From 524a8bba89b95840b4e9215c403947a8bb76d7b2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 30 Nov 2020 16:05:10 +0100 Subject: Complete rebuild of static docs of dev version --- docs/dev/articles/FOCUS_D.html | 12 +- docs/dev/articles/FOCUS_L.html | 44 +-- docs/dev/articles/mkin.html | 2 +- docs/dev/articles/twa.html | 2 +- docs/dev/articles/web_only/FOCUS_Z.html | 76 ++--- docs/dev/articles/web_only/NAFTA_examples.html | 2 +- docs/dev/articles/web_only/benchmarks.html | 48 +-- docs/dev/articles/web_only/compiled_models.html | 28 +- docs/dev/pkgdown.yml | 2 +- docs/dev/reference/CAKE_export.html | 41 +-- docs/dev/reference/D24_2014.html | 8 +- docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 13 +- docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 13 +- docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html | 13 +- docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html | 13 +- docs/dev/reference/FOCUS_2006_datasets.html | 23 +- docs/dev/reference/NAFTA_SOP_2015-1.png | Bin 41379 -> 64838 bytes docs/dev/reference/NAFTA_SOP_2015.html | 37 +-- docs/dev/reference/NAFTA_SOP_Attachment-1.png | Bin 42204 -> 66148 bytes docs/dev/reference/NAFTA_SOP_Attachment.html | 37 +-- docs/dev/reference/Rplot001.png | Bin 14324 -> 14180 bytes docs/dev/reference/Rplot002.png | Bin 56035 -> 13753 bytes docs/dev/reference/Rplot003.png | Bin 55725 -> 28735 bytes docs/dev/reference/Rplot004.png | Bin 57095 -> 49269 bytes docs/dev/reference/Rplot008.png | Bin 11762 -> 0 bytes docs/dev/reference/Rplot009.png | Bin 21414 -> 0 bytes docs/dev/reference/Rplot010.png | Bin 5643 -> 0 bytes docs/dev/reference/Rplot011.png | Bin 26192 -> 0 bytes docs/dev/reference/Rplot012.png | Bin 23686 -> 0 bytes docs/dev/reference/Rplot013.png | Bin 23097 -> 0 bytes docs/dev/reference/Rplot014.png | Bin 18299 -> 0 bytes docs/dev/reference/Rplot015.png | Bin 23097 -> 0 bytes docs/dev/reference/add_err.html | 2 +- docs/dev/reference/aw.html | 29 +- docs/dev/reference/confint.mkinfit.html | 14 +- docs/dev/reference/create_deg_func.html | 20 +- docs/dev/reference/dot-plot_mixed.html | 203 ------------- docs/dev/reference/experimental_data_for_UBA.html | 28 +- docs/dev/reference/loftest-1.png | Bin 27354 -> 41288 bytes docs/dev/reference/loftest-2.png | Bin 27721 -> 40668 bytes docs/dev/reference/loftest-3.png | Bin 78754 -> 78452 bytes docs/dev/reference/loftest-4.png | Bin 76899 -> 76132 bytes docs/dev/reference/loftest-5.png | Bin 75806 -> 74691 bytes docs/dev/reference/loftest.html | 88 +++--- docs/dev/reference/logLik.mkinfit.html | 6 +- docs/dev/reference/logistic.solution.html | 2 +- docs/dev/reference/lrtest.mkinfit.html | 32 +- docs/dev/reference/mccall81_245T.html | 4 +- docs/dev/reference/mkin_long_to_wide.html | 16 +- docs/dev/reference/mkin_wide_to_long.html | 18 +- docs/dev/reference/mkinerrmin.html | 28 +- docs/dev/reference/mkinerrplot.html | 4 +- docs/dev/reference/mkinfit.html | 30 +- docs/dev/reference/mkinmod.html | 91 +++--- docs/dev/reference/mkinparplot.html | 8 +- docs/dev/reference/mkinplot.html | 13 +- docs/dev/reference/mkinpredict.html | 8 +- docs/dev/reference/mkinresplot.html | 4 +- docs/dev/reference/mkinsub.html | 234 -------------- docs/dev/reference/mmkin.html | 20 +- docs/dev/reference/nlme-2.png | Bin 89236 -> 89493 bytes docs/dev/reference/nlme.html | 7 +- docs/dev/reference/nlme.mmkin-1.png | Bin 119655 -> 122068 bytes docs/dev/reference/nlme.mmkin-2.png | Bin 159253 -> 160690 bytes docs/dev/reference/nlme.mmkin-3.png | Bin 158883 -> 161800 bytes docs/dev/reference/nlme.mmkin-4.png | Bin 162990 -> 0 bytes docs/dev/reference/nlme.mmkin-5.png | Bin 81513 -> 0 bytes docs/dev/reference/nlme.mmkin-6.png | Bin 80989 -> 0 bytes docs/dev/reference/nlme.mmkin-7.png | Bin 81584 -> 0 bytes docs/dev/reference/nlme.mmkin.html | 184 +++++------ docs/dev/reference/nobs.mkinfit.html | 10 +- docs/dev/reference/plot.mixed.mmkin-2.png | Bin 164488 -> 163684 bytes docs/dev/reference/plot.mixed.mmkin.html | 10 +- docs/dev/reference/plot.mkinfit.html | 6 +- docs/dev/reference/plot.nafta.html | 13 +- docs/dev/reference/plot.nlme.mmkin-1.png | Bin 86076 -> 0 bytes docs/dev/reference/plot.nlme.mmkin-2.png | Bin 164488 -> 0 bytes docs/dev/reference/plot.nlme.mmkin.html | 302 ------------------ docs/dev/reference/plot.saem.mmkin-1.png | Bin 86076 -> 0 bytes docs/dev/reference/plot.saem.mmkin-2.png | Bin 164014 -> 0 bytes docs/dev/reference/plot.saem.mmkin.html | 308 ------------------- docs/dev/reference/plot_mixed-1.png | Bin 86076 -> 0 bytes docs/dev/reference/plot_mixed-2.png | Bin 164488 -> 0 bytes docs/dev/reference/plot_mixed-3.png | Bin 164014 -> 0 bytes docs/dev/reference/plot_mixed.html | 336 --------------------- docs/dev/reference/print.mkinds.html | 194 ------------ docs/dev/reference/print.mkinmod.html | 217 ------------- docs/dev/reference/residuals.mkinfit.html | 20 +- docs/dev/reference/saem.html | 52 ++-- docs/dev/reference/saemix-1.png | Bin 46062 -> 0 bytes docs/dev/reference/saemix-10.png | Bin 17011 -> 0 bytes docs/dev/reference/saemix-11.png | Bin 64787 -> 0 bytes docs/dev/reference/saemix-12.png | Bin 59464 -> 0 bytes docs/dev/reference/saemix-13.png | Bin 7742 -> 0 bytes docs/dev/reference/saemix-2.png | Bin 47804 -> 0 bytes docs/dev/reference/saemix-3.png | Bin 40694 -> 0 bytes docs/dev/reference/saemix-4.png | Bin 38144 -> 0 bytes docs/dev/reference/saemix-5.png | Bin 39988 -> 0 bytes docs/dev/reference/saemix-6.png | Bin 39720 -> 0 bytes docs/dev/reference/saemix-7.png | Bin 7742 -> 0 bytes docs/dev/reference/saemix-8.png | Bin 35501 -> 0 bytes docs/dev/reference/saemix-9.png | Bin 7742 -> 0 bytes docs/dev/reference/schaefer07_complex_case-1.png | Bin 67741 -> 67659 bytes docs/dev/reference/schaefer07_complex_case.html | 42 +-- docs/dev/reference/summary.mkinfit.html | 8 +- docs/dev/reference/summary.nlme.mmkin.html | 230 +++++++------- docs/dev/reference/summary.saem.mmkin-1.png | Bin 7742 -> 0 bytes docs/dev/reference/summary.saem.mmkin.html | 14 +- .../reference/synthetic_data_for_UBA_2014-1.png | Bin 70430 -> 70005 bytes .../dev/reference/synthetic_data_for_UBA_2014.html | 224 +++++++------- docs/dev/reference/test_data_from_UBA_2014-1.png | Bin 59294 -> 59592 bytes docs/dev/reference/test_data_from_UBA_2014-2.png | Bin 78194 -> 76645 bytes docs/dev/reference/test_data_from_UBA_2014.html | 76 +++-- docs/dev/reference/transform_odeparms.html | 8 +- docs/dev/reference/update.mkinfit-1.png | Bin 28678 -> 43366 bytes docs/dev/reference/update.mkinfit-2.png | Bin 28541 -> 44304 bytes docs/dev/reference/update.mkinfit.html | 24 +- 117 files changed, 949 insertions(+), 2652 deletions(-) delete mode 100644 docs/dev/reference/Rplot008.png delete mode 100644 docs/dev/reference/Rplot009.png delete mode 100644 docs/dev/reference/Rplot010.png delete mode 100644 docs/dev/reference/Rplot011.png delete mode 100644 docs/dev/reference/Rplot012.png delete mode 100644 docs/dev/reference/Rplot013.png delete mode 100644 docs/dev/reference/Rplot014.png delete mode 100644 docs/dev/reference/Rplot015.png delete mode 100644 docs/dev/reference/dot-plot_mixed.html delete mode 100644 docs/dev/reference/mkinsub.html delete mode 100644 docs/dev/reference/nlme.mmkin-4.png delete mode 100644 docs/dev/reference/nlme.mmkin-5.png delete mode 100644 docs/dev/reference/nlme.mmkin-6.png delete mode 100644 docs/dev/reference/nlme.mmkin-7.png delete mode 100644 docs/dev/reference/plot.nlme.mmkin-1.png delete mode 100644 docs/dev/reference/plot.nlme.mmkin-2.png delete mode 100644 docs/dev/reference/plot.nlme.mmkin.html delete mode 100644 docs/dev/reference/plot.saem.mmkin-1.png delete mode 100644 docs/dev/reference/plot.saem.mmkin-2.png delete mode 100644 docs/dev/reference/plot.saem.mmkin.html delete mode 100644 docs/dev/reference/plot_mixed-1.png delete mode 100644 docs/dev/reference/plot_mixed-2.png delete mode 100644 docs/dev/reference/plot_mixed-3.png delete mode 100644 docs/dev/reference/plot_mixed.html delete mode 100644 docs/dev/reference/print.mkinds.html delete mode 100644 docs/dev/reference/print.mkinmod.html delete mode 100644 docs/dev/reference/saemix-1.png delete mode 100644 docs/dev/reference/saemix-10.png delete mode 100644 docs/dev/reference/saemix-11.png delete mode 100644 docs/dev/reference/saemix-12.png delete mode 100644 docs/dev/reference/saemix-13.png delete mode 100644 docs/dev/reference/saemix-2.png delete mode 100644 docs/dev/reference/saemix-3.png delete mode 100644 docs/dev/reference/saemix-4.png delete mode 100644 docs/dev/reference/saemix-5.png delete mode 100644 docs/dev/reference/saemix-6.png delete mode 100644 docs/dev/reference/saemix-7.png delete mode 100644 docs/dev/reference/saemix-8.png delete mode 100644 docs/dev/reference/saemix-9.png delete mode 100644 docs/dev/reference/summary.saem.mmkin-1.png (limited to 'docs') diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html index e526b3a7..dd86f677 100644 --- a/docs/dev/articles/FOCUS_D.html +++ b/docs/dev/articles/FOCUS_D.html @@ -102,7 +102,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2020-11-19

