From a37ba8f8898e4629dfc9d2558fc19a180551de2d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 19 Jan 2018 16:01:47 +0100 Subject: Reweighting with two-component error model Static documentation except articles rebuilt by pkgdown --- DESCRIPTION | 2 +- NEWS.md | 8 + R/mkinfit.R | 109 ++++++-- R/sigma_rl.R | 3 + README.html | 4 +- README.md | 2 +- _pkgdown.yml | 1 + check.log | 12 +- docs/index.html | 2 +- docs/news/index.html | 10 + docs/reference/index.html | 6 + docs/reference/mkinfit.html | 576 ++++++++++++++++++++++--------------------- docs/reference/sigma_rl.html | 167 +++++++++++++ man/mkinfit.Rd | 28 ++- man/sigma_rl.Rd | 25 ++ test.log | 6 +- tests/testthat/test_irls.R | 46 ++++ 17 files changed, 679 insertions(+), 328 deletions(-) create mode 100644 R/sigma_rl.R create mode 100644 docs/reference/sigma_rl.html create mode 100644 man/sigma_rl.Rd create mode 100644 tests/testthat/test_irls.R diff --git a/DESCRIPTION b/DESCRIPTION index 27d81005..e3c7de4e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 0.9.47.1 -Date: 2018-01-05 +Date: 2018-01-30 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", comment = c(ORCID = "0000-0003-4371-6538")), diff --git a/NEWS.md b/NEWS.md index 630d38de..26da68bd 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,11 @@ +# mkin 0.9.47.1 (2017-01-30) + +- 'test_data_from_UBA_2014': Added this list of datasets containing experimental data used in the expertise from 2014 + +- 'mkinfit': Added the iterative reweighting method 'tc' using the two-component error model from Rocke and Lorenzato. NA values in the data are not returned any more. + +- 'summary.mkinfit': Improved output regarding weighting method. No predictions are returned for NA values in the model (see above). + # mkin 0.9.46.3 (2017-11-16) - `README.md`, `vignettes/mkin.Rmd`: URLs were updated diff --git a/R/mkinfit.R b/R/mkinfit.R index 55734bac..adc20a9f 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -1,4 +1,4 @@ -# Copyright (C) 2010-2016 Johannes Ranke +# Copyright (C) 2010-2018 Johannes Ranke # Portions of this code are copyright (C) 2013 Eurofins Regulatory AG # Contact: jranke@uni-bremen.de # The summary function is an adapted and extended version of summary.modFit @@ -36,7 +36,10 @@ mkinfit <- function(mkinmod, observed, transform_rates = TRUE, transform_fractions = TRUE, plot = FALSE, quiet = FALSE, - err = NULL, weight = "none", scaleVar = FALSE, + err = NULL, + weight = c("none", "std", "mean", "tc"), + tc = c(sigma_low = 0.5, rsd_high = 0.07), + scaleVar = FALSE, atol = 1e-8, rtol = 1e-10, n.outtimes = 100, reweight.method = NULL, reweight.tol = 1e-8, reweight.max.iter = 10, @@ -77,8 +80,9 @@ mkinfit <- function(mkinmod, observed, # Get the names of observed variables obs_vars <- names(mkinmod$spec) - # Subset observed data with names of observed data in the model + # Subset observed data with names of observed data in the model and remove NA values observed <- subset(observed, name %in% obs_vars) + observed <- subset(observed, !is.na(value)) # Obtain data for decline from maximum mean value if requested if (from_max_mean) { @@ -249,11 +253,17 @@ mkinfit <- function(mkinmod, observed, # Define outtimes for model solution. # Include time points at which observed data are available - # Make sure we include time 0, so initial values for state variables are for time 0 outtimes = sort(unique(c(observed$time, seq(min(observed$time), max(observed$time), length.out = n.outtimes)))) + weight.ini <- weight <- match.arg(weight) + if (weight.ini == "tc") { + observed$err = sigma_rl(observed$value, tc["sigma_low"], tc["rsd_high"]) + err <- "err" + } else { + if (!is.null(err)) weight.ini = "manual" + } cost.old <- 1e100 # The first model cost should be smaller than this value calls <- 0 # Counter for number of model solutions @@ -387,33 +397,73 @@ mkinfit <- function(mkinmod, observed, # Reiterate the fit until convergence of the variance components (IRLS) # if requested by the user - weight.ini = weight - if (!is.null(err)) weight.ini = "manual" if (!is.null(reweight.method)) { - if (reweight.method != "obs") stop("Only reweighting method 'obs' is implemented") - if(!quiet) { - cat("IRLS based on variance estimates for each observed variable\n") + if (! reweight.method %in% c("obs", "tc")) stop("Only reweighting methods 'obs' and 'tc' are implemented") + + if (reweight.method == "obs") { + if(!quiet) { + cat("IRLS based on variance estimates for each observed variable\n") + cat("Initial variance estimates are:\n") + print(signif(fit$var_ms_unweighted, 8)) + } } - if (!quiet) { - cat("Initial variance estimates are:\n") - print(signif(fit$var_ms_unweighted, 8)) + if (reweight.method == "tc") { + # We need unweighted residuals to update the weighting + cost_tmp <- cost(fit$par) + + tc_fit <- nls(abs(res.unweighted) ~ sigma_rl(obs, sigma_low, rsd_high), + start = list(sigma_low = tc["sigma_low"], rsd_high = tc["rsd_high"]), + data = cost_tmp$residuals, + algorithm = "port") + + tc_fitted <- coef(tc_fit) + if(!quiet) { + cat("IRLS based on variance estimates according to the Rocke and Lorenzato model\n") + cat("Initial variance components are:\n") + print(signif(tc_fitted)) + } } reweight.diff = 1 n.iter <- 0 if (!is.null(err)) observed$err.ini <- observed[[err]] err = "err.irls" + while (reweight.diff > reweight.tol & n.iter < reweight.max.iter) { n.iter <- n.iter + 1 - sigma.old <- sqrt(fit$var_ms_unweighted) - observed[err] <- sqrt(fit$var_ms_unweighted)[as.character(observed$name)] + # Store squared residual predictors used for weighting in sr_old and define new weights + if (reweight.method == "obs") { + sr_old <- fit$var_ms_unweighted + observed[err] <- sqrt(fit$var_ms_unweighted[as.character(observed$name)]) + } + if (reweight.method == "tc") { + sr_old <- tc_fitted + observed[err] <- predict(tc_fit) + + } fit <- modFit(cost, fit$par, method = method.modFit, control = control.modFit, lower = lower, upper = upper, ...) - reweight.diff = sum((sqrt(fit$var_ms_unweighted) - sigma.old)^2) + + if (reweight.method == "obs") { + sr_new <- fit$var_ms_unweighted + } + if (reweight.method == "tc") { + cost_tmp <- cost(fit$par) + + tc_fit <- nls(abs(res.unweighted) ~ sigma_rl(obs, sigma_low, rsd_high), + start = as.list(tc_fitted), + data = cost_tmp$residuals, + algorithm = "port") + + tc_fitted <- coef(tc_fit) + sr_new <- tc_fitted + } + + reweight.diff = sum((sr_new - sr_old)^2) if (!quiet) { cat("Iteration", n.iter, "yields variance estimates:\n") - print(signif(fit$var_ms_unweighted, 8)) - cat("Sum of squared differences to last variance estimates:", + print(signif(sr_new, 8)) + cat("Sum of squared differences to last variance (component) estimates:", signif(reweight.diff, 2), "\n") } } @@ -530,9 +580,11 @@ mkinfit <- function(mkinmod, observed, fit$atol <- atol fit$rtol <- rtol fit$weight.ini <- weight.ini + fit$tc.ini <- tc fit$reweight.method <- reweight.method fit$reweight.tol <- reweight.tol fit$reweight.max.iter <- reweight.max.iter + if (exists("tc_fitted")) fit$tc_fitted <- tc_fitted # Return different sets of backtransformed parameters for summary and plotting fit$bparms.optim <- bparms.optim @@ -624,6 +676,9 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05, use_of_ff = object$mkinmod$use_of_ff, weight.ini = object$weight.ini, reweight.method = object$reweight.method, + tc.ini = object$tc.ini, + var_ms_unweighted = object$var_ms_unweighted, + tc_fitted = object$tc_fitted, residuals = object$residuals, residualVariance = resvar, sigma = sqrt(resvar), @@ -679,9 +734,23 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), . "using", x$calls, "model solutions performed in", x$time[["elapsed"]], "s\n") cat("\nWeighting:", x$weight.ini) - if(!is.null(x$reweight.method)) cat(" then iterative reweighting method", - x$reweight.method) - cat("\n") + if (x$weight.ini == "tc") { + cat(" with variance components\n") + print(x$tc.ini) + } else { + cat ("\n") + } + if(!is.null(x$reweight.method)) { + cat("\nIterative reweighting with method", x$reweight.method, "\n") + if (x$reweight.method == "obs") { + cat("Final mean squared residuals of observed variables:\n") + print(x$var_ms_unweighted) + } + if (x$reweight.method == "tc") { + cat("Final components of fitted standard deviation:\n") + print(x$tc_fitted) + } + } cat("\nStarting values for parameters to be optimised:\n") print(x$start) diff --git a/R/sigma_rl.R b/R/sigma_rl.R new file mode 100644 index 00000000..2b921d29 --- /dev/null +++ b/R/sigma_rl.R @@ -0,0 +1,3 @@ + sigma_rl <- function(y, sigma_low, rsd_high) { + sqrt(sigma_low^2 + y^2 * rsd_high^2) + } diff --git a/README.html b/README.html index a38856bd..f4999a38 100644 --- a/README.html +++ b/README.html @@ -121,7 +121,7 @@ $(document).ready(function () {

