From d75378911cef79b3ed95daef71bf67db413d2ac8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 17 Nov 2021 12:59:49 +0100 Subject: Update required saemix version, update tests --- R/saem.R | 5 +- test.log | 60 +- ...t-for-saem-object-with-mkin-transformations.svg | 2306 ++++++++++---------- ...for-saem-object-with-saemix-transformations.svg | 572 ++--- tests/testthat/print_sfo_saem_1.txt | 8 +- tests/testthat/setup_script.R | 2 +- tests/testthat/summary_saem_biphasic_s.txt | 38 +- vignettes/FOCUS_D.html | 8 +- vignettes/FOCUS_L.html | 52 +- 9 files changed, 1525 insertions(+), 1526 deletions(-) diff --git a/R/saem.R b/R/saem.R index 9db2c04a..2c20f788 100644 --- a/R/saem.R +++ b/R/saem.R @@ -231,9 +231,8 @@ print.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...) { saemix_model <- function(object, solution_type = "auto", transformations = c("mkin", "saemix"), degparms_start = numeric(), test_log_parms = FALSE, verbose = FALSE, ...) { - if (packageVersion("saemix") < "3.1.9000") { - stop("To use the interface to saemix, you need to install a development version\n", - "preferably https://github.com/jranke/saemixextension@warp_combined") + if (packageVersion("saemix") < "3.0") { + stop("To use the interface to saemix, you need to install a version >= 3.0\n") } if (nrow(object) > 1) stop("Only row objects allowed") diff --git a/test.log b/test.log index f68ec45a..4d5012a0 100644 --- a/test.log +++ b/test.log @@ -1,42 +1,42 @@ ℹ Loading mkin Loading required package: parallel ℹ Testing mkin -✔ | OK F W S | Context -✔ | 5 | AIC calculation -✔ | 5 | Analytical solutions for coupled models [3.4 s] -✔ | 5 | Calculation of Akaike weights -✔ | 2 | Export dataset for reading into CAKE -✔ | 12 | Confidence intervals and p-values [1.0 s] -✔ | 14 | Error model fitting [4.6 s] -✔ | 5 | Time step normalisation -✔ | 4 | Calculation of FOCUS chi2 error levels [0.5 s] -✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8 s] -✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3 s] -✔ | 1 | Fitting the logistic model [0.2 s] -✔ | 35 1 | Nonlinear mixed-effects models [26.3 s] +✔ | F W S OK | Context +✔ | 5 | AIC calculation +✔ | 5 | Analytical solutions for coupled models [3.5s] +✔ | 5 | Calculation of Akaike weights +✔ | 2 | Export dataset for reading into CAKE +✔ | 12 | Confidence intervals and p-values [1.0s] +✔ | 14 | Error model fitting [5.0s] +✔ | 5 | Time step normalisation +✔ | 4 | Calculation of FOCUS chi2 error levels [0.6s] +✔ | 14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s] +✔ | 4 | Test fitting the decline of metabolites from their maximum [0.3s] +✔ | 1 | Fitting the logistic model [0.2s] +✔ | 1 35 | Nonlinear mixed-effects models [26.8s] ──────────────────────────────────────────────────────────────────────────────── Skip (test_mixed.R:161:3): saem results are reproducible for biphasic fits Reason: Fitting with saemix takes around 10 minutes when using deSolve ──────────────────────────────────────────────────────────────────────────────── -✔ | 2 | Test dataset classes mkinds and mkindsg -✔ | 10 | Special cases of mkinfit calls [0.4 s] -✔ | 1 | mkinfit features [0.3 s] -✔ | 8 | mkinmod model generation and printing [0.2 s] -✔ | 3 | Model predictions with mkinpredict [0.3 s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.4 s] -✔ | 9 | Nonlinear mixed-effects models with nlme [7.9 s] -✔ | 16 | Plotting [1.3 s] -✔ | 4 | Residuals extracted from mkinfit models -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5 s] -✔ | 7 | Fitting the SFORB model [3.7 s] -✔ | 1 | Summaries of old mkinfit objects -✔ | 4 | Summary [0.1 s] -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s] -✔ | 9 | Hypothesis tests [8.4 s] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3 s] +✔ | 2 | Test dataset classes mkinds and mkindsg +✔ | 10 | Special cases of mkinfit calls [0.4s] +✔ | 1 | mkinfit features [0.4s] +✔ | 8 | mkinmod model generation and printing [0.2s] +✔ | 3 | Model predictions with mkinpredict [0.3s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.5s] +✔ | 9 | Nonlinear mixed-effects models with nlme [8.2s] +✔ | 16 | Plotting [1.3s] +✔ | 4 | Residuals extracted from mkinfit models +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s] +✔ | 7 | Fitting the SFORB model [3.8s] +✔ | 1 | Summaries of old mkinfit objects +✔ | 4 | Summary [0.1s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3s] +✔ | 9 | Hypothesis tests [8.6s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 67.6 s +Duration: 69.5 s ── Skipped tests ────────────────────────────────────────────────────────────── • Fitting with saemix takes around 10 minutes when using deSolve (1) diff --git a/tests/testthat/_snaps/plot/mixed-model-fit-for-saem-object-with-mkin-transformations.svg b/tests/testthat/_snaps/plot/mixed-model-fit-for-saem-object-with-mkin-transformations.svg index d3ca239b..6346a383 100644 --- a/tests/testthat/_snaps/plot/mixed-model-fit-for-saem-object-with-mkin-transformations.svg +++ b/tests/testthat/_snaps/plot/mixed-model-fit-for-saem-object-with-mkin-transformations.svg @@ -96,7 +96,7 @@ - + @@ -157,7 +157,7 @@ - + @@ -176,7 +176,7 @@ - + @@ -213,7 +213,7 @@ - + @@ -250,7 +250,7 @@ - + @@ -269,7 +269,7 @@ - + @@ -288,7 +288,7 @@ - + @@ -343,7 +343,7 @@ - + @@ -416,7 +416,7 @@ - + @@ -471,7 +471,7 @@ - + @@ -526,7 +526,7 @@ - + @@ -563,7 +563,7 @@ - + @@ -618,7 +618,7 @@ - + @@ -673,7 +673,7 @@ - + @@ -710,7 +710,7 @@ - + @@ -729,7 +729,7 @@ - + @@ -739,30 +739,30 @@ - + - - - - - + + + + + 0 -20 -40 -60 -80 -100 - - - +20 +40 +60 +80 +100 + + + - - --4 --2 + + +-4 +-2 0 -2 -4 +2 +4 @@ -776,582 +776,582 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -1359,7 +1359,7 @@ - + @@ -1416,7 +1416,7 @@ - + @@ -1431,7 +1431,7 @@ - + @@ -1464,7 +1464,7 @@ - + @@ -1497,7 +1497,7 @@ - + @@ -1514,7 +1514,7 @@ - + @@ -1530,7 +1530,7 @@ - + @@ -1579,7 +1579,7 @@ - + @@ -1644,7 +1644,7 @@ - + @@ -1693,7 +1693,7 @@ - + @@ -1742,7 +1742,7 @@ - + @@ -1775,7 +1775,7 @@ - + @@ -1824,7 +1824,7 @@ - + @@ -1873,7 +1873,7 @@ - + @@ -1906,7 +1906,7 @@ - + @@ -1923,7 +1923,7 @@ - + @@ -1933,28 +1933,28 @@ - + - - - - + + + + 0 -10 -20 -30 -40 - - - +10 +20 +30 +40 + + + - - --4 --2 + + +-4 +-2 0 -2 -4 +2 +4 @@ -1968,515 +1968,515 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/_snaps/plot/mixed-model-fit-for-saem-object-with-saemix-transformations.svg b/tests/testthat/_snaps/plot/mixed-model-fit-for-saem-object-with-saemix-transformations.svg index 072154ee..13590b9b 100644 --- a/tests/testthat/_snaps/plot/mixed-model-fit-for-saem-object-with-saemix-transformations.svg +++ b/tests/testthat/_snaps/plot/mixed-model-fit-for-saem-object-with-saemix-transformations.svg @@ -51,7 +51,7 @@ - + @@ -108,7 +108,7 @@ - + @@ -127,7 +127,7 @@ - + @@ -160,7 +160,7 @@ - + @@ -201,7 +201,7 @@ - + @@ -218,7 +218,7 @@ - + @@ -228,30 +228,30 @@ - + - + - - + + 0 -20 +20 40 60 -80 -100 - - - +80 +100 + + + - - --4 --2 + + +-4 +-2 