+

2020-11-30

Source: vignettes/FOCUS_D.rmd @@ -163,8 +163,8 @@

Next we specify the degradation model: The parent compound degrades with simple first-order kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.

The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector $diffs of the mkinmod object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.

-SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
-
## Successfully compiled differential equation model from auto-generated C code.
+SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) +
## Temporary DLL for differentials generated and loaded
 print(SFO_SFO$diffs)
##                                                    parent 
@@ -189,8 +189,8 @@
 summary(fit)
## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:06 2020 
-## Date of summary: Thu Nov 19 15:00:06 2020 
+## Date of fit:     Mon Nov 30 16:01:50 2020 
+## Date of summary: Mon Nov 30 16:01:50 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -198,7 +198,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 401 model solutions performed in 0.188 s
+## Fitted using 401 model solutions performed in 0.161 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/dev/articles/FOCUS_L.html b/docs/dev/articles/FOCUS_L.html
index 1fbe5c76..2695db5e 100644
--- a/docs/dev/articles/FOCUS_L.html
+++ b/docs/dev/articles/FOCUS_L.html
@@ -102,7 +102,7 @@
       
Example evaluation of FOCUS Laboratory Data L1 to L3

                         
Johannes Ranke

             
-            
2020-11-19

+            
2020-11-30

       
       Source: vignettes/FOCUS_L.rmd
       
@@ -130,15 +130,15 @@
 summary(m.L1.SFO)
## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:09 2020 
-## Date of summary: Thu Nov 19 15:00:09 2020 
+## Date of fit:     Mon Nov 30 16:01:52 2020 
+## Date of summary: Mon Nov 30 16:01:52 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.034 s
+## Fitted using 133 model solutions performed in 0.032 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -236,15 +236,15 @@
 ## doubtful
## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:09 2020 
-## Date of summary: Thu Nov 19 15:00:09 2020 
+## Date of fit:     Mon Nov 30 16:01:53 2020 
+## Date of summary: Mon Nov 30 16:01:53 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 380 model solutions performed in 0.085 s
+## Fitted using 380 model solutions performed in 0.087 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -348,15 +348,15 @@
 summary(m.L2.FOMC, data = FALSE)
## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:10 2020 
-## Date of summary: Thu Nov 19 15:00:10 2020 
+## Date of fit:     Mon Nov 30 16:01:54 2020 
+## Date of summary: Mon Nov 30 16:01:54 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.051 s
+## Fitted using 239 model solutions performed in 0.05 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -429,8 +429,8 @@
 summary(m.L2.DFOP, data = FALSE)
## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:10 2020 
-## Date of summary: Thu Nov 19 15:00:10 2020 
+## Date of fit:     Mon Nov 30 16:01:54 2020 
+## Date of summary: Mon Nov 30 16:01:54 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -439,7 +439,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 581 model solutions performed in 0.138 s
+## Fitted using 581 model solutions performed in 0.136 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -535,8 +535,8 @@
 summary(mm.L3[["DFOP", 1]])
## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:11 2020 
-## Date of summary: Thu Nov 19 15:00:11 2020 
+## Date of fit:     Mon Nov 30 16:01:55 2020 
+## Date of summary: Mon Nov 30 16:01:55 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -545,7 +545,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 376 model solutions performed in 0.083 s
+## Fitted using 376 model solutions performed in 0.081 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -648,15 +648,15 @@
 summary(mm.L4[["SFO", 1]], data = FALSE)
## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:12 2020 
-## Date of summary: Thu Nov 19 15:00:12 2020 
+## Date of fit:     Mon Nov 30 16:01:55 2020 
+## Date of summary: Mon Nov 30 16:01:55 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.031 s
+## Fitted using 142 model solutions performed in 0.03 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -713,15 +713,15 @@
 summary(mm.L4[["FOMC", 1]], data = FALSE)
## mkin version used for fitting:    0.9.50.4 
 ## R version used for fitting:       4.0.3 
-## Date of fit:     Thu Nov 19 15:00:12 2020 
-## Date of summary: Thu Nov 19 15:00:12 2020 
+## Date of fit:     Mon Nov 30 16:01:55 2020 
+## Date of summary: Mon Nov 30 16:01:56 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.05 s
+## Fitted using 224 model solutions performed in 0.045 s
 ## 
 ## Error model: Constant variance 
 ## 
diff --git a/docs/dev/articles/mkin.html b/docs/dev/articles/mkin.html
index 75e53bbd..2de8b9f0 100644
--- a/docs/dev/articles/mkin.html
+++ b/docs/dev/articles/mkin.html
@@ -102,7 +102,7 @@
       
Introduction to mkin

                         
Johannes Ranke

             
-            
2020-11-27

+            
2020-11-30

       
       Source: vignettes/mkin.rmd
       
diff --git a/docs/dev/articles/twa.html b/docs/dev/articles/twa.html
index d778b773..42ed6fa5 100644
--- a/docs/dev/articles/twa.html
+++ b/docs/dev/articles/twa.html
@@ -102,7 +102,7 @@
       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2020-11-19

+            
2020-11-30

       
       Source: vignettes/twa.rmd
       
diff --git a/docs/dev/articles/web_only/FOCUS_Z.html b/docs/dev/articles/web_only/FOCUS_Z.html
index 4cfe6c31..15c41eb7 100644
--- a/docs/dev/articles/web_only/FOCUS_Z.html
+++ b/docs/dev/articles/web_only/FOCUS_Z.html
@@ -102,7 +102,7 @@
       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2020-11-19

+            
2020-11-30

       
       Source: vignettes/web_only/FOCUS_Z.rmd
       
@@ -138,9 +138,9 @@
 Parent and one metabolite
 
The next step is to set up the models used for the kinetic analysis. As the simultaneous fit of parent and the first metabolite is usually straightforward, Step 1 (SFO for parent only) is skipped here. We start with the model 2a, with formation and decline of metabolite Z1 and the pathway from parent directly to sink included (default in mkin).

 
-Z.2a <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
-                Z1 = mkinsub("SFO"))

-
## Successfully compiled differential equation model from auto-generated C code.

+Z.2a <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
+                Z1 = mkinsub("SFO"))
+
## Temporary DLL for differentials generated and loaded
 m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE)
## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
@@ -159,10 +159,10 @@
 
As obvious from the parameter summary (the  component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.

 
A similar result can be obtained when formation fractions are used in the model formulation:

 
-Z.2a.ff <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
-                   Z1 = mkinsub("SFO"),
+Z.2a.ff <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
+                   Z1 = mkinsub("SFO"),
                    use_of_ff = "max")

-
## Successfully compiled differential equation model from auto-generated C code.

+
## Temporary DLL for differentials generated and loaded

 
 m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE)

 
## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
@@ -182,9 +182,9 @@
 
A simplified model is obtained by removing the pathway to the sink. 

 
In the following, we use the parameterisation with formation fractions in order to be able to compare with the results in the FOCUS guidance, and as it makes it easier to use parameters obtained in a previous fit when adding a further metabolite.

 
-Z.3 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-               Z1 = mkinsub("SFO"), use_of_ff = "max")

-
## Successfully compiled differential equation model from auto-generated C code.

+Z.3 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
+               Z1 = mkinsub("SFO"), use_of_ff = "max")

+
## Temporary DLL for differentials generated and loaded

 
 m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE)

 
## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
@@ -206,10 +206,10 @@
 Metabolites Z2 and Z3
 
As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as well in the next step. While this step appears questionable on the basis of the above results, it is followed here for the purpose of comparison. Also, in the FOCUS report, it is assumed that there is additional empirical evidence that Z1 quickly and exclusively hydrolyses to Z2.

 
-Z.5 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-               Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-               Z2 = mkinsub("SFO"), use_of_ff = "max")

-
## Successfully compiled differential equation model from auto-generated C code.

+Z.5 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
+               Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+               Z2 = mkinsub("SFO"), use_of_ff = "max")

+
## Temporary DLL for differentials generated and loaded

 
 m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE)

 
## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
@@ -219,12 +219,12 @@
 

 
Finally, metabolite Z3 is added to the model. We use the optimised differential equation parameter values from the previous fit in order to accelerate the optimization.

 
-Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-                   Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                   Z2 = mkinsub("SFO", "Z3"),
-                   Z3 = mkinsub("SFO"),
+Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
+                   Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+                   Z2 = mkinsub("SFO", "Z3"),
+                   Z3 = mkinsub("SFO"),
                    use_of_ff = "max")

-
## Successfully compiled differential equation model from auto-generated C code.

+
## Temporary DLL for differentials generated and loaded

 
 m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin,
                      parms.ini = m.Z.5$bparms.ode,
@@ -266,11 +266,11 @@
 
As the FOCUS report states, there is a certain tailing of the time course of metabolite Z3. Also, the time course of the parent compound is not fitted very well using the SFO model, as residues at a certain low level remain.