mkin

-

+

The R package mkin provides calculation routines for the analysis of chemical degradation data, including multicompartment kinetics as needed for modelling the formation and decline of transformation products, or if several compartments are involved.

Installation

@@ -162,7 +162,7 @@ $(document).ready(function () {

News

-

Yes, there is a ChangeLog, for the latest CRAN release and one for the github master branch.

+

There is a ChangeLog, for the latest CRAN release and one for the github master branch.

Credits and historical remarks

diff --git a/README.md b/README.md index 05911f62..af933f66 100644 --- a/README.md +++ b/README.md @@ -100,7 +100,7 @@ for installation instructions and a manual. ## News -Yes, there is a ChangeLog, for the latest [CRAN release](https://cran.r-project.org/package=mkin/news.html) +There is a ChangeLog, for the latest [CRAN release](https://cran.r-project.org/package=mkin/news.html) and one for the [github master branch](https://github.com/jranke/mkin/blob/master/NEWS.md). ## Credits and historical remarks diff --git a/_pkgdown.yml b/_pkgdown.yml index f7d868ef..2630bca0 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -48,6 +48,7 @@ reference: - print.mkinmod - transform_odeparms - ilr + - sigma_rl - title: Analytical solutions desc: Parent only model solutions contents: diff --git a/check.log b/check.log index be621e26..436a78b0 100644 --- a/check.log +++ b/check.log @@ -52,12 +52,10 @@ Maintainer: ‘Johannes Ranke ’ * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK +* checking sizes of PDF files under ‘inst/doc’ ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... NOTE -Examples with CPU or elapsed time > 5s - user system elapsed -test_data_from_UBA_2014 5.736 1.888 5.427 +* checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK @@ -66,9 +64,5 @@ test_data_from_UBA_2014 5.736 1.888 5.427 * checking PDF version of manual ... OK * DONE -Status: 1 NOTE -See - ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ -for details. - +Status: OK diff --git a/docs/index.html b/docs/index.html index f228bbe2..1eefd772 100644 --- a/docs/index.html +++ b/docs/index.html @@ -124,7 +124,7 @@

News

-

Yes, there is a ChangeLog, for the latest CRAN release and one for the github master branch.

+

There is a ChangeLog, for the latest CRAN release and one for the github master branch.

diff --git a/docs/news/index.html b/docs/news/index.html index f442d89c..28ec949f 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -103,6 +103,15 @@

+
+

+mkin 0.9.47.1 (2017-01-30)

+
    +

  • ‘test_data_from_UBA_2014’: Added this list of datasets containing experimental data used in the expertise from 2014

    • +

  • ‘mkinfit’: Added the iterative reweighting method ‘tc’ using the two-component error model from Rocke and Lorenzato. NA values in the data are not returned any more.

    • +

  • ‘summary.mkinfit’: Improved output regarding weighting method. No predictions are returned for NA values in the model (see above).