0 -2 -4 +2 +4 @@ -265,132 +265,132 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -398,7 +398,7 @@ - + @@ -453,7 +453,7 @@ - + @@ -470,7 +470,7 @@ - + @@ -499,7 +499,7 @@ - + @@ -536,7 +536,7 @@ - + @@ -551,7 +551,7 @@ - + @@ -561,30 +561,30 @@ - + - - - - - + + + + + 0 -5 -10 -15 -20 -25 - - - +5 +10 +15 +20 +25 + + + - - --4 --2 + + +-4 +-2 0 -2 -4 +2 +4 @@ -598,118 +598,118 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tests/testthat/print_sfo_saem_1.txt b/tests/testthat/print_sfo_saem_1.txt index 0c0e32ce..3fc9ca3b 100644 --- a/tests/testthat/print_sfo_saem_1.txt +++ b/tests/testthat/print_sfo_saem_1.txt @@ -7,15 +7,15 @@ Data: Likelihood computed by importance sampling AIC BIC logLik - 1310 1315 -649 + 1311 1315 -649 Fitted parameters: estimate lower upper -parent_0 1e+02 98.87 1e+02 +parent_0 1e+02 98.96 1e+02 k_parent 4e-02 0.03 4e-02 -Var.parent_0 1e+00 -1.72 5e+00 +Var.parent_0 8e-01 -1.94 3e+00 Var.k_parent 1e-01 0.03 2e-01 a.1 9e-01 0.75 1e+00 b.1 5e-02 0.04 5e-02 -SD.parent_0 1e+00 -0.12 3e+00 +SD.parent_0 9e-01 -0.67 2e+00 SD.k_parent 3e-01 0.20 4e-01 diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R index 96e865d4..cb3713aa 100644 --- a/tests/testthat/setup_script.R +++ b/tests/testthat/setup_script.R @@ -185,7 +185,7 @@ ds_biphasic <- lapply(ds_biphasic_mean, function(ds) { # Mixed model fits saemix_available <- FALSE if (requireNamespace("saemix", quietly = TRUE)) { - if(packageVersion("saemix") >= "3.1.9000") saemix_available <- TRUE + if(packageVersion("saemix") >= "3.0") saemix_available <- TRUE } mmkin_sfo_1 <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc", cores = n_cores) mmkin_dfop_1 <- mmkin("DFOP", ds_dfop, quiet = TRUE, cores = n_cores) diff --git a/tests/testthat/summary_saem_biphasic_s.txt b/tests/testthat/summary_saem_biphasic_s.txt index 8dfae367..bab4bf98 100644 --- a/tests/testthat/summary_saem_biphasic_s.txt +++ b/tests/testthat/summary_saem_biphasic_s.txt @@ -34,33 +34,33 @@ Results: Likelihood computed by importance sampling AIC BIC logLik - 2702 2711 -1338 + 2679 2689 -1327 Optimised parameters: est. lower upper parent_0 1.0e+02 1.0e+02 1.0e+02 -k_m1 4.7e-03 3.9e-03 5.6e-03 +k_m1 4.8e-03 4.1e-03 5.5e-03 f_parent_to_m1 4.8e-01 4.3e-01 5.2e-01 -k1 4.8e-02 3.1e-02 6.5e-02 -k2 1.3e-02 8.7e-03 1.7e-02 -g 5.0e-01 4.1e-01 5.8e-01 +k1 5.9e-02 4.6e-02 7.2e-02 +k2 1.1e-02 9.0e-03 1.3e-02 +g 4.9e-01 4.3e-01 5.4e-01 Correlation: prnt_0 k_m1 f_p__1 k1 k2 -k_m1 -0.152 -f_parent_to_m1 -0.143 0.366 -k1 0.097 -0.014 -0.021 -k2 0.022 0.083 0.023 0.101 -g -0.084 -0.144 -0.044 -0.303 -0.364 +k_m1 -0.168 +f_parent_to_m1 -0.141 0.379 +k1 0.139 -0.004 -0.024 +k2 0.055 0.154 0.033 0.246 +g -0.078 -0.206 -0.058 -0.435 -0.601 Random effects: - est. lower upper -SD.parent_0 1.22 0.316 2.12 -SD.k_m1 0.15 -0.079 0.38 -SD.f_parent_to_m1 0.32 0.191 0.44 -SD.k1 0.66 0.416 0.90 -SD.k2 0.59 0.368 0.80 -SD.g 0.16 -0.373 0.70 + est. lower upper +SD.parent_0 1.1986 0.28 2.12 +SD.k_m1 0.0034 -6.85 6.86 +SD.f_parent_to_m1 0.3369 0.21 0.46 +SD.k1 0.3790 0.24 0.52 +SD.k2 0.2666 0.16 0.37 +SD.g 0.0401 -0.67 0.75 Variance model: est. lower upper @@ -73,5 +73,5 @@ parent_sink 0.52 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 -parent 26 127 38 14 54 -m1 146 485 NA NA NA +parent 25 150 45 12 64 +m1 145 483 NA NA NA diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index ba514c18..d9127473 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -360,7 +360,7 @@ pre code {