 
Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the \(\chi^2\) error level is lower for metabolite Z3 using this model and the graphical fit for Z3 is improved. However, the covariance matrix is not returned.

 
-Z.mkin.1 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO", "Z3"),
-                    Z3 = mkinsub("SFORB"))

-
## Successfully compiled differential equation model from auto-generated C code.

+Z.mkin.1 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
+                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+                    Z2 = mkinsub("SFO", "Z3"),
+                    Z3 = mkinsub("SFORB"))

+
## Temporary DLL for differentials generated and loaded

 
 m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE)

 
## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
@@ -283,10 +283,10 @@
 
## NULL

 
Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.

 
-Z.mkin.3 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO"))

-
## Successfully compiled differential equation model from auto-generated C code.

+Z.mkin.3 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
+                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+                    Z2 = mkinsub("SFO"))

+
## Temporary DLL for differentials generated and loaded

 
 m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE)

 
## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
@@ -297,11 +297,11 @@
 
This results in a much better representation of the behaviour of the parent compound Z0.

 
Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.

 
-Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO", "Z3"),
-                    Z3 = mkinsub("SFO"))

-
## Successfully compiled differential equation model from auto-generated C code.

+Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
+                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+                    Z2 = mkinsub("SFO", "Z3"),
+                    Z3 = mkinsub("SFO"))

+
## Temporary DLL for differentials generated and loaded

 
 m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin,
                       parms.ini = m.Z.mkin.3$bparms.ode,
@@ -313,11 +313,11 @@
 

 
The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.

 
-Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO", "Z3"),
-                    Z3 = mkinsub("SFORB"))

-
## Successfully compiled differential equation model from auto-generated C code.

+Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
+                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+                    Z2 = mkinsub("SFO", "Z3"),
+                    Z3 = mkinsub("SFORB"))

+
## Temporary DLL for differentials generated and loaded

 
 m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
                       parms.ini = m.Z.mkin.4$bparms.ode[1:4],
diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html
index c3192b37..fca15672 100644
--- a/docs/dev/articles/web_only/NAFTA_examples.html
+++ b/docs/dev/articles/web_only/NAFTA_examples.html
@@ -102,7 +102,7 @@
       
Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance

                         
Johannes Ranke

             
-            
2020-11-19

+            
2020-11-30

       
       Source: vignettes/web_only/NAFTA_examples.rmd
       
diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html
index ff70847e..8e157c0f 100644
--- a/docs/dev/articles/web_only/benchmarks.html
+++ b/docs/dev/articles/web_only/benchmarks.html
@@ -102,7 +102,7 @@
       
Benchmark timings for mkin

                         
Johannes Ranke

             
-            
2020-11-19

+            
2020-11-30

       
       Source: vignettes/web_only/benchmarks.rmd
       
@@ -127,14 +127,14 @@
 
One metabolite:

 
 SFO_SFO <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
+  parent = mkinsub("SFO", "m1"),
+  m1 = mkinsub("SFO"))
 FOMC_SFO <- mkinmod(
-  parent = mkinsub("FOMC", "m1"),
-  m1 = mkinsub("SFO"))
+  parent = mkinsub("FOMC", "m1"),
+  m1 = mkinsub("SFO"))
 DFOP_SFO <- mkinmod(
-  parent = mkinsub("FOMC", "m1"),
-  m1 = mkinsub("SFO"))
+  parent = mkinsub("FOMC", "m1"),
+  m1 = mkinsub("SFO"))
 t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[["elapsed"]]
 t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
     error_model = "tc"))[["elapsed"]]

@@ -148,14 +148,14 @@
     error_model = "obs"))[["elapsed"]]

 
Two metabolites, synthetic data:

 
-m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
-                           M1 = mkinsub("SFO", "M2"),
-                           M2 = mkinsub("SFO"),
+m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
+                           M1 = mkinsub("SFO", "M2"),
+                           M2 = mkinsub("SFO"),
                            use_of_ff = "max", quiet = TRUE)
 
-m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
-                           M1 = mkinsub("SFO"),
-                           M2 = mkinsub("SFO"),
+m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
+                           M1 = mkinsub("SFO"),
+                           M2 = mkinsub("SFO"),
                            use_of_ff = "max", quiet = TRUE)
 
 SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
@@ -232,8 +232,8 @@
 
 
 0.9.50.4
-1.702
-3.717
+1.786
+3.729
 
 
 
@@ -294,9 +294,9 @@
 
 
 0.9.50.4
-1.355
-7.015
-2.729
+1.397
+7.251
+2.810
 
 
 
@@ -381,12 +381,12 @@
 
 
 0.9.50.4
-0.759
-1.245
-1.436
-3.687
-1.886
-3.028
+0.783
+1.282
+1.486
+3.815
+1.958
+3.105
 
 
 
diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html
index 3d1c7fcd..a444f4bc 100644
--- a/docs/dev/articles/web_only/compiled_models.html
+++ b/docs/dev/articles/web_only/compiled_models.html
@@ -102,7 +102,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2020-11-19

+            
2020-11-30

       
       Source: vignettes/web_only/compiled_models.rmd
       
@@ -134,9 +134,9 @@
 
 library("mkin", quietly = TRUE)
 SFO_SFO <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))

-
## Successfully compiled differential equation model from auto-generated C code.

+  parent = mkinsub("SFO", "m1"),
+  m1 = mkinsub("SFO"))

+
## Temporary DLL for differentials generated and loaded

 
 FOCUS_D <- subset(FOCUS_2006_D, value != 0)

 
We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package. In the output of below code, the warnings about zero being removed from the FOCUS D dataset are suppressed. Since mkin version 0.9.49.11, an analytical solution is also implemented, which is included in the tests below.

@@ -160,10 +160,10 @@
   print("R package rbenchmark is not available")
 }

 
##                    test replications relative elapsed
-## 4            analytical            1    1.000   0.186
-## 3     deSolve, compiled            1    1.742   0.324
-## 2      Eigenvalue based            1    2.048   0.381
-## 1 deSolve, not compiled            1   42.532   7.911

+## 4            analytical            1    1.000   0.187
+## 3     deSolve, compiled            1    1.807   0.338
+## 2      Eigenvalue based            1    2.032   0.380
+## 1 deSolve, not compiled            1   43.048   8.050

We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.

@@ -173,8 +173,8 @@ 
 if (require(rbenchmark)) {
   FOMC_SFO <- mkinmod(
-    parent = mkinsub("FOMC", "m1"),
-    m1 = mkinsub( "SFO"))
+    parent = mkinsub("FOMC", "m1"),
+    m1 = mkinsub( "SFO"))
 
   b.2 <- benchmark(
     "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_D,
@@ -188,11 +188,11 @@
   factor_FOMC_SFO <- NA
   print("R package benchmark is not available")
 }
-
## Successfully compiled differential equation model from auto-generated C code.
+
## Temporary DLL for differentials generated and loaded
##                    test replications relative elapsed
-## 2     deSolve, compiled            1    1.000   0.465
-## 1 deSolve, not compiled            1   30.852  14.346
-

Here we get a performance benefit of a factor of 31 using the version of the differential equation model compiled from C code!

+## 2 deSolve, compiled 1 1.000 0.483 +## 1 deSolve, not compiled 1 29.969 14.475 +

Here we get a performance benefit of a factor of 30 using the version of the differential equation model compiled from C code!

This vignette was built with mkin 0.9.50.4 on

## R version 4.0.3 (2020-10-10)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index f8ab4012..b3db5e23 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
   web_only/NAFTA_examples: NAFTA_examples.html
   web_only/benchmarks: benchmarks.html
   web_only/compiled_models: compiled_models.html
-last_built: 2020-11-27T20:47Z
+last_built: 2020-11-30T14:47Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/CAKE_export.html b/docs/dev/reference/CAKE_export.html
index ce8a3444..d3f45bf0 100644
--- a/docs/dev/reference/CAKE_export.html
+++ b/docs/dev/reference/CAKE_export.html
@@ -73,7 +73,7 @@ specified as well." />
       
       
         mkin
-        0.9.50.3
+        0.9.50.4
@@ -121,7 +121,7 @@ specified as well." />
  • - + @@ -140,7 +140,7 @@ specified as well." />

    Export a list of datasets format to a CAKE study file

    - Source: R/CAKE_export.R + Source: R/CAKE_export.R
    @@ -149,21 +149,21 @@ specified as well." /> specified as well.

    - 
    CAKE_export(
-  ds,
-  map = c(parent = "Parent"),
-  links = NA,
-  filename = "CAKE_export.csf",
-  path = ".",
-  overwrite = FALSE,
-  study = "Codlemone aerobic soil degradation",
-  description = "",
-  time_unit = "days",
-  res_unit = "% AR",
-  comment = "Created using mkin::CAKE_export",
-  date = Sys.Date(),
-  optimiser = "IRLS"
-)
    + 
    CAKE_export(
+  ds,
+  map = c(parent = "Parent"),
+  links = NA,
+  filename = "CAKE_export.csf",
+  path = ".",
+  overwrite = FALSE,
+  study = "Codlemone aerobic soil degradation",
+  description = "",
+  time_unit = "days",
+  res_unit = "% AR",
+  comment = "Created using mkin::CAKE_export",
+  date = Sys.Date(),
+  optimiser = "IRLS"
+)

    Arguments

    @@ -230,6 +230,9 @@ compatible with CAKE.

    Value

    The function is called for its side effect.

    +

    Author

    + +

    Johannes Ranke

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.6.1.

    diff --git a/docs/dev/reference/D24_2014.html b/docs/dev/reference/D24_2014.html index ba768186..e4a3216d 100644 --- a/docs/dev/reference/D24_2014.html +++ b/docs/dev/reference/D24_2014.html @@ -217,10 +217,10 @@ specific pieces of information in the comments.

