Improve error model fitting

Now we have a three stage fitting process for nonconstant error models: - Unweighted least squares - Only optimize the error model - Optimize both Static documentation rebuilt by pkgdown
author: Johannes Ranke <jranke@uni-bremen.de> 2019-05-03 19:14:15 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2019-05-03 19:14:15 +0200
commit: 1ef7008be2a72a0847064ad9c2ddcfa16b055482 (patch)
tree: ecc3f90e5d18c75aea14ad774aad9214039c0674
parent: de7b6acdd75a0f95f2a9522c22625810f4aa329a (diff)
49 files changed, 622 insertions, 592 deletions
diff --git a/R/mkinds.R b/R/mkinds.R
index 257a17c4..5333ca26 100644
--- a/R/mkinds.R
+++ b/R/mkinds.R
@@ -42,7 +42,6 @@ mkinds <- R6Class("mkinds",
   )
 )
 
-#' @export
 print.mkinds <- function(x, ...) {
   cat("<mkinds> with $title: ",  x$title, "\n")
   cat("Observed compounds $observed: ", paste(x$observed, collapse = ", "), "\n")
diff --git a/R/mkinfit.R b/R/mkinfit.R
index dca71ecf..cca75690 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -263,7 +263,7 @@ mkinfit <- function(mkinmod, observed,
       errparms = rep(3, length(obs_vars))
     }
     if (err_mod == "tc") {
-      errparms <- c(sigma_low = 3, rsd_high = 0.01)
+      errparms <- c(sigma_low = 0.1, rsd_high = 0.1)
     }
     names(errparms) <- errparm_names
   }
@@ -275,13 +275,20 @@ mkinfit <- function(mkinmod, observed,
                                               length.out = n.outtimes))))
 
   # Define log-likelihood function for optimisation, including (back)transformations
-  nlogLik <- function(P, trans = TRUE, OLS = FALSE, update_data = TRUE, ...)
+  nlogLik <- function(P, trans = TRUE, OLS = FALSE, local = FALSE, update_data = TRUE, ...)
   {
     assign("calls", calls + 1, inherits = TRUE) # Increase the model solution counter
+    P.orig <- P
 
     # Trace parameter values if requested
     if(trace_parms) cat(P, "\n")
 
+    # If we do a local optimisation of the error model, the initials
+    # for the state variabels and the parameters are given as 'local'
+    if (local[1] != FALSE) {
+      P <- local
+    }
+
     # Initial states for t0
     if(length(state.ini.optim) > 0) {
       odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed)
@@ -291,7 +298,7 @@ mkinfit <- function(mkinmod, observed,
       names(odeini) <- state.ini.fixed.boxnames
     }
 
-    if (OLS) {
+    if (OLS | identical(P, local)) {
       odeparms.optim <- P[(length(state.ini.optim) + 1):length(P)]
     } else {
       odeparms.optim <- P[(length(state.ini.optim) + 1):(length(P) - length(errparms))]
@@ -314,6 +321,9 @@ mkinfit <- function(mkinmod, observed,
                        method.ode = method.ode,
                        atol = atol, rtol = rtol, ...)
 
+    # Get back the original parameter vector to get the error model parameters
+    P <- P.orig
+
     out_long <- mkin_wide_to_long(out, time = "time")
 
     if (err_mod == "const") {
@@ -411,16 +421,17 @@ mkinfit <- function(mkinmod, observed,
 
   # Do the fit and take the time until the hessians are calculated
   fit_time <- system.time({
-    # For constant variance, we do not include sigma in the optimisation, as it
-    # is unnecessary and leads to instability of the fit which are most obvious
-    # when fitting the IORE model
-    if (err_mod == "const") {
-      fit.ols <- nlminb(c(state.ini.optim, transparms.optim),
-                    nlogLik, control = control,
-                    lower = lower, upper = upper, OLS = TRUE, ...)
+    # In the inital run, we assume a constant standard deviation and do
+    # not optimise it, as this is unnecessary and leads to instability of the
+    # fit (most obvious when fitting the IORE model)
+    if (!quiet) message("Ordinary least squares optimisation")
+    parms.start <- c(state.ini.optim, transparms.optim)
+    fit.ols <- nlminb(parms.start, nlogLik, control = control,
+      lower = lower[names(parms.start)], 
+      upper = upper[names(parms.start)], OLS = TRUE, ...)
 
+    if (err_mod == "const") {
       # Get the maximum likelihood estimate for sigma at the optimum parameter values
-      # This is equivalent to including sigma in the optimisation, but more stable
       data_errmod$residual <- data_errmod$value.observed - data_errmod$value.predicted
       sigma_mle = sqrt(sum(data_errmod$residual^2)/nrow(data_errmod))
 
@@ -428,9 +439,20 @@ mkinfit <- function(mkinmod, observed,
       fit <- fit.ols
       fit$logLik <- - nlogLik(c(fit$par, sigma = sigma_mle), OLS = FALSE)
     } else {
-      fit <- nlminb(c(state.ini.optim, transparms.optim, errparms),
-                    nlogLik, control = control,
-                    lower = lower, upper = upper, ...)
+      # After the OLS stop we fit the error model with fixed degradation model
+      # parameters
+      if (!quiet) message("Optimising the error model")
+      fit.err <- nlminb(errparms, nlogLik, control = control,
+        lower = lower[names(errparms)], 
+        upper = upper[names(errparms)],
+        local = fit.ols$par, ...)
+      errparms.tmp <- fit.err$par
+      if (!quiet) message("Optimising the complete model")
+      parms.start <- c(state.ini.optim, transparms.optim, errparms.tmp)
+      fit <- nlminb(parms.start, nlogLik,
+        lower = lower[names(parms.start)], 
+        upper = upper[names(parms.start)],
+        control = control, ...)
       fit$logLik <- - nlogLik.current
     }
 
diff --git a/build.log b/build.log
index 980d0de0..9728241a 100644
--- a/build.log
+++ b/build.log
@@ -6,7 +6,5 @@
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
 * looking to see if a ‘data/datalist’ file should be added
-  NB: this package now depends on R (>= 3.5.0)
-  WARNING: Added dependency on R >= 3.5.0 because serialized objects in  serialize/load version 3 cannot be read in older versions of R.  File(s) containing such objects: 'mkin/vignettes/mkin_benchmarks.rda'
-* building 'mkin_0.9.49.4.tar.gz'
+* building ‘mkin_0.9.49.4.tar.gz’
 
diff --git a/check.log b/check.log
index 325b690c..49ba0af6 100644
--- a/check.log
+++ b/check.log
@@ -17,6 +17,7 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
 * checking for hidden files and directories ... OK
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
+* checking serialization versions ... OK
 * checking whether package ‘mkin’ can be installed ... OK
 * checking installed package size ... OK
 * checking package directory ... OK
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 3ce94de7..ae895cc3 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -88,7 +88,7 @@
       <h1>Example evaluation of FOCUS Example Dataset D</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2019-05-02</h4>
+            <h4 class="date">2019-05-03</h4>
       
       
       <div class="hidden name"><code>FOCUS_D.Rmd</code></div>
@@ -168,8 +168,8 @@
 <div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 18:49:13 2019 
-## Date of summary: Thu May  2 18:49:14 2019 
+## Date of fit:     Fri May  3 19:08:45 2019 
+## Date of summary: Fri May  3 19:08:46 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -177,7 +177,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted using 396 model solutions performed in 0.999 s
+## Fitted using 389 model solutions performed in 0.983 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -216,13 +216,13 @@
 ## log_k_parent_sink  6.067e-01         1.000e+00      -8.550e-02
 ## log_k_parent_m1   -6.372e-02        -8.550e-02       1.000e+00
 ## log_k_m1_sink     -1.688e-01        -6.252e-01       4.731e-01
-## sigma             -3.368e-07         3.365e-08       8.420e-07
+## sigma              1.164e-09        -8.908e-10       1.652e-08
 ##                   log_k_m1_sink      sigma
-## parent_0             -1.688e-01 -3.368e-07
-## log_k_parent_sink    -6.252e-01  3.365e-08
-## log_k_parent_m1       4.731e-01  8.420e-07
-## log_k_m1_sink         1.000e+00  1.958e-08
-## sigma                 1.958e-08  1.000e+00
+## parent_0             -1.688e-01  1.164e-09
+## log_k_parent_sink    -6.252e-01 -8.908e-10
+## log_k_parent_m1       4.731e-01  1.652e-08
+## log_k_m1_sink         1.000e+00 -1.340e-10
+## sigma                -1.340e-10  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -258,10 +258,10 @@
 ##     0   parent   102.04  99.59848  2.442e+00
 ##     1   parent    93.50  90.23787  3.262e+00
 ##     1   parent    92.50  90.23787  2.262e+00
-##     3   parent    63.23  74.07319 -1.084e+01
-##     3   parent    68.99  74.07319 -5.083e+00
-##     7   parent    52.32  49.91206  2.408e+00
-##     7   parent    55.13  49.91206  5.218e+00
+##     3   parent    63.23  74.07320 -1.084e+01
+##     3   parent    68.99  74.07320 -5.083e+00
+##     7   parent    52.32  49.91207  2.408e+00
+##     7   parent    55.13  49.91207  5.218e+00
 ##    14   parent    27.27  25.01257  2.257e+00
 ##    14   parent    26.64  25.01257  1.627e+00
 ##    21   parent    11.50  12.53462 -1.035e+00
@@ -271,23 +271,23 @@
 ##    50   parent     0.69   0.71624 -2.624e-02
 ##    50   parent     0.63   0.71624 -8.624e-02
 ##    75   parent     0.05   0.06074 -1.074e-02
-##    75   parent     0.06   0.06074 -7.381e-04
+##    75   parent     0.06   0.06074 -7.382e-04
 ##     1       m1     4.84   4.80296  3.704e-02
 ##     1       m1     5.64   4.80296  8.370e-01
 ##     3       m1    12.91  13.02400 -1.140e-01
 ##     3       m1    12.96  13.02400 -6.400e-02
 ##     7       m1    22.97  25.04476 -2.075e+00
 ##     7       m1    24.47  25.04476 -5.748e-01
-##    14       m1    41.69  36.69003  5.000e+00
-##    14       m1    33.21  36.69003 -3.480e+00
+##    14       m1    41.69  36.69002  5.000e+00
+##    14       m1    33.21  36.69002 -3.480e+00
 ##    21       m1    44.37  41.65310  2.717e+00
 ##    21       m1    46.44  41.65310  4.787e+00
 ##    35       m1    41.22  43.31312 -2.093e+00
 ##    35       m1    37.95  43.31312 -5.363e+00
-##    50       m1    41.19  41.21832 -2.832e-02
-##    50       m1    40.01  41.21832 -1.208e+00
-##    75       m1    40.09  36.44704  3.643e+00
-##    75       m1    33.85  36.44704 -2.597e+00
+##    50       m1    41.19  41.21831 -2.831e-02
+##    50       m1    40.01  41.21831 -1.208e+00
+##    75       m1    40.09  36.44703  3.643e+00
+##    75       m1    33.85  36.44703 -2.597e+00
 ##   100       m1    31.04  31.98163 -9.416e-01
 ##   100       m1    33.13  31.98163  1.148e+00
 ##   120       m1    25.15  28.78984 -3.640e+00
diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png
index b8f2fe94..0cd6596d 100644
--- a/docs/articles/FOCUS_D_files/figure-html/plot-1.png
+++ b/docs/articles/FOCUS_D_files/figure-html/plot-1.png
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 42f2dc60..9507139c 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -88,7 +88,7 @@
       <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2019-05-02</h4>
+            <h4 class="date">2019-05-03</h4>
       
