From 8a3475c59f3d91ce5ce7d980d6de09360617e7fe Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 7 May 2019 08:12:27 +0200 Subject: After the OLS step, use OLS parameter estimates - Fix the respective error in the code - Static documentation rebuilt by pkgdown --- docs/reference/NAFTA_SOP_2015.html | 32 +-- docs/reference/NAFTA_SOP_Attachment.html | 32 +-- docs/reference/logLik.mkinfit.html | 2 +- docs/reference/logistic.solution.html | 18 +- docs/reference/mccall81_245T.html | 45 ++-- docs/reference/mkinfit.html | 339 ++++++++++++---------------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinparplot-1.png | Bin 16549 -> 17306 bytes docs/reference/mkinparplot.html | 2 +- docs/reference/mkinpredict.html | 8 +- docs/reference/mmkin.html | 4 +- docs/reference/nafta.html | 32 +-- docs/reference/summary.mkinfit.html | 30 ++- docs/reference/test_data_from_UBA_2014.html | 54 ++--- docs/reference/transform_odeparms.html | 90 ++++---- 15 files changed, 300 insertions(+), 390 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 84341a17..9fbc71c6 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -155,7 +155,7 @@

Examples

- 
  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
+    
  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#> Warning: Could not calculate correlation; no covariance matrix
#> Warning: Could not calculate correlation; no covariance matrix
#> Warning: Could not calculate correlation; no covariance matrix
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
 #>       SFO      IORE      DFOP 
 #> 1378.6832  615.7730  517.8836 
 #> 
@@ -164,25 +164,25 @@
 #> 
 #> Parameters:
 #> $SFO
-#>               Estimate   Pr(>t)    Lower   Upper
-#> parent_0       83.7558 1.80e-14 77.18268 90.3288
-#> k_parent_sink   0.0017 7.43e-05  0.00112  0.0026
-#> sigma           8.7518 1.22e-05  5.64278 11.8608
+#>               Estimate Pr(>t) Lower Upper
+#> parent_0       83.7558     NA    NA    NA
+#> k_parent_sink   0.0017     NA    NA    NA
+#> sigma           8.7518     NA    NA    NA
 #> 
 #> $IORE
-#>                     Estimate Pr(>t)    Lower    Upper
-#> parent_0            9.69e+01     NA 8.88e+01 1.05e+02
-#> k__iore_parent_sink 8.40e-14     NA 1.79e-18 3.94e-09
-#> N_parent            6.68e+00     NA 4.19e+00 9.17e+00
-#> sigma               5.85e+00     NA 3.76e+00 7.94e+00
+#>                     Estimate Pr(>t) Lower Upper
+#> parent_0            9.69e+01     NA    NA    NA
+#> k__iore_parent_sink 8.40e-14     NA    NA    NA
+#> N_parent            6.68e+00     NA    NA    NA
+#> sigma               5.85e+00     NA    NA    NA
 #> 
 #> $DFOP
-#>          Estimate   Pr(>t)    Lower    Upper
-#> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02
-#> k1       4.24e-02 5.92e-03 2.03e-02 8.88e-02
-#> k2       8.24e-04 6.48e-03 3.89e-04 1.75e-03
-#> g        2.88e-01 2.47e-05 1.95e-01 4.03e-01
-#> sigma    5.36e+00 2.22e-05 3.43e+00 7.30e+00
+#>          Estimate Pr(>t) Lower Upper
+#> parent_0 9.76e+01     NA    NA    NA
+#> k1       4.24e-02     NA    NA    NA
+#> k2       8.24e-04     NA    NA    NA
+#> g        2.88e-01     NA    NA    NA
+#> sigma    5.36e+00     NA    NA    NA
 #> 
 #> 
 #> DTx values:
diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html
index 76d91c40..149b4d82 100644
--- a/docs/reference/NAFTA_SOP_Attachment.html
+++ b/docs/reference/NAFTA_SOP_Attachment.html
@@ -152,7 +152,7 @@
     
 
     