    #> 10 114 18.0 #> 11 183 11.3 #> 12 273 9.9 -#> 13 365 6.3
    m_D24 = mkinmod(D24 = mkinsub("SFO", to = "DCP"), - DCP = mkinsub("SFO", to = "DCA"), - DCA = mkinsub("SFO")) -
    #> Successfully compiled differential equation model from auto-generated C code.
    +#> 13 365 6.3
    m_D24 = mkinmod(D24 = mkinsub("SFO", to = "DCP"), + DCP = mkinsub("SFO", to = "DCA"), + DCA = mkinsub("SFO")) +
    #> Temporary DLL for differentials generated and loaded
    @@ -124,7 +124,7 @@ in this fit." />
    • - + @@ -155,12 +155,12 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.

      - 
      FOCUS_2006_DFOP_ref_A_to_B
      + 
      FOCUS_2006_DFOP_ref_A_to_B

      Format

      -

      A data frame containing the following variables.

      +

      A data frame containing the following variables.

      package

      a factor giving the name of the software package

      M0

      The fitted initial concentration of the parent compound

      f

      The fitted f parameter

      @@ -181,7 +181,8 @@ in this fit.

      http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

      Examples

      - 
      data(FOCUS_2006_DFOP_ref_A_to_B)
      + 
      data(FOCUS_2006_DFOP_ref_A_to_B)
+
      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html index 666a1123..6b8a6119 100644 --- a/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -76,7 +76,7 @@ in this fit." /> mkin - 0.9.50.3 + 0.9.50.4 @@ -124,7 +124,7 @@ in this fit." />
    • - + @@ -155,12 +155,12 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.

      - 
      FOCUS_2006_FOMC_ref_A_to_F
      + 
      FOCUS_2006_FOMC_ref_A_to_F

      Format

      -

      A data frame containing the following variables.

      +

      A data frame containing the following variables.

      package

      a factor giving the name of the software package

      M0

      The fitted initial concentration of the parent compound

      alpha

      The fitted alpha parameter

      @@ -180,7 +180,8 @@ in this fit.

      http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

      Examples

      - 
      data(FOCUS_2006_FOMC_ref_A_to_F)
      + 
      data(FOCUS_2006_FOMC_ref_A_to_F)
+
      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html index b07abb0d..076a66c6 100644 --- a/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -76,7 +76,7 @@ in this fit." /> mkin - 0.9.50.3 + 0.9.50.4 @@ -124,7 +124,7 @@ in this fit." />
    • - + @@ -155,12 +155,12 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.

      - 
      FOCUS_2006_HS_ref_A_to_F
      + 
      FOCUS_2006_HS_ref_A_to_F

      Format

      -

      A data frame containing the following variables.

      +

      A data frame containing the following variables.

      package

      a factor giving the name of the software package

      M0

      The fitted initial concentration of the parent compound

      tb

      The fitted tb parameter

      @@ -181,7 +181,8 @@ in this fit.

      http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

      Examples

      - 
      data(FOCUS_2006_HS_ref_A_to_F)
      + 
      data(FOCUS_2006_HS_ref_A_to_F)
+
      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html index 1e3b91f6..08f1d416 100644 --- a/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -76,7 +76,7 @@ in this fit." /> mkin - 0.9.50.3 + 0.9.50.4 @@ -124,7 +124,7 @@ in this fit." />
    • - + @@ -155,12 +155,12 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.

      - 
      FOCUS_2006_SFO_ref_A_to_F
      + 
      FOCUS_2006_SFO_ref_A_to_F

      Format

      -

      A data frame containing the following variables.

      +

      A data frame containing the following variables.

      package

      a factor giving the name of the software package

      M0

      The fitted initial concentration of the parent compound

      k

      The fitted first-order degradation rate constant

      @@ -179,7 +179,8 @@ in this fit.

      http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

      Examples

      - 
      data(FOCUS_2006_SFO_ref_A_to_F)
      + 
      data(FOCUS_2006_SFO_ref_A_to_F)
+
      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/dev/reference/FOCUS_2006_datasets.html b/docs/dev/reference/FOCUS_2006_datasets.html index 9836adac..df4651f8 100644 --- a/docs/dev/reference/FOCUS_2006_datasets.html +++ b/docs/dev/reference/FOCUS_2006_datasets.html @@ -72,7 +72,7 @@ mkin - 0.9.50.3 + 0.9.50.4 @@ -120,7 +120,7 @@
    • - + @@ -147,17 +147,17 @@

      Data taken from FOCUS (2006), p. 258.

      - 
      FOCUS_2006_A
-  FOCUS_2006_B
-  FOCUS_2006_C
-  FOCUS_2006_D
-  FOCUS_2006_E
-  FOCUS_2006_F
      + 
      FOCUS_2006_A
+  FOCUS_2006_B
+  FOCUS_2006_C
+  FOCUS_2006_D
+  FOCUS_2006_E
+  FOCUS_2006_F

      Format

      -

      6 datasets with observations on the following variables.

      +

      6 datasets with observations on the following variables.

      name

      a factor containing the name of the observed variable

      time

      a numeric vector containing time points

      value

      a numeric vector containing concentrations in percent of applied radioactivity

      @@ -173,7 +173,8 @@ http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

      Examples

      - 
      FOCUS_2006_C
      #>     name time value
+    
      FOCUS_2006_C
+
      #>     name time value
 #> 1 parent    0  85.1
 #> 2 parent    1  57.9
 #> 3 parent    3  29.9
@@ -198,7 +199,7 @@
 
      
 
 
      
-  
      Site built with pkgdown 1.5.1.
      
+  
      Site built with pkgdown 1.6.1.
      
 
      
 
       
diff --git a/docs/dev/reference/NAFTA_SOP_2015-1.png b/docs/dev/reference/NAFTA_SOP_2015-1.png
index 9025f2bb..4d823d77 100644
Binary files a/docs/dev/reference/NAFTA_SOP_2015-1.png and b/docs/dev/reference/NAFTA_SOP_2015-1.png differ
diff --git a/docs/dev/reference/NAFTA_SOP_2015.html b/docs/dev/reference/NAFTA_SOP_2015.html
index c7e20a45..4243faba 100644
--- a/docs/dev/reference/NAFTA_SOP_2015.html
+++ b/docs/dev/reference/NAFTA_SOP_2015.html
@@ -72,7 +72,7 @@
       
       
         mkin
-        0.9.50.3
+        0.9.50.4
       
     
      
 
@@ -120,7 +120,7 @@
    • - + @@ -147,13 +147,13 @@

      Data taken from US EPA (2015), p. 19 and 23.

      - 
      NAFTA_SOP_Appendix_B
-  NAFTA_SOP_Appendix_D
      + 
      NAFTA_SOP_Appendix_B
+  NAFTA_SOP_Appendix_D

      Format

      -

      2 datasets with observations on the following variables.

      +

      2 datasets with observations on the following variables.

      name

      a factor containing the name of the observed variable

      time

      a numeric vector containing time points

      value

      a numeric vector containing concentrations

      @@ -172,7 +172,9 @@ https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance

      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)
+
      #> 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 
 #> 
@@ -181,17 +183,17 @@
 #> 
 #> 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 1.80e-14 77.18268 90.3288
+#> k_parent   0.0017 7.43e-05  0.00112  0.0026
+#> sigma      8.7518 1.22e-05  5.64278 11.8608
 #> 
 #> $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 8.88e+01 1.05e+02
+#> k__iore_parent 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
 #> 
 #> $DFOP
 #>          Estimate   Pr(>t)    Lower    Upper
@@ -209,7 +211,8 @@
 #> DFOP  429    2380      841
 #> 
 #> Representative half-life:
-#> [1] 841.41
        plot(nafta_evaluation)
      
+#> [1] 841.41
        plot(nafta_evaluation)
+
      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/dev/reference/NAFTA_SOP_Attachment-1.png b/docs/dev/reference/NAFTA_SOP_Attachment-1.png index 19da6da7..6eb10cde 100644 Binary files a/docs/dev/reference/NAFTA_SOP_Attachment-1.png and b/docs/dev/reference/NAFTA_SOP_Attachment-1.png differ diff --git a/docs/dev/reference/NAFTA_SOP_Attachment.html b/docs/dev/reference/NAFTA_SOP_Attachment.html index 7bc7817e..de984984 100644 --- a/docs/dev/reference/NAFTA_SOP_Attachment.html +++ b/docs/dev/reference/NAFTA_SOP_Attachment.html @@ -72,7 +72,7 @@ mkin - 0.9.50.3 + 0.9.50.4 @@ -120,7 +120,7 @@
    • - + @@ -147,7 +147,7 @@

      Data taken from from Attachment 1 of the SOP.

      - 
      NAFTA_SOP_Attachment
      + 
      NAFTA_SOP_Attachment

      Format

      @@ -166,7 +166,9 @@ https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance

      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)
+
      #> 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 
 #> 
@@ -175,23 +177,23 @@
 #> 
 #> 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 4.67e-21 92.245 99.4357
+#> k_parent   0.0102 3.92e-12  0.009  0.0117
+#> sigma      4.8230 3.81e-06  3.214  6.4318
 #> 
 #> $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 9.91e+01 1.02e+02
+#> k__iore_parent 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
 #> 
 #> $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
+#> k2       2.42e-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
 #> 
@@ -200,10 +202,11 @@
 #>      DT50     DT90 DT50_rep
 #> SFO  67.7 2.25e+02 6.77e+01
 #> IORE 58.2 1.07e+03 3.22e+02
-#> DFOP 55.5 4.42e+11 2.42e+11
+#> DFOP 55.5 5.22e+11 2.86e+11
 #> 
 #> Representative half-life:
-#> [1] 321.51
        plot(nafta_att_p5a)
      