       
       <div class="hidden name"><code>FOCUS_L.Rmd</code></div>
@@ -114,15 +114,15 @@
 <a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 18:49:16 2019 
-## Date of summary: Thu May  2 18:49:16 2019 
+## Date of fit:     Fri May  3 19:08:47 2019 
+## Date of summary: Fri May  3 19:08:47 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.278 s
+## Fitted using 133 model solutions performed in 0.281 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -215,8 +215,8 @@
 ## finite result is doubtful</code></pre>
 <pre><code>## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 18:49:17 2019 
-## Date of summary: Thu May  2 18:49:17 2019 
+## Date of fit:     Fri May  3 19:08:50 2019 
+## Date of summary: Fri May  3 19:08:50 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -228,7 +228,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 599 model solutions performed in 1.26 s
+## Fitted using 899 model solutions performed in 1.885 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -238,41 +238,41 @@
 ## parent_0 89.850000  state
 ## alpha     1.000000 deparm
 ## beta     10.000000 deparm
-## sigma     2.779868  error
+## sigma     2.779871  error
 ## 
 ## Starting values for the transformed parameters actually optimised:
 ##               value lower upper
 ## parent_0  89.850000  -Inf   Inf
 ## log_alpha  0.000000  -Inf   Inf
 ## log_beta   2.302585  -Inf   Inf
-## sigma      2.779868     0   Inf
+## sigma      2.779871     0   Inf
 ## 
 ## Fixed parameter values:
 ## None
 ## 
 ## Optimised, transformed parameters with symmetric confidence intervals:
 ##           Estimate Std. Error  Lower  Upper
-## parent_0     92.47     1.2810 89.720 95.220
-## log_alpha    10.66        NaN    NaN    NaN
-## log_beta     13.01        NaN    NaN    NaN
-## sigma         2.78     0.4599  1.794  3.766
+## parent_0     92.47     1.2800 89.730 95.220
+## log_alpha    10.58        NaN    NaN    NaN
+## log_beta     12.93        NaN    NaN    NaN
+## sigma         2.78     0.4507  1.813  3.747
 ## 
 ## Parameter correlation:
-##           parent_0 log_alpha log_beta    sigma
-## parent_0  1.000000       NaN      NaN 0.003475
-## log_alpha      NaN         1      NaN      NaN
-## log_beta       NaN       NaN        1      NaN
-## sigma     0.003475       NaN      NaN 1.000000
+##           parent_0 log_alpha log_beta   sigma
+## parent_0   1.00000       NaN      NaN 0.01452
+## log_alpha      NaN         1      NaN     NaN
+## log_beta       NaN       NaN        1     NaN
+## sigma      0.01452       NaN      NaN 1.00000
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
 ## t-test (unrealistically) based on the assumption of normal distribution
 ## for estimators of untransformed parameters.
 ##           Estimate  t value    Pr(&gt;t)  Lower  Upper
-## parent_0     92.47 72.13000 1.052e-19 89.720 95.220
-## alpha     42700.00  0.02298 4.910e-01     NA     NA
-## beta     446600.00  0.02298 4.910e-01     NA     NA
-## sigma         2.78  6.00000 1.628e-05  1.794  3.766
+## parent_0     92.47 72.13000 1.052e-19 89.730 95.220
+## alpha     39440.00  0.02397 4.906e-01     NA     NA
+## beta     412500.00  0.02397 4.906e-01     NA     NA
+## sigma         2.78  6.00000 1.628e-05  1.813  3.747
 ## 
 ## FOCUS Chi2 error levels in percent:
 ##          err.min n.optim df
@@ -281,7 +281,7 @@
 ## 
 ## Estimated disappearance times:
 ##         DT50  DT90 DT50back
-## parent 7.249 24.08     7.25</code></pre>
+## parent 7.249 24.08    7.249</code></pre>
 <p>We get a warning that the default optimisation algorithm <code>Port</code> did not converge, which is an indication that the model is overparameterised, <em>i.e.</em> contains too many parameters that are ill-defined as a consequence.</p>
 <p>And in fact, due to the higher number of parameters, and the lower number of degrees of freedom of the fit, the <span class="math inline">\(\chi^2\)</span> error level is actually higher for the FOMC model (3.6%) than for the SFO model (3.4%). Additionally, the parameters <code>log_alpha</code> and <code>log_beta</code> internally fitted in the model have excessive confidence intervals, that span more than 25 orders of magnitude (!) when backtransformed to the scale of <code>alpha</code> and <code>beta</code>. Also, the t-test for significant difference from zero does not indicate such a significant difference, with p-values greater than 0.1, and finally, the parameter correlation of <code>log_alpha</code> and <code>log_beta</code> is 1.000, clearly indicating that the model is overparameterised.</p>
 <p>The <span class="math inline">\(\chi^2\)</span> error levels reported in Appendix 3 and Appendix 7 to the FOCUS kinetics report are rounded to integer percentages and partly deviate by one percentage point from the results calculated by mkin. The reason for this is not known. However, mkin gives the same <span class="math inline">\(\chi^2\)</span> error levels as the kinfit package and the calculation routines of the kinfit package have been extensively compared to the results obtained by the KinGUI software, as documented in the kinfit package vignette. KinGUI was the first widely used standard package in this field. Also, the calculation of <span class="math inline">\(\chi^2\)</span> error levels was compared with KinGUII, CAKE and DegKin manager in a project sponsored by the German Umweltbundesamt <span class="citation">(Ranke 2014)</span>.</p>
@@ -319,15 +319,15 @@
 <div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 18:49:18 2019 
-## Date of summary: Thu May  2 18:49:18 2019 
+## Date of fit:     Fri May  3 19:08:51 2019 
+## Date of summary: Fri May  3 19:08:51 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 240 model solutions performed in 0.486 s
+## Fitted using 239 model solutions performed in 0.486 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -358,10 +358,10 @@
 ## 
 ## Parameter correlation:
 ##             parent_0  log_alpha   log_beta      sigma
-## parent_0   1.000e+00 -1.151e-01 -2.085e-01  1.606e-08
-## log_alpha -1.151e-01  1.000e+00  9.741e-01 -1.168e-07
-## log_beta  -2.085e-01  9.741e-01  1.000e+00 -1.029e-07
-## sigma      1.606e-08 -1.168e-07 -1.029e-07  1.000e+00
+## parent_0   1.000e+00 -1.151e-01 -2.085e-01 -7.637e-09
+## log_alpha -1.151e-01  1.000e+00  9.741e-01 -1.617e-07
+## log_beta  -2.085e-01  9.741e-01  1.000e+00 -1.387e-07
+## sigma     -7.637e-09 -1.617e-07 -1.387e-07  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -394,8 +394,8 @@
 <div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 18:49:20 2019 
-## Date of summary: Thu May  2 18:49:20 2019 
+## Date of fit:     Fri May  3 19:08:52 2019 
+## Date of summary: Fri May  3 19:08:52 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -404,7 +404,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 587 model solutions performed in 1.223 s
+## Fitted using 572 model solutions performed in 1.193 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -431,18 +431,18 @@
 ## Optimised, transformed parameters with symmetric confidence intervals:
 ##          Estimate Std. Error      Lower     Upper
 ## parent_0  93.9500  9.998e-01    91.5900   96.3100
-## log_k1     3.1330  2.265e+03 -5354.0000 5360.0000
+## log_k1     3.1370  2.376e+03 -5616.0000 5622.0000
 ## log_k2    -1.0880  6.285e-02    -1.2370   -0.9394
 ## g_ilr     -0.2821  7.033e-02    -0.4484   -0.1158
 ## sigma      1.4140  2.886e-01     0.7314    2.0960
 ## 
 ## Parameter correlation:
 ##            parent_0     log_k1     log_k2      g_ilr      sigma
-## parent_0  1.000e+00  5.434e-07 -9.989e-11  2.665e-01 -3.978e-10
-## log_k1    5.434e-07  1.000e+00  8.888e-05 -1.748e-04 -8.207e-06
-## log_k2   -9.989e-11  8.888e-05  1.000e+00 -7.903e-01  5.751e-10
-## g_ilr     2.665e-01 -1.748e-04 -7.903e-01  1.000e+00 -7.109e-10
-## sigma    -3.978e-10 -8.207e-06  5.751e-10 -7.109e-10  1.000e+00
+## parent_0  1.000e+00  5.155e-07  2.371e-09  2.665e-01 -6.849e-09
+## log_k1    5.155e-07  1.000e+00  8.434e-05 -1.659e-04 -7.791e-06
+## log_k2    2.371e-09  8.434e-05  1.000e+00 -7.903e-01 -1.262e-08
+## g_ilr     2.665e-01 -1.659e-04 -7.903e-01  1.000e+00  3.241e-08
+## sigma    -6.849e-09 -7.791e-06 -1.262e-08  3.241e-08  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -450,7 +450,7 @@
 ## for estimators of untransformed parameters.
 ##          Estimate   t value    Pr(&gt;t)   Lower   Upper
 ## parent_0  93.9500 9.397e+01 2.036e-12 91.5900 96.3100
-## k1        22.9300 4.514e-04 4.998e-01  0.0000     Inf
+## k1        23.0400 4.303e-04 4.998e-01  0.0000     Inf
 ## k2         0.3369 1.591e+01 4.697e-07  0.2904  0.3909
 ## g          0.4016 1.680e+01 3.238e-07  0.3466  0.4591
 ## sigma      1.4140 4.899e+00 8.776e-04  0.7314  2.0960
@@ -462,7 +462,7 @@
 ## 
 ## Estimated disappearance times:
 ##          DT50  DT90 DT50_k1 DT50_k2
-## parent 0.5335 5.311 0.03023   2.058</code></pre>
+## parent 0.5335 5.311 0.03009   2.058</code></pre>
 <p>Here, the DFOP model is clearly the best-fit model for dataset L2 based on the chi^2 error level criterion. However, the failure to calculate the covariance matrix indicates that the parameter estimates correlate excessively. Therefore, the FOMC model may be preferred for this dataset.</p>
 </div>
 </div>
@@ -493,8 +493,8 @@
 <div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 18:49:21 2019 
-## Date of summary: Thu May  2 18:49:22 2019 
+## Date of fit:     Fri May  3 19:08:54 2019 
+## Date of summary: Fri May  3 19:08:54 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -503,7 +503,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 372 model solutions performed in 0.768 s
+## Fitted using 373 model solutions performed in 0.775 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -536,12 +536,12 @@
 ## sigma      1.0170    0.25430  0.2079   1.827000
 ## 
 ## Parameter correlation:
-##           parent_0     log_k1     log_k2      g_ilr      sigma
-## parent_0 1.000e+00  1.732e-01  2.282e-02  4.009e-01  1.660e-07
-## log_k1   1.732e-01  1.000e+00  4.945e-01 -5.809e-01  6.635e-08
-## log_k2   2.282e-02  4.945e-01  1.000e+00 -6.812e-01  3.880e-07
-## g_ilr    4.009e-01 -5.809e-01 -6.812e-01  1.000e+00 -3.822e-07
-## sigma    1.660e-07  6.635e-08  3.880e-07 -3.822e-07  1.000e+00
+##            parent_0     log_k1     log_k2      g_ilr      sigma
+## parent_0  1.000e+00  1.732e-01  2.282e-02  4.009e-01 -6.872e-07
+## log_k1    1.732e-01  1.000e+00  4.945e-01 -5.809e-01  3.200e-07
+## log_k2    2.282e-02  4.945e-01  1.000e+00 -6.812e-01  7.673e-07
+## g_ilr     4.009e-01 -5.809e-01 -6.812e-01  1.000e+00 -8.731e-07
+## sigma    -6.872e-07  3.200e-07  7.673e-07 -8.731e-07  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -598,15 +598,15 @@
 <div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 18:49:22 2019 
-## Date of summary: Thu May  2 18:49:23 2019 
+## Date of fit:     Fri May  3 19:08:55 2019 
+## Date of summary: Fri May  3 19:08:55 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 146 model solutions performed in 0.294 s
+## Fitted using 142 model solutions performed in 0.29 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -633,10 +633,10 @@
 ## sigma                3.162    0.79050  1.130   5.194
 ## 
 ## Parameter correlation:
-##                    parent_0 log_k_parent_sink      sigma
-## parent_0          1.000e+00         5.938e-01  4.256e-10
-## log_k_parent_sink 5.938e-01         1.000e+00 -7.280e-10
-## sigma             4.256e-10        -7.280e-10  1.000e+00
+##                    parent_0 log_k_parent_sink     sigma
+## parent_0          1.000e+00         5.938e-01 3.440e-07
+## log_k_parent_sink 5.938e-01         1.000e+00 5.885e-07
+## sigma             3.440e-07         5.885e-07 1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -662,15 +662,15 @@
 <div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
 <pre><code>## mkin version used for fitting:    0.9.49.4 
 ## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 18:49:23 2019 
-## Date of summary: Thu May  2 18:49:23 2019 
+## Date of fit:     Fri May  3 19:08:55 2019 
+## Date of summary: Fri May  3 19:08:55 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.454 s
+## Fitted using 224 model solutions performed in 0.451 s
 ## 
 ## Error model:
 ## Constant variance 
@@ -701,10 +701,10 @@
 ## 
 ## Parameter correlation:
 ##             parent_0  log_alpha   log_beta      sigma
-## parent_0   1.000e+00 -4.696e-01 -5.543e-01 -2.473e-07
-## log_alpha -4.696e-01  1.000e+00  9.889e-01  2.429e-08
-## log_beta  -5.543e-01  9.889e-01  1.000e+00  5.183e-08
-## sigma     -2.473e-07  2.429e-08  5.183e-08  1.000e+00
+## parent_0   1.000e+00 -4.696e-01 -5.543e-01 -2.563e-07
+## log_alpha -4.696e-01  1.000e+00  9.889e-01  4.066e-08
+## log_beta  -5.543e-01  9.889e-01  1.000e+00  6.818e-08
+## sigma     -2.563e-07  4.066e-08  6.818e-08  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png
index 7f695ecf..cc28c092 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png
index 850df1e1..46d85b73 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-12-1.png
diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png
index 5ed0b4de..3dd8565c 100644
--- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png
+++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-6-1.png
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 132e0c14..b0af83ce 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -88,7 +88,7 @@
       <h1>Introduction to mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2019-05-02</h4>
+            <h4 class="date">2019-05-03</h4>
       
       
       <div class="hidden name"><code>mkin.Rmd</code></div>
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 7d9d1c4e..7f68d39e 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -88,7 +88,7 @@
       <h1>Calculation of time weighted average concentrations with mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2019-05-02</h4>
+            <h4 class="date">2019-05-03</h4>
       
       
       <div class="hidden name"><code>twa.Rmd</code></div>
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 950e8eab..9e64ae3a 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -88,7 +88,7 @@
       <h1>Example evaluation of FOCUS dataset Z</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2019-05-02</h4>
+            <h4 class="date">2019-05-03</h4>
       
       
       <div class="hidden name"><code>FOCUS_Z.Rmd</code></div>
@@ -132,11 +132,11 @@
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p>
 <div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
 <pre><code>##             Estimate se_notrans    t value     Pr(&gt;t)    Lower    Upper
-## Z0_0      9.7015e+01   3.394776 2.8578e+01 6.5093e-21 91.66556 102.3642
-## k_Z0_sink 4.0301e-10   0.225510 1.7871e-09 5.0000e-01  0.00000      Inf
-## k_Z0_Z1   2.2360e+00   0.159161 1.4049e+01 1.1412e-13  1.95303   2.5600
-## k_Z1_sink 4.8212e-01   0.065499 7.3608e+00 5.1791e-08  0.40341   0.5762
-## sigma     4.8041e+00   0.637657 7.5340e+00 3.4468e-08  3.52677   6.0815</code></pre>
+## Z0_0      9.7015e+01   3.393176 2.8591e+01 6.4352e-21 91.66556 102.3642
+## k_Z0_sink 7.2231e-10   0.225254 3.2067e-09 5.0000e-01  0.00000      Inf
+## k_Z0_Z1   2.2360e+00   0.159134 1.4051e+01 1.1369e-13  1.95303   2.5600
+## k_Z1_sink 4.8212e-01   0.065454 7.3658e+00 5.1186e-08  0.40341   0.5762
+## sigma     4.8041e+00   0.637618 7.5345e+00 3.4431e-08  3.52677   6.0815</code></pre>
 <p>As obvious from the parameter summary (the  component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.</p>
 <p>A similar result can be obtained when formation fractions are used in the model formulation:</p>
 <div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">Z<span class="fl">.2</span>a.ff &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),</a>
@@ -199,20 +199,18 @@
 <a class="sourceLine" id="cb30-3" title="3">                     <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
 <pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.
 ## 5$bparms.ode, : Observations with value of zero were removed from the data</code></pre>
-<pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation did not converge:
-## false convergence (8)</code></pre>
-<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.FOCUS)</a></code></pre></div>
+<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb32-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.FOCUS)</a></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p>
-<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
+<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div>
 <pre><code>##             Estimate se_notrans t value     Pr(&gt;t)     Lower      Upper
-## Z0_0       96.838619   1.994272 48.5584 4.0282e-42 92.826596 100.850642
-## k_Z0        2.215408   0.118459 18.7018 1.0415e-23  1.989468   2.467007
-## k_Z1        0.478300   0.028257 16.9267 6.2407e-22  0.424701   0.538663
-## k_Z2        0.451618   0.042138 10.7177 1.6308e-14  0.374327   0.544869
-## k_Z3        0.058693   0.015246  3.8498 1.7805e-04  0.034804   0.098981
-## f_Z2_to_Z3  0.471508   0.058352  8.0804 9.6647e-11  0.357725   0.588332
+## Z0_0       96.838607   1.994273 48.5584 4.0283e-42 92.826626 100.850589
+## k_Z0        2.215405   0.118459 18.7018 1.0415e-23  1.989465   2.467003
+## k_Z1        0.478300   0.028257 16.9267 6.2408e-22  0.424701   0.538662
+## k_Z2        0.451618   0.042138 10.7177 1.6308e-14  0.374328   0.544867
+## k_Z3        0.058693   0.015246  3.8498 1.7806e-04  0.034805   0.098978
+## f_Z2_to_Z3  0.471508   0.058352  8.0804 9.6648e-11  0.357735   0.588320
 ## sigma       3.984431   0.383402 10.3923 4.5575e-14  3.213126   4.755736</code></pre>
-<div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" title="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.FOCUS)</a></code></pre></div>
+<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb35-1" title="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.FOCUS)</a></code></pre></div>
 <pre><code>## $ff
 ##   Z2_Z3 Z2_sink 
 ## 0.47151 0.52849 
@@ -225,7 +223,7 @@
 ## Z0  0.31288  1.0394
 ## Z1  1.44919  4.8141
 ## Z2  1.53481  5.0985
-## Z3 11.80962 39.2307</code></pre>
+## Z3 11.80965 39.2308</code></pre>
 <p>This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.</p>
 </div>
 <div id="using-the-sforb-model" class="section level1">
@@ -233,17 +231,17 @@
 <a href="#using-the-sforb-model" class="anchor"></a>Using the SFORB model</h1>
 <p>As the FOCUS report states, there is a certain tailing of the time course of metabolite Z3. Also, the time course of the parent compound is not fitted very well using the SFO model, as residues at a certain low level remain.</p>
 <p>Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the <span class="math inline">\(\chi^2\)</span> error level is lower for metabolite Z3 using this model and the graphical fit for Z3 is improved. However, the covariance matrix is not returned.</p>
-<div class="sourceCode" id="cb38"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb38-1" title="1">Z.mkin<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb38-2" title="2">                    <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb38-3" title="3">                    <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a>
-<a class="sourceLine" id="cb38-4" title="4">                    <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" title="1">Z.mkin<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
+<a class="sourceLine" id="cb37-2" title="2">                    <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
+<a class="sourceLine" id="cb37-3" title="3">                    <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a>
+<a class="sourceLine" id="cb37-4" title="4">                    <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div>
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" title="1">m.Z.mkin<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.1</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb39"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb39-1" title="1">m.Z.mkin<span class="fl">.1</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.1</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
 <pre><code>## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations
 ## with value of zero were removed from the data</code></pre>
-<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.1</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb41"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb41-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.1</span>)</a></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p>
-<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div>
+<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div>
 <pre><code>##                            Z0_0 log_k_Z0_Z1 log_k_Z1_Z2 log_k_Z2_sink
 ## Z0_0                 3.8375e+00  5.4918e-03  3.0584e-02    1.2969e-01
 ## log_k_Z0_Z1          5.4918e-03  2.7613e-03 -1.8820e-04    2.6634e-04
@@ -251,9 +249,9 @@
 ## log_k_Z2_sink        1.2969e-01  2.6634e-04  3.2177e-03    3.4256e-02
 ## log_k_Z2_Z3_free    -2.4223e-02 -2.6169e-04 -1.1845e-03   -8.1134e-03
 ## log_k_Z3_free_sink  -6.5467e-02 -4.0815e-04 -3.2978e-03   -3.6010e-02
-## log_k_Z3_free_bound -6.0658e-02 -4.4768e-04 -3.0588e-03   -3.9074e-02
-## log_k_Z3_bound_free  4.7821e+00  5.5819e-03  1.0267e-01    1.1956e+00
-## sigma               -1.4345e-08  8.6519e-11 -6.1861e-10   -4.7499e-10
+## log_k_Z3_free_bound -6.0659e-02 -4.4768e-04 -3.0588e-03   -3.9074e-02
+## log_k_Z3_bound_free  5.2844e-01  4.5458e-03  7.9800e-03    4.6274e-02
+## sigma                2.0366e-10 -3.4658e-10  8.9910e-11   -2.5946e-10
 ##                     log_k_Z2_Z3_free log_k_Z3_free_sink
 ## Z0_0                     -2.4223e-02        -6.5467e-02
 ## log_k_Z0_Z1              -2.6169e-04        -4.0815e-04
@@ -262,84 +260,84 @@
 ## log_k_Z2_Z3_free          1.5500e-02         2.1583e-02
 ## log_k_Z3_free_sink        2.1583e-02         7.5705e-02
 ## log_k_Z3_free_bound       2.5836e-02         1.1964e-01
-## log_k_Z3_bound_free      -2.1303e-01        -9.0584e-01
-## sigma                     5.8776e-10         1.0773e-09
+## log_k_Z3_bound_free       5.2534e-02         2.9441e-01
+## sigma                     1.3063e-10         3.4170e-10
 ##                     log_k_Z3_free_bound log_k_Z3_bound_free       sigma
-## Z0_0                        -6.0658e-02          4.7821e+00 -1.4345e-08
-## log_k_Z0_Z1                 -4.4768e-04          5.5819e-03  8.6519e-11
-## log_k_Z1_Z2                 -3.0588e-03          1.0267e-01 -6.1861e-10
-## log_k_Z2_sink               -3.9074e-02          1.1956e+00 -4.7499e-10
-## log_k_Z2_Z3_free             2.5836e-02         -2.1303e-01  5.8776e-10
-## log_k_Z3_free_sink           1.1964e-01         -9.0584e-01  1.0773e-09
-## log_k_Z3_free_bound          6.5902e-01          4.2011e+00  2.1743e-09
-## log_k_Z3_bound_free          4.2011e+00          3.6036e+08  7.2404e-02
-## sigma                        2.1743e-09          7.2404e-02  1.4170e-01</code></pre>
+## Z0_0                        -6.0659e-02          5.2844e-01  2.0366e-10
+## log_k_Z0_Z1                 -4.4768e-04          4.5458e-03 -3.4658e-10
+## log_k_Z1_Z2                 -3.0588e-03          7.9800e-03  8.9910e-11
+## log_k_Z2_sink               -3.9074e-02          4.6274e-02 -2.5946e-10
+## log_k_Z2_Z3_free             2.5836e-02          5.2534e-02  1.3063e-10
+## log_k_Z3_free_sink           1.1964e-01          2.9441e-01  3.4170e-10
+## log_k_Z3_free_bound          6.5902e-01          5.4737e+00 -6.7704e-10
+## log_k_Z3_bound_free          5.4737e+00          2.8722e+08  7.2421e-02
+## sigma                       -6.7704e-10          7.2421e-02  1.4170e-01</code></pre>
 <p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p>
-<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" title="1">Z.mkin<span class="fl">.3</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb45-2" title="2">                    <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb45-3" title="3">                    <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" title="1">Z.mkin<span class="fl">.3</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
+<a class="sourceLine" id="cb44-2" title="2">                    <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
+<a class="sourceLine" id="cb44-3" title="3">                    <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div>
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" title="1">m.Z.mkin<span class="fl">.3</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" title="1">m.Z.mkin<span class="fl">.3</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
 <pre><code>## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations
 ## with value of zero were removed from the data</code></pre>
-<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.3</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.3</span>)</a></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="700"></p>
 <p>This results in a much better representation of the behaviour of the parent compound Z0.</p>
 <p>Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.</p>
-<div class="sourceCode" id="cb50"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb50-1" title="1">Z.mkin<span class="fl">.4</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb50-2" title="2">                    <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb50-3" title="3">                    <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a>
-<a class="sourceLine" id="cb50-4" title="4">                    <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" title="1">Z.mkin<span class="fl">.4</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
+<a class="sourceLine" id="cb49-2" title="2">                    <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
+<a class="sourceLine" id="cb49-3" title="3">                    <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a>
+<a class="sourceLine" id="cb49-4" title="4">                    <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div>
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb52"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb52-1" title="1">m.Z.mkin<span class="fl">.4</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.4</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a>
-<a class="sourceLine" id="cb52-2" title="2">                      <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.3</span><span class="op">$</span>bparms.ode,</a>
-<a class="sourceLine" id="cb52-3" title="3">                      <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" title="1">m.Z.mkin<span class="fl">.4</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.4</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a>
+<a class="sourceLine" id="cb51-2" title="2">                      <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.3</span><span class="op">$</span>bparms.ode,</a>
+<a class="sourceLine" id="cb51-3" title="3">                      <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
 <pre><code>## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin.
 ## 3$bparms.ode, : Observations with value of zero were removed from the data</code></pre>
-<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.4</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb53"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb53-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.4</span>)</a></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png" width="700"></p>
 <p>The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.</p>
-<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" title="1">Z.mkin<span class="fl">.5</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb55-2" title="2">                    <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
-<a class="sourceLine" id="cb55-3" title="3">                    <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a>
-<a class="sourceLine" id="cb55-4" title="4">                    <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1">Z.mkin<span class="fl">.5</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
+<a class="sourceLine" id="cb54-2" title="2">                    <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a>
+<a class="sourceLine" id="cb54-3" title="3">                    <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a>
+<a class="sourceLine" id="cb54-4" title="4">                    <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div>
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1">m.Z.mkin<span class="fl">.5</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a>
-<a class="sourceLine" id="cb57-2" title="2">                      <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.4</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>],</a>
-<a class="sourceLine" id="cb57-3" title="3">                      <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb56"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb56-1" title="1">m.Z.mkin<span class="fl">.5</span> &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a>
+<a class="sourceLine" id="cb56-2" title="2">                      <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.4</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>],</a>
+<a class="sourceLine" id="cb56-3" title="3">                      <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
 <pre><code>## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin.
 ## 4$bparms.ode[1:4], : Observations with value of zero were removed from the
 ## data</code></pre>
-<div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb58"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb58-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>)</a></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png" width="700"></p>
 <p>The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized  is excessively small, it seems reasonable to fix it to zero.</p>
-<div class="sourceCode" id="cb60"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb60-1" title="1">m.Z.mkin<span class="fl">.5</span>a &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a>
-<a class="sourceLine" id="cb60-2" title="2">                       <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(m.Z.mkin<span class="fl">.5</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">7</span>],</a>
-<a class="sourceLine" id="cb60-3" title="3">                                     <span class="dt">k_Z3_bound_free =</span> <span class="dv">0</span>),</a>
-<a class="sourceLine" id="cb60-4" title="4">                       <span class="dt">fixed_parms =</span> <span class="st">"k_Z3_bound_free"</span>,</a>
-<a class="sourceLine" id="cb60-5" title="5">                       <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" title="1">m.Z.mkin<span class="fl">.5</span>a &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a>
+<a class="sourceLine" id="cb59-2" title="2">                       <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(m.Z.mkin<span class="fl">.5</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">7</span>],</a>
+<a class="sourceLine" id="cb59-3" title="3">                                     <span class="dt">k_Z3_bound_free =</span> <span class="dv">0</span>),</a>
+<a class="sourceLine" id="cb59-4" title="4">                       <span class="dt">fixed_parms =</span> <span class="st">"k_Z3_bound_free"</span>,</a>
+<a class="sourceLine" id="cb59-5" title="5">                       <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div>
 <pre><code>## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = c(m.Z.mkin.
 ## 5$bparms.ode[1:7], : Observations with value of zero were removed from the
 ## data</code></pre>
-<div class="sourceCode" id="cb62"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb62-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div>
+<div class="sourceCode" id="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png" width="700"></p>
 <p>As expected, the residual plots for Z0 and Z3 are more random than in the case of the all SFO model for which they were shown above. In conclusion, the model  is proposed as the best-fit model for the dataset from Appendix 7 of the FOCUS report.</p>
 <p>A graphical representation of the confidence intervals can finally be obtained.</p>
-<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb63-1" title="1"><span class="kw"><a href="../../reference/mkinparplot.html">mkinparplot</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div>
+<div class="sourceCode" id="cb62"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb62-1" title="1"><span class="kw"><a href="../../reference/mkinparplot.html">mkinparplot</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div>
 <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png" width="700"></p>
 <p>The endpoints obtained with this model are</p>
-<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" title="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div>
+<div class="sourceCode" id="cb63"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb63-1" title="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div>
 <pre><code>## $ff
 ##   Z0_free_Z1        Z1_Z2      Z2_sink   Z2_Z3_free Z3_free_sink 
 ##      1.00000      1.00000      0.46344      0.53656      1.00000 
 ## 
 ## $SFORB
 ##     Z0_b1     Z0_b2     Z3_b1     Z3_b2 
-## 2.4471329 0.0075123 0.0800074 0.0000000 
+## 2.4471381 0.0075124 0.0800075 0.0000000 
 ## 
 ## $distimes
 ##      DT50   DT90 DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2
-## Z0 0.3043 1.1848    0.28325     92.268         NA         NA
+## Z0 0.3043 1.1848    0.28325     92.267         NA         NA
 ## Z1 1.5148 5.0320         NA         NA         NA         NA
 ## Z2 1.6414 5.4526         NA         NA         NA         NA
 ## Z3     NA     NA         NA         NA     8.6635        Inf</code></pre>
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png
index 3dfb6477..1a92365e 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png
index bb909e98..debf3cb8 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png
index c7cbb448..89020a0a 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png
index e39a2e6a..8188c4cf 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png
index 7213dac1..a11e0092 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png
diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png
index 27c51525..acd197f2 100644
--- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png
+++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index 0ae02f3c..04a60db6 100644
--- a/docs/articles/web_only/NAFTA_examples.html
+++ b/docs/articles/web_only/NAFTA_examples.html
@@ -88,7 +88,7 @@
       <h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2019-05-02</h4>
+            <h4 class="date">2019-05-03</h4>
       