    • +
+

mkin 0.9.46.3 (2017-11-16)

@@ -578,6 +587,7 @@

Contents

@@ -130,7 +128,9 @@ control.modFit = list(), transform_rates = TRUE, transform_fractions = TRUE, - plot = FALSE, quiet = FALSE, err = NULL, weight = "none", + plot = FALSE, quiet = FALSE, err = NULL, + weight = c("none", "std", "mean", "tc"), + tc = c(sigma_low = 0.5, rsd_high = 0.07), scaleVar = FALSE, atol = 1e-8, rtol = 1e-10, n.outtimes = 100, reweight.method = NULL, @@ -293,7 +293,13 @@ weight

only if err=NULL: how to weight the residuals, one of "none", - "std", "mean", see details of modCost.

+ "std", "mean", see details of modCost, or "tc" for the + two component error model of Rocke and Lorenzato.

+ + + tc +

The two components of the Rocke and Lorenzato error model as used + for (initial) weighting

scaleVar @@ -321,12 +327,19 @@ reweight.method

The method used for iteratively reweighting residuals, also known as iteratively reweighted least squares (IRLS). Default is NULL, - the other method implemented is called "obs", meaning that each - observed variable is assumed to have its own variance, this is - estimated from the fit and used for weighting the residuals - in each iteration until convergence of this estimate up to + i.e. no iterative weighting. + The first reweighting method is called "obs", meaning that each + observed variable is assumed to have its own variance. This variance + is estimated from the fit (mean squared residuals) and used for weighting + the residuals in each iteration until convergence of this estimate up to reweight.tol or up to the maximum number of iterations - specified by reweight.max.iter.

+ specified by reweight.max.iter. + The second reweighting method is called "tc" (two-component error model). + When using this method, the two components of the error model according + to Rocke and Lorenzato (1995) are estimated from the fit and the resulting + variances are used for weighting the residuals in each iteration until + convergence of these components or up to the maximum number of iterations + specified.

reweight.tol @@ -373,21 +386,26 @@ numerical ODE solver. In this situation it may help to switch off the internal rate transformation.

+

Source

+ +

Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for + measurement error in analytical chemistry. Technometrics 37(2), 176-184.