Examples

-    
  nafta_att_p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]], cores = 1)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The half-life obtained from the IORE model may be used
  print(nafta_att_p5a)
#> Sums of squares:
+    
  nafta_att_p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]], cores = 1)
#> Warning: Could not calculate correlation; no covariance matrix
#> Warning: Could not calculate correlation; no covariance matrix
#> Warning: Could not calculate correlation; no covariance matrix
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The half-life obtained from the IORE model may be used
  print(nafta_att_p5a)
#> Sums of squares:
 #>       SFO      IORE      DFOP 
 #> 465.21753  56.27506  32.06401 
 #> 
@@ -161,25 +161,25 @@
 #> 
 #> Parameters:
 #> $SFO
-#>               Estimate   Pr(>t)  Lower   Upper
-#> parent_0       95.8401 4.67e-21 92.245 99.4357
-#> k_parent_sink   0.0102 3.92e-12  0.009  0.0117
-#> sigma           4.8230 3.81e-06  3.214  6.4318
+#>               Estimate Pr(>t) Lower Upper
+#> parent_0       95.8401     NA    NA    NA
+#> k_parent_sink   0.0102     NA    NA    NA
+#> sigma           4.8230     NA    NA    NA
 #> 
 #> $IORE
-#>                     Estimate Pr(>t)    Lower    Upper
-#> parent_0            1.01e+02     NA 9.91e+01 1.02e+02
-#> k__iore_parent_sink 1.54e-05     NA 4.08e-06 5.84e-05
-#> N_parent            2.57e+00     NA 2.25e+00 2.89e+00
-#> sigma               1.68e+00     NA 1.12e+00 2.24e+00
+#>                     Estimate Pr(>t) Lower Upper
+#> parent_0            1.01e+02     NA    NA    NA
+#> k__iore_parent_sink 1.54e-05     NA    NA    NA
+#> N_parent            2.57e+00     NA    NA    NA
+#> sigma               1.68e+00     NA    NA    NA
 #> 
 #> $DFOP
-#>          Estimate   Pr(>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       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
+#>          Estimate Pr(>t) Lower Upper
+#> parent_0 9.99e+01     NA    NA    NA
+#> k1       2.67e-02     NA    NA    NA
+#> k2       2.86e-12     NA    NA    NA
+#> g        6.47e-01     NA    NA    NA
+#> sigma    1.27e+00     NA    NA    NA
 #> 
 #> 
 #> DTx values:
diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html
index f5844a8e..0184d573 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
   f_nw <- mkinfit(sfo_sfo, d_t, quiet = TRUE) # no weighting (weights are unity)
#> Warning: Observations with value of zero were removed from the data
  f_obs <- mkinfit(sfo_sfo, d_t, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
  f_tc <- mkinfit(sfo_sfo, d_t, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
  AIC(f_nw, f_obs, f_tc)
#>       df      AIC
 #> f_nw   5 204.4486
 #> f_obs  6 205.8727
-#> f_tc   6 148.1802
  

+#> f_tc   6 141.9656
  

   

   
  summary(m)$bpar
#>              Estimate   se_notrans   t value       Pr(>t)        Lower
-#> parent_0 1.057896e+02 1.9023449649 55.610120 3.768361e-16 1.016451e+02
-#> kmax     6.398190e-02 0.0143201029  4.467978 3.841828e-04 3.929235e-02
-#> k0       1.612775e-04 0.0005866813  0.274898 3.940351e-01 5.846685e-08
-#> r        2.263946e-01 0.1718110773  1.317695 1.061044e-01 4.335843e-02
-#> sigma    5.332935e+00 0.9145907310  5.830952 4.036926e-05 3.340213e+00
-#>                Upper
-#> parent_0 109.9341588
-#> kmax       0.1041853
-#> k0         0.4448750
-#> r          1.1821121
-#> sigma      7.3256566
  endpoints(m)$distimes
#>            DT50     DT90  DT50_k0 DT50_kmax
+  plot_sep(m)
  summary(m)$bpar
#> Warning: Could not calculate correlation; no covariance matrix
#>              Estimate se_notrans t value Pr(>t) Lower Upper
+#> parent_0 1.057896e+02         NA      NA     NA    NA    NA
+#> kmax     6.398190e-02         NA      NA     NA    NA    NA
+#> k0       1.612775e-04         NA      NA     NA    NA    NA
+#> r        2.263946e-01         NA      NA     NA    NA    NA
+#> sigma    5.332935e+00         NA      NA     NA    NA    NA
  endpoints(m)$distimes
#>            DT50     DT90  DT50_k0 DT50_kmax
 #> parent 36.86533 62.41511 4297.854  10.83349