       
       <div class="hidden name"><code>NAFTA_examples.Rmd</code></div>
@@ -141,7 +141,7 @@
 ##          Estimate   Pr(&gt;t)   Lower    Upper
 ## parent_0 9.99e+01 1.41e-26 98.8116 101.0810
 ## k1       2.67e-02 5.05e-06  0.0243   0.0295
-## k2       3.41e-12 5.00e-01  0.0000      Inf
+## k2       2.86e-12 5.00e-01  0.0000      Inf
 ## g        6.47e-01 3.67e-06  0.6248   0.6677
 ## sigma    1.27e+00 8.91e-06  0.8395   1.6929
 ## 
@@ -150,7 +150,7 @@
 ##      DT50     DT90 DT50_rep
 ## SFO  67.7 2.25e+02 6.77e+01
 ## IORE 58.2 1.07e+03 3.22e+02
-## DFOP 55.5 3.70e+11 2.03e+11
+## DFOP 55.5 4.42e+11 2.42e+11
 ## 
 ## Representative half-life:
 ## [1] 321.51</code></pre>
@@ -189,7 +189,7 @@
 ##          Estimate   Pr(&gt;t)   Lower   Upper
 ## parent_0 9.84e+01 1.24e-27 97.8078 98.9187
 ## k1       1.55e-02 4.10e-04  0.0143  0.0167
-## k2       8.28e-12 5.00e-01  0.0000     Inf
+## k2       1.16e-11 5.00e-01  0.0000     Inf
 ## g        6.89e-01 2.92e-03  0.6626  0.7142
 ## sigma    6.48e-01 2.38e-05  0.4147  0.8813
 ## 
@@ -198,7 +198,7 @@
 ##      DT50     DT90 DT50_rep
 ## SFO  86.6 2.88e+02 8.66e+01
 ## IORE 85.5 7.17e+02 2.16e+02
-## DFOP 83.6 1.37e+11 8.37e+10
+## DFOP 83.6 9.80e+10 5.98e+10
 ## 
 ## Representative half-life:
 ## [1] 215.87</code></pre>
@@ -222,7 +222,7 @@
 ## Parameters:
 ## $SFO
 ##               Estimate   Pr(&gt;t)   Lower   Upper
-## parent_0       94.7759 7.29e-24 92.3479 97.2039
+## parent_0       94.7759 7.29e-24 92.3478 97.2039
 ## k_parent_sink   0.0179 8.02e-16  0.0166  0.0194
 ## sigma           3.0696 3.81e-06  2.0456  4.0936
 ## 
@@ -237,7 +237,7 @@
 ##          Estimate   Pr(&gt;t)   Lower   Upper
 ## parent_0 9.66e+01 1.57e-25 95.3476 97.8979
 ## k1       2.55e-02 7.33e-06  0.0233  0.0278
-## k2       3.87e-11 5.00e-01  0.0000     Inf
+## k2       4.90e-11 5.00e-01  0.0000     Inf
 ## g        8.61e-01 7.55e-06  0.8314  0.8867
 ## sigma    1.46e+00 6.93e-06  0.9661  1.9483
 ## 
@@ -246,7 +246,7 @@
 ##      DT50     DT90 DT50_rep
 ## SFO  38.6 1.28e+02 3.86e+01
 ## IORE 34.0 1.77e+02 5.32e+01
-## DFOP 34.1 8.43e+09 1.79e+10
+## DFOP 34.1 6.66e+09 1.41e+10
 ## 
 ## Representative half-life:
 ## [1] 53.17</code></pre>
@@ -285,7 +285,7 @@
 ##          Estimate   Pr(&gt;t)   Lower    Upper
 ## parent_0 9.89e+01 9.44e-49 95.4640 102.2573
 ## k1       1.81e-02 1.75e-01  0.0116   0.0281
-## k2       2.46e-10 5.00e-01  0.0000      Inf
+## k2       1.97e-10 5.00e-01  0.0000      Inf
 ## g        6.06e-01 2.19e-01  0.4826   0.7178
 ## sigma    7.40e+00 2.97e-15  6.0201   8.7754
 ## 
@@ -294,7 +294,7 @@
 ##      DT50     DT90 DT50_rep
 ## SFO  94.3 3.13e+02 9.43e+01
 ## IORE 96.7 1.51e+03 4.55e+02
-## DFOP 96.4 5.58e+09 2.82e+09
+## DFOP 96.4 6.97e+09 3.52e+09
 ## 
 ## Representative half-life:
 ## [1] 454.55</code></pre>
@@ -397,7 +397,7 @@
 ##          Estimate   Pr(&gt;t)  Lower  Upper
 ## parent_0 9.85e+01 2.54e-20 97.390 99.672
 ## k1       1.38e-01 3.52e-05  0.131  0.146
-## k2       5.75e-13 5.00e-01  0.000    Inf
+## k2       6.02e-13 5.00e-01  0.000    Inf
 ## g        6.52e-01 8.13e-06  0.642  0.661
 ## sigma    7.88e-01 6.13e-02  0.481  1.095
 ## 
@@ -406,7 +406,7 @@
 ##      DT50     DT90 DT50_rep
 ## SFO  16.9 5.63e+01 1.69e+01
 ## IORE 11.6 3.37e+02 1.01e+02
-## DFOP 10.5 2.17e+12 1.21e+12
+## DFOP 10.5 2.07e+12 1.15e+12
 ## 
 ## Representative half-life:
 ## [1] 101.43</code></pre>
@@ -416,12 +416,16 @@
 <h2 class="hasAnchor">
 <a href="#example-on-page-9-lower-panel" class="anchor"></a>Example on page 9, lower panel</h2>
 <div class="sourceCode" id="cb38"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb38-1" title="1">p9b &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div>
+<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre>
 <pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre>
+<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre>
+<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
+## finite result is doubtful</code></pre>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div>
+<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p>
-<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div>
+<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 35.64867 23.22334 35.64867 
@@ -446,9 +450,9 @@
 ## $DFOP
 ##          Estimate   Pr(&gt;t)   Lower   Upper
 ## parent_0  94.7123 1.61e-16 93.1355 96.2891
-## k1         0.0389      NaN  0.0306  0.0495
-## k2         0.0389 1.10e-06  0.0186  0.0812
-## g          0.7598      NaN  0.0000  1.0000
+## k1         0.0389 1.43e-06  0.0312  0.0485
+## k2         0.0389 6.67e-03  0.0186  0.0812
+## g          0.7742      NaN      NA      NA
 ## sigma      1.5957 2.50e-04  0.9135  2.2779
 ## 
 ## 
@@ -465,12 +469,12 @@
 <div id="example-on-page-10" class="section level2">
 <h2 class="hasAnchor">
 <a href="#example-on-page-10" class="anchor"></a>Example on page 10</h2>
-<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" title="1">p10 &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p10"</span>]])</a></code></pre></div>
+<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1">p10 &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p10"</span>]])</a></code></pre></div>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div>
+<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p>
-<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div>
+<div class="sourceCode" id="cb52"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb52-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 899.4089 336.4348 899.4089 
@@ -495,8 +499,8 @@
 ## $DFOP
 ##          Estimate   Pr(&gt;t)   Lower    Upper
 ## parent_0 101.7315 1.41e-09 91.6534 111.8097
-## k1         0.0495 6.41e-04  0.0303   0.0809
-## k2         0.0495 1.66e-02  0.0201   0.1219
+## k1         0.0495 6.42e-04  0.0301   0.0814
+## k2         0.0495 1.66e-02  0.0200   0.1225
 ## g          0.6634 5.00e-01  0.0000   1.0000
 ## sigma      8.0152 2.50e-04  4.5886  11.4418
 ## 
@@ -518,12 +522,12 @@
 <div id="example-on-page-11" class="section level2">
 <h2 class="hasAnchor">
 <a href="#example-on-page-11" class="anchor"></a>Example on page 11</h2>
-<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" title="1">p11 &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p11"</span>]])</a></code></pre></div>
+<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1">p11 &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p11"</span>]])</a></code></pre></div>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div>
+<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p>
-<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div>
+<div class="sourceCode" id="cb58"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb58-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 579.6805 204.7932 144.7783 
@@ -549,7 +553,7 @@
 ##          Estimate   Pr(&gt;t)    Lower    Upper
 ## parent_0 1.05e+02 9.47e-13  99.9990 109.1224
 ## k1       4.41e-02 5.95e-03   0.0296   0.0658
-## k2       9.20e-13 5.00e-01   0.0000      Inf
+## k2       7.25e-13 5.00e-01   0.0000      Inf
 ## g        3.22e-01 1.45e-03   0.2814   0.3650
 ## sigma    3.22e+00 3.52e-04   1.8410   4.5906
 ## 
@@ -558,7 +562,7 @@
 ##          DT50     DT90 DT50_rep
 ## SFO  2.16e+02 7.18e+02 2.16e+02
 ## IORE 9.73e+02 1.37e+08 4.11e+07
-## DFOP 3.31e+11 2.08e+12 7.53e+11
+## DFOP 4.21e+11 2.64e+12 9.56e+11
 ## 
 ## Representative half-life:
 ## [1] 41148169</code></pre>
@@ -572,19 +576,14 @@
 <div id="example-on-page-12-upper-panel" class="section level2">
 <h2 class="hasAnchor">
 <a href="#example-on-page-12-upper-panel" class="anchor"></a>Example on page 12, upper panel</h2>
-<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1">p12a &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></code></pre></div>
+<div class="sourceCode" id="cb60"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb60-1" title="1">p12a &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></code></pre></div>
 <pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
 ## singular system.</code></pre>
-<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre>
-<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre>
-<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre>
-<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
-## finite result is doubtful</code></pre>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb65"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb65-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12a)</a></code></pre></div>
+<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12a)</a></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p>
-<div class="sourceCode" id="cb66"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb66-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12a)</a></code></pre></div>
+<div class="sourceCode" id="cb65"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb65-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12a)</a></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 695.4440 220.0685 695.4440 
@@ -609,9 +608,9 @@
 ## $DFOP
 ##          Estimate   Pr(&gt;t)   Lower   Upper
 ## parent_0  100.521 2.74e-10 92.2366 108.805
-## k1          0.124 5.43e-06  0.0959   0.161
-## k2          0.124 6.45e-02  0.0315   0.490
-## g           0.880      NaN      NA      NA
+## k1          0.124 5.74e-06  0.0958   0.161
+## k2          0.124 6.61e-02  0.0319   0.484
+## g           0.877 5.00e-01  0.0000   1.000
 ## sigma       7.048 2.50e-04  4.0349  10.061
 ## 
 ## 
@@ -627,7 +626,7 @@
 <div id="example-on-page-12-lower-panel" class="section level2">
 <h2 class="hasAnchor">
 <a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2>
-<div class="sourceCode" id="cb68"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb68-1" title="1">p12b &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div>
+<div class="sourceCode" id="cb67"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb67-1" title="1">p12b &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div>
 <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre>
 <pre><code>## Warning in qt(alpha/2, rdf): NaNs wurden erzeugt</code></pre>
 <pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs wurden erzeugt</code></pre>
@@ -638,9 +637,9 @@
 ## finite result is doubtful</code></pre>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb78"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb78-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div>
+<div class="sourceCode" id="cb77"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb77-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p>
-<div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div>
+<div class="sourceCode" id="cb78"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb78-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 58.90242 19.06353 58.90242 
@@ -667,7 +666,7 @@
 ## parent_0  97.6840    NaN   NaN   NaN
 ## k1         0.0589    NaN    NA    NA
 ## k2         0.0589    NaN    NA    NA
-## g          0.8275    NaN    NA    NA
+## g          0.6902    NaN    NA    NA
 ## sigma      3.4323    NaN   NaN   NaN
 ## 
 ## 
@@ -683,12 +682,16 @@
 <div id="example-on-page-13" class="section level2">
 <h2 class="hasAnchor">
 <a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2>
-<div class="sourceCode" id="cb81"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb81-1" title="1">p13 &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div>
+<div class="sourceCode" id="cb80"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb80-1" title="1">p13 &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div>
+<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre>
+<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre>
+<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
+## finite result is doubtful</code></pre>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb84"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb84-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div>
+<div class="sourceCode" id="cb86"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb86-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p>
-<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div>
+<div class="sourceCode" id="cb87"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb87-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 174.5971 142.3951 174.5971 
@@ -713,9 +716,9 @@
 ## $DFOP
 ##          Estimate   Pr(&gt;t)    Lower    Upper
 ## parent_0 92.73500 9.25e-15 8.95e+01 9.59e+01
-## k1        0.00258 4.28e-01 1.25e-08 5.31e+02
+## k1        0.00258 4.28e-01 1.70e-08 3.92e+02
 ## k2        0.00258 3.69e-08 2.20e-03 3.03e-03
-## g         0.00442 5.00e-01 0.00e+00 1.00e+00
+## g         0.00442 5.00e-01       NA       NA
 ## sigma     3.41172 1.35e-04 2.02e+00 4.80e+00
 ## 
 ## 
@@ -732,16 +735,16 @@
 <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1">
 <h1 class="hasAnchor">
 <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1>
-<div class="sourceCode" id="cb87"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb87-1" title="1">p14 &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div>
+<div class="sourceCode" id="cb89"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb89-1" title="1">p14 &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div>
 <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre>
 <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre>
 <pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
 ## finite result is doubtful</code></pre>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb93"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb93-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div>
+<div class="sourceCode" id="cb95"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb95-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p>
-<div class="sourceCode" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div>
+<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 48.43249 28.67746 27.26248 
@@ -767,7 +770,7 @@
 ##          Estimate   Pr(&gt;t)    Lower    Upper
 ## parent_0 1.00e+02 2.96e-28 99.40280 101.2768
 ## k1       9.53e-03 1.20e-01  0.00638   0.0143
-## k2       5.42e-12 5.00e-01  0.00000      Inf
+## k2       7.29e-12 5.00e-01  0.00000      Inf
 ## g        3.98e-01 2.19e-01  0.30481   0.4998
 ## sigma    1.17e+00 7.68e-06  0.77406   1.5610
 ## 
@@ -776,7 +779,7 @@
 ##          DT50     DT90 DT50_rep
 ## SFO  2.48e+02 8.25e+02 2.48e+02
 ## IORE 4.34e+02 2.22e+04 6.70e+03
-## DFOP 3.41e+10 3.31e+11 1.28e+11
+## DFOP 2.54e+10 2.46e+11 9.51e+10
 ## 
 ## Representative half-life:
 ## [1] 6697.44</code></pre>
@@ -785,7 +788,7 @@
 <div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1">
 <h1 class="hasAnchor">
 <a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1>
-<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" title="1">p15a &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15a"</span>]])</a></code></pre></div>
+<div class="sourceCode" id="cb98"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb98-1" title="1">p15a &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15a"</span>]])</a></code></pre></div>
 <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre>
 <pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre>
 <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre>
@@ -793,9 +796,9 @@
 ## finite result is doubtful</code></pre>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb103"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb103-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div>
+<div class="sourceCode" id="cb105"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb105-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p>
-<div class="sourceCode" id="cb104"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb104-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div>
+<div class="sourceCode" id="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 245.5248 135.0132 245.5248 
@@ -819,10 +822,10 @@
 ## 
 ## $DFOP
 ##          Estimate   Pr(&gt;t)    Lower    Upper
-## parent_0 97.96751 2.85e-13 94.21913 101.7159
-## k1        0.00952 5.68e-02  0.00262   0.0347
-## k2        0.00952 1.52e-04  0.00639   0.0142
-## g         0.22357      NaN       NA       NA
+## parent_0 97.96752 2.85e-13 94.21914 101.7159
+## k1        0.00952 6.80e-02  0.00277   0.0327
+## k2        0.00952 3.82e-06  0.00902   0.0100
+## g         0.17247      NaN       NA       NA
 ## sigma     4.18778 2.50e-04  2.39747   5.9781
 ## 
 ## 
@@ -834,12 +837,16 @@
 ## 
 ## Representative half-life:
 ## [1] 41.33</code></pre>
-<div class="sourceCode" id="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" title="1">p15b &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div>
+<div class="sourceCode" id="cb108"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb108-1" title="1">p15b &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div>
+<pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre>
+<pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre>
+<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
+## finite result is doubtful</code></pre>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The half-life obtained from the IORE model may be used</code></pre>
-<div class="sourceCode" id="cb109"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb109-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div>
+<div class="sourceCode" id="cb114"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb114-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p>
-<div class="sourceCode" id="cb110"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb110-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div>
+<div class="sourceCode" id="cb115"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb115-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div>
 <pre><code>## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 106.91629  68.55574 106.91629 
@@ -864,9 +871,9 @@
 ## $DFOP
 ##          Estimate Pr(&gt;t)    Lower    Upper
 ## parent_0 1.01e+02     NA 9.82e+01 1.04e+02
-## k1       4.86e-03     NA 6.49e-04 3.64e-02
-## k2       4.86e-03     NA 3.36e-03 7.03e-03
-## g        1.50e-01     NA 0.00e+00 1.00e+00
+## k1       4.86e-03     NA 6.75e-04 3.49e-02
+## k2       4.86e-03     NA 3.37e-03 6.99e-03
+## g        1.50e-01     NA       NA       NA
 ## sigma    2.76e+00     NA 1.58e+00 3.94e+00
 ## 
 ## 
@@ -883,14 +890,14 @@
 <div id="the-dfop-fraction-parameter-is-greater-than-1" class="section level1">
 <h1 class="hasAnchor">
 <a href="#the-dfop-fraction-parameter-is-greater-than-1" class="anchor"></a>The DFOP fraction parameter is greater than 1</h1>
-<div class="sourceCode" id="cb112"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb112-1" title="1">p16 &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p16"</span>]])</a></code></pre></div>
+<div class="sourceCode" id="cb117"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb117-1" title="1">p16 &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p16"</span>]])</a></code></pre></div>
 <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre>
 <pre><code>## The representative half-life of the IORE model is longer than the one corresponding</code></pre>
 <pre><code>## to the terminal degradation rate found with the DFOP model.</code></pre>
 <pre><code>## The representative half-life obtained from the DFOP model may be used</code></pre>
-<div class="sourceCode" id="cb117"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb117-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div>
+<div class="sourceCode" id="cb122"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb122-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div>
 <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p>
-<div class="sourceCode" id="cb118"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb118-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div>
+<div class="sourceCode" id="cb123"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb123-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div>
 <pre><code>## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 3831.804 2062.008 1550.980 
@@ -915,7 +922,7 @@
 ## $DFOP
 ##          Estimate   Pr(&gt;t)   Lower  Upper
 ## parent_0  88.5333 7.40e-18 79.9836 97.083
-## k1        18.6315 5.00e-01  0.0000    Inf
+## k1        18.5561 5.00e-01  0.0000    Inf
 ## k2         0.0776 1.41e-05  0.0518  0.116
 ## g          0.4733 1.41e-09  0.3674  0.582
 ## sigma      7.1902 2.11e-08  5.2785  9.102
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png
index 8ffc5375..396828c3 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p14-1.png
diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png
index 48d65737..57bf4014 100644
--- a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png
+++ b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 5f6312ce..6df96c14 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -88,7 +88,7 @@
       <h1>Benchmark timings for mkin on various systems</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2019-05-02</h4>
+            <h4 class="date">2019-05-03</h4>
       