+

Examples

# Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version:    0.9.46 
-#> R version:       3.4.1 
-#> Date of fit:     Sat Jul 29 15:14:18 2017 
-#> Date of summary: Sat Jul 29 15:14:18 2017 
+summary(fit)
#> mkin version:    0.9.47.1 
+#> R version:       3.4.3 
+#> Date of fit:     Tue Jan 30 10:05:48 2018 
+#> Date of summary: Tue Jan 30 10:05:48 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 64 model solutions performed in 0.141 s
+#> Fitted with method Port using 64 model solutions performed in 0.31 s
 #> 
 #> Weighting: none
 #> 
@@ -456,7 +474,7 @@
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#>    user  system elapsed 
-#>   0.888   0.000   0.890 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   1.196   0.000   1.195 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
@@ -535,7 +553,7 @@
 #> Model cost at call  153 :  371.2134 
 #> Optimisation by method Port successfully terminated.
 #>    user  system elapsed 
-#>   0.728   0.000   0.729 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   1.008   0.000   1.006 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
@@ -576,10 +594,10 @@
 # Weighted fits, including IRLS
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
                       m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
-summary(f.noweight)
#> mkin version:    0.9.46 
-#> R version:       3.4.1 
-#> Date of fit:     Sat Jul 29 15:14:28 2017 
-#> Date of summary: Sat Jul 29 15:14:28 2017 
+summary(f.noweight)
#> mkin version:    0.9.47.1 
+#> R version:       3.4.3 
+#> Date of fit:     Tue Jan 30 10:06:00 2018 
+#> Date of summary: Tue Jan 30 10:06:00 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -587,7 +605,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 185 model solutions performed in 0.746 s
+#> Fitted with method Port using 185 model solutions performed in 0.739 s
 #> 
 #> Weighting: none
 #> 
@@ -653,54 +671,50 @@
 #> 
 #> Data:
 #>  time variable observed predicted   residual
-#>     0   parent    99.46 9.960e+01 -1.385e-01
-#>     0   parent   102.04 9.960e+01  2.442e+00
-#>     1   parent    93.50 9.024e+01  3.262e+00
-#>     1   parent    92.50 9.024e+01  2.262e+00
-#>     3   parent    63.23 7.407e+01 -1.084e+01
-#>     3   parent    68.99 7.407e+01 -5.083e+00
-#>     7   parent    52.32 4.991e+01  2.408e+00
-#>     7   parent    55.13 4.991e+01  5.218e+00
-#>    14   parent    27.27 2.501e+01  2.257e+00
-#>    14   parent    26.64 2.501e+01  1.627e+00
-#>    21   parent    11.50 1.253e+01 -1.035e+00
-#>    21   parent    11.64 1.253e+01 -8.946e-01
-#>    35   parent     2.85 3.148e+00 -2.979e-01
-#>    35   parent     2.91 3.148e+00 -2.379e-01
-#>    50   parent     0.69 7.162e-01 -2.624e-02
-#>    50   parent     0.63 7.162e-01 -8.624e-02
-#>    75   parent     0.05 6.074e-02 -1.074e-02
-#>    75   parent     0.06 6.074e-02 -7.381e-04
-#>   100   parent       NA 5.151e-03         NA
-#>   100   parent       NA 5.151e-03         NA
-#>   120   parent       NA 7.155e-04         NA
-#>   120   parent       NA 7.155e-04         NA
-#>     0       m1     0.00 0.000e+00  0.000e+00
-#>     0       m1     0.00 0.000e+00  0.000e+00
-#>     1       m1     4.84 4.803e+00  3.704e-02
-#>     1       m1     5.64 4.803e+00  8.370e-01
-#>     3       m1    12.91 1.302e+01 -1.140e-01
-#>     3       m1    12.96 1.302e+01 -6.400e-02
-#>     7       m1    22.97 2.504e+01 -2.075e+00
-#>     7       m1    24.47 2.504e+01 -5.748e-01
-#>    14       m1    41.69 3.669e+01  5.000e+00
-#>    14       m1    33.21 3.669e+01 -3.480e+00
-#>    21       m1    44.37 4.165e+01  2.717e+00
-#>    21       m1    46.44 4.165e+01  4.787e+00
-#>    35       m1    41.22 4.331e+01 -2.093e+00
-#>    35       m1    37.95 4.331e+01 -5.363e+00
-#>    50       m1    41.19 4.122e+01 -2.831e-02
-#>    50       m1    40.01 4.122e+01 -1.208e+00
-#>    75       m1    40.09 3.645e+01  3.643e+00
-#>    75       m1    33.85 3.645e+01 -2.597e+00
-#>   100       m1    31.04 3.198e+01 -9.416e-01
-#>   100       m1    33.13 3.198e+01  1.148e+00
-#>   120       m1    25.15 2.879e+01 -3.640e+00
-#>   120       m1    33.31 2.879e+01  4.520e+00
f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE)
-summary(f.irls)
#> mkin version:    0.9.46 
-#> R version:       3.4.1 
-#> Date of fit:     Sat Jul 29 15:14:30 2017 
-#> Date of summary: Sat Jul 29 15:14:30 2017 
+#>     0   parent    99.46  99.59848 -1.385e-01
+#>     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
+#>    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
+#>    21   parent    11.64  12.53462 -8.946e-01
+#>    35   parent     2.85   3.14787 -2.979e-01
+#>    35   parent     2.91   3.14787 -2.379e-01
+#>    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
+#>     0       m1     0.00   0.00000  0.000e+00
+#>     0       m1     0.00   0.00000  0.000e+00
+#>     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  36.69002  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  41.21831 -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
+#>   120       m1    33.31  28.78984  4.520e+00
f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE)
+summary(f.irls)
#> mkin version:    0.9.47.1 
+#> R version:       3.4.3 
+#> Date of fit:     Tue Jan 30 10:06:02 2018 
+#> Date of summary: Tue Jan 30 10:06:02 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -708,9 +722,14 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 468 model solutions performed in 1.914 s
+#> Fitted with method Port using 523 model solutions performed in 2.151 s
+#> 
+#> Weighting: none
 #> 
-#> Weighting: none then iterative reweighting method obs
+#> Iterative reweighting with method obs 
+#> Final mean squared residuals of observed variables:
+#>    parent        m1 
+#> 11.573408  7.407845 
 #> 
 #> Starting values for parameters to be optimised:
 #>                   value   type
@@ -739,10 +758,10 @@
 #> 
 #> Parameter correlation:
 #>                parent_0 log_k_parent log_k_m1 f_parent_ilr_1
-#> parent_0         1.0000       0.5083  -0.1979        -0.6147
+#> parent_0         1.0000       0.5083  -0.1979        -0.6148
 #> log_k_parent     0.5083       1.0000  -0.3894        -0.6062
 #> log_k_m1        -0.1979      -0.3894   1.0000         0.7417
-#> f_parent_ilr_1  -0.6147      -0.6062   0.7417         1.0000
+#> f_parent_ilr_1  -0.6148      -0.6062   0.7417         1.0000
 #> 
 #> Residual standard error: 1.054 on 36 degrees of freedom
 #> 
@@ -751,9 +770,9 @@
 #> t-test (unrealistically) based on the assumption of normal distribution
 #> for estimators of untransformed parameters.
 #>                Estimate t value    Pr(>t)     Lower     Upper
-#> parent_0       99.67000  55.630 8.181e-37 96.040000 1.033e+02
+#> parent_0       99.67000  55.630 8.184e-37 96.040000 1.033e+02
 #> k_parent        0.09906  21.930 1.016e-22  0.090310 1.087e-01
-#> k_m1            0.00524   7.996 8.487e-10  0.004066 6.753e-03
+#> k_m1            0.00524   7.996 8.486e-10  0.004066 6.753e-03
 #> f_parent_to_m1  0.51340  23.000 2.038e-23  0.468100 5.584e-01