   

   
   
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.002       0.000       0.001 
  system.time(
+#>       0.001       0.000       0.001 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve", use_compiled = FALSE)[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.022       0.000       0.021 

+#>       0.021       0.000       0.022 

   
    # Predict from a fitted model
     f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Ordinary least squares optimisation
#> Sum of squared residuals at call 1: 552.5739
 #> Sum of squared residuals at call 3: 552.5739
@@ -368,9 +368,7 @@
 #> Sum of squared residuals at call 59: 196.5334
 #> Sum of squared residuals at call 65: 196.5334
 #> Sum of squared residuals at call 73: 196.5334
-#> Negative log-likelihood at call 75: 26.64668
-#> Negative log-likelihood at call 103: 26.64668
-#> Optimisation successfully terminated.
    head(mkinpredict(f))
#>   time   parent       m1
+#> Negative log-likelihood at call 75: 26.64668
#> Optimisation successfully terminated.
    head(mkinpredict(f))
#>   time   parent       m1
 #> 1  0.0 82.49216 0.000000
 #> 2  0.1 80.00563 1.179955
 #> 3  0.2 77.59404 2.312580
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index c730ecb0..849e619e 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -194,8 +194,8 @@
 time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
#>        User      System verstrichen 
-#>       0.042       0.028       5.095 
time_1
#>        User      System verstrichen 
-#>       19.29        0.00       19.30 

+#>       0.039       0.031       3.113 
time_1
#>        User      System verstrichen 
+#>      10.445       0.001      10.456 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
 #>   0.7340481   0.2659519   0.7505684   0.2494316 
diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html
index a9ee2f76..62027fab 100644
--- a/docs/reference/nafta.html
+++ b/docs/reference/nafta.html
@@ -182,7 +182,7 @@
     
 
     
Examples

-    
  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
+    
  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#> Warning: Could not calculate correlation; no covariance matrix
#> Warning: Could not calculate correlation; no covariance matrix
#> Warning: Could not calculate correlation; no covariance matrix
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
 #>       SFO      IORE      DFOP 
 #> 1378.6832  615.7730  517.8836 
 #> 
@@ -191,25 +191,25 @@
 #> 
 #> Parameters:
 #> $SFO
-#>               Estimate   Pr(>t)    Lower   Upper
-#> parent_0       83.7558 1.80e-14 77.18268 90.3288
-#> k_parent_sink   0.0017 7.43e-05  0.00112  0.0026
-#> sigma           8.7518 1.22e-05  5.64278 11.8608
+#>               Estimate Pr(>t) Lower Upper
+#> parent_0       83.7558     NA    NA    NA
+#> k_parent_sink   0.0017     NA    NA    NA
+#> sigma           8.7518     NA    NA    NA
 #> 
 #> $IORE
-#>                     Estimate Pr(>t)    Lower    Upper
-#> parent_0            9.69e+01     NA 8.88e+01 1.05e+02
-#> k__iore_parent_sink 8.40e-14     NA 1.79e-18 3.94e-09
-#> N_parent            6.68e+00     NA 4.19e+00 9.17e+00
-#> sigma               5.85e+00     NA 3.76e+00 7.94e+00
+#>                     Estimate Pr(>t) Lower Upper
+#> parent_0            9.69e+01     NA    NA    NA
+#> k__iore_parent_sink 8.40e-14     NA    NA    NA
+#> N_parent            6.68e+00     NA    NA    NA
+#> sigma               5.85e+00     NA    NA    NA
 #> 
 #> $DFOP
-#>          Estimate   Pr(>t)    Lower    Upper
-#> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02
-#> k1       4.24e-02 5.92e-03 2.03e-02 8.88e-02
-#> k2       8.24e-04 6.48e-03 3.89e-04 1.75e-03
-#> g        2.88e-01 2.47e-05 1.95e-01 4.03e-01
-#> sigma    5.36e+00 2.22e-05 3.43e+00 7.30e+00
+#>          Estimate Pr(>t) Lower Upper
+#> parent_0 9.76e+01     NA    NA    NA
+#> k1       4.24e-02     NA    NA    NA
+#> k2       8.24e-04     NA    NA    NA
+#> g        2.88e-01     NA    NA    NA
+#> sigma    5.36e+00     NA    NA    NA
 #> 
 #> 
 #> DTx values:
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 351d7a7e..a4f3d04f 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -209,17 +209,17 @@
     