       
       <div class="hidden name"><code>benchmarks.Rmd</code></div>
@@ -115,32 +115,32 @@
 <a class="sourceLine" id="cb1-12" title="12">}</a></code></pre></div>
 <div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="co"># Parent only</span></a>
 <a class="sourceLine" id="cb2-2" title="2">t1 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a>
-<a class="sourceLine" id="cb2-3" title="3">t2 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a></code></pre></div>
-<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
-## false convergence (8)</code></pre>
-<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="co"># One metabolite</span></a>
-<a class="sourceLine" id="cb4-2" title="2">SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a>
-<a class="sourceLine" id="cb4-3" title="3">  <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),</a>
-<a class="sourceLine" id="cb4-4" title="4">  <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div>
+<a class="sourceLine" id="cb2-3" title="3">t2 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"HS"</span>), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_C, FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a>
+<a class="sourceLine" id="cb2-4" title="4"></a>
+<a class="sourceLine" id="cb2-5" title="5"><span class="co"># One metabolite</span></a>
+<a class="sourceLine" id="cb2-6" title="6">SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a>
+<a class="sourceLine" id="cb2-7" title="7">  <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),</a>
+<a class="sourceLine" id="cb2-8" title="8">  <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div>
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">FOMC_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a>
+<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">FOMC_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a>
+<a class="sourceLine" id="cb4-2" title="2">  <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a>
+<a class="sourceLine" id="cb4-3" title="3">  <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div>
+<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
+<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">DFOP_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a>
 <a class="sourceLine" id="cb6-2" title="2">  <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a>
 <a class="sourceLine" id="cb6-3" title="3">  <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div>
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">DFOP_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a>
-<a class="sourceLine" id="cb8-2" title="2">  <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a>
-<a class="sourceLine" id="cb8-3" title="3">  <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div>
-<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">t3 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a></code></pre></div>
-<pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
-## Observations with value of zero were removed from the data</code></pre>
+<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">t3 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D)))[[<span class="st">"elapsed"</span>]]</a></code></pre></div>
 <pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
 ## Observations with value of zero were removed from the data
 
 ## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Observations with value of zero were removed from the data
+
+## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
 ## Observations with value of zero were removed from the data</code></pre>
-<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1">t4 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/subset">subset</a></span>(FOCUS_<span class="dv">2006</span>_D, value <span class="op">!=</span><span class="st"> </span><span class="dv">0</span>)), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a>
-<a class="sourceLine" id="cb13-2" title="2">t5 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[[<span class="st">"elapsed"</span>]]</a></code></pre></div>
+<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">t4 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/subset">subset</a></span>(FOCUS_<span class="dv">2006</span>_D, value <span class="op">!=</span><span class="st"> </span><span class="dv">0</span>)), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[[<span class="st">"elapsed"</span>]]</a>
+<a class="sourceLine" id="cb10-2" title="2">t5 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_SFO, FOMC_SFO, DFOP_SFO), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(FOCUS_<span class="dv">2006</span>_D), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[[<span class="st">"elapsed"</span>]]</a></code></pre></div>
 <pre><code>## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
 ## Observations with value of zero were removed from the data
 
@@ -149,32 +149,32 @@
 
 ## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
 ## Observations with value of zero were removed from the data</code></pre>
-<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1"><span class="co"># Two metabolites, synthetic data</span></a>
-<a class="sourceLine" id="cb15-2" title="2">m_synth_SFO_lin &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),</a>
-<a class="sourceLine" id="cb15-3" title="3">                           <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),</a>
-<a class="sourceLine" id="cb15-4" title="4">                           <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a>
-<a class="sourceLine" id="cb15-5" title="5">                           <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a>
-<a class="sourceLine" id="cb15-6" title="6"></a>
-<a class="sourceLine" id="cb15-7" title="7">m_synth_DFOP_par &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"DFOP"</span>, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"M1"</span>, <span class="st">"M2"</span>)),</a>
-<a class="sourceLine" id="cb15-8" title="8">                           <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a>
-<a class="sourceLine" id="cb15-9" title="9">                           <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a>
-<a class="sourceLine" id="cb15-10" title="10">                           <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a>
-<a class="sourceLine" id="cb15-11" title="11"></a>
-<a class="sourceLine" id="cb15-12" title="12">SFO_lin_a &lt;-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">1</span>]]<span class="op">$</span>data</a>
-<a class="sourceLine" id="cb15-13" title="13"></a>
-<a class="sourceLine" id="cb15-14" title="14">DFOP_par_c &lt;-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">12</span>]]<span class="op">$</span>data</a>
-<a class="sourceLine" id="cb15-15" title="15"></a>
-<a class="sourceLine" id="cb15-16" title="16">t6 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a)))[<span class="st">"elapsed"</span>]</a>
-<a class="sourceLine" id="cb15-17" title="17">t7 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c)))[<span class="st">"elapsed"</span>]</a>
-<a class="sourceLine" id="cb15-18" title="18"></a>
-<a class="sourceLine" id="cb15-19" title="19">t8 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a>
-<a class="sourceLine" id="cb15-20" title="20">t9 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a>
-<a class="sourceLine" id="cb15-21" title="21"></a>
-<a class="sourceLine" id="cb15-22" title="22">t10 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a>
-<a class="sourceLine" id="cb15-23" title="23">t11 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a>
-<a class="sourceLine" id="cb15-24" title="24"></a>
-<a class="sourceLine" id="cb15-25" title="25">mkin_benchmarks[system_string, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste0</a></span>(<span class="st">"t"</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">11</span>)] &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)</a>
-<a class="sourceLine" id="cb15-26" title="26">mkin_benchmarks</a></code></pre></div>
+<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="co"># Two metabolites, synthetic data</span></a>
+<a class="sourceLine" id="cb12-2" title="2">m_synth_SFO_lin &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),</a>
+<a class="sourceLine" id="cb12-3" title="3">                           <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),</a>
+<a class="sourceLine" id="cb12-4" title="4">                           <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a>
+<a class="sourceLine" id="cb12-5" title="5">                           <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a>
+<a class="sourceLine" id="cb12-6" title="6"></a>
+<a class="sourceLine" id="cb12-7" title="7">m_synth_DFOP_par &lt;-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"DFOP"</span>, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"M1"</span>, <span class="st">"M2"</span>)),</a>
+<a class="sourceLine" id="cb12-8" title="8">                           <span class="dt">M1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a>
+<a class="sourceLine" id="cb12-9" title="9">                           <span class="dt">M2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a>
+<a class="sourceLine" id="cb12-10" title="10">                           <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a>
+<a class="sourceLine" id="cb12-11" title="11"></a>
+<a class="sourceLine" id="cb12-12" title="12">SFO_lin_a &lt;-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">1</span>]]<span class="op">$</span>data</a>
+<a class="sourceLine" id="cb12-13" title="13"></a>
+<a class="sourceLine" id="cb12-14" title="14">DFOP_par_c &lt;-<span class="st"> </span>synthetic_data_for_UBA_<span class="dv">2014</span>[[<span class="dv">12</span>]]<span class="op">$</span>data</a>
+<a class="sourceLine" id="cb12-15" title="15"></a>
+<a class="sourceLine" id="cb12-16" title="16">t6 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a)))[<span class="st">"elapsed"</span>]</a>
+<a class="sourceLine" id="cb12-17" title="17">t7 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c)))[<span class="st">"elapsed"</span>]</a>
+<a class="sourceLine" id="cb12-18" title="18"></a>
+<a class="sourceLine" id="cb12-19" title="19">t8 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a>
+<a class="sourceLine" id="cb12-20" title="20">t9 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"tc"</span>))[<span class="st">"elapsed"</span>]</a>
+<a class="sourceLine" id="cb12-21" title="21"></a>
+<a class="sourceLine" id="cb12-22" title="22">t10 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_SFO_lin), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(SFO_lin_a), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a>
+<a class="sourceLine" id="cb12-23" title="23">t11 &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/system.time">system.time</a></span>(<span class="kw">mmkin_bench</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(m_synth_DFOP_par), <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(DFOP_par_c), <span class="dt">error_model =</span> <span class="st">"obs"</span>))[<span class="st">"elapsed"</span>]</a>
+<a class="sourceLine" id="cb12-24" title="24"></a>
+<a class="sourceLine" id="cb12-25" title="25">mkin_benchmarks[system_string, <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste0</a></span>(<span class="st">"t"</span>, <span class="dv">1</span><span class="op">:</span><span class="dv">11</span>)] &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)</a>
+<a class="sourceLine" id="cb12-26" title="26">mkin_benchmarks</a></code></pre></div>
 <pre><code>##                                                                                                       CPU
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 AMD Ryzen 7 1700 Eight-Core Processor
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 AMD Ryzen 7 1700 Eight-Core Processor
@@ -198,68 +198,68 @@
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.850
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.864
 ##                                                                         t2
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.019
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 23.254
 ##                                                                        t3
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.293
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.544
 ##                                                                         t4
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  8.461
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 14.570
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.757
 ##                                                                        t5
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.772
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.870
 ##                                                                        t6
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.647
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.554
 ##                                                                        t7
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.257
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  4.22
 ##                                                                        t8
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.02
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.703
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.479
 ##                                                                         t9
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  8.171
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  7.618
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  7.742
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 11.236
 ##                                                                       t10
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.421
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.803
 ##                                                                        t11
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  5.636
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.574
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.365
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  5.614</code></pre>
-<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/save">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</a></code></pre></div>
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  7.688</code></pre>
+<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/save">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</a></code></pre></div>
 </div>
   </div>
 