 #> 
 #> Chi2 error levels in percent:
@@ -774,54 +793,50 @@
 #> 
 #> Data:
 #>  time variable observed predicted   residual   err
-#>     0   parent    99.46 9.967e+01 -2.122e-01 3.402
-#>     0   parent   102.04 9.967e+01  2.368e+00 3.402
-#>     1   parent    93.50 9.027e+01  3.228e+00 3.402
-#>     1   parent    92.50 9.027e+01  2.228e+00 3.402
-#>     3   parent    63.23 7.405e+01 -1.082e+01 3.402
-#>     3   parent    68.99 7.405e+01 -5.056e+00 3.402
-#>     7   parent    52.32 4.982e+01  2.499e+00 3.402
-#>     7   parent    55.13 4.982e+01  5.309e+00 3.402
-#>    14   parent    27.27 2.490e+01  2.367e+00 3.402
-#>    14   parent    26.64 2.490e+01  1.737e+00 3.402
-#>    21   parent    11.50 1.245e+01 -9.476e-01 3.402
-#>    21   parent    11.64 1.245e+01 -8.076e-01 3.402
-#>    35   parent     2.85 3.110e+00 -2.600e-01 3.402
-#>    35   parent     2.91 3.110e+00 -2.000e-01 3.402
-#>    50   parent     0.69 7.037e-01 -1.374e-02 3.402
-#>    50   parent     0.63 7.037e-01 -7.374e-02 3.402
-#>    75   parent     0.05 5.913e-02 -9.133e-03 3.402
-#>    75   parent     0.06 5.913e-02  8.666e-04 3.402
-#>   100   parent       NA 4.969e-03         NA 3.402
-#>   100   parent       NA 4.969e-03         NA 3.402
-#>   120   parent       NA 6.852e-04         NA 3.402
-#>   120   parent       NA 6.852e-04         NA 3.402
-#>     0       m1     0.00 0.000e+00  0.000e+00 2.722
-#>     0       m1     0.00 0.000e+00  0.000e+00 2.722
-#>     1       m1     4.84 4.813e+00  2.672e-02 2.722
-#>     1       m1     5.64 4.813e+00  8.267e-01 2.722
-#>     3       m1    12.91 1.305e+01 -1.378e-01 2.722
-#>     3       m1    12.96 1.305e+01 -8.779e-02 2.722
-#>     7       m1    22.97 2.508e+01 -2.106e+00 2.722
-#>     7       m1    24.47 2.508e+01 -6.062e-01 2.722
-#>    14       m1    41.69 3.671e+01  4.983e+00 2.722
-#>    14       m1    33.21 3.671e+01 -3.497e+00 2.722
-#>    21       m1    44.37 4.165e+01  2.720e+00 2.722
-#>    21       m1    46.44 4.165e+01  4.790e+00 2.722
-#>    35       m1    41.22 4.329e+01 -2.069e+00 2.722
-#>    35       m1    37.95 4.329e+01 -5.339e+00 2.722
-#>    50       m1    41.19 4.119e+01 -3.376e-03 2.722
-#>    50       m1    40.01 4.119e+01 -1.183e+00 2.722
-#>    75       m1    40.09 3.644e+01  3.652e+00 2.722
-#>    75       m1    33.85 3.644e+01 -2.588e+00 2.722
-#>   100       m1    31.04 3.199e+01 -9.497e-01 2.722
-#>   100       m1    33.13 3.199e+01  1.140e+00 2.722
-#>   120       m1    25.15 2.881e+01 -3.659e+00 2.722
-#>   120       m1    33.31 2.881e+01  4.501e+00 2.722
f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE)
-summary(f.w.mean)
#> mkin version:    0.9.46 
-#> R version:       3.4.1 
-#> Date of fit:     Sat Jul 29 15:14:31 2017 
-#> Date of summary: Sat Jul 29 15:14:31 2017 
+#>     0   parent    99.46  99.67218 -2.122e-01 3.402
+#>     0   parent   102.04  99.67218  2.368e+00 3.402
+#>     1   parent    93.50  90.27153  3.228e+00 3.402
+#>     1   parent    92.50  90.27153  2.228e+00 3.402
+#>     3   parent    63.23  74.04648 -1.082e+01 3.402
+#>     3   parent    68.99  74.04648 -5.056e+00 3.402
+#>     7   parent    52.32  49.82092  2.499e+00 3.402
+#>     7   parent    55.13  49.82092  5.309e+00 3.402
+#>    14   parent    27.27  24.90287  2.367e+00 3.402
+#>    14   parent    26.64  24.90287  1.737e+00 3.402
+#>    21   parent    11.50  12.44764 -9.476e-01 3.402
+#>    21   parent    11.64  12.44764 -8.076e-01 3.402
+#>    35   parent     2.85   3.11002 -2.600e-01 3.402
+#>    35   parent     2.91   3.11002 -2.000e-01 3.402
+#>    50   parent     0.69   0.70374 -1.374e-02 3.402
+#>    50   parent     0.63   0.70374 -7.374e-02 3.402
+#>    75   parent     0.05   0.05913 -9.134e-03 3.402
+#>    75   parent     0.06   0.05913  8.662e-04 3.402
+#>     0       m1     0.00   0.00000  0.000e+00 2.722
+#>     0       m1     0.00   0.00000  0.000e+00 2.722
+#>     1       m1     4.84   4.81328  2.672e-02 2.722
+#>     1       m1     5.64   4.81328  8.267e-01 2.722
+#>     3       m1    12.91  13.04779 -1.378e-01 2.722
+#>     3       m1    12.96  13.04779 -8.779e-02 2.722
+#>     7       m1    22.97  25.07615 -2.106e+00 2.722
+#>     7       m1    24.47  25.07615 -6.062e-01 2.722
+#>    14       m1    41.69  36.70729  4.983e+00 2.722
+#>    14       m1    33.21  36.70729 -3.497e+00 2.722
+#>    21       m1    44.37  41.65050  2.720e+00 2.722
+#>    21       m1    46.44  41.65050  4.790e+00 2.722
+#>    35       m1    41.22  43.28866 -2.069e+00 2.722
+#>    35       m1    37.95  43.28866 -5.339e+00 2.722
+#>    50       m1    41.19  41.19338 -3.383e-03 2.722
+#>    50       m1    40.01  41.19338 -1.183e+00 2.722
+#>    75       m1    40.09  36.43820  3.652e+00 2.722
+#>    75       m1    33.85  36.43820 -2.588e+00 2.722
+#>   100       m1    31.04  31.98971 -9.497e-01 2.722
+#>   100       m1    33.13  31.98971  1.140e+00 2.722
+#>   120       m1    25.15  28.80897 -3.659e+00 2.722
+#>   120       m1    33.31  28.80897  4.501e+00 2.722
f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE)
+summary(f.w.mean)
#> mkin version:    0.9.47.1 
+#> R version:       3.4.3 
+#> Date of fit:     Tue Jan 30 10:06:03 2018 
+#> Date of summary: Tue Jan 30 10:06:03 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -829,7 +844,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 155 model solutions performed in 0.692 s
+#> Fitted with method Port using 155 model solutions performed in 0.675 s
 #> 
 #> Weighting: mean
 #> 
@@ -895,55 +910,51 @@
 #> 
 #> Data:
 #>  time variable observed predicted   residual
-#>     0   parent    99.46 99.730570  -0.270570
-#>     0   parent   102.04 99.730570   2.309430
-#>     1   parent    93.50 90.298055   3.201945
-#>     1   parent    92.50 90.298055   2.201945
-#>     3   parent    63.23 74.025028 -10.795028
-#>     3   parent    68.99 74.025028  -5.035028
-#>     7   parent    52.32 49.748382   2.571618
-#>     7   parent    55.13 49.748382   5.381618
-#>    14   parent    27.27 24.815876   2.454124
-#>    14   parent    26.64 24.815876   1.824124
-#>    21   parent    11.50 12.378849  -0.878849
-#>    21   parent    11.64 12.378849  -0.738849
-#>    35   parent     2.85  3.080219  -0.230219
-#>    35   parent     2.91  3.080219  -0.170219
-#>    50   parent     0.69  0.693958  -0.003958
-#>    50   parent     0.63  0.693958  -0.063958
-#>    75   parent     0.05  0.057888  -0.007888
-#>    75   parent     0.06  0.057888   0.002112
-#>   100   parent       NA  0.004829         NA
-#>   100   parent       NA  0.004829         NA
-#>   120   parent       NA  0.000662         NA
-#>   120   parent       NA  0.000662         NA
-#>     0       m1     0.00  0.000000   0.000000
-#>     0       m1     0.00  0.000000   0.000000
-#>     1       m1     4.84  4.821488   0.018512
-#>     1       m1     5.64  4.821488   0.818512
-#>     3       m1    12.91 13.066692  -0.156692
-#>     3       m1    12.96 13.066692  -0.106692
-#>     7       m1    22.97 25.101058  -2.131058
-#>     7       m1    24.47 25.101058  -0.631058
-#>    14       m1    41.69 36.720923   4.969077