+#> [1] 321.51
        plot(nafta_att_p5a)
+
      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png index f001da49..ae5db971 100644 Binary files a/docs/dev/reference/Rplot001.png and b/docs/dev/reference/Rplot001.png differ diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png index c6c75f42..51e51cf4 100644 Binary files a/docs/dev/reference/Rplot002.png and b/docs/dev/reference/Rplot002.png differ diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png index 41711ba6..ff6bc722 100644 Binary files a/docs/dev/reference/Rplot003.png and b/docs/dev/reference/Rplot003.png differ diff --git a/docs/dev/reference/Rplot004.png b/docs/dev/reference/Rplot004.png index 875d6daf..98dd019e 100644 Binary files a/docs/dev/reference/Rplot004.png and b/docs/dev/reference/Rplot004.png differ diff --git a/docs/dev/reference/Rplot008.png b/docs/dev/reference/Rplot008.png deleted file mode 100644 index 5d1701b8..00000000 Binary files a/docs/dev/reference/Rplot008.png and /dev/null differ diff --git a/docs/dev/reference/Rplot009.png b/docs/dev/reference/Rplot009.png deleted file mode 100644 index 7788b2d0..00000000 Binary files a/docs/dev/reference/Rplot009.png and /dev/null differ diff --git a/docs/dev/reference/Rplot010.png b/docs/dev/reference/Rplot010.png deleted file mode 100644 index 86ddd790..00000000 Binary files a/docs/dev/reference/Rplot010.png and /dev/null differ diff --git a/docs/dev/reference/Rplot011.png b/docs/dev/reference/Rplot011.png deleted file mode 100644 index 30861f3e..00000000 Binary files a/docs/dev/reference/Rplot011.png and /dev/null differ diff --git a/docs/dev/reference/Rplot012.png b/docs/dev/reference/Rplot012.png deleted file mode 100644 index 4286bb2a..00000000 Binary files a/docs/dev/reference/Rplot012.png and /dev/null differ diff --git a/docs/dev/reference/Rplot013.png b/docs/dev/reference/Rplot013.png deleted file mode 100644 index 65903441..00000000 Binary files a/docs/dev/reference/Rplot013.png and /dev/null differ diff --git a/docs/dev/reference/Rplot014.png b/docs/dev/reference/Rplot014.png deleted file mode 100644 index fe2cf0d9..00000000 Binary files a/docs/dev/reference/Rplot014.png and /dev/null differ diff --git a/docs/dev/reference/Rplot015.png b/docs/dev/reference/Rplot015.png deleted file mode 100644 index 65903441..00000000 Binary files a/docs/dev/reference/Rplot015.png and /dev/null differ diff --git a/docs/dev/reference/add_err.html b/docs/dev/reference/add_err.html index ae10e863..6ea30515 100644 --- a/docs/dev/reference/add_err.html +++ b/docs/dev/reference/add_err.html @@ -224,7 +224,7 @@ https://jrwb.de/posters/piacenza_2015.pdf

      # The kinetic model m_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"), M1 = mkinsub("SFO"), use_of_ff = "max") -
      #> Successfully compiled differential equation model from auto-generated C code.
      +
      #> Temporary DLL for differentials generated and loaded
      # Generate a prediction for a specific set of parameters sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) diff --git a/docs/dev/reference/aw.html b/docs/dev/reference/aw.html index 267c3b0b..ef808dd8 100644 --- a/docs/dev/reference/aw.html +++ b/docs/dev/reference/aw.html @@ -74,7 +74,7 @@ by Burnham and Anderson (2004)." /> mkin - 0.9.50.3 + 0.9.50.4
      @@ -122,7 +122,7 @@ by Burnham and Anderson (2004)." />
    • - + @@ -141,7 +141,7 @@ by Burnham and Anderson (2004)." />

      Calculate Akaike weights for model averaging

      - Source: R/aw.R + Source: R/aw.R
      @@ -151,13 +151,13 @@ expected Kullback-Leibler information as specified by Burnham and Anderson (2004).

      - 
      aw(object, ...)
+    
      aw(object, ...)
 
 # S3 method for mkinfit
-aw(object, ...)
+aw(object, ...)
 
 # S3 method for mmkin
-aw(object, ...)
      
+aw(object, ...)

      Arguments

    @@ -185,11 +185,16 @@ Inference: Understanding AIC and BIC in Model Selection.

    Examples

    # \dontrun{
-f_sfo <- mkinfit("SFO", FOCUS_2006_D, quiet = TRUE)
-f_dfop <- mkinfit("DFOP", FOCUS_2006_D, quiet = TRUE)
-aw_sfo_dfop <- aw(f_sfo, f_dfop)
-sum(aw_sfo_dfop)
    #> [1] 1
    aw_sfo_dfop # SFO gets more weight as it has less parameters and a similar fit
    #> [1] 0.5970258 0.4029742
    f <- mmkin(c("SFO", "FOMC", "DFOP"), list("FOCUS D" = FOCUS_2006_D), cores = 1, quiet = TRUE)
-aw(f)
    #> [1] 0.4808722 0.1945539 0.3245740
    sum(aw(f))
    #> [1] 1
    aw(f[c("SFO", "DFOP")])
    #> [1] 0.5970258 0.4029742
    # }
+f_sfo <- mkinfit("SFO", FOCUS_2006_D, quiet = TRUE)
+f_dfop <- mkinfit("DFOP", FOCUS_2006_D, quiet = TRUE)
+aw_sfo_dfop <- aw(f_sfo, f_dfop)
+sum(aw_sfo_dfop)
+
    #> [1] 1
    aw_sfo_dfop # SFO gets more weight as it has less parameters and a similar fit
+
    #> [1] 0.5970258 0.4029742
    f <- mmkin(c("SFO", "FOMC", "DFOP"), list("FOCUS D" = FOCUS_2006_D), cores = 1, quiet = TRUE)
+aw(f)
+
    #> [1] 0.4808722 0.1945539 0.3245740
    sum(aw(f))
+
    #> [1] 1
    aw(f[c("SFO", "DFOP")])
+
    #> [1] 0.5970258 0.4029742
    # }
    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.6.1.

    diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html index 745f2dc4..515a7c9e 100644 --- a/docs/dev/reference/confint.mkinfit.html +++ b/docs/dev/reference/confint.mkinfit.html @@ -278,19 +278,19 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, if(Sys.getenv("TRAVIS")!="")n_cores=1if(Sys.info()["sysname"]=="Windows")n_cores=1 -SFO_SFO<-mkinmod(parent =mkinsub("SFO", "m1"), m1 =mkinsub("SFO"), quiet =TRUE) -SFO_SFO.ff<-mkinmod(parent =mkinsub("SFO", "m1"), m1 =mkinsub("SFO"), +SFO_SFO<-mkinmod(parent =mkinsub("SFO", "m1"), m1 =mkinsub("SFO"), quiet =TRUE) +SFO_SFO.ff<-mkinmod(parent =mkinsub("SFO", "m1"), m1 =mkinsub("SFO"), use_of_ff ="max", quiet =TRUE)f_d_1<-mkinfit(SFO_SFO, subset(FOCUS_2006_D, value!=0), quiet =TRUE)system.time(ci_profile<-confint(f_d_1, method ="profile", cores =1, quiet =TRUE))
    #> user system elapsed -#> 3.829 1.000 3.519
    # Using more cores does not save much time here, as parent_0 takes up most of the time +#> 3.900 0.929 3.548
    # Using more cores does not save much time here, as parent_0 takes up most of the time # If we additionally exclude parent_0 (the confidence of which is often of # minor interest), we get a nice performance improvement from about 50 # seconds to about 12 seconds if we use at least four cores system.time(ci_profile_no_parent_0 <- confint(f_d_1, method = "profile", c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores)) -
    #> Profiling the likelihood
    #> Warning: scheduled cores 2, 1, 3 encountered errors in user code, all values of the jobs will be affected
    #> Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent
    #> Timing stopped at: 0.011 0.029 0.241
    ci_profile +
    #> Profiling the likelihood
    #> Warning: scheduled cores 3, 2, 1 encountered errors in user code, all values of the jobs will be affected
    #> Error in dimnames(x) <- dn: length of 'dimnames' [2] not equal to array extent
    #> Timing stopped at: 0.009 0.034 0.257
    ci_profile
    #> 2.5% 97.5% #> parent_0 96.456003640 1.027703e+02 #> k_parent 0.090911032 1.071578e-01 @@ -386,9 +386,9 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, #> sigma 0.0550252516 0.0327066836
    # The profiling for the following fit does not finish in a reasonable time, # therefore we use the quadratic approximation -m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), - M1 = mkinsub("SFO"), - M2 = mkinsub("SFO"), +m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), + M1 = mkinsub("SFO"), + M2 = mkinsub("SFO"), use_of_ff = "max", quiet = TRUE) DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data f_tc_2 <- mkinfit(m_synth_DFOP_par, DFOP_par_c, error_model = "tc", diff --git a/docs/dev/reference/create_deg_func.html b/docs/dev/reference/create_deg_func.html index 9f2e4deb..4945d157 100644 --- a/docs/dev/reference/create_deg_func.html +++ b/docs/dev/reference/create_deg_func.html @@ -169,9 +169,9 @@

    Examples

    
 SFO_SFO <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
-
    #> Successfully compiled differential equation model from auto-generated C code.
    FOCUS_D <- subset(FOCUS_2006_D, value != 0) # to avoid warnings
+  parent = mkinsub("SFO", "m1"),
+  m1 = mkinsub("SFO"))
+
    #> Temporary DLL for differentials generated and loaded
    FOCUS_D <- subset(FOCUS_2006_D, value != 0) # to avoid warnings
 fit_1 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE)
 fit_2 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE)
 # \dontrun{
@@ -181,20 +181,20 @@
     deSolve = mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE),
     replications = 2)
 
    #> Loading required package: rbenchmark
    #>         test replications elapsed relative user.self sys.self user.child
-#> 1 analytical            2   0.397    1.000     0.397    0.001          0
-#> 2    deSolve            2   0.684    1.723     0.683    0.000          0
+#> 1 analytical            2   0.396    1.000     0.395        0          0
+#> 2    deSolve            2   0.694    1.753     0.693        0          0
 #>   sys.child
 #> 1         0
 #> 2         0
      DFOP_SFO <- mkinmod(
-    parent = mkinsub("DFOP", "m1"),
-    m1 = mkinsub("SFO"))
-
    #> Successfully compiled differential equation model from auto-generated C code.
      benchmark(
+    parent = mkinsub("DFOP", "m1"),
+    m1 = mkinsub("SFO"))
+
    #> Temporary DLL for differentials generated and loaded
      benchmark(
     analytical = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE),
     deSolve = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE),
     replications = 2)
 