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 362bc72c..feba6e23 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -88,7 +88,7 @@
       <h1>Performance benefit by using compiled model definitions in mkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2019-05-02</h4>
+            <h4 class="date">2019-05-03</h4>
       
       
       <div class="hidden name"><code>compiled_models.Rmd</code></div>
@@ -163,9 +163,9 @@
 ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
 ## = TRUE): Observations with value of zero were removed from the data</code></pre>
 <pre><code>##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   3.174    1.000     3.172        0
-## 1 deSolve, not compiled            3  28.777    9.066    28.764        0
-## 2      Eigenvalue based            3   4.386    1.382     4.383        0
+## 3     deSolve, compiled            3   3.075    1.000     3.072    0.000
+## 1 deSolve, not compiled            3  28.192    9.168    28.168    0.008
+## 2      Eigenvalue based            3   4.351    1.415     4.349    0.000
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -214,8 +214,8 @@
 ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
 ## value of zero were removed from the data</code></pre>
 <pre><code>##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.561    1.000     4.559        0
-## 1 deSolve, not compiled            3  49.847   10.929    49.823        0
+## 2     deSolve, compiled            3   4.933    1.000     4.930        0
+## 1 deSolve, not compiled            3  52.879   10.719    52.853        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0</code></pre>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 3b7209b1..652dfee0 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -189,7 +189,7 @@
     <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span>]]
   )</div><div class='output co'>#&gt; $par
 #&gt;  parent_0 log_alpha  log_beta     sigma 
-#&gt; 99.666193  2.549850  5.050586  1.890202 
+#&gt; 99.666193  2.549849  5.050586  1.890202 
 #&gt; 
 #&gt; $objective
 #&gt; [1] 28.58291
@@ -202,7 +202,7 @@
 #&gt; 
 #&gt; $evaluations
 #&gt; function gradient 
-#&gt;       25       76 
+#&gt;       25       72 
 #&gt; 
 #&gt; $message
 #&gt; [1] "both X-convergence and relative convergence (5)"
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index c9b79512..c67c2a37 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -182,9 +182,9 @@
 
     <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='no'>fit.fomc</span>$<span class='no'>par</span>, <span class='no'>fit.iore</span>$<span class='no'>par</span>, <span class='no'>fit.iore.deS</span>$<span class='no'>par</span>,
                      <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"model par"</span>, <span class='fl'>1</span>:<span class='fl'>4</span>)))</div><div class='output co'>#&gt;             fit.fomc.par fit.iore.par fit.iore.deS.par
-#&gt; model par 1  85.87488995    85.874890        85.874890
-#&gt; model par 2   0.05192228    -4.826631        -4.826631
-#&gt; model par 3   0.65096650     1.949403         1.949403
+#&gt; model par 1  85.87489063    85.874890        85.874890
+#&gt; model par 2   0.05192238    -4.826631        -4.826631
+#&gt; model par 3   0.65096665     1.949403         1.949403
 #&gt; model par 4   1.85744396     1.857444         1.857444</div><div class='input'>    <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/cbind'>rbind</a></span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>,
                 <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>))</div><div class='output co'>#&gt;              DT50    DT90 DT50back
 #&gt; fomc     1.785233 15.1479 4.559973
diff --git a/docs/reference/NAFTA_SOP_Attachment-1.png b/docs/reference/NAFTA_SOP_Attachment-1.png
index 87068d7c..a40cb689 100644
--- a/docs/reference/NAFTA_SOP_Attachment-1.png
+++ b/docs/reference/NAFTA_SOP_Attachment-1.png
diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html
index 48a1495f..76d91c40 100644
--- a/docs/reference/NAFTA_SOP_Attachment.html
+++ b/docs/reference/NAFTA_SOP_Attachment.html
@@ -177,7 +177,7 @@
 #&gt;          Estimate   Pr(&gt;t)   Lower    Upper
 #&gt; parent_0 9.99e+01 1.41e-26 98.8116 101.0810
 #&gt; k1       2.67e-02 5.05e-06  0.0243   0.0295
-#&gt; k2       3.41e-12 5.00e-01  0.0000      Inf
+#&gt; k2       2.86e-12 5.00e-01  0.0000      Inf
 #&gt; g        6.47e-01 3.67e-06  0.6248   0.6677
 #&gt; sigma    1.27e+00 8.91e-06  0.8395   1.6929
 #&gt; 
@@ -186,7 +186,7 @@
 #&gt;      DT50     DT90 DT50_rep
 #&gt; SFO  67.7 2.25e+02 6.77e+01
 #&gt; IORE 58.2 1.07e+03 3.22e+02
-#&gt; DFOP 55.5 3.70e+11 2.03e+11
+#&gt; DFOP 55.5 4.42e+11 2.42e+11
 #&gt; 
 #&gt; Representative half-life:
 #&gt; [1] 321.51</div><div class='input'>  <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='img'><img src='NAFTA_SOP_Attachment-1.png' alt='' width='700' height='433' /></div></pre>
diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png
index 2f60fdf7..61f00d9b 100644
--- a/docs/reference/add_err-1.png
+++ b/docs/reference/add_err-1.png
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index 0184d573..f5844a8e 100644
--- a/docs/reference/logLik.mkinfit.html
+++ b/docs/reference/logLik.mkinfit.html
@@ -180,7 +180,7 @@ The total number of estimated parameters returned with the value
   <span class='no'>f_nw</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># no weighting (weights are unity)</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>  <span class='no'>f_obs</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>  <span class='no'>f_tc</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>  <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f_nw</span>, <span class='no'>f_obs</span>, <span class='no'>f_tc</span>)</div><div class='output co'>#&gt;       df      AIC
 #&gt; f_nw   5 204.4486
 #&gt; f_obs  6 205.8727
-#&gt; f_tc   6 141.9656</div><div class='input'>  </div></pre>
+#&gt; f_tc   6 148.1802</div><div class='input'>  </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
index 4ce03e83..3b45b14f 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.html
@@ -206,18 +206,18 @@
 