 
     
Examples

-    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.4 
+    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> Warning: Could not calculate correlation; no covariance matrix
#> mkin version used for fitting:    0.9.49.4 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Fri May  3 19:08:31 2019 
-#> Date of summary: Fri May  3 19:08:31 2019 
+#> Date of fit:     Tue May  7 08:09:03 2019 
+#> Date of summary: Tue May  7 08:09:03 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 131 model solutions performed in 0.27 s
+#> Fitted using 39 model solutions performed in 0.08 s
 #> 
 #> Error model:
 #> Constant variance 
@@ -240,25 +240,21 @@
 #> None
 #> 
 #> Optimised, transformed parameters with symmetric confidence intervals:
-#>                   Estimate Std. Error  Lower   Upper
-#> parent_0           109.200    3.70400 99.630 118.700
-#> log_k_parent_sink   -3.291    0.09176 -3.527  -3.055
-#> sigma                5.266    1.31600  1.882   8.649
+#>                   Estimate Std. Error Lower Upper
+#> parent_0           109.200         NA    NA    NA
+#> log_k_parent_sink   -3.291         NA    NA    NA
+#> sigma                5.266         NA    NA    NA
 #> 
 #> Parameter correlation:
-#>                    parent_0 log_k_parent_sink     sigma
-#> parent_0          1.000e+00         5.428e-01 1.648e-07
-#> log_k_parent_sink 5.428e-01         1.000e+00 2.513e-07
-#> sigma             1.648e-07         2.513e-07 1.000e+00
-#> 
+#> No covariance matrix
 #> 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(>t)   Lower     Upper
-#> parent_0      109.20000   29.47 4.218e-07 99.6300 118.70000
-#> k_parent_sink   0.03722   10.90 5.650e-05  0.0294   0.04712
-#> sigma           5.26600    4.00 5.162e-03  1.8820   8.64900
+#>                Estimate t value Pr(>t) Lower Upper
+#> parent_0      109.20000      NA     NA    NA    NA
+#> k_parent_sink   0.03722      NA     NA    NA    NA
+#> sigma           5.26600      NA     NA    NA    NA
 #> 
 #> FOCUS Chi2 error levels in percent:
 #>          err.min n.optim df
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index bc988340..11cb6420 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -159,20 +159,13 @@
   # model).
   m_ws <- mkinmod(parent_w = mkinsub("SFO", "parent_s"),
                   parent_s = mkinsub("SFO", "parent_w"))
#> Successfully compiled differential equation model from auto-generated C code.
  f_river <- mkinfit(m_ws, test_data_from_UBA_2014[[1]]$data, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
  plot_sep(f_river)

-  summary(f_river)$bpar
#>                         Estimate se_notrans      t value       Pr(>t)
-#> parent_w_0          9.598567e+01 2.12351789 4.520126e+01 9.476190e-18
-#> k_parent_w_sink     3.603743e-01 0.03149282 1.144306e+01 4.126593e-09
-#> k_parent_w_parent_s 6.031371e-02 0.01603582 3.761186e+00 9.436275e-04
-#> k_parent_s_sink     5.108964e-11 0.09482736 5.387647e-10 5.000000e-01
-#> k_parent_s_parent_w 7.419672e-02 0.10737376 6.910135e-01 2.500560e-01
-#> sigma               2.982879e+00 0.50545649 5.901356e+00 1.454535e-05
-#>                           Lower       Upper
-#> parent_w_0          91.48420503 100.4871438
-#> k_parent_w_sink      0.30668904   0.4234571
-#> k_parent_w_parent_s  0.03423904   0.1062455
-#> k_parent_s_sink      0.00000000         Inf
-#> k_parent_s_parent_w  0.02289956   0.2404043
-#> sigma                2.00184022   3.9639169
  mkinerrmin(f_river)
#>             err.min n.optim df
+  summary(f_river)$bpar
#> Warning: Could not calculate correlation; no covariance matrix
#>                         Estimate se_notrans t value Pr(>t) Lower Upper
+#> parent_w_0          9.598567e+01         NA      NA     NA    NA    NA
+#> k_parent_w_sink     3.603743e-01         NA      NA     NA    NA    NA
+#> k_parent_w_parent_s 6.031371e-02         NA      NA     NA    NA    NA
+#> k_parent_s_sink     5.108964e-11         NA      NA     NA    NA    NA
+#> k_parent_s_parent_w 7.419672e-02         NA      NA     NA    NA    NA
+#> sigma               2.982879e+00         NA      NA     NA    NA    NA
  mkinerrmin(f_river)
#>             err.min n.optim df
 #> All data 0.09246946       5  6
 #> parent_w 0.06377096       3  3
 #> parent_s 0.20882325       2  3