-#>    14       m1    33.21 36.720923  -3.510923
-#>    21       m1    44.37 41.648353   2.721647
-#>    21       m1    46.44 41.648353   4.791647
-#>    35       m1    41.22 43.269225  -2.049225
-#>    35       m1    37.95 43.269225  -5.319225
-#>    50       m1    41.19 41.173639   0.016361
-#>    50       m1    40.01 41.173639  -1.163639
-#>    75       m1    40.09 36.431224   3.658776
-#>    75       m1    33.85 36.431224  -2.581224
-#>   100       m1    31.04 31.996124  -0.956124
-#>   100       m1    33.13 31.996124   1.133876
-#>   120       m1    25.15 28.824128  -3.674128
-#>   120       m1    33.31 28.824128   4.485872
f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value",
+#>     0   parent    99.46  99.73057  -0.270570
+#>     0   parent   102.04  99.73057   2.309430
+#>     1   parent    93.50  90.29805   3.201945
+#>     1   parent    92.50  90.29805   2.201945
+#>     3   parent    63.23  74.02503 -10.795028
+#>     3   parent    68.99  74.02503  -5.035028
+#>     7   parent    52.32  49.74838   2.571618
+#>     7   parent    55.13  49.74838   5.381618
+#>    14   parent    27.27  24.81588   2.454124
+#>    14   parent    26.64  24.81588   1.824124
+#>    21   parent    11.50  12.37885  -0.878849
+#>    21   parent    11.64  12.37885  -0.738849
+#>    35   parent     2.85   3.08022  -0.230219
+#>    35   parent     2.91   3.08022  -0.170219
+#>    50   parent     0.69   0.69396  -0.003958
+#>    50   parent     0.63   0.69396  -0.063958
+#>    75   parent     0.05   0.05789  -0.007888
+#>    75   parent     0.06   0.05789   0.002112
+#>     0       m1     0.00   0.00000   0.000000
+#>     0       m1     0.00   0.00000   0.000000
+#>     1       m1     4.84   4.82149   0.018512
+#>     1       m1     5.64   4.82149   0.818512
+#>     3       m1    12.91  13.06669  -0.156692
+#>     3       m1    12.96  13.06669  -0.106692
+#>     7       m1    22.97  25.10106  -2.131058
+#>     7       m1    24.47  25.10106  -0.631058
+#>    14       m1    41.69  36.72092   4.969077
+#>    14       m1    33.21  36.72092  -3.510923
+#>    21       m1    44.37  41.64835   2.721647
+#>    21       m1    46.44  41.64835   4.791647
+#>    35       m1    41.22  43.26923  -2.049225
+#>    35       m1    37.95  43.26923  -5.319225
+#>    50       m1    41.19  41.17364   0.016361
+#>    50       m1    40.01  41.17364  -1.163639
+#>    75       m1    40.09  36.43122   3.658776
+#>    75       m1    33.85  36.43122  -2.581224
+#>   100       m1    31.04  31.99612  -0.956124
+#>   100       m1    33.13  31.99612   1.133876
+#>   120       m1    25.15  28.82413  -3.674128
+#>   120       m1    33.31  28.82413   4.485872
f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value",
                      quiet = TRUE)
-summary(f.w.value)
#> mkin version:    0.9.46 
-#> R version:       3.4.1 
-#> Date of fit:     Sat Jul 29 15:14:32 2017 
-#> Date of summary: Sat Jul 29 15:14:32 2017 
+summary(f.w.value)
#> mkin version:    0.9.47.1 
+#> R version:       3.4.3 
+#> Date of fit:     Tue Jan 30 10:06:04 2018 
+#> Date of summary: Tue Jan 30 10:06:04 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -951,7 +962,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 174 model solutions performed in 0.701 s
+#> Fitted with method Port using 174 model solutions performed in 0.68 s
 #> 
 #> Weighting: manual
 #> 
@@ -1062,10 +1073,10 @@
 errors <- c(parent = 2, m1 = 1)
 dw$err.man <- errors[FOCUS_2006_D$name]
 f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE)
-summary(f.w.man)
#> mkin version:    0.9.46 
-#> R version:       3.4.1 
-#> Date of fit:     Sat Jul 29 15:14:33 2017 
-#> Date of summary: Sat Jul 29 15:14:33 2017 
+summary(f.w.man)
#> mkin version:    0.9.47.1 
+#> R version:       3.4.3 
+#> Date of fit:     Tue Jan 30 10:06:05 2018 
+#> Date of summary: Tue Jan 30 10:06:05 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1073,7 +1084,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 297 model solutions performed in 1.223 s
+#> Fitted with method Port using 297 model solutions performed in 1.178 s
 #> 
 #> Weighting: manual
 #> 
@@ -1139,55 +1150,51 @@
 #> 
 #> Data:
 #>  time variable observed predicted   residual err
-#>     0   parent    99.46 99.485976  -0.025976   1
-#>     0   parent   102.04 99.485976   2.554024   1
-#>     1   parent    93.50 90.186117   3.313883   1
-#>     1   parent    92.50 90.186117   2.313883   1
-#>     3   parent    63.23 74.113162 -10.883162   1
-#>     3   parent    68.99 74.113162  -5.123162   1
-#>     7   parent    52.32 50.050295   2.269705   1
-#>     7   parent    55.13 50.050295   5.079705   1
-#>    14   parent    27.27 25.179750   2.090250   1
-#>    14   parent    26.64 25.179750   1.460250   1
-#>    21   parent    11.50 12.667654  -1.167654   1
-#>    21   parent    11.64 12.667654  -1.027654   1
-#>    35   parent     2.85  3.206164  -0.356164   1
-#>    35   parent     2.91  3.206164  -0.296164   1
-#>    50   parent     0.69  0.735619  -0.045619   1
-#>    50   parent     0.63  0.735619  -0.105619   1
-#>    75   parent     0.05  0.063256  -0.013256   1
-#>    75   parent     0.06  0.063256  -0.003256   1
-#>   100   parent       NA  0.005439         NA   1
-#>   100   parent       NA  0.005439         NA   1
-#>   120   parent       NA  0.000764         NA   1
-#>   120   parent       NA  0.000764         NA   1
-#>     0       m1     0.00  0.000000   0.000000   2
-#>     0       m1     0.00  0.000000   0.000000   2
-#>     1       m1     4.84  4.787287   0.052713   2
-#>     1       m1     5.64  4.787287   0.852713   2
-#>     3       m1    12.91 12.987848  -0.077848   2
-#>     3       m1    12.96 12.987848  -0.027848   2
-#>     7       m1    22.97 24.996945  -2.026945   2
-#>     7       m1    24.47 24.996945  -0.526945   2
-#>    14       m1    41.69 36.663527   5.026473   2
-#>    14       m1    33.21 36.663527  -3.453527   2
-#>    21       m1    44.37 41.656813   2.713187   2
-#>    21       m1    46.44 41.656813   4.783187   2
-#>    35       m1    41.22 43.350312  -2.130312   2
-#>    35       m1    37.95 43.350312  -5.400312   2
-#>    50       m1    41.19 41.256365  -0.066365   2
-#>    50       m1    40.01 41.256365  -1.246365   2
-#>    75       m1    40.09 36.460567   3.629433   2
-#>    75       m1    33.85 36.460567  -2.610567   2
-#>   100       m1    31.04 31.969288  -0.929288   2
-#>   100       m1    33.13 31.969288   1.160712   2
-#>   120       m1    25.15 28.760616  -3.610616   2
-#>   120       m1    33.31 28.760616   4.549384   2
f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE,
+#>     0   parent    99.46  99.48598  -0.025976   1
+#>     0   parent   102.04  99.48598   2.554024   1
+#>     1   parent    93.50  90.18612   3.313883   1
+#>     1   parent    92.50  90.18612   2.313883   1
+#>     3   parent    63.23  74.11316 -10.883162   1
+#>     3   parent    68.99  74.11316  -5.123162   1
+#>     7   parent    52.32  50.05029   2.269705   1
+#>     7   parent    55.13  50.05029   5.079705   1
+#>    14   parent    27.27  25.17975   2.090250   1