   <span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
   <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt;              Estimate   se_notrans   t value       Pr(&gt;t)        Lower
-#&gt; parent_0 1.057896e+02 1.9023449643 55.610120 3.768361e-16 1.016451e+02
+#&gt; parent_0 1.057896e+02 1.9023449649 55.610120 3.768361e-16 1.016451e+02
 #&gt; kmax     6.398190e-02 0.0143201029  4.467978 3.841828e-04 3.929235e-02
-#&gt; k0       1.612775e-04 0.0005866813  0.274898 3.940351e-01 5.846687e-08
-#&gt; r        2.263946e-01 0.1718110718  1.317695 1.061044e-01 4.335843e-02
+#&gt; k0       1.612775e-04 0.0005866813  0.274898 3.940351e-01 5.846685e-08
+#&gt; r        2.263946e-01 0.1718110773  1.317695 1.061044e-01 4.335843e-02
 #&gt; sigma    5.332935e+00 0.9145907310  5.830952 4.036926e-05 3.340213e+00
 #&gt;                Upper
 #&gt; parent_0 109.9341588
 #&gt; kmax       0.1041853
-#&gt; k0         0.4448749
+#&gt; k0         0.4448750
 #&gt; r          1.1821121
 #&gt; sigma      7.3256566</div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt;            DT50     DT90  DT50_k0 DT50_kmax
-#&gt; parent 36.86533 62.41511 4297.853  10.83349</div></pre>
+#&gt; parent 36.86533 62.41511 4297.854  10.83349</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 1f0f6b50..1db9a9d9 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -160,14 +160,14 @@
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>  <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>),
                          <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>),
-                         <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>  </div><div class='input'>    <span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>    <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt;                      Estimate  se_notrans   t value       Pr(&gt;t)        Lower
-#&gt; T245_0           1.038550e+02 2.150809526 48.286486 3.542195e-18 99.246062243
-#&gt; k_T245_sink      1.636106e-02         NaN       NaN          NaN  0.012661558
-#&gt; k_T245_phenol    2.700936e-02         NaN       NaN          NaN  0.024487315
-#&gt; k_phenol_sink    1.187912e-10         NaN       NaN          NaN  0.000000000
-#&gt; k_phenol_anisole 4.050581e-01 0.105378416  3.843843 7.969195e-04  0.218013983
-#&gt; k_anisole_sink   6.678742e-03 0.000620576 10.762166 9.426361e-09  0.005370739
-#&gt; sigma            2.514628e+00 0.338361458  7.431780 1.053891e-06  1.706607296
+                         <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>  </div><div class='input'>    <span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>    <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt;                      Estimate   se_notrans   t value       Pr(&gt;t)        Lower
+#&gt; T245_0           1.038550e+02 2.1508110557 48.286452 3.542232e-18 99.246062215
+#&gt; k_T245_sink      1.636106e-02          NaN       NaN          NaN  0.012661558
+#&gt; k_T245_phenol    2.700936e-02          NaN       NaN          NaN  0.024487315
+#&gt; k_phenol_sink    1.788604e-10          NaN       NaN          NaN  0.000000000
+#&gt; k_phenol_anisole 4.050581e-01 0.1053801116  3.843781 7.970202e-04  0.218013982
+#&gt; k_anisole_sink   6.678742e-03 0.0006205844 10.762020 9.428076e-09  0.005370739
+#&gt; sigma            2.514628e+00 0.3383670685  7.431657 1.054101e-06  1.706607296
 #&gt;                         Upper
 #&gt; T245_0           1.084640e+02
 #&gt; k_T245_sink      2.114150e-02
@@ -177,7 +177,7 @@
 #&gt; k_anisole_sink   8.305299e-03
 #&gt; sigma            3.322649e+00</div><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#&gt; $ff
 #&gt;      T245_sink    T245_phenol    phenol_sink phenol_anisole   anisole_sink 
-#&gt;   3.772401e-01   6.227599e-01   2.932696e-10   1.000000e+00   1.000000e+00 
+#&gt;   3.772401e-01   6.227599e-01   4.415672e-10   1.000000e+00   1.000000e+00 
 #&gt; 
 #&gt; $SFORB
 #&gt; logical(0)
@@ -191,21 +191,21 @@
     <span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
                    <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
                    <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>    <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.2</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt;                      Estimate   se_notrans   t value       Pr(&gt;t)        Lower
-#&gt; T245_0           1.038550e+02 2.1623652988 48.028441 4.993105e-19 99.271024566
-#&gt; k_T245_sink      1.636106e-02 0.0019676253  8.315129 1.673677e-07  0.012679144
-#&gt; k_T245_phenol    2.700936e-02 0.0012421965 21.743225 1.314080e-13  0.024500318
-#&gt; k_phenol_anisole 4.050581e-01 0.1177235385  3.440757 1.679236e-03  0.218746681
-#&gt; k_anisole_sink   6.678743e-03 0.0006829745  9.778904 1.872891e-08  0.005377084
+#&gt; T245_0           1.038550e+02 2.1623653063 48.028441 4.993105e-19 99.271025146
+#&gt; k_T245_sink      1.636106e-02 0.0019676255  8.315130 1.673674e-07  0.012679148
+#&gt; k_T245_phenol    2.700936e-02 0.0012421966 21.743224 1.314080e-13  0.024500319
+#&gt; k_phenol_anisole 4.050581e-01 0.1177235488  3.440757 1.679237e-03  0.218746679
+#&gt; k_anisole_sink   6.678742e-03 0.0006829745  9.778904 1.872892e-08  0.005377084
 #&gt; sigma            2.514628e+00 0.3790944250  6.633250 2.875782e-06  1.710983655
 #&gt;                         Upper
-#&gt; T245_0           1.084390e+02
-#&gt; k_T245_sink      2.111217e-02
-#&gt; k_T245_phenol    2.977534e-02
-#&gt; k_phenol_anisole 7.500550e-01
-#&gt; k_anisole_sink   8.295501e-03
-#&gt; sigma            3.318272e+00</div><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#&gt; $ff
+#&gt; T245_0           108.43904395
+#&gt; k_T245_sink        0.02111217
+#&gt; k_T245_phenol      0.02977535
+#&gt; k_phenol_anisole   0.75005504
+#&gt; k_anisole_sink     0.00829550
+#&gt; sigma              3.31827222</div><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.1</span>)</div><div class='output co'>#&gt; $ff
 #&gt;      T245_sink    T245_phenol    phenol_sink phenol_anisole   anisole_sink 
-#&gt;   3.772401e-01   6.227599e-01   2.932696e-10   1.000000e+00   1.000000e+00 
+#&gt;   3.772401e-01   6.227599e-01   4.415672e-10   1.000000e+00   1.000000e+00 
 #&gt; 
 #&gt; $SFORB
 #&gt; logical(0)
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 545ed8ab..8c14fc9d 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -362,15 +362,15 @@ Per default, parameters in the kinetic models are internally transformed in
 <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.4 
 #&gt; R version used for fitting:       3.6.0 
-#&gt; Date of fit:     Thu May  2 18:47:43 2019 
-#&gt; Date of summary: Thu May  2 18:47:43 2019 
+#&gt; Date of fit:     Fri May  3 19:07:19 2019 
+#&gt; Date of summary: Fri May  3 19:07:19 2019 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #&gt; 
 #&gt; Model predictions using solution type analytical 
 #&gt; 
-#&gt; Fitted using 221 model solutions performed in 0.458 s
+#&gt; Fitted using 222 model solutions performed in 0.463 s
 #&gt; 
 #&gt; Error model:
 #&gt; Constant variance 
@@ -400,11 +400,11 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt; sigma      1.85700     0.4378  0.73200  2.9830
 #&gt; 
 #&gt; Parameter correlation:
-#&gt;             parent_0  log_alpha   log_beta      sigma
-#&gt; parent_0   1.000e+00 -1.565e-01 -3.142e-01 -1.317e-07
-#&gt; log_alpha -1.565e-01  1.000e+00  9.564e-01 -2.640e-07
-#&gt; log_beta  -3.142e-01  9.564e-01  1.000e+00 -2.205e-07
-#&gt; sigma     -1.317e-07 -2.640e-07 -2.205e-07  1.000e+00
+#&gt;             parent_0  log_alpha   log_beta     sigma
+#&gt; parent_0   1.000e+00 -1.565e-01 -3.142e-01 4.770e-08
+#&gt; log_alpha -1.565e-01  1.000e+00  9.564e-01 9.974e-08
+#&gt; log_beta  -3.142e-01  9.564e-01  1.000e+00 8.468e-08
+#&gt; sigma      4.770e-08  9.974e-08  8.468e-08 1.000e+00
 #&gt; 
 #&gt; Backtransformed parameters:
 #&gt; Confidence intervals for internally transformed parameters are asymmetric.
@@ -443,7 +443,7 @@ Per default, parameters in the kinetic models are internally transformed in
   <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
                            <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       1.524       0.000       1.525 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
+#&gt;       1.493       0.000       1.494 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
 #&gt; parent_sink   parent_m1     m1_sink 
 #&gt;    0.485524    0.514476    1.000000 
 #&gt; 
@@ -452,75 +452,72 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt; 
 #&gt; $distimes
 #&gt;              DT50      DT90
-#&gt; parent   7.022928  23.32966
-#&gt; m1     131.760715 437.69962
+#&gt; parent   7.022929  23.32967
+#&gt; m1     131.760712 437.69961
 #&gt; </div><div class='input'><span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</span>
 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit.deSolve</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
-                           <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; Sum of squared residuals at call 1: 18915.53
+                           <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#&gt; Sum of squared residuals at call 1: 18915.53
 #&gt; Sum of squared residuals at call 2: 18915.53
 #&gt; Sum of squared residuals at call 6: 11424.02
 #&gt; Sum of squared residuals at call 10: 11424
-#&gt; Sum of squared residuals at call 13: 2367.052
-#&gt; Sum of squared residuals at call 14: 2367.05
-#&gt; Sum of squared residuals at call 19: 1314.716
-#&gt; Sum of squared residuals at call 22: 1314.714
-#&gt; Sum of squared residuals at call 25: 991.8311
-#&gt; Sum of squared residuals at call 28: 991.8305
-#&gt; Sum of squared residuals at call 30: 893.6462
-#&gt; Sum of squared residuals at call 33: 893.6457
-#&gt; Sum of squared residuals at call 35: 569.4049
-#&gt; Sum of squared residuals at call 38: 569.4047
-#&gt; Sum of squared residuals at call 40: 565.0651
-#&gt; Sum of squared residuals at call 41: 565.065
-#&gt; Sum of squared residuals at call 42: 565.0637
-#&gt; Sum of squared residuals at call 45: 428.0188
-#&gt; Sum of squared residuals at call 46: 428.0185
-#&gt; Sum of squared residuals at call 50: 406.732
-#&gt; Sum of squared residuals at call 52: 406.732
-#&gt; Sum of squared residuals at call 55: 398.9115
-#&gt; Sum of squared residuals at call 57: 398.9113
-#&gt; Sum of squared residuals at call 60: 394.5943
-#&gt; Sum of squared residuals at call 62: 394.5943
-#&gt; Sum of squared residuals at call 66: 385.26
-#&gt; Sum of squared residuals at call 67: 385.2599
-#&gt; Sum of squared residuals at call 69: 385.2599
-#&gt; Sum of squared residuals at call 70: 385.2597
-#&gt; Sum of squared residuals at call 71: 374.7604
-#&gt; Sum of squared residuals at call 72: 374.7603
-#&gt; Sum of squared residuals at call 76: 373.199
-#&gt; Sum of squared residuals at call 79: 373.199
-#&gt; Sum of squared residuals at call 80: 373.199
-#&gt; Sum of squared residuals at call 81: 372.3772
-#&gt; Sum of squared residuals at call 84: 372.3772
-#&gt; Sum of squared residuals at call 86: 371.2615
-#&gt; Sum of squared residuals at call 89: 371.2615
-#&gt; Sum of squared residuals at call 90: 371.2615
-#&gt; Sum of squared residuals at call 92: 371.2439
-#&gt; Sum of squared residuals at call 93: 371.2439
-#&gt; Sum of squared residuals at call 94: 371.2439
-#&gt; Sum of squared residuals at call 97: 371.2198
-#&gt; Sum of squared residuals at call 98: 371.2198
-#&gt; Sum of squared residuals at call 102: 371.2174
-#&gt; Sum of squared residuals at call 104: 371.2174
-#&gt; Sum of squared residuals at call 107: 371.2147
-#&gt; Sum of squared residuals at call 110: 371.2147
-#&gt; Sum of squared residuals at call 111: 371.2147
-#&gt; Sum of squared residuals at call 112: 371.2145
-#&gt; Sum of squared residuals at call 113: 371.2145
-#&gt; Sum of squared residuals at call 116: 371.2145
-#&gt; Sum of squared residuals at call 119: 371.2135
-#&gt; Sum of squared residuals at call 121: 371.2135
-#&gt; Sum of squared residuals at call 124: 371.2135
-#&gt; Sum of squared residuals at call 126: 371.2135
-#&gt; Sum of squared residuals at call 127: 371.2135
-#&gt; Sum of squared residuals at call 133: 371.2134
+#&gt; Sum of squared residuals at call 12: 4094.396
+#&gt; Sum of squared residuals at call 16: 4094.396
+#&gt; Sum of squared residuals at call 19: 1340.595
+#&gt; Sum of squared residuals at call 20: 1340.593
+#&gt; Sum of squared residuals at call 25: 1072.239
+#&gt; Sum of squared residuals at call 28: 1072.236
+#&gt; Sum of squared residuals at call 30: 874.2615
+#&gt; Sum of squared residuals at call 33: 874.2611
+#&gt; Sum of squared residuals at call 35: 616.2375
+#&gt; Sum of squared residuals at call 37: 616.237
+#&gt; Sum of squared residuals at call 40: 467.4386
+#&gt; Sum of squared residuals at call 42: 467.438
+#&gt; Sum of squared residuals at call 46: 398.2913
+#&gt; Sum of squared residuals at call 48: 398.2913
+#&gt; Sum of squared residuals at call 49: 398.2912
+#&gt; Sum of squared residuals at call 51: 395.0711
+#&gt; Sum of squared residuals at call 54: 395.071
+#&gt; Sum of squared residuals at call 56: 378.3298
+#&gt; Sum of squared residuals at call 59: 378.3298
+#&gt; Sum of squared residuals at call 62: 376.9812
+#&gt; Sum of squared residuals at call 64: 376.9811
+#&gt; Sum of squared residuals at call 67: 375.2085
+#&gt; Sum of squared residuals at call 69: 375.2085
+#&gt; Sum of squared residuals at call 70: 375.2085
+#&gt; Sum of squared residuals at call 71: 375.2085
+#&gt; Sum of squared residuals at call 72: 374.5723
+#&gt; Sum of squared residuals at call 74: 374.5723
+#&gt; Sum of squared residuals at call 77: 374.0075
+#&gt; Sum of squared residuals at call 79: 374.0075
+#&gt; Sum of squared residuals at call 80: 374.0075
+#&gt; Sum of squared residuals at call 82: 373.1711
+#&gt; Sum of squared residuals at call 84: 373.1711
+#&gt; Sum of squared residuals at call 87: 372.6445
+#&gt; Sum of squared residuals at call 88: 372.1615
+#&gt; Sum of squared residuals at call 90: 372.1615
+#&gt; Sum of squared residuals at call 91: 372.1615
+#&gt; Sum of squared residuals at call 94: 371.6464
+#&gt; Sum of squared residuals at call 99: 371.4299
+#&gt; Sum of squared residuals at call 101: 371.4299
+#&gt; Sum of squared residuals at call 104: 371.4071
+#&gt; Sum of squared residuals at call 106: 371.4071
+#&gt; Sum of squared residuals at call 107: 371.4071
+#&gt; Sum of squared residuals at call 109: 371.2524
+#&gt; Sum of squared residuals at call 113: 371.2524
+#&gt; Sum of squared residuals at call 114: 371.2136
+#&gt; Sum of squared residuals at call 115: 371.2136
+#&gt; Sum of squared residuals at call 116: 371.2136
+#&gt; Sum of squared residuals at call 119: 371.2134
+#&gt; Sum of squared residuals at call 120: 371.2134
+#&gt; Sum of squared residuals at call 122: 371.2134
+#&gt; Sum of squared residuals at call 123: 371.2134
+#&gt; Sum of squared residuals at call 125: 371.2134
+#&gt; Sum of squared residuals at call 126: 371.2134
 #&gt; Sum of squared residuals at call 135: 371.2134
-#&gt; Sum of squared residuals at call 138: 371.2134
-#&gt; Sum of squared residuals at call 142: 371.2134
-#&gt; Negative log-likelihood at call 152: 97.22429
+#&gt; Negative log-likelihood at call 145: 97.22429
 #&gt; Optimisation successfully terminated.
 #&gt;        User      System verstrichen 
-#&gt;       1.095       0.000       1.096 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
+#&gt;       1.082       0.000       1.083 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
 #&gt; parent_sink   parent_m1     m1_sink 
 #&gt;    0.485524    0.514476    1.000000 
 #&gt; 
@@ -529,8 +526,8 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt; 
 #&gt; $distimes
 #&gt;              DT50      DT90
-#&gt; parent   7.022928  23.32966
-#&gt; m1     131.760710 437.69961
+#&gt; parent   7.022929  23.32967
+#&gt; m1     131.760712 437.69961
 #&gt; </div><div class='input'>
 # Use stepwise fitting, using optimised parameters from parent only fit, FOMC
 </div><div class='input'><span class='no'>FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
@@ -552,8 +549,8 @@ Per default, parameters in the kinetic models are internally transformed in
 <span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
                       <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.4 
 #&gt; R version used for fitting:       3.6.0 
-#&gt; Date of fit:     Thu May  2 18:47:59 2019 
-#&gt; Date of summary: Thu May  2 18:47:59 2019 
+#&gt; Date of fit:     Fri May  3 19:07:35 2019 
+#&gt; Date of summary: Fri May  3 19:07:35 2019 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent * parent
@@ -561,7 +558,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted using 404 model solutions performed in 1.047 s
+#&gt; Fitted using 421 model solutions performed in 1.099 s
 #&gt; 
 #&gt; Error model:
 #&gt; Constant variance 
@@ -596,11 +593,11 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt; 
 #&gt; Parameter correlation:
 #&gt;                  parent_0 log_k_parent   log_k_m1 f_parent_ilr_1      sigma
-#&gt; parent_0        1.000e+00    5.174e-01 -1.688e-01     -5.471e-01 -5.940e-09
-#&gt; log_k_parent    5.174e-01    1.000e+00 -3.263e-01     -5.426e-01 -1.406e-08
-#&gt; log_k_m1       -1.688e-01   -3.263e-01  1.000e+00      7.478e-01 -2.306e-08
-#&gt; f_parent_ilr_1 -5.471e-01   -5.426e-01  7.478e-01      1.000e+00 -6.664e-09
-#&gt; sigma          -5.940e-09   -1.406e-08 -2.306e-08     -6.664e-09  1.000e+00
+#&gt; parent_0        1.000e+00    5.174e-01 -1.688e-01     -5.471e-01 -2.265e-07
+#&gt; log_k_parent    5.174e-01    1.000e+00 -3.263e-01     -5.426e-01  3.785e-07
+#&gt; log_k_m1       -1.688e-01   -3.263e-01  1.000e+00      7.478e-01 -1.386e-07
+#&gt; f_parent_ilr_1 -5.471e-01   -5.426e-01  7.478e-01      1.000e+00 -3.641e-08
+#&gt; sigma          -2.265e-07    3.785e-07 -1.386e-07     -3.641e-08  1.000e+00
 #&gt; 
 #&gt; Backtransformed parameters:
 #&gt; Confidence intervals for internally transformed parameters are asymmetric.
@@ -635,10 +632,10 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt;     0   parent   102.04  99.59848  2.442e+00
 #&gt;     1   parent    93.50  90.23787  3.262e+00
 #&gt;     1   parent    92.50  90.23787  2.262e+00
-#&gt;     3   parent    63.23  74.07320 -1.084e+01
-#&gt;     3   parent    68.99  74.07320 -5.083e+00
-#&gt;     7   parent    52.32  49.91207  2.408e+00
-#&gt;     7   parent    55.13  49.91207  5.218e+00
+#&gt;     3   parent    63.23  74.07319 -1.084e+01
+#&gt;     3   parent    68.99  74.07319 -5.083e+00
+#&gt;     7   parent    52.32  49.91206  2.408e+00
+#&gt;     7   parent    55.13  49.91206  5.218e+00
 #&gt;    14   parent    27.27  25.01257  2.257e+00
 #&gt;    14   parent    26.64  25.01257  1.627e+00
 #&gt;    21   parent    11.50  12.53462 -1.035e+00
@@ -648,7 +645,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt;    50   parent     0.69   0.71624 -2.624e-02
 #&gt;    50   parent     0.63   0.71624 -8.624e-02
 #&gt;    75   parent     0.05   0.06074 -1.074e-02
-#&gt;    75   parent     0.06   0.06074 -7.382e-04
+#&gt;    75   parent     0.06   0.06074 -7.381e-04
 #&gt;     1       m1     4.84   4.80296  3.704e-02
 #&gt;     1       m1     5.64   4.80296  8.370e-01
 #&gt;     3       m1    12.91  13.02400 -1.140e-01
@@ -670,8 +667,8 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt;   120       m1    25.15  28.78984 -3.640e+00
 #&gt;   120       m1    33.31  28.78984  4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.4 
 #&gt; R version used for fitting:       3.6.0 
-#&gt; Date of fit:     Thu May  2 18:48:00 2019 
-#&gt; Date of summary: Thu May  2 18:48:00 2019 
+#&gt; Date of fit:     Fri May  3 19:07:37 2019 
+#&gt; Date of summary: Fri May  3 19:07:37 2019 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent * parent
@@ -679,7 +676,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted using 558 model solutions performed in 1.45 s
+#&gt; Fitted using 756 model solutions performed in 1.973 s
 #&gt; 
 #&gt; Error model:
 #&gt; Variance unique to each observed variable 
@@ -717,17 +714,17 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt; 
 #&gt; Parameter correlation:
 #&gt;                parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_parent
-#&gt; parent_0        1.00000      0.51078 -0.19133       -0.59997     0.035671
-#&gt; log_k_parent    0.51078      1.00000 -0.37458       -0.59239     0.069834
-#&gt; log_k_m1       -0.19133     -0.37458  1.00000        0.74398    -0.026158
-#&gt; f_parent_ilr_1 -0.59997     -0.59239  0.74398        1.00000    -0.041369
-#&gt; sigma_parent    0.03567      0.06983 -0.02616       -0.04137     1.000000
-#&gt; sigma_m1       -0.03385     -0.06627  0.02482        0.03926    -0.004628
+#&gt; parent_0        1.00000      0.51078 -0.19133       -0.59997     0.035685
+#&gt; log_k_parent    0.51078      1.00000 -0.37458       -0.59239     0.069840
+#&gt; log_k_m1       -0.19133     -0.37458  1.00000        0.74398    -0.026160
+#&gt; f_parent_ilr_1 -0.59997     -0.59239  0.74398        1.00000    -0.041377
+#&gt; sigma_parent    0.03569      0.06984 -0.02616       -0.04138     1.000000
+#&gt; sigma_m1       -0.03385     -0.06626  0.02482        0.03925    -0.004628
 #&gt;                 sigma_m1
 #&gt; parent_0       -0.033847
-#&gt; log_k_parent   -0.066265
+#&gt; log_k_parent   -0.066264
 #&gt; log_k_m1        0.024822
-#&gt; f_parent_ilr_1  0.039256
+#&gt; f_parent_ilr_1  0.039254
 #&gt; sigma_parent   -0.004628
 #&gt; sigma_m1        1.000000
 #&gt; 
@@ -761,47 +758,47 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt; 
 #&gt; Data:
 #&gt;  time variable observed predicted   residual
-#&gt;     0   parent    99.46  99.65417 -1.942e-01
-#&gt;     0   parent   102.04  99.65417  2.386e+00
-#&gt;     1   parent    93.50  90.26333  3.237e+00
-#&gt;     1   parent    92.50  90.26333  2.237e+00
-#&gt;     3   parent    63.23  74.05306 -1.082e+01
-#&gt;     3   parent    68.99  74.05306 -5.063e+00
-#&gt;     7   parent    52.32  49.84325  2.477e+00
-#&gt;     7   parent    55.13  49.84325  5.287e+00
-#&gt;    14   parent    27.27  24.92971  2.340e+00
-#&gt;    14   parent    26.64  24.92971  1.710e+00
-#&gt;    21   parent    11.50  12.46890 -9.689e-01
-#&gt;    21   parent    11.64  12.46890 -8.289e-01
-#&gt;    35   parent     2.85   3.11925 -2.692e-01
-#&gt;    35   parent     2.91   3.11925 -2.092e-01
-#&gt;    50   parent     0.69   0.70679 -1.679e-02
-#&gt;    50   parent     0.63   0.70679 -7.679e-02
-#&gt;    75   parent     0.05   0.05952 -9.523e-03
-#&gt;    75   parent     0.06   0.05952  4.772e-04
+#&gt;     0   parent    99.46  99.65425 -1.942e-01
+#&gt;     0   parent   102.04  99.65425  2.386e+00
+#&gt;     1   parent    93.50  90.26338  3.237e+00
+#&gt;     1   parent    92.50  90.26338  2.237e+00
+#&gt;     3   parent    63.23  74.05309 -1.082e+01
+#&gt;     3   parent    68.99  74.05309 -5.063e+00
+#&gt;     7   parent    52.32  49.84326  2.477e+00
+#&gt;     7   parent    55.13  49.84326  5.287e+00
+#&gt;    14   parent    27.27  24.92970  2.340e+00
+#&gt;    14   parent    26.64  24.92970  1.710e+00
+#&gt;    21   parent    11.50  12.46888 -9.689e-01
+#&gt;    21   parent    11.64  12.46888 -8.289e-01
+#&gt;    35   parent     2.85   3.11924 -2.692e-01
+#&gt;    35   parent     2.91   3.11924 -2.092e-01
+#&gt;    50   parent     0.69   0.70678 -1.678e-02
+#&gt;    50   parent     0.63   0.70678 -7.678e-02
+#&gt;    75   parent     0.05   0.05952 -9.522e-03
+#&gt;    75   parent     0.06   0.05952  4.776e-04
 #&gt;     1       m1     4.84   4.81075  2.925e-02
 #&gt;     1       m1     5.64   4.81075  8.292e-01
 #&gt;     3       m1    12.91  13.04197 -1.320e-01
 #&gt;     3       m1    12.96  13.04197 -8.197e-02
-#&gt;     7       m1    22.97  25.06847 -2.098e+00
-#&gt;     7       m1    24.47  25.06847 -5.985e-01
+#&gt;     7       m1    22.97  25.06848 -2.098e+00
+#&gt;     7       m1    24.47  25.06848 -5.985e-01
 #&gt;    14       m1    41.69  36.70308  4.987e+00
 #&gt;    14       m1    33.21  36.70308 -3.493e+00
 #&gt;    21       m1    44.37  41.65115  2.719e+00
 #&gt;    21       m1    46.44  41.65115  4.789e+00
-#&gt;    35       m1    41.22  43.29465 -2.075e+00
-#&gt;    35       m1    37.95  43.29465 -5.345e+00
-#&gt;    50       m1    41.19  41.19948 -9.482e-03
-#&gt;    50       m1    40.01  41.19948 -1.189e+00
-#&gt;    75       m1    40.09  36.44036  3.650e+00
-#&gt;    75       m1    33.85  36.44036 -2.590e+00
-#&gt;   100       m1    31.04  31.98774 -9.477e-01
-#&gt;   100       m1    33.13  31.98774  1.142e+00
+#&gt;    35       m1    41.22  43.29464 -2.075e+00
+#&gt;    35       m1    37.95  43.29464 -5.345e+00
+#&gt;    50       m1    41.19  41.19947 -9.473e-03
+#&gt;    50       m1    40.01  41.19947 -1.189e+00
+#&gt;    75       m1    40.09  36.44035  3.650e+00
+#&gt;    75       m1    33.85  36.44035 -2.590e+00
+#&gt;   100       m1    31.04  31.98773 -9.477e-01
+#&gt;   100       m1    33.13  31.98773  1.142e+00
 #&gt;   120       m1    25.15  28.80430 -3.654e+00
-#&gt;   120       m1    33.31  28.80430  4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.4 
+#&gt;   120       m1    33.31  28.80430  4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt; <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.4 
 #&gt; R version used for fitting:       3.6.0 
-#&gt; Date of fit:     Thu May  2 18:48:04 2019 
-#&gt; Date of summary: Thu May  2 18:48:04 2019 
+#&gt; Date of fit:     Fri May  3 19:07:40 2019 
+#&gt; Date of summary: Fri May  3 19:07:40 2019 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent * parent
@@ -809,7 +806,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt; 
 #&gt; Model predictions using solution type deSolve 
 #&gt; 
-#&gt; Fitted using 844 model solutions performed in 3.407 s
+#&gt; Fitted using 888 model solutions performed in 3.579 s
 #&gt; 
 #&gt; Error model:
 #&gt; Two-component variance function 
@@ -820,8 +817,8 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt; k_parent         0.1000 deparm
 #&gt; k_m1             0.1001 deparm
 #&gt; f_parent_to_m1   0.5000 deparm
-#&gt; sigma_low        3.0000  error
-#&gt; rsd_high         0.0100  error
+#&gt; sigma_low        0.1000  error
+#&gt; rsd_high         0.1000  error
 #&gt; 
 #&gt; Starting values for the transformed parameters actually optimised:
 #&gt;                     value lower upper
@@ -829,99 +826,106 @@ Per default, parameters in the kinetic models are internally transformed in
 #&gt; log_k_parent    -2.302585  -Inf   Inf
 #&gt; log_k_m1        -2.301586  -Inf   Inf
 #&gt; f_parent_ilr_1   0.000000  -Inf   Inf
-#&gt; sigma_low        3.000000     0   Inf
-#&gt; rsd_high         0.010000     0   Inf
+#&gt; sigma_low        0.100000     0   Inf
+#&gt; rsd_high         0.100000     0   Inf
 #&gt; 
 #&gt; Fixed parameter values:
 #&gt;      value  type
 #&gt; m1_0     0 state
 #&gt; 
 #&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt;                 Estimate Std. Error     Lower     Upper
-#&gt; parent_0       100.70000   2.621000 95.400000 106.10000
-#&gt; log_k_parent    -2.29700   0.008862 -2.315000  -2.27900
-#&gt; log_k_m1        -5.26600   0.091310 -5.452000  -5.08000
-#&gt; f_parent_ilr_1   0.02374   0.055300 -0.088900   0.13640
-#&gt; sigma_low        0.00305   0.004829 -0.006786   0.01289
-#&gt; rsd_high         0.07928   0.009418  0.060100   0.09847
+#&gt;                 Estimate Std. Error    Lower     Upper
+#&gt; parent_0       100.30000    3.06400 94.08000 106.60000
+#&gt; log_k_parent    -2.31100    0.02913 -2.37100  -2.25200
+#&gt; log_k_m1        -5.27800    0.10890 -5.49900  -5.05600
+#&gt; f_parent_ilr_1   0.02128    0.07223 -0.12590   0.16840
+#&gt; sigma_low        0.99650        NaN      NaN       NaN
+#&gt; rsd_high         0.07560    0.01059  0.05402   0.09717
 #&gt; 
 #&gt; Parameter correlation:
-#&gt;                parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_low rsd_high
-#&gt; parent_0        1.00000      0.67644 -0.10215       -0.76822   0.14294 -0.08783
-#&gt; log_k_parent    0.67644      1.00000 -0.15102       -0.59491   0.34611 -0.08125
-#&gt; log_k_m1       -0.10215     -0.15102  1.00000        0.51808  -0.05236  0.01240
-#&gt; f_parent_ilr_1 -0.76822     -0.59491  0.51808        1.00000  -0.13900  0.03248
-#&gt; sigma_low       0.14294      0.34611 -0.05236       -0.13900   1.00000 -0.16546
-#&gt; rsd_high       -0.08783     -0.08125  0.01240        0.03248  -0.16546  1.00000
+#&gt;                parent_0 log_k_parent  log_k_m1 f_parent_ilr_1 sigma_low
+#&gt; parent_0        1.00000      0.64703 -0.220160       -0.79035       NaN
+#&gt; log_k_parent    0.64703      1.00000 -0.339633       -0.67982       NaN
+#&gt; log_k_m1       -0.22016     -0.33963  1.000000        0.62815       NaN
+#&gt; f_parent_ilr_1 -0.79035     -0.67982  0.628148        1.00000       NaN
+#&gt; sigma_low           NaN          NaN       NaN            NaN         1
+#&gt; rsd_high       -0.05745     -0.01123  0.003502        0.00568       NaN
+#&gt;                 rsd_high
+#&gt; parent_0       -0.057450
+#&gt; log_k_parent   -0.011230
+#&gt; log_k_m1        0.003502
+#&gt; f_parent_ilr_1  0.005680
+#&gt; sigma_low            NaN
+#&gt; rsd_high        1.000000
 #&gt; 
 #&gt; Backtransformed parameters:
 #&gt; Confidence intervals for internally transformed parameters are asymmetric.
 #&gt; t-test (unrealistically) based on the assumption of normal distribution
 #&gt; for estimators of untransformed parameters.
-#&gt;                 Estimate  t value    Pr(&gt;t)     Lower     Upper
-#&gt; parent_0       1.007e+02  38.4300 1.180e-28 95.400000 1.061e+02
-#&gt; k_parent       1.006e-01 112.8000 1.718e-43  0.098760 1.024e-01
-#&gt; k_m1           5.167e-03  10.9500 1.171e-12  0.004290 6.223e-03
-#&gt; f_parent_to_m1 5.084e-01  26.0100 2.146e-23  0.468600 5.481e-01
-#&gt; sigma_low      3.050e-03   0.6314 2.661e-01 -0.006786 1.289e-02
-#&gt; rsd_high       7.928e-02   8.4170 6.418e-10  0.060100 9.847e-02
+#&gt;                 Estimate t value    Pr(&gt;t)     Lower     Upper
+#&gt; parent_0       1.003e+02  32.740 1.759e-26 94.080000 1.066e+02
+#&gt; k_parent       9.914e-02  34.330 4.045e-27  0.093430 1.052e-01
+#&gt; k_m1           5.105e-03   9.186 8.682e-11  0.004089 6.372e-03
+#&gt; f_parent_to_m1 5.075e-01  19.880 7.143e-20  0.455600 5.593e-01
+#&gt; sigma_low      9.965e-01     NaN       NaN       NaN       NaN
+#&gt; rsd_high       7.560e-02   7.137 2.114e-08  0.054020 9.717e-02
 #&gt; 
 #&gt; FOCUS Chi2 error levels in percent:
 #&gt;          err.min n.optim df
-#&gt; All data   6.475       4 15
-#&gt; parent     6.573       2  7
-#&gt; m1         4.671       2  8
+#&gt; All data   6.433       4 15
+#&gt; parent     6.506       2  7
+#&gt; m1         4.692       2  8
 #&gt; 
 #&gt; Resulting formation fractions:
 #&gt;                 ff
-#&gt; parent_m1   0.5084
-#&gt; parent_sink 0.4916
+#&gt; parent_m1   0.5075
+#&gt; parent_sink 0.4925
 #&gt; 
 #&gt; Estimated disappearance times:
-#&gt;           DT50  DT90
-#&gt; parent   6.893  22.9
-#&gt; m1     134.156 445.7
+#&gt;           DT50   DT90
+#&gt; parent   6.992  23.23
+#&gt; m1     135.787 451.08
 #&gt; 
 #&gt; Data:
 #&gt;  time variable observed predicted   residual
-#&gt;     0   parent    99.46 100.73434  -1.274339
-#&gt;     0   parent   102.04 100.73434   1.305661
-#&gt;     1   parent    93.50  91.09751   2.402486
-#&gt;     1   parent    92.50  91.09751   1.402486
-#&gt;     3   parent    63.23  74.50141 -11.271410
-#&gt;     3   parent    68.99  74.50141  -5.511410
-#&gt;     7   parent    52.32  49.82880   2.491201
-#&gt;     7   parent    55.13  49.82880   5.301201
-#&gt;    14   parent    27.27  24.64809   2.621908
-#&gt;    14   parent    26.64  24.64809   1.991908
-#&gt;    21   parent    11.50  12.19232  -0.692315
-#&gt;    21   parent    11.64  12.19232  -0.552315
-#&gt;    35   parent     2.85   2.98327  -0.133266
-#&gt;    35   parent     2.91   2.98327  -0.073266
-#&gt;    50   parent     0.69   0.66013   0.029874
-#&gt;    50   parent     0.63   0.66013  -0.030126
-#&gt;    75   parent     0.05   0.05344  -0.003438
-#&gt;    75   parent     0.06   0.05344   0.006562
-#&gt;     1       m1     4.84   4.88645  -0.046451
-#&gt;     1       m1     5.64   4.88645   0.753549
-#&gt;     3       m1    12.91  13.22867  -0.318669
-#&gt;     3       m1    12.96  13.22867  -0.268669
-#&gt;     7       m1    22.97  25.36417  -2.394167
-#&gt;     7       m1    24.47  25.36417  -0.894167
-#&gt;    14       m1    41.69  37.00974   4.680263
-#&gt;    14       m1    33.21  37.00974  -3.799737
-#&gt;    21       m1    44.37  41.90133   2.468668
-#&gt;    21       m1    46.44  41.90133   4.538668
-#&gt;    35       m1    41.22  43.45691  -2.236914
-#&gt;    35       m1    37.95  43.45691  -5.506914
-#&gt;    50       m1    41.19  41.34199  -0.151986
-#&gt;    50       m1    40.01  41.34199  -1.331986
-#&gt;    75       m1    40.09  36.61471   3.475294
-#&gt;    75       m1    33.85  36.61471  -2.764706
-#&gt;   100       m1    31.04  32.20082  -1.160824
-#&gt;   100       m1    33.13  32.20082   0.929176
-#&gt;   120       m1    25.15  29.04130  -3.891305
-#&gt;   120       m1    33.31  29.04130   4.268695</div><div class='input'>
+#&gt;     0   parent    99.46 100.32122  -0.861220
+#&gt;     0   parent   102.04 100.32122   1.718780
+#&gt;     1   parent    93.50  90.85266   2.647340
+#&gt;     1   parent    92.50  90.85266   1.647340
+#&gt;     3   parent    63.23  74.51219 -11.282190
+#&gt;     3   parent    68.99  74.51219  -5.522190
+#&gt;     7   parent    52.32  50.11950   2.200504
+#&gt;     7   parent    55.13  50.11950   5.010504
+#&gt;    14   parent    27.27  25.03921   2.230792
+#&gt;    14   parent    26.64  25.03921   1.600792
+#&gt;    21   parent    11.50  12.50934  -1.009342
+#&gt;    21   parent    11.64  12.50934  -0.869342
+#&gt;    35   parent     2.85   3.12221  -0.272211
+#&gt;    35   parent     2.91   3.12221  -0.212211
+#&gt;    50   parent     0.69   0.70572  -0.015724
+#&gt;    50   parent     0.63   0.70572  -0.075724
+#&gt;    75   parent     0.05   0.05919  -0.009191
+#&gt;    75   parent     0.06   0.05919   0.000809
+#&gt;     1       m1     4.84   4.79307   0.046928
+#&gt;     1       m1     5.64   4.79307   0.846928
+#&gt;     3       m1    12.91  12.99398  -0.083980
+#&gt;     3       m1    12.96  12.99398  -0.033980
+#&gt;     7       m1    22.97  24.97744  -2.007441
+#&gt;     7       m1    24.47  24.97744  -0.507441
+#&gt;    14       m1    41.69  36.57917   5.110827
+#&gt;    14       m1    33.21  36.57917  -3.369173
+#&gt;    21       m1    44.37  41.52931   2.840692
+#&gt;    21       m1    46.44  41.52931   4.910692
+#&gt;    35       m1    41.22  43.22614  -2.006138
+#&gt;    35       m1    37.95  43.22614  -5.276138
+#&gt;    50       m1    41.19  41.20972  -0.019717
+#&gt;    50       m1    40.01  41.20972  -1.199717
+#&gt;    75       m1    40.09  36.57312   3.516882
+#&gt;    75       m1    33.85  36.57312  -2.723118
+#&gt;   100       m1    31.04  32.21655  -1.176546
+#&gt;   100       m1    33.13  32.21655   0.913454
+#&gt;   120       m1    25.15  29.09181  -3.941814
+#&gt;   120       m1    33.31  29.09181   4.218186</div><div class='input'>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 23139c0f..9ba463e3 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -234,7 +234,7 @@ For the definition of model types and their parameters, the equations given
 <span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
   <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
   <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; Compilation argument:
-#&gt;  /usr/lib/R/bin/R CMD SHLIB file26cc3b169ccf.c 2&gt; file26cc3b169ccf.c.err.txt 
+#&gt;  /usr/lib/R/bin/R CMD SHLIB file2b304be466d0.c 2&gt; file2b304be466d0.c.err.txt 
 #&gt; Program source:
 #&gt;   1: #include &lt;R.h&gt;
 #&gt;   2: 
diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png
index 798722a2..65918d53 100644
--- a/docs/reference/mkinparplot-1.png
+++ b/docs/reference/mkinparplot-1.png
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index c90acf4a..8cfb9374 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -154,8 +154,7 @@
     <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
   <span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"phenol"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
   <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"anisole"</span>)),
-  <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation did not converge:</span>
-#&gt; <span class='warning'>false convergence (8)</span></div><div class='input'><span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div></pre>
+  <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 7b75b85d..074ac3ac 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -333,14 +333,14 @@
                 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
                 <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt;     time   parent       m1
 #&gt; 201   20 4.978707 27.46227</div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       0.002       0.000       0.002 </div><div class='input'>  <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
+#&gt;       0.002       0.000       0.001 </div><div class='input'>  <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
     <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
                 <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
                 <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt;     time   parent       m1
 #&gt; 201   20 4.978707 27.46227</div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       0.021       0.000       0.021 </div><div class='input'>
+#&gt;       0.022       0.000       0.021 </div><div class='input'>
   </div><div class='input'>    <span class='co'># Predict from a fitted model</span>
-    <span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#&gt; Sum of squared residuals at call 1: 552.5739
+    <span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#&gt; <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#&gt; Sum of squared residuals at call 1: 552.5739
 #&gt; Sum of squared residuals at call 3: 552.5739
 #&gt; Sum of squared residuals at call 4: 552.5739
 #&gt; Sum of squared residuals at call 6: 279.9345
@@ -350,6 +350,7 @@
 #&gt; Sum of squared residuals at call 12: 200.3629
 #&gt; Sum of squared residuals at call 13: 200.3629
 #&gt; Sum of squared residuals at call 18: 197.9039
+#&gt; Sum of squared residuals at call 23: 197.9039
 #&gt; Sum of squared residuals at call 25: 196.6754
 #&gt; Sum of squared residuals at call 27: 196.6754
 #&gt; Sum of squared residuals at call 32: 196.5742
@@ -366,15 +367,16 @@
 #&gt; Sum of squared residuals at call 58: 196.5334
 #&gt; Sum of squared residuals at call 59: 196.5334
 #&gt; Sum of squared residuals at call 65: 196.5334
+#&gt; Sum of squared residuals at call 73: 196.5334
 #&gt; Negative log-likelihood at call 75: 26.64668
 #&gt; Negative log-likelihood at call 103: 26.64668
 #&gt; Optimisation successfully terminated.</div><div class='input'>    <span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</span>))</div><div class='output co'>#&gt;   time   parent       m1
 #&gt; 1  0.0 82.49216 0.000000
-#&gt; 2  0.1 80.00563 1.179956
-#&gt; 3  0.2 77.59404 2.312583
-#&gt; 4  0.3 75.25515 3.399424
-#&gt; 5  0.4 72.98675 4.441974
-#&gt; 6  0.5 70.78673 5.441685</div><div class='input'>  </div></pre>
+#&gt; 2  0.1 80.00563 1.179955
+#&gt; 3  0.2 77.59404 2.312580
+#&gt; 4  0.3 75.25515 3.399419
+#&gt; 5  0.4 72.98675 4.441969
+#&gt; 6  0.5 70.78673 5.441679</div><div class='input'>  </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png
index 5b7180ee..344561de 100644
--- a/docs/reference/mkinresplot-1.png
+++ b/docs/reference/mkinresplot-1.png
diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png
index c66b0beb..59d293d5 100644
--- a/docs/reference/mmkin-2.png
+++ b/docs/reference/mmkin-2.png
diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png
index 761778f8..a947ac65 100644
--- a/docs/reference/mmkin-3.png
+++ b/docs/reference/mmkin-3.png
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 49d41270..c730ecb0 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -194,11 +194,11 @@
 <span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
 