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

Last change 31 January 2019 (rebuilt 2021-09-16)

+

Last change 31 January 2019 (rebuilt 2021-11-17)

@@ -435,9 +435,9 @@ print(FOCUS_2006_D)

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

summary(fit)
## mkin version used for fitting:    1.1.0 
-## R version used for fitting:       4.1.1 
-## Date of fit:     Thu Sep 16 13:57:32 2021 
-## Date of summary: Thu Sep 16 13:57:33 2021 
+## R version used for fitting:       4.1.2 
+## Date of fit:     Wed Nov 17 12:15:48 2021 
+## Date of summary: Wed Nov 17 12:15:49 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index b6ebb606..96a823cf 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -1513,7 +1513,7 @@ div.tocify {
 
 
Example evaluation of FOCUS Laboratory Data L1 to L3

 
Johannes Ranke

-
Last change 17 November 2016 (rebuilt 2021-09-16)

+
Last change 17 November 2016 (rebuilt 2021-11-17)

 
 
 
@@ -1533,16 +1533,16 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)
m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)
## mkin version used for fitting:    1.1.0 
-## R version used for fitting:       4.1.1 
-## Date of fit:     Thu Sep 16 13:57:35 2021 
-## Date of summary: Thu Sep 16 13:57:35 2021 
+## R version used for fitting:       4.1.2 
+## Date of fit:     Wed Nov 17 12:15:51 2021 
+## Date of summary: Wed Nov 17 12:15:51 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.031 s
+## Fitted using 133 model solutions performed in 0.032 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1634,9 +1634,9 @@ summary(m.L1.SFO)
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
 ## doubtful
## mkin version used for fitting:    1.1.0 
-## R version used for fitting:       4.1.1 
-## Date of fit:     Thu Sep 16 13:57:35 2021 
-## Date of summary: Thu Sep 16 13:57:35 2021 
+## R version used for fitting:       4.1.2 
+## Date of fit:     Wed Nov 17 12:15:51 2021 
+## Date of summary: Wed Nov 17 12:15:51 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -1739,16 +1739,16 @@ plot(m.L2.FOMC, show_residuals = TRUE,
 

 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version used for fitting:    1.1.0 
-## R version used for fitting:       4.1.1 
-## Date of fit:     Thu Sep 16 13:57:35 2021 
-## Date of summary: Thu Sep 16 13:57:35 2021 
+## R version used for fitting:       4.1.2 
+## Date of fit:     Wed Nov 17 12:15:52 2021 
+## Date of summary: Wed Nov 17 12:15:52 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.048 s
+## Fitted using 239 model solutions performed in 0.049 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1817,9 +1817,9 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
 

 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version used for fitting:    1.1.0 
-## R version used for fitting:       4.1.1 
-## Date of fit:     Thu Sep 16 13:57:36 2021 
-## Date of summary: Thu Sep 16 13:57:36 2021 
+## R version used for fitting:       4.1.2 
+## Date of fit:     Wed Nov 17 12:15:52 2021 
+## Date of summary: Wed Nov 17 12:15:52 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1828,7 +1828,7 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 581 model solutions performed in 0.133 s
+## Fitted using 581 model solutions performed in 0.134 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -1917,9 +1917,9 @@ plot(mm.L3)

 
We can extract the summary and plot for e.g. the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.

 
summary(mm.L3[["DFOP", 1]])

 
## mkin version used for fitting:    1.1.0 
-## R version used for fitting:       4.1.1 
-## Date of fit:     Thu Sep 16 13:57:36 2021 
-## Date of summary: Thu Sep 16 13:57:36 2021 
+## R version used for fitting:       4.1.2 
+## Date of fit:     Wed Nov 17 12:15:52 2021 
+## Date of summary: Wed Nov 17 12:15:52 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -1928,7 +1928,7 @@ plot(mm.L3)

 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 376 model solutions performed in 0.079 s
+## Fitted using 376 model solutions performed in 0.08 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -2025,9 +2025,9 @@ plot(mm.L4)

 
The χ2 error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the χ2 test passes is slightly lower for the FOMC model. However, the difference appears negligible.

 
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version used for fitting:    1.1.0 
-## R version used for fitting:       4.1.1 
-## Date of fit:     Thu Sep 16 13:57:36 2021 
-## Date of summary: Thu Sep 16 13:57:36 2021 
+## R version used for fitting:       4.1.2 
+## Date of fit:     Wed Nov 17 12:15:53 2021 
+## Date of summary: Wed Nov 17 12:15:53 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -2089,9 +2089,9 @@ plot(mm.L4)

 ## parent  106  352
summary(mm.L4[["FOMC", 1]], data = FALSE)
## mkin version used for fitting:    1.1.0 
-## R version used for fitting:       4.1.1 
-## Date of fit:     Thu Sep 16 13:57:36 2021 
-## Date of summary: Thu Sep 16 13:57:36 2021 
+## R version used for fitting:       4.1.2 
+## Date of fit:     Wed Nov 17 12:15:53 2021 
+## Date of summary: Wed Nov 17 12:15:53 2021 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
-- 
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