+#>    14   parent    26.64  25.17975   1.460250   1
+#>    21   parent    11.50  12.66765  -1.167654   1
+#>    21   parent    11.64  12.66765  -1.027654   1
+#>    35   parent     2.85   3.20616  -0.356164   1
+#>    35   parent     2.91   3.20616  -0.296164   1
+#>    50   parent     0.69   0.73562  -0.045619   1
+#>    50   parent     0.63   0.73562  -0.105619   1
+#>    75   parent     0.05   0.06326  -0.013256   1
+#>    75   parent     0.06   0.06326  -0.003256   1
+#>     0       m1     0.00   0.00000   0.000000   2
+#>     0       m1     0.00   0.00000   0.000000   2
+#>     1       m1     4.84   4.78729   0.052713   2
+#>     1       m1     5.64   4.78729   0.852713   2
+#>     3       m1    12.91  12.98785  -0.077848   2
+#>     3       m1    12.96  12.98785  -0.027848   2
+#>     7       m1    22.97  24.99695  -2.026945   2
+#>     7       m1    24.47  24.99695  -0.526945   2
+#>    14       m1    41.69  36.66353   5.026473   2
+#>    14       m1    33.21  36.66353  -3.453527   2
+#>    21       m1    44.37  41.65681   2.713187   2
+#>    21       m1    46.44  41.65681   4.783187   2
+#>    35       m1    41.22  43.35031  -2.130312   2
+#>    35       m1    37.95  43.35031  -5.400312   2
+#>    50       m1    41.19  41.25637  -0.066365   2
+#>    50       m1    40.01  41.25637  -1.246365   2
+#>    75       m1    40.09  36.46057   3.629433   2
+#>    75       m1    33.85  36.46057  -2.610567   2
+#>   100       m1    31.04  31.96929  -0.929288   2
+#>   100       m1    33.13  31.96929   1.160712   2
+#>   120       m1    25.15  28.76062  -3.610616   2
+#>   120       m1    33.31  28.76062   4.549384   2
f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE,
                        reweight.method = "obs")
-summary(f.w.man.irls)
#> mkin version:    0.9.46 
-#> R version:       3.4.1 
-#> Date of fit:     Sat Jul 29 15:14:36 2017 
-#> Date of summary: Sat Jul 29 15:14:36 2017 
+summary(f.w.man.irls)
#> mkin version:    0.9.47.1 
+#> R version:       3.4.3 
+#> Date of fit:     Tue Jan 30 10:06:08 2018 
+#> Date of summary: Tue Jan 30 10:06:08 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1195,9 +1202,14 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 628 model solutions performed in 2.578 s
+#> Fitted with method Port using 692 model solutions performed in 2.733 s
+#> 
+#> Weighting: manual
 #> 
-#> Weighting: manual then iterative reweighting method obs
+#> Iterative reweighting with method obs 
+#> Final mean squared residuals of observed variables:
+#>    parent        m1 
+#> 11.573407  7.407845 
 #> 
 #> Starting values for parameters to be optimised:
 #>                   value   type
@@ -1226,10 +1238,10 @@
 #> 
 #> Parameter correlation:
 #>                parent_0 log_k_parent log_k_m1 f_parent_ilr_1
-#> parent_0         1.0000       0.5083  -0.1979        -0.6147
+#> parent_0         1.0000       0.5083  -0.1979        -0.6148
 #> log_k_parent     0.5083       1.0000  -0.3894        -0.6062
 #> log_k_m1        -0.1979      -0.3894   1.0000         0.7417
-#> f_parent_ilr_1  -0.6147      -0.6062   0.7417         1.0000
+#> f_parent_ilr_1  -0.6148      -0.6062   0.7417         1.0000
 #> 
 #> Residual standard error: 1.054 on 36 degrees of freedom
 #> 
@@ -1238,10 +1250,10 @@
 #> t-test (unrealistically) based on the assumption of normal distribution
 #> for estimators of untransformed parameters.
 #>                Estimate t value    Pr(>t)     Lower     Upper
-#> parent_0       99.67000  55.630 8.179e-37 96.040000 1.033e+02
-#> k_parent        0.09906  21.930 1.015e-22  0.090310 1.087e-01
-#> k_m1            0.00524   7.996 8.488e-10  0.004066 6.753e-03
-#> f_parent_to_m1  0.51340  23.000 2.039e-23  0.468100 5.584e-01
+#> parent_0       99.67000  55.630 8.184e-37 96.040000 1.033e+02
+#> k_parent        0.09906  21.930 1.016e-22  0.090310 1.087e-01
+#> k_m1            0.00524   7.996 8.486e-10  0.004066 6.753e-03
+#> f_parent_to_m1  0.51340  23.000 2.038e-23  0.468100 5.584e-01
 #> 
 #> Chi2 error levels in percent:
 #>          err.min n.optim df
@@ -1257,54 +1269,50 @@
 #> Estimated disappearance times:
 #>           DT50   DT90
 #> parent   6.997  23.24
-#> m1     132.281 439.43
+#> m1     132.282 439.43
 #> 
 #> Data:
 #>  time variable observed predicted   residual err.ini   err
-#>     0   parent    99.46 9.967e+01 -2.122e-01       1 3.402
-#>     0   parent   102.04 9.967e+01  2.368e+00       1 3.402
-#>     1   parent    93.50 9.027e+01  3.228e+00       1 3.402
-#>     1   parent    92.50 9.027e+01  2.228e+00       1 3.402
-#>     3   parent    63.23 7.405e+01 -1.082e+01       1 3.402
-#>     3   parent    68.99 7.405e+01 -5.056e+00       1 3.402
-#>     7   parent    52.32 4.982e+01  2.499e+00       1 3.402
-#>     7   parent    55.13 4.982e+01  5.309e+00       1 3.402
-#>    14   parent    27.27 2.490e+01  2.367e+00       1 3.402
-#>    14   parent    26.64 2.490e+01  1.737e+00       1 3.402
-#>    21   parent    11.50 1.245e+01 -9.477e-01       1 3.402
-#>    21   parent    11.64 1.245e+01 -8.077e-01       1 3.402
-#>    35   parent     2.85 3.110e+00 -2.600e-01       1 3.402
-#>    35   parent     2.91 3.110e+00 -2.000e-01       1 3.402
-#>    50   parent     0.69 7.037e-01 -1.375e-02       1 3.402
-#>    50   parent     0.63 7.037e-01 -7.375e-02       1 3.402
-#>    75   parent     0.05 5.913e-02 -9.134e-03       1 3.402
-#>    75   parent     0.06 5.913e-02  8.659e-04       1 3.402
-#>   100   parent       NA 4.969e-03         NA       1 3.402
-#>   100   parent       NA 4.969e-03         NA       1 3.402
-#>   120   parent       NA 6.852e-04         NA       1 3.402
-#>   120   parent       NA 6.852e-04         NA       1 3.402
-#>     0       m1     0.00 0.000e+00  0.000e+00       2 2.722
-#>     0       m1     0.00 0.000e+00  0.000e+00       2 2.722
-#>     1       m1     4.84 4.813e+00  2.672e-02       2 2.722
-#>     1       m1     5.64 4.813e+00  8.267e-01       2 2.722
-#>     3       m1    12.91 1.305e+01 -1.378e-01       2 2.722
-#>     3       m1    12.96 1.305e+01 -8.778e-02       2 2.722
-#>     7       m1    22.97 2.508e+01 -2.106e+00       2 2.722
-#>     7       m1    24.47 2.508e+01 -6.061e-01       2 2.722
-#>    14       m1    41.69 3.671e+01  4.983e+00       2 2.722
-#>    14       m1    33.21 3.671e+01 -3.497e+00       2 2.722
-#>    21       m1    44.37 4.165e+01  2.719e+00       2 2.722
-#>    21       m1    46.44 4.165e+01  4.789e+00       2 2.722
-#>    35       m1    41.22 4.329e+01 -2.069e+00       2 2.722
-#>    35       m1    37.95 4.329e+01 -5.339e+00       2 2.722
-#>    50       m1    41.19 4.119e+01 -3.394e-03       2 2.722
-#>    50       m1    40.01 4.119e+01 -1.183e+00       2 2.722
-#>    75       m1    40.09 3.644e+01  3.652e+00       2 2.722
-#>    75       m1    33.85 3.644e+01 -2.588e+00       2 2.722
-#>   100       m1    31.04 3.199e+01 -9.497e-01       2 2.722
-#>   100       m1    33.13 3.199e+01  1.140e+00       2 2.722
-#>   120       m1    25.15 2.881e+01 -3.659e+00       2 2.722
-#>   120       m1    33.31 2.881e+01  4.501e+00       2 2.722