    #>         test replications elapsed relative user.self sys.self user.child
-#> 1 analytical            2   0.834    1.000     0.833    0.001          0
-#> 2    deSolve            2   1.545    1.853     1.541    0.001          0
+#> 1 analytical            2   0.838    1.000     0.838    0.001          0
+#> 2    deSolve            2   1.573    1.877     1.572    0.000          0
 #>   sys.child
 #> 1         0
 #> 2         0
    # }
diff --git a/docs/dev/reference/dot-plot_mixed.html b/docs/dev/reference/dot-plot_mixed.html
deleted file mode 100644
index e359c5ea..00000000
--- a/docs/dev/reference/dot-plot_mixed.html
+++ /dev/null
@@ -1,203 +0,0 @@
-
-
-
-  
-  
-
-
-
-Not intended to be called directly by the user — .plot_mixed • mkin
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-  
-
-  
-    
    
-      
    
-      
-
-      
-
-      
    
-
-
    
-  
    
-    
    
-    
    Not intended to be called directly by the user
    
-    Source: R/plot_mixed.R
-    
-    
    
-
-    
    
-    
    Not intended to be called directly by the user
    
-    
    
-
-    
    .plot_mixed(
-  x,
-  i = 1:ncol(x$mmkin),
-  degparms_optim,
-  degparms_pop,
-  residuals,
-  obs_vars = names(x$mkinmod$map),
-  standardized = TRUE,
-  xlab = "Time",
-  xlim = range(x$data$time),
-  resplot = c("predicted", "time"),
-  ymax = "auto",
-  maxabs = "auto",
-  ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
-  nrow.legend = ceiling((length(i) + 1)/ncol.legend),
-  rel.height.legend = 0.03 + 0.08 * nrow.legend,
-  rel.height.bottom = 1.1,
-  pch_ds = 1:length(i),
-  col_ds = pch_ds + 1,
-  lty_ds = col_ds,
-  frame = TRUE,
-  ...
-)
    
-
-
-
-  
    
-  
-
    
-
-
-      
    
-      
    
-  
    Developed by Johannes Ranke.
    
-
    
-
-
    
-  
    Site built with pkgdown 1.6.1.
    
-
    
-
-      
    
-   
    
-
-  
-
-
-  
-
-
-
diff --git a/docs/dev/reference/experimental_data_for_UBA.html b/docs/dev/reference/experimental_data_for_UBA.html
index cd098b7d..78e57fb0 100644
--- a/docs/dev/reference/experimental_data_for_UBA.html
+++ b/docs/dev/reference/experimental_data_for_UBA.html
@@ -242,31 +242,31 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
 
 # Model definitions
 sfo_sfo <- mkinmod(
-  parent = mkinsub("SFO", to = "A1"),
-  A1 = mkinsub("SFO"),
+  parent = mkinsub("SFO", to = "A1"),
+  A1 = mkinsub("SFO"),
   use_of_ff = "max"
 )
-
    #> Successfully compiled differential equation model from auto-generated C code.
    
+
    #> Temporary DLL for differentials generated and loaded
    
 dfop_sfo <- mkinmod(
-  parent = mkinsub("DFOP", to = "A1"),
-  A1 = mkinsub("SFO"),
+  parent = mkinsub("DFOP", to = "A1"),
+  A1 = mkinsub("SFO"),
   use_of_ff = "max"
 )
-
    #> Successfully compiled differential equation model from auto-generated C code.
    
+
    #> Temporary DLL for differentials generated and loaded
    
 sfo_sfo_sfo <- mkinmod(
-  parent = mkinsub("SFO", to = "A1"),
-  A1 = mkinsub("SFO", to = "A2"),
-  A2 = mkinsub("SFO"),
+  parent = mkinsub("SFO", to = "A1"),
+  A1 = mkinsub("SFO", to = "A2"),
+  A2 = mkinsub("SFO"),
   use_of_ff = "max"
 )
-
    #> Successfully compiled differential equation model from auto-generated C code.
    
+
    #> Temporary DLL for differentials generated and loaded
    
 dfop_sfo_sfo <- mkinmod(
-  parent = mkinsub("DFOP", to = "A1"),
-  A1 = mkinsub("SFO", to = "A2"),
-  A2 = mkinsub("SFO"),
+  parent = mkinsub("DFOP", to = "A1"),
+  A1 = mkinsub("SFO", to = "A2"),
+  A2 = mkinsub("SFO"),
   use_of_ff = "max"
 )
-
    #> Successfully compiled differential equation model from auto-generated C code.
    d_1_2 <- lapply(experimental_data_for_UBA_2019[1:2], function(x) x$data)
+
    #> Temporary DLL for differentials generated and loaded
    d_1_2 <- lapply(experimental_data_for_UBA_2019[1:2], function(x) x$data)
 names(d_1_2) <- paste("Soil", 1:2)
 
 
diff --git a/docs/dev/reference/loftest-1.png b/docs/dev/reference/loftest-1.png
index 3d20f41e..6b918fec 100644
Binary files a/docs/dev/reference/loftest-1.png and b/docs/dev/reference/loftest-1.png differ
diff --git a/docs/dev/reference/loftest-2.png b/docs/dev/reference/loftest-2.png
index be8bf815..60874bd3 100644
Binary files a/docs/dev/reference/loftest-2.png and b/docs/dev/reference/loftest-2.png differ
diff --git a/docs/dev/reference/loftest-3.png b/docs/dev/reference/loftest-3.png
index cb55838c..4837e7f2 100644
Binary files a/docs/dev/reference/loftest-3.png and b/docs/dev/reference/loftest-3.png differ
diff --git a/docs/dev/reference/loftest-4.png b/docs/dev/reference/loftest-4.png
index e2b8ac5c..9c18ac30 100644
Binary files a/docs/dev/reference/loftest-4.png and b/docs/dev/reference/loftest-4.png differ
diff --git a/docs/dev/reference/loftest-5.png b/docs/dev/reference/loftest-5.png
index a4d9fd48..11f2bda7 100644
Binary files a/docs/dev/reference/loftest-5.png and b/docs/dev/reference/loftest-5.png differ
diff --git a/docs/dev/reference/loftest.html b/docs/dev/reference/loftest.html
index b93b3aa3..abbbd3b9 100644
--- a/docs/dev/reference/loftest.html
+++ b/docs/dev/reference/loftest.html
@@ -75,7 +75,7 @@ lrtest.default from the lmtest package." />
       
       
         mkin
-        0.9.50.3
+        0.9.50.4
       
     
    
 
@@ -123,7 +123,7 @@ lrtest.default from the lmtest package." />
       
       
      
         
    • 
-  
+  
     
      
   
@@ -142,7 +142,7 @@ lrtest.default from the lmtest package." />
   
      
     
      
     
      Lack-of-fit test for models fitted to data with replicates
      
-    Source: R/loftest.R
+    Source: R/loftest.R
     
     
      
 
@@ -153,10 +153,10 @@ compares the likelihoods using the likelihood ratio test
 lrtest.default from the lmtest package.
      
     
      
 
-    
      loftest(object, ...)
+    
      loftest(object, ...)
 
 # S3 method for mkinfit
-loftest(object, ...)
      
+loftest(object, ...)
      
 
     
      Arguments
    @@ -183,9 +183,11 @@ of replicate samples.

    Examples

    # \dontrun{
-test_data <- subset(synthetic_data_for_UBA_2014[[12]]$data, name == "parent")
-sfo_fit <- mkinfit("SFO", test_data, quiet = TRUE)
-plot_res(sfo_fit) # We see a clear pattern in the residuals
    loftest(sfo_fit)  # We have a clear lack of fit
    #> Likelihood ratio test
+test_data <- subset(synthetic_data_for_UBA_2014[[12]]$data, name == "parent")
+sfo_fit <- mkinfit("SFO", test_data, quiet = TRUE)
+plot_res(sfo_fit) # We see a clear pattern in the residuals
+
    loftest(sfo_fit)  # We have a clear lack of fit
+
    #> Likelihood ratio test
 #> 
 #> Model 1: ANOVA with error model const
 #> Model 2: SFO with error model const
@@ -195,9 +197,11 @@ of replicate samples.
    
 #> ---
 #> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
    #
 # We try a different model (the one that was used to generate the data)
-dfop_fit <- mkinfit("DFOP", test_data, quiet = TRUE)
-plot_res(dfop_fit) # We don't see systematic deviations, but heteroscedastic residuals
    # therefore we should consider adapting the error model, although we have
-loftest(dfop_fit) # no lack of fit
    #> Likelihood ratio test
+dfop_fit <- mkinfit("DFOP", test_data, quiet = TRUE)
+plot_res(dfop_fit) # We don't see systematic deviations, but heteroscedastic residuals
+
    # therefore we should consider adapting the error model, although we have
+loftest(dfop_fit) # no lack of fit
+
    #> Likelihood ratio test
 #> 
 #> Model 1: ANOVA with error model const
 #> Model 2: DFOP with error model const
@@ -205,10 +209,11 @@ of replicate samples.
    
 #> 1  10 -40.710                    
 #> 2   5 -42.453 -5 3.485     0.6257
    #
 # This is the anova model used internally for the comparison
-test_data_anova <- test_data
-test_data_anova$time <- as.factor(test_data_anova$time)
-anova_fit <- lm(value ~ time, data = test_data_anova)
-summary(anova_fit)
    #> 
+test_data_anova <- test_data
+test_data_anova$time <- as.factor(test_data_anova$time)
+anova_fit <- lm(value ~ time, data = test_data_anova)
+summary(anova_fit)
+
    #> 
 #> Call:
 #> lm(formula = value ~ time, data = test_data_anova)
 #> 
@@ -233,12 +238,16 @@ of replicate samples.
    