 <span class='no'>time_default</span></div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       0.047       0.041       7.417 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;      21.251       0.000      21.263 </div><div class='input'>
+#&gt;       0.042       0.028       5.095 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt;        User      System verstrichen 
+#&gt;       19.29        0.00       19.30 </div><div class='input'>
 <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
 #&gt;   parent_M1 parent_sink       M1_M2     M1_sink 
-#&gt;   0.7340481   0.2659519   0.7505683   0.2494317 
+#&gt;   0.7340481   0.2659519   0.7505684   0.2494316 
 #&gt; 
 #&gt; $SFORB
 #&gt; logical(0)
@@ -206,8 +206,8 @@
 #&gt; $distimes
 #&gt;              DT50       DT90
 #&gt; parent  0.8777689   2.915885
-#&gt; M1      2.3257442   7.725955
-#&gt; M2     33.7200941 112.015728
+#&gt; M1      2.3257449   7.725957
+#&gt; M2     33.7200958 112.015734
 #&gt; </div><div class='input'>
 <span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span>
 <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><div class='img'><img src='mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><div class='img'><img src='mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span>
diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png
index 115792db..e7b3bac7 100644
--- a/docs/reference/plot.mkinfit-1.png
+++ b/docs/reference/plot.mkinfit-1.png
diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png
index 412c7244..7f32afe2 100644
--- a/docs/reference/plot.mmkin-3.png
+++ b/docs/reference/plot.mmkin-3.png
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index f645e6a7..09f6d1e2 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -167,7 +167,7 @@
   <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>  </div><div class='input'>    <span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
     <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></div><div class='input'>    <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
 #&gt;   parent_A1   parent_B1   parent_C1 parent_sink       A1_A2     A1_sink 
-#&gt;   0.3809619   0.1954667   0.4235714   0.0000000   0.4479603   0.5520397 
+#&gt;   0.3809619   0.1954667   0.4235714   0.0000000   0.4479620   0.5520380 
 #&gt; 
 #&gt; $SFORB
 #&gt; logical(0)
@@ -175,10 +175,10 @@
 #&gt; $distimes
 #&gt;            DT50      DT90
 #&gt; parent 13.95078  46.34350
-#&gt; A1     49.75343 165.27733
-#&gt; B1     37.26907 123.80518
-#&gt; C1     11.23131  37.30959
-#&gt; A2     28.50644  94.69635
+#&gt; A1     49.75344 165.27737
+#&gt; B1     37.26907 123.80517
+#&gt; C1     11.23131  37.30960
+#&gt; A2     28.50627  94.69577
 #&gt; </div><div class='input'>  </div><div class='input'> <span class='co'># Compare with the results obtained in the original publication</span>
  <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>schaefer07_complex_results</span>)</div><div class='output co'>#&gt;         compound          parameter  KinGUI ModelMaker deviation
 #&gt; 1         parent   degradation rate  0.0496     0.0506       2.0
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 89a8b9a6..351d7a7e 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -211,15 +211,15 @@
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>  <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting:    0.9.49.4 
 #&gt; R version used for fitting:       3.6.0 
-#&gt; Date of fit:     Thu May  2 18:48:59 2019 
-#&gt; Date of summary: Thu May  2 18:48:59 2019 
+#&gt; Date of fit:     Fri May  3 19:08:31 2019 
+#&gt; Date of summary: Fri May  3 19:08:31 2019 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - k_parent_sink * parent
 #&gt; 
 #&gt; Model predictions using solution type analytical 
 #&gt; 
-#&gt; Fitted using 131 model solutions performed in 0.274 s
+#&gt; Fitted using 131 model solutions performed in 0.27 s
 #&gt; 
 #&gt; Error model:
 #&gt; Constant variance 
@@ -247,9 +247,9 @@
 #&gt; 
 #&gt; Parameter correlation:
 #&gt;                    parent_0 log_k_parent_sink     sigma
-#&gt; parent_0          1.000e+00         5.428e-01 1.642e-07
-#&gt; log_k_parent_sink 5.428e-01         1.000e+00 2.507e-07
-#&gt; sigma             1.642e-07         2.507e-07 1.000e+00
+#&gt; parent_0          1.000e+00         5.428e-01 1.648e-07
+#&gt; log_k_parent_sink 5.428e-01         1.000e+00 2.513e-07
+#&gt; sigma             1.648e-07         2.513e-07 1.000e+00
 #&gt; 
 #&gt; Backtransformed parameters:
 #&gt; Confidence intervals for internally transformed parameters are asymmetric.
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 688baf32..bc988340 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -160,14 +160,14 @@
   <span class='no'>m_ws</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent_w</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span>),
                   <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>  <span class='no'>f_river</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'>
   <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt;                         Estimate se_notrans      t value       Pr(&gt;t)
-#&gt; parent_w_0          9.598567e+01 2.12352039 4.520120e+01 9.476357e-18
-#&gt; k_parent_w_sink     3.603743e-01 0.03149366 1.144276e+01 4.128096e-09
-#&gt; k_parent_w_parent_s 6.031371e-02 0.01603582 3.761185e+00 9.436293e-04
-#&gt; k_parent_s_sink     7.560341e-11 0.09483761 7.971881e-10 5.000000e-01
-#&gt; k_parent_s_parent_w 7.419672e-02 0.10738374 6.909493e-01 2.500756e-01
-#&gt; sigma               2.982879e+00 0.50546582 5.901247e+00 1.454824e-05
+#&gt; parent_w_0          9.598567e+01 2.12351789 4.520126e+01 9.476190e-18
+#&gt; k_parent_w_sink     3.603743e-01 0.03149282 1.144306e+01 4.126593e-09
+#&gt; k_parent_w_parent_s 6.031371e-02 0.01603582 3.761186e+00 9.436275e-04
+#&gt; k_parent_s_sink     5.108964e-11 0.09482736 5.387647e-10 5.000000e-01
+#&gt; k_parent_s_parent_w 7.419672e-02 0.10737376 6.910135e-01 2.500560e-01
+#&gt; sigma               2.982879e+00 0.50545649 5.901356e+00 1.454535e-05
 #&gt;                           Lower       Upper
-#&gt; parent_w_0          91.48420501 100.4871438
+#&gt; parent_w_0          91.48420503 100.4871438
 #&gt; k_parent_w_sink      0.30668904   0.4234571
 #&gt; k_parent_w_parent_s  0.03423904   0.1062455
 #&gt; k_parent_s_sink      0.00000000         Inf
@@ -184,25 +184,25 @@
                     <span class='kw'>M3</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>),
                     <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
   <span class='no'>f_soil</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt;                   Estimate  se_notrans    t value       Pr(&gt;t)        Lower
-#&gt; parent_0       76.55425583 0.859186612 89.1008482 1.113866e-26 74.755959748
-#&gt; k_parent        0.12081956 0.004601921 26.2541551 1.077372e-16  0.111561582
-#&gt; k_M1            0.84258650 0.806231456  1.0450926 1.545475e-01  0.113839804
-#&gt; k_M2            0.04210878 0.017083049  2.4649452 1.170195e-02  0.018013807
+#&gt; parent_0       76.55425584 0.859186619 89.1008474 1.113866e-26 74.755959756
+#&gt; k_parent        0.12081956 0.004601922 26.2541544 1.077373e-16  0.111561582
+#&gt; k_M1            0.84258649 0.806231419  1.0450926 1.545475e-01  0.113839803
+#&gt; k_M2            0.04210878 0.017083049  2.4649453 1.170195e-02  0.018013807
 #&gt; k_M3            0.01122919 0.007245890  1.5497322 6.885127e-02  0.002909463
-#&gt; f_parent_to_M1  0.32240199 0.240803564  1.3388589 9.820820e-02           NA
-#&gt; f_parent_to_M2  0.16099854 0.033691991  4.7785403 6.531225e-05           NA
-#&gt; f_M1_to_M3      0.27921500 0.269443517  1.0362654 1.565440e-01  0.022992933
-#&gt; f_M2_to_M3      0.55641333 0.595125466  0.9349513 1.807725e-01  0.008003317
+#&gt; f_parent_to_M1  0.32240199 0.240803555  1.3388589 9.820820e-02           NA
+#&gt; f_parent_to_M2  0.16099854 0.033691991  4.7785403 6.531224e-05           NA
+#&gt; f_M1_to_M3      0.27921501 0.269443514  1.0362655 1.565440e-01  0.022992937
+#&gt; f_M2_to_M3      0.55641331 0.595125445  0.9349513 1.807725e-01  0.008003317
 #&gt; sigma           1.14005399 0.149696423  7.6157731 1.727024e-07  0.826735778
 #&gt;                      Upper
 #&gt; parent_0       78.35255192
 #&gt; k_parent        0.13084582
-#&gt; k_M1            6.23641283
+#&gt; k_M1            6.23641265
 #&gt; k_M2            0.09843279
 #&gt; k_M3            0.04333950
 #&gt; f_parent_to_M1          NA
 #&gt; f_parent_to_M2          NA
-#&gt; f_M1_to_M3      0.86443084
+#&gt; f_M1_to_M3      0.86443083
 #&gt; f_M2_to_M3      0.99489847
 #&gt; sigma           1.45337221</div><div class='input'>  <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#&gt;             err.min n.optim df
 #&gt; All data 0.09649963       9 20
diff --git a/test.log b/test.log
index b1e9b9f3..bd6c6d0e 100644
--- a/test.log
+++ b/test.log
@@ -2,26 +2,26 @@ Loading mkin
 Testing mkin
 ✔ |  OK F W S | Context
 