@@ -183,28 +176,17 @@
                     M2 = mkinsub("SFO", "M3"),
                     M3 = mkinsub("SFO"),
                     use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

-  f_soil <- mkinfit(m_soil, test_data_from_UBA_2014[[3]]$data, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
  plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright"))
  summary(f_soil)$bpar
#>                   Estimate  se_notrans    t value       Pr(>t)        Lower
-#> parent_0       76.55425584 0.859186619 89.1008474 1.113866e-26 74.755959756
-#> k_parent        0.12081956 0.004601922 26.2541544 1.077373e-16  0.111561582
-#> k_M1            0.84258649 0.806231419  1.0450926 1.545475e-01  0.113839803
-#> k_M2            0.04210878 0.017083049  2.4649453 1.170195e-02  0.018013807
-#> k_M3            0.01122919 0.007245890  1.5497322 6.885127e-02  0.002909463
-#> f_parent_to_M1  0.32240199 0.240803555  1.3388589 9.820820e-02           NA
-#> f_parent_to_M2  0.16099854 0.033691991  4.7785403 6.531224e-05           NA
-#> f_M1_to_M3      0.27921501 0.269443514  1.0362655 1.565440e-01  0.022992937
-#> f_M2_to_M3      0.55641331 0.595125445  0.9349513 1.807725e-01  0.008003317
-#> sigma           1.14005399 0.149696423  7.6157731 1.727024e-07  0.826735778
-#>                      Upper
-#> parent_0       78.35255192
-#> k_parent        0.13084582
-#> k_M1            6.23641265
-#> k_M2            0.09843279
-#> k_M3            0.04333950
-#> f_parent_to_M1          NA
-#> f_parent_to_M2          NA
-#> f_M1_to_M3      0.86443083
-#> f_M2_to_M3      0.99489847
-#> sigma           1.45337221
  mkinerrmin(f_soil)
#>             err.min n.optim df
+  f_soil <- mkinfit(m_soil, test_data_from_UBA_2014[[3]]$data, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
  plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright"))
  summary(f_soil)$bpar
#> Warning: Could not calculate correlation; no covariance matrix
#>                   Estimate se_notrans t value Pr(>t) Lower Upper
+#> parent_0       76.55425584         NA      NA     NA    NA    NA
+#> k_parent        0.12081956         NA      NA     NA    NA    NA
+#> k_M1            0.84258649         NA      NA     NA    NA    NA
+#> k_M2            0.04210878         NA      NA     NA    NA    NA
+#> k_M3            0.01122919         NA      NA     NA    NA    NA
+#> f_parent_to_M1  0.32240199         NA      NA     NA    NA    NA
+#> f_parent_to_M2  0.16099854         NA      NA     NA    NA    NA
+#> f_M1_to_M3      0.27921501         NA      NA     NA    NA    NA
+#> f_M2_to_M3      0.55641331         NA      NA     NA    NA    NA
+#> sigma           1.14005399         NA      NA     NA    NA    NA
  mkinerrmin(f_soil)
#>             err.min n.optim df
 #> All data 0.09649963       9 20
 #> parent   0.04721283       2  6
 #> M1       0.26551209       2  5
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 7e05480e..c91565b9 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -202,32 +202,30 @@ The transformation of sets of formation fractions is fragile, as it supposes
     