 #> Residual standard error: 3.285 on 9 degrees of freedom
 #> Multiple R-squared:  0.9953,	Adjusted R-squared:  0.9912 
 #> F-statistic: 240.5 on 8 and 9 DF,  p-value: 1.417e-09
-#> 
    logLik(anova_fit) # We get the same likelihood and degrees of freedom
    #> 'log Lik.' -40.71015 (df=10)
    #
-test_data_2 <- synthetic_data_for_UBA_2014[[12]]$data
-m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
-  M1 = list(type = "SFO", to = "M2"),
-  M2 = list(type = "SFO"), use_of_ff = "max")
    #> Successfully compiled differential equation model from auto-generated C code.
    sfo_lin_fit <- mkinfit(m_synth_SFO_lin, test_data_2, quiet = TRUE)
-plot_res(sfo_lin_fit) # not a good model, we try parallel formation
    loftest(sfo_lin_fit)
    #> Likelihood ratio test
+#> 
    logLik(anova_fit) # We get the same likelihood and degrees of freedom
+
    #> 'log Lik.' -40.71015 (df=10)
    #
+test_data_2 <- synthetic_data_for_UBA_2014[[12]]$data
+m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
+  M1 = list(type = "SFO", to = "M2"),
+  M2 = list(type = "SFO"), use_of_ff = "max")
+
    #> Temporary DLL for differentials generated and loaded
    sfo_lin_fit <- mkinfit(m_synth_SFO_lin, test_data_2, quiet = TRUE)
+plot_res(sfo_lin_fit) # not a good model, we try parallel formation
+
    loftest(sfo_lin_fit)
+
    #> Likelihood ratio test
 #> 
 #> Model 1: ANOVA with error model const
 #> Model 2: m_synth_SFO_lin with error model const and fixed parameter(s) M1_0, M2_0
@@ -247,10 +256,13 @@ of replicate samples.
    
 #> 2   7 -171.927 -21 156.64  < 2.2e-16 ***
 #> ---
 #> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
    #
-m_synth_SFO_par <- mkinmod(parent = list(type = "SFO", to = c("M1", "M2")),
-  M1 = list(type = "SFO"),
-  M2 = list(type = "SFO"), use_of_ff = "max")
    #> Successfully compiled differential equation model from auto-generated C code.
    sfo_par_fit <- mkinfit(m_synth_SFO_par, test_data_2, quiet = TRUE)
-plot_res(sfo_par_fit) # much better for metabolites
    loftest(sfo_par_fit)
    #> Likelihood ratio test
+m_synth_SFO_par <- mkinmod(parent = list(type = "SFO", to = c("M1", "M2")),
+  M1 = list(type = "SFO"),
+  M2 = list(type = "SFO"), use_of_ff = "max")
+
    #> Temporary DLL for differentials generated and loaded
    sfo_par_fit <- mkinfit(m_synth_SFO_par, test_data_2, quiet = TRUE)
+plot_res(sfo_par_fit) # much better for metabolites
+
    loftest(sfo_par_fit)
+
    #> Likelihood ratio test
 #> 
 #> Model 1: ANOVA with error model const
 #> Model 2: m_synth_SFO_par with error model const and fixed parameter(s) M1_0, M2_0
@@ -259,10 +271,13 @@ of replicate samples.
    
 #> 2   7 -156.331 -21 125.45  < 2.2e-16 ***
 #> ---
 #> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
    #
-m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2")),
-  M1 = list(type = "SFO"),
-  M2 = list(type = "SFO"), use_of_ff = "max")
    #> Successfully compiled differential equation model from auto-generated C code.
    dfop_par_fit <- mkinfit(m_synth_DFOP_par, test_data_2, quiet = TRUE)
-plot_res(dfop_par_fit) # No visual lack of fit
    loftest(dfop_par_fit)  # no lack of fit found by the test
    #> Likelihood ratio test
+m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2")),
+  M1 = list(type = "SFO"),
+  M2 = list(type = "SFO"), use_of_ff = "max")
+
    #> Temporary DLL for differentials generated and loaded
    dfop_par_fit <- mkinfit(m_synth_DFOP_par, test_data_2, quiet = TRUE)
+plot_res(dfop_par_fit) # No visual lack of fit
+
    loftest(dfop_par_fit)  # no lack of fit found by the test
+
    #> Likelihood ratio test
 #> 
 #> Model 1: ANOVA with error model const
 #> Model 2: m_synth_DFOP_par with error model const and fixed parameter(s) M1_0, M2_0
@@ -270,11 +285,12 @@ of replicate samples.
    
 #> 1  28  -93.606                      
 #> 2   9 -102.763 -19 18.313     0.5016
    #
 # The anova model used for comparison in the case of transformation products
-test_data_anova_2 <- dfop_par_fit$data
-test_data_anova_2$variable <- as.factor(test_data_anova_2$variable)
-test_data_anova_2$time <- as.factor(test_data_anova_2$time)
-anova_fit_2 <- lm(observed ~ time:variable - 1, data = test_data_anova_2)
-summary(anova_fit_2)
    #> 
+test_data_anova_2 <- dfop_par_fit$data
+test_data_anova_2$variable <- as.factor(test_data_anova_2$variable)
+test_data_anova_2$time <- as.factor(test_data_anova_2$time)
+anova_fit_2 <- lm(observed ~ time:variable - 1, data = test_data_anova_2)
+summary(anova_fit_2)
+
    #> 
 #> Call:
 #> lm(formula = observed ~ time:variable - 1, data = test_data_anova_2)
 #> 
@@ -317,7 +333,7 @@ of replicate samples.
    
 #> Residual standard error: 2.225 on 25 degrees of freedom
 #> Multiple R-squared:  0.9979,	Adjusted R-squared:  0.9957 
 #> F-statistic: 469.2 on 25 and 25 DF,  p-value: < 2.2e-16
-#> 
    # }
+#> 
    # }
    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.6.1.

    diff --git a/docs/dev/reference/logLik.mkinfit.html b/docs/dev/reference/logLik.mkinfit.html index dbeeef60..66539dbd 100644 --- a/docs/dev/reference/logLik.mkinfit.html +++ b/docs/dev/reference/logLik.mkinfit.html @@ -193,10 +193,10 @@ and the fitted error model parameters.

    
   # \dontrun{
   sfo_sfo <- mkinmod(
-    parent = mkinsub("SFO", to = "m1"),
-    m1 = mkinsub("SFO")
+    parent = mkinsub("SFO", to = "m1"),
+    m1 = mkinsub("SFO")
   )
-
    #> Successfully compiled differential equation model from auto-generated C code.
      d_t <- FOCUS_2006_D
+
    #> Temporary DLL for differentials generated and loaded
      d_t <- FOCUS_2006_D
   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)
diff --git a/docs/dev/reference/logistic.solution.html b/docs/dev/reference/logistic.solution.html
index 86be11a7..950e8a8e 100644
--- a/docs/dev/reference/logistic.solution.html
+++ b/docs/dev/reference/logistic.solution.html
@@ -225,7 +225,7 @@ Version 1.1, 18 December 2014
          lty = 1:5, col = 1:5)
 
    
   # Fit with synthetic data
-  logistic <- mkinmod(parent = mkinsub("logistic"))
+  logistic <- mkinmod(parent = mkinsub("logistic"))
 
   sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
   parms_logistic <- c(kmax = 0.08, k0 = 0.0001, r = 0.2)
diff --git a/docs/dev/reference/lrtest.mkinfit.html b/docs/dev/reference/lrtest.mkinfit.html
index 712cfcfb..b76ebc87 100644
--- a/docs/dev/reference/lrtest.mkinfit.html
+++ b/docs/dev/reference/lrtest.mkinfit.html
@@ -76,7 +76,7 @@ and can be expressed by fixing the parameters of the other." />
       
       
         mkin
-        0.9.50.3
+        0.9.50.4
       
     
    
 
@@ -124,7 +124,7 @@ and can be expressed by fixing the parameters of the other." />
       
       
      
         
    • 
-  
+  
     
      
   
@@ -143,7 +143,7 @@ and can be expressed by fixing the parameters of the other." />
   
      
     
      
     
      Likelihood ratio test for mkinfit models
      
-    Source: R/lrtest.mkinfit.R
+    Source: R/lrtest.mkinfit.R
     
     
      
 
@@ -156,10 +156,10 @@ and can be expressed by fixing the parameters of the other.
      
     
      
 
     
      # S3 method for mkinfit
-lrtest(object, object_2 = NULL, ...)
+lrtest(object, object_2 = NULL, ...)
 
 # S3 method for mmkin
-lrtest(object, ...)
      
+lrtest(object, ...)

    Arguments

    @@ -191,10 +191,11 @@ lower number of fitted parameters (null hypothesis).

    Examples

    # \dontrun{
-test_data <- subset(synthetic_data_for_UBA_2014[[12]]$data, name == "parent")
-sfo_fit <- mkinfit("SFO", test_data, quiet = TRUE)
-dfop_fit <- mkinfit("DFOP", test_data, quiet = TRUE)
-lrtest(dfop_fit, sfo_fit)
    #> Likelihood ratio test
+test_data <- subset(synthetic_data_for_UBA_2014[[12]]$data, name == "parent")
+sfo_fit <- mkinfit("SFO", test_data, quiet = TRUE)
+dfop_fit <- mkinfit("DFOP", test_data, quiet = TRUE)
+lrtest(dfop_fit, sfo_fit)
+
    #> Likelihood ratio test
 #> 
 #> Model 1: DFOP with error model const
 #> Model 2: SFO with error model const
@@ -202,7 +203,8 @@ lower number of fitted parameters (null hypothesis).
    
 #> 1   5 -42.453                         
 #> 2   3 -63.954 -2 43.002  4.594e-10 ***
 #> ---
-#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
    lrtest(sfo_fit, dfop_fit)
    #> Likelihood ratio test
+#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
    lrtest(sfo_fit, dfop_fit)
+
    #> Likelihood ratio test
 #> 
 #> Model 1: DFOP with error model const
 #> Model 2: SFO with error model const
@@ -217,7 +219,8 @@ lower number of fitted parameters (null hypothesis).
    
 #lrtest(dfop_fit, fixed_parms = c(k2 = 0))
 
 # However, this equivalent syntax also works for static help pages
-lrtest(dfop_fit, update(dfop_fit, error_model = "tc"))
    #> Likelihood ratio test
+lrtest(dfop_fit, update(dfop_fit, error_model = "tc"))
+
    #> Likelihood ratio test
 #> 
 #> Model 1: DFOP with error model tc
 #> Model 2: DFOP with error model const
@@ -225,7 +228,8 @@ lower number of fitted parameters (null hypothesis).
    