 ⠏ |   0       | Export dataset for reading into CAKE
 ✔ |   1       | Export dataset for reading into CAKE
-
-⠏ |   0       | Error model fitting
-⠋ |   1       | Error model fitting
-⠹ |   3       | Error model fitting
-⠸ |   4       | Error model fitting
-⠼ |   5       | Error model fitting
-⠴ |   6       | Error model fitting
-⠧ |   8       | Error model fitting
-⠏ |  10       | Error model fitting
-⠋ |  11       | Error model fitting
-✔ |  12       | Error model fitting [147.8 s]
-
-⠏ |   0       | Calculation of FOCUS chi2 error levels
-⠋ |   1       | Calculation of FOCUS chi2 error levels
-⠹ |   3       | Calculation of FOCUS chi2 error levels
-✔ |   3       | Calculation of FOCUS chi2 error levels [2.3 s]
-
-⠏ |   0       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
-⠋ |   1       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
-⠙ |   2       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
-⠸ |   4       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
-⠇ |   9       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
-✔ |  13       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.7 s]
+
+⠏ |   0       | Error model fitting
+⠋ |   1       | Error model fitting
+⠹ |   3       | Error model fitting
+⠸ |   4       | Error model fitting
+⠼ |   5       | Error model fitting
+⠴ |   6       | Error model fitting
+⠧ |   8       | Error model fitting
+⠏ |  10       | Error model fitting
+⠋ |  11       | Error model fitting
+✔ |  12       | Error model fitting [219.8 s]
+
+⠏ |   0       | Calculation of FOCUS chi2 error levels
+⠋ |   1       | Calculation of FOCUS chi2 error levels
+⠹ |   3       | Calculation of FOCUS chi2 error levels
+✔ |   3       | Calculation of FOCUS chi2 error levels [2.4 s]
+
+⠏ |   0       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
+⠋ |   1       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
+⠙ |   2       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
+⠸ |   4       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
+⠇ |   9       | Results for FOCUS D established in expertise for UBA (Ranke 2014)
+✔ |  13       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [4.0 s]
 
 ⠏ |   0       | Test fitting the decline of metabolites from their maximum
 ⠋ |   1       | Test fitting the decline of metabolites from their maximum
 ⠹ |   3       | Test fitting the decline of metabolites from their maximum
 ⠼ |   5       | Test fitting the decline of metabolites from their maximum
 ✔ |   6       | Test fitting the decline of metabolites from their maximum [0.9 s]
 
 ⠏ |   0       | Fitting the logistic model
 ⠋ |   1       | Fitting the logistic model
 ✔ |   1       | Fitting the logistic model [0.9 s]
 
 ⠏ |   0       | Test dataset class mkinds used in gmkin
 ✔ |   1       | Test dataset class mkinds used in gmkin
-
-⠏ |   0       | Special cases of mkinfit calls
-⠋ |   1       | Special cases of mkinfit calls
-⠇ |   9       | Special cases of mkinfit calls
-⠏ |  10       | Special cases of mkinfit calls
-⠋ |  11       | Special cases of mkinfit calls
-⠙ |  12       | Special cases of mkinfit calls
-✔ |  12       | Special cases of mkinfit calls [2.7 s]
+
+⠏ |   0       | Special cases of mkinfit calls
+⠋ |   1       | Special cases of mkinfit calls
+⠇ |   9       | Special cases of mkinfit calls
+⠏ |  10       | Special cases of mkinfit calls
+⠋ |  11       | Special cases of mkinfit calls
+⠙ |  12       | Special cases of mkinfit calls
+✔ |  12       | Special cases of mkinfit calls [2.9 s]
 
 ⠏ |   0       | mkinmod model generation and printing
 ⠇ |   9       | mkinmod model generation and printing
 ✔ |   9       | mkinmod model generation and printing [0.2 s]
 
 ⠏ |   0       | Model predictions with mkinpredict
 ⠋ |   1       | Model predictions with mkinpredict
 ✔ |   3       | Model predictions with mkinpredict [0.3 s]
-
-⠏ |   0       | Evaluations according to 2015 NAFTA guidance
-⠙ |   2       | Evaluations according to 2015 NAFTA guidance
-⠇ |   9       | Evaluations according to 2015 NAFTA guidance
-⠏ |  10       | Evaluations according to 2015 NAFTA guidance
-⠴ |  16       | Evaluations according to 2015 NAFTA guidance
-✔ |  16       | Evaluations according to 2015 NAFTA guidance [3.9 s]
-
-⠏ |   0       | Fitting of parent only models
-⠋ |   1       | Fitting of parent only models
-⠙ |   2       | Fitting of parent only models
-⠹ |   3       | Fitting of parent only models
-⠸ |   4       | Fitting of parent only models
-⠼ |   5       | Fitting of parent only models
-⠴ |   6       | Fitting of parent only models
-⠦ |   7       | Fitting of parent only models
-⠧ |   8       | Fitting of parent only models
-⠇ |   9       | Fitting of parent only models
-⠏ |  10       | Fitting of parent only models
-⠋ |  11       | Fitting of parent only models
-⠙ |  12       | Fitting of parent only models
-⠹ |  13       | Fitting of parent only models
-⠴ |  16       | Fitting of parent only models
-⠧ |  18       | Fitting of parent only models
-⠏ |  20       | Fitting of parent only models
-✔ |  21       | Fitting of parent only models [40.1 s]
+
+⠏ |   0       | Evaluations according to 2015 NAFTA guidance
+⠙ |   2       | Evaluations according to 2015 NAFTA guidance
+⠇ |   9       | Evaluations according to 2015 NAFTA guidance
+⠏ |  10       | Evaluations according to 2015 NAFTA guidance
+⠴ |  16       | Evaluations according to 2015 NAFTA guidance
+✔ |  16       | Evaluations according to 2015 NAFTA guidance [4.0 s]
+
+⠏ |   0       | Fitting of parent only models
+⠋ |   1       | Fitting of parent only models
+⠙ |   2       | Fitting of parent only models
+⠹ |   3       | Fitting of parent only models
+⠸ |   4       | Fitting of parent only models
+⠼ |   5       | Fitting of parent only models
+⠴ |   6       | Fitting of parent only models
+⠦ |   7       | Fitting of parent only models
+⠧ |   8       | Fitting of parent only models
+⠇ |   9       | Fitting of parent only models
+⠏ |  10       | Fitting of parent only models
+⠋ |  11       | Fitting of parent only models
+⠙ |  12       | Fitting of parent only models
+⠹ |  13       | Fitting of parent only models
+⠴ |  16       | Fitting of parent only models
+⠧ |  18       | Fitting of parent only models
+⠏ |  20       | Fitting of parent only models
+✔ |  21       | Fitting of parent only models [40.8 s]
 
 ⠏ |   0       | Calculation of maximum time weighted average concentrations (TWAs)
 ⠋ |   1       | Calculation of maximum time weighted average concentrations (TWAs)
 ⠙ |   2       | Calculation of maximum time weighted average concentrations (TWAs)
 ⠹ |   3       | Calculation of maximum time weighted average concentrations (TWAs)
 ⠸ |   4       | Calculation of maximum time weighted average concentrations (TWAs)
 ✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
 
 ⠏ |   0       | Summary
 ✔ |   1       | Summary
 
 ⠏ |   0       | Plotting
 ⠹ |   3       | Plotting
 ✔ |   4       | Plotting [0.3 s]
 
 ⠏ |   0       | AIC calculation
 ✔ |   2       | AIC calculation
-
-⠏ |   0       | Complex test case from Schaefer et al. (2007) Piacenza paper
-⠋ |   1       | Complex test case from Schaefer et al. (2007) Piacenza paper
-✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s]
+
+⠏ |   0       | Complex test case from Schaefer et al. (2007) Piacenza paper
+⠋ |   1       | Complex test case from Schaefer et al. (2007) Piacenza paper
+✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.4 s]
 
 ⠏ |   0       | Results for synthetic data established in expertise for UBA (Ranke 2014)
 ⠋ |   1       | Results for synthetic data established in expertise for UBA (Ranke 2014)
 ⠹ |   3       | Results for synthetic data established in expertise for UBA (Ranke 2014)
 ✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.1 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 223.4 s
+Duration: 297.0 s
 
 OK:       115
 Failed:   0
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index 07488d5e..02c7893f 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -5,7 +5,7 @@ Description:
 MeasurementUnits: % AR
 TimeUnits: days
 Comments: Created using mkin::CAKE_export
-Date: 2019-05-02
+Date: 2019-05-03
 Optimiser: IRLS
 
 [Data]
diff --git a/vignettes/mkin_benchmarks.rda b/vignettes/mkin_benchmarks.rda
index 61f03620..985cdac6 100644
--- a/vignettes/mkin_benchmarks.rda
+++ b/vignettes/mkin_benchmarks.rda
author	Johannes Ranke <jranke@uni-bremen.de>	2019-05-03 19:14:15 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2019-05-03 19:14:15 +0200
commit	1ef7008be2a72a0847064ad9c2ddcfa16b055482 (patch)
tree	ecc3f90e5d18c75aea14ad774aad9214039c0674
parent	de7b6acdd75a0f95f2a9522c22625810f4aa329a (diff)