SFO_SFO <- mkinmod(
   parent = list(type = "SFO", to = "m1", sink = TRUE),
   m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.s <- summary(fit)
-# Transformed and backtransformed parameters
-print(fit.s$par, 3)
#>                   Estimate Std. Error Lower  Upper
-#> parent_0             99.60     1.5702 96.40 102.79
-#> log_k_parent_sink    -3.04     0.0763 -3.19  -2.88
-#> log_k_parent_m1      -2.98     0.0403 -3.06  -2.90
-#> log_k_m1_sink        -5.25     0.1332 -5.52  -4.98
-#> sigma                 3.13     0.3585  2.40   3.85
print(fit.s$bpar, 3)
#>               Estimate se_notrans t value   Pr(>t)    Lower    Upper
-#> parent_0      99.59848    1.57022   63.43 2.30e-36 96.40384 102.7931
-#> k_parent_sink  0.04792    0.00365   13.11 6.13e-15  0.04103   0.0560
-#> k_parent_m1    0.05078    0.00205   24.80 3.27e-23  0.04678   0.0551
-#> k_m1_sink      0.00526    0.00070    7.51 6.16e-09  0.00401   0.0069
-#> sigma          3.12550    0.35852    8.72 2.24e-10  2.39609   3.8549

+fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.s <- summary(fit)
#> Warning: Could not calculate correlation; no covariance matrix
# Transformed and backtransformed parameters
+print(fit.s$par, 3)
#>                   Estimate Std. Error Lower Upper
+#> parent_0             99.60         NA    NA    NA
+#> log_k_parent_sink    -3.04         NA    NA    NA
+#> log_k_parent_m1      -2.98         NA    NA    NA
+#> log_k_m1_sink        -5.25         NA    NA    NA
+#> sigma                 3.13         NA    NA    NA
print(fit.s$bpar, 3)
#>               Estimate se_notrans t value Pr(>t) Lower Upper
+#> parent_0      99.59848         NA      NA     NA    NA    NA
+#> k_parent_sink  0.04792         NA      NA     NA    NA    NA
+#> k_parent_m1    0.05078         NA      NA     NA    NA    NA
+#> k_m1_sink      0.00526         NA      NA     NA    NA    NA
+#> sigma          3.12550         NA      NA     NA    NA    NA

 
# Compare to the version without transforming rate parameters
-fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.2.s <- summary(fit.2)
-print(fit.2.s$par, 3)
#>               Estimate Std. Error    Lower    Upper
-#> parent_0      99.59848    1.57022 96.40384 1.03e+02
-#> k_parent_sink  0.04792    0.00365  0.04049 5.54e-02
-#> k_parent_m1    0.05078    0.00205  0.04661 5.49e-02
-#> k_m1_sink      0.00526    0.00070  0.00384 6.69e-03
-#> sigma          3.12550    0.35852  2.39609 3.85e+00
print(fit.2.s$bpar, 3)
#>               Estimate se_notrans t value   Pr(>t)    Lower    Upper
-#> parent_0      99.59848    1.57022   63.43 2.30e-36 96.40384 1.03e+02
-#> k_parent_sink  0.04792    0.00365   13.11 6.13e-15  0.04049 5.54e-02
-#> k_parent_m1    0.05078    0.00205   24.80 3.27e-23  0.04661 5.49e-02
-#> k_m1_sink      0.00526    0.00070    7.51 6.16e-09  0.00384 6.69e-03
-#> sigma          3.12550    0.35852    8.72 2.24e-10  2.39609 3.85e+00

+fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.2.s <- summary(fit.2)
#> Warning: Could not calculate correlation; no covariance matrix
print(fit.2.s$par, 3)
#>               Estimate Std. Error Lower Upper
+#> parent_0      99.59848         NA    NA    NA
+#> k_parent_sink  0.04792         NA    NA    NA
+#> k_parent_m1    0.05078         NA    NA    NA
+#> k_m1_sink      0.00526         NA    NA    NA
+#> sigma          3.12550         NA    NA    NA
print(fit.2.s$bpar, 3)
#>               Estimate se_notrans t value Pr(>t) Lower Upper
+#> parent_0      99.59848         NA      NA     NA    NA    NA
+#> k_parent_sink  0.04792         NA      NA     NA    NA    NA
+#> k_parent_m1    0.05078         NA      NA     NA    NA    NA
+#> k_m1_sink      0.00526         NA      NA     NA    NA    NA
+#> sigma          3.12550         NA      NA     NA    NA    NA

 initials <- fit$start$value
 names(initials) <- rownames(fit$start)
 transformed <- fit$start_transformed$value
@@ -240,18 +238,17 @@ The transformation of sets of formation fractions is fragile, as it supposes
   parent = list(type = "SFO", to = "m1", sink = TRUE),
   m1 = list(type = "SFO"),
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

-fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.ff.s <- summary(fit.ff)
-print(fit.ff.s$par, 3)
#>                Estimate Std. Error   Lower   Upper
-#> parent_0         99.598     1.5702 96.4038 102.793
-#> log_k_parent     -2.316     0.0409 -2.3988  -2.233
-#> log_k_m1         -5.248     0.1332 -5.5184  -4.977
-#> f_parent_ilr_1    0.041     0.0631 -0.0875   0.169
-#> sigma             3.126     0.3585  2.3961   3.855
print(fit.ff.s$bpar, 3)
#>                Estimate se_notrans t value   Pr(>t)    Lower    Upper
-#> parent_0       99.59848    1.57022   63.43 2.30e-36 96.40384 102.7931
-#> k_parent        0.09870    0.00403   24.47 4.96e-23  0.09082   0.1073
-#> k_m1            0.00526    0.00070    7.51 6.16e-09  0.00401   0.0069
-#> f_parent_to_m1  0.51448    0.02230   23.07 3.10e-22  0.46912   0.5596
-#> sigma           3.12550    0.35852    8.72 2.24e-10  2.39609   3.8549
initials <- c("f_parent_to_m1" = 0.5)
+fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.ff.s <- summary(fit.ff)
#> Warning: Could not calculate correlation; no covariance matrix
print(fit.ff.s$par, 3)
#>                Estimate Std. Error Lower Upper
+#> parent_0         99.598         NA    NA    NA
+#> log_k_parent     -2.316         NA    NA    NA
+#> log_k_m1         -5.248         NA    NA    NA
+#> f_parent_ilr_1    0.041         NA    NA    NA
+#> sigma             3.126         NA    NA    NA
print(fit.ff.s$bpar, 3)
#>                Estimate se_notrans t value Pr(>t) Lower Upper
+#> parent_0       99.59848         NA      NA     NA    NA    NA
+#> k_parent        0.09870         NA      NA     NA    NA    NA
+#> k_m1            0.00526         NA      NA     NA    NA    NA
+#> f_parent_to_m1  0.51448         NA      NA     NA    NA    NA
+#> sigma           3.12550         NA      NA     NA    NA    NA
initials <- c("f_parent_to_m1" = 0.5)
 transformed <- transform_odeparms(initials, SFO_SFO.ff)
 backtransform_odeparms(transformed, SFO_SFO.ff)
#> f_parent_to_m1 
 #>            0.5 

@@ -261,16 +258,15 @@ The transformation of sets of formation fractions is fragile, as it supposes
   m1 = list(type = "SFO"),
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 
-fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.ff.2.s <- summary(fit.ff.2)
-print(fit.ff.2.s$par, 3)
#>              Estimate Std. Error Lower Upper
-#> parent_0        84.79      3.012 78.67 90.91
-#> log_k_parent    -2.76      0.082 -2.92 -2.59
-#> log_k_m1        -4.21      0.123 -4.46 -3.96
-#> sigma            8.22      0.943  6.31 10.14
print(fit.ff.2.s$bpar, 3)
#>          Estimate se_notrans t value   Pr(>t)   Lower  Upper
-#> parent_0  84.7916    3.01203   28.15 1.92e-25 78.6704 90.913
-#> k_parent   0.0635    0.00521   12.19 2.91e-14  0.0538  0.075
-#> k_m1       0.0148    0.00182    8.13 8.81e-10  0.0115  0.019
-#> sigma      8.2229    0.94323    8.72 1.73e-10  6.3060 10.140

+fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.ff.2.s <- summary(fit.ff.2)
#> Warning: Could not calculate correlation; no covariance matrix
print(fit.ff.2.s$par, 3)
#>              Estimate Std. Error Lower Upper
+#> parent_0        84.79         NA    NA    NA
+#> log_k_parent    -2.76         NA    NA    NA
+#> log_k_m1        -4.21         NA    NA    NA
+#> sigma            8.22         NA    NA    NA
print(fit.ff.2.s$bpar, 3)
#>          Estimate se_notrans t value Pr(>t) Lower Upper
+#> parent_0  84.7916         NA      NA     NA    NA    NA
+#> k_parent   0.0635         NA      NA     NA    NA    NA
+#> k_m1       0.0148         NA      NA     NA    NA    NA
+#> sigma      8.2229         NA      NA     NA    NA    NA