+#>     0   parent    99.46  99.67218 -2.122e-01       1 3.402
+#>     0   parent   102.04  99.67218  2.368e+00       1 3.402
+#>     1   parent    93.50  90.27153  3.228e+00       1 3.402
+#>     1   parent    92.50  90.27153  2.228e+00       1 3.402
+#>     3   parent    63.23  74.04648 -1.082e+01       1 3.402
+#>     3   parent    68.99  74.04648 -5.056e+00       1 3.402
+#>     7   parent    52.32  49.82092  2.499e+00       1 3.402
+#>     7   parent    55.13  49.82092  5.309e+00       1 3.402
+#>    14   parent    27.27  24.90288  2.367e+00       1 3.402
+#>    14   parent    26.64  24.90288  1.737e+00       1 3.402
+#>    21   parent    11.50  12.44765 -9.476e-01       1 3.402
+#>    21   parent    11.64  12.44765 -8.076e-01       1 3.402
+#>    35   parent     2.85   3.11002 -2.600e-01       1 3.402
+#>    35   parent     2.91   3.11002 -2.000e-01       1 3.402
+#>    50   parent     0.69   0.70375 -1.375e-02       1 3.402
+#>    50   parent     0.63   0.70375 -7.375e-02       1 3.402
+#>    75   parent     0.05   0.05913 -9.134e-03       1 3.402
+#>    75   parent     0.06   0.05913  8.662e-04       1 3.402
+#>     0       m1     0.00   0.00000  0.000e+00       2 2.722
+#>     0       m1     0.00   0.00000  0.000e+00       2 2.722
+#>     1       m1     4.84   4.81328  2.672e-02       2 2.722
+#>     1       m1     5.64   4.81328  8.267e-01       2 2.722
+#>     3       m1    12.91  13.04779 -1.378e-01       2 2.722
+#>     3       m1    12.96  13.04779 -8.779e-02       2 2.722
+#>     7       m1    22.97  25.07615 -2.106e+00       2 2.722
+#>     7       m1    24.47  25.07615 -6.062e-01       2 2.722
+#>    14       m1    41.69  36.70729  4.983e+00       2 2.722
+#>    14       m1    33.21  36.70729 -3.497e+00       2 2.722
+#>    21       m1    44.37  41.65050  2.720e+00       2 2.722
+#>    21       m1    46.44  41.65050  4.790e+00       2 2.722
+#>    35       m1    41.22  43.28866 -2.069e+00       2 2.722
+#>    35       m1    37.95  43.28866 -5.339e+00       2 2.722
+#>    50       m1    41.19  41.19339 -3.386e-03       2 2.722
+#>    50       m1    40.01  41.19339 -1.183e+00       2 2.722
+#>    75       m1    40.09  36.43820  3.652e+00       2 2.722
+#>    75       m1    33.85  36.43820 -2.588e+00       2 2.722
+#>   100       m1    31.04  31.98971 -9.497e-01       2 2.722
+#>   100       m1    33.13  31.98971  1.140e+00       2 2.722
+#>   120       m1    25.15  28.80897 -3.659e+00       2 2.722
+#>   120       m1    33.31  28.80897  4.501e+00       2 2.722