 #> 1   6 -34.587                         
 #> 2   5 -42.453 -1 15.731  7.302e-05 ***
 #> ---
-#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
    lrtest(dfop_fit, update(dfop_fit, fixed_parms = c(k2 = 0)))
    #> Likelihood ratio test
+#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
    lrtest(dfop_fit, update(dfop_fit, fixed_parms = c(k2 = 0)))
+
    #> Likelihood ratio test
 #> 
 #> Model 1: DFOP with error model const
 #> Model 2: DFOP with error model const and fixed parameter(s) k2
@@ -233,7 +237,7 @@ lower number of fitted parameters (null hypothesis).
    
 #> 1   5 -42.453                         
 #> 2   4 -57.340 -1 29.776  4.851e-08 ***
 #> ---
-#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
    # }
+#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
    # }
    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.6.1.

    diff --git a/docs/dev/reference/mccall81_245T.html b/docs/dev/reference/mccall81_245T.html index 255c3568..c23bfda2 100644 --- a/docs/dev/reference/mccall81_245T.html +++ b/docs/dev/reference/mccall81_245T.html @@ -177,7 +177,7 @@ 
      SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"),
     phenol = list(type = "SFO", to = "anisole"),
     anisole = list(type = "SFO"))
-
    #> Successfully compiled differential equation model from auto-generated C code.
      # \dontrun{
+
    #> Temporary DLL for differentials generated and loaded
      # \dontrun{
     fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
 
    #> Warning: Observations with value of zero were removed from the data
        summary(fit.1)$bpar
 
    #>                         Estimate   se_notrans   t value       Pr(>t)
@@ -211,7 +211,7 @@
     SFO_SFO_SFO_2 <- mkinmod(T245 = list(type = "SFO", to = "phenol"),
       phenol = list(type = "SFO", to = "anisole", sink = FALSE),
       anisole = list(type = "SFO"))
-
    #> Successfully compiled differential equation model from auto-generated C code.
        fit.2 <- mkinfit(SFO_SFO_SFO_2, subset(mccall81_245T, soil == "Commerce"),
+
    #> Temporary DLL for differentials generated and loaded
        fit.2 <- mkinfit(SFO_SFO_SFO_2, subset(mccall81_245T, soil == "Commerce"),
       quiet = TRUE)
 
    #> Warning: Observations with value of zero were removed from the data
        summary(fit.2)$bpar
 
    #>                      Estimate   se_notrans   t value       Pr(>t)        Lower
diff --git a/docs/dev/reference/mkin_long_to_wide.html b/docs/dev/reference/mkin_long_to_wide.html
index 143eb12a..28a37800 100644
--- a/docs/dev/reference/mkin_long_to_wide.html
+++ b/docs/dev/reference/mkin_long_to_wide.html
@@ -74,7 +74,7 @@ variable and several dependent variables as columns." />
       
       
         mkin
-        0.9.50.3
+        0.9.50.4
       
     
    
 
@@ -122,7 +122,7 @@ variable and several dependent variables as columns." />
       
       
      
         
    • 
-  
+  
     
      
   
@@ -141,7 +141,7 @@ variable and several dependent variables as columns." />
   
      
     
      
     
      Convert a dataframe from long to wide format
      
-    Source: R/mkin_long_to_wide.R
+    Source: R/mkin_long_to_wide.R
     
     
      
 
@@ -151,7 +151,7 @@ observed value, and converts it into a dataframe with one independent
 variable and several dependent variables as columns.
      
     
      
 
-    
      mkin_long_to_wide(long_data, time = "time", outtime = "time")
      
+    
      mkin_long_to_wide(long_data, time = "time", outtime = "time")
      
 
     
      Arguments
    @@ -176,10 +176,14 @@ observed values called "value".

    Value

    Dataframe in wide format.

    +

    Author

    + +

    Johannes Ranke

    Examples

    
-mkin_long_to_wide(FOCUS_2006_D)
    #>    time parent    m1
+mkin_long_to_wide(FOCUS_2006_D)
+
    #>    time parent    m1
 #> 1     0  99.46  0.00
 #> 2     0 102.04  0.00
 #> 3     1  93.50  4.84
@@ -218,7 +222,7 @@ observed values called "value".
    
 
    
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.6.1.
    
 
    
 
       
diff --git a/docs/dev/reference/mkin_wide_to_long.html b/docs/dev/reference/mkin_wide_to_long.html
index 14419558..f085d162 100644
--- a/docs/dev/reference/mkin_wide_to_long.html
+++ b/docs/dev/reference/mkin_wide_to_long.html
@@ -74,7 +74,7 @@ mkinfit." />
       
       
         mkin
-        0.9.50.3
+        0.9.50.4
       
     
 
@@ -122,7 +122,7 @@ mkinfit." />
       
       
      
         
    • 
-  
+  
     
      
   
@@ -141,7 +141,7 @@ mkinfit." />
   
      
     
      
     
      Convert a dataframe with observations over time into long format
      
-    Source: R/mkin_wide_to_long.R
+    Source: R/mkin_wide_to_long.R
     
     
      
 
@@ -151,7 +151,7 @@ several dependent variable and converts it into the long form as required by
 mkinfit.
      
     
      
 
-    
      mkin_wide_to_long(wide_data, time = "t")
      
+    
      mkin_wide_to_long(wide_data, time = "t")
      
 
     
      Arguments
    @@ -171,11 +171,15 @@ column of observed values.

    Value

    Dataframe in long format as needed for mkinfit.

    +

    Author

    + +

    Johannes Ranke

    Examples

    
-wide <- data.frame(t = c(1,2,3), x = c(1,4,7), y = c(3,4,5))
-mkin_wide_to_long(wide)
    #>   name time value
+wide <- data.frame(t = c(1,2,3), x = c(1,4,7), y = c(3,4,5))
+mkin_wide_to_long(wide)
+
    #>   name time value
 #> 1    x    1     1
 #> 2    x    2     4
 #> 3    x    3     7
@@ -198,7 +202,7 @@ column of observed values.
    
 
    
 
 
    
-  
    Site built with pkgdown 1.5.1.
    
+  
    Site built with pkgdown 1.6.1.
    
 
    
 
       
diff --git a/docs/dev/reference/mkinerrmin.html b/docs/dev/reference/mkinerrmin.html
index 9f58dfaa..1cff040d 100644
--- a/docs/dev/reference/mkinerrmin.html
+++ b/docs/dev/reference/mkinerrmin.html
@@ -73,7 +73,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />
       
       
         mkin
-        0.9.50.3
+        0.9.50.4
       
     
 
@@ -121,7 +121,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />
       
       
      
         
    • 
-  
+  
     
      
   
@@ -140,7 +140,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />
   
      
     
      
     
      Calculate the minimum error to assume in order to pass the variance test
      
-    Source: R/mkinerrmin.R
+    Source: R/mkinerrmin.R
     
     
      
 
@@ -149,7 +149,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." />
 the chi-squared test as defined in the FOCUS kinetics report from 2006.
      
     
      
 
-    
      mkinerrmin(fit, alpha = 0.05)
      
+    
      mkinerrmin(fit, alpha = 0.05)
      
 
     
      Arguments
    @@ -189,18 +189,22 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp,

    Examples

    
-SFO_SFO = mkinmod(parent = mkinsub("SFO", to = "m1"),
-                  m1 = mkinsub("SFO"),
-                  use_of_ff = "max")
    #> Successfully compiled differential equation model from auto-generated C code.
    
-fit_FOCUS_D = mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
    #> Warning: Observations with value of zero were removed from the data
    round(mkinerrmin(fit_FOCUS_D), 4)
    #>          err.min n.optim df
+SFO_SFO = mkinmod(parent = mkinsub("SFO", to = "m1"),
+                  m1 = mkinsub("SFO"),
+                  use_of_ff = "max")
+
    #> Temporary DLL for differentials generated and loaded
    
+fit_FOCUS_D = mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+
    #> Warning: Observations with value of zero were removed from the data
    round(mkinerrmin(fit_FOCUS_D), 4)
+
    #>          err.min n.optim df
 #> All data  0.0640       4 15
 #> parent    0.0646       2  7
 #> m1        0.0469       2  8
    # \dontrun{
-  fit_FOCUS_E = mkinfit(SFO_SFO, FOCUS_2006_E, quiet = TRUE)
-  round(mkinerrmin(fit_FOCUS_E), 4)
    #>          err.min n.optim df
+  fit_FOCUS_E = mkinfit(SFO_SFO, FOCUS_2006_E, quiet = TRUE)
+  round(mkinerrmin(fit_FOCUS_E), 4)
+
    #>          err.min n.optim df
 #> All data  0.1544       4 13
 #> parent    0.1659       2  7
-#> m1        0.1095       2  6
    # }
+#> m1        0.1095       2  6
    # }
    @@ -218,7 +222,7 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp,
    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.6.1.

    diff --git a/docs/dev/reference/mkinerrplot.html b/docs/dev/reference/mkinerrplot.html index 48d20ca8..2324b968 100644 --- a/docs/dev/reference/mkinerrplot.html +++ b/docs/dev/reference/mkinerrplot.html @@ -242,8 +242,8 @@ lines of the mkinfit object.

    Examples

    
 # \dontrun{
-model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
-
    #> Successfully compiled differential equation model from auto-generated C code.
    fit <- mkinfit(model, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
+model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
+
    #> Temporary DLL for differentials generated and loaded
    fit <- mkinfit(model, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
 
    #> Warning: Observations with value of zero were removed from the data
    mkinerrplot(fit)
 
    # }
 
diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html
index f5a913b2..73c09c1f 100644
--- a/docs/dev/reference/mkinfit.html
+++ b/docs/dev/reference/mkinfit.html
@@ -432,15 +432,15 @@ Degradation Data. Environments 6(12) 124
 summary(fit)
 
    #> mkin version used for fitting:    0.9.50.4 
 #> R version used for fitting:       4.0.3 
-#> Date of fit:     Thu Nov 19 14:49:38 2020 
-#> Date of summary: Thu Nov 19 14:49:38 2020 
+#> Date of fit:     Mon Nov 30 15:48:34 2020 
+#> Date of summary: Mon Nov 30 15:48:34 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.045 s
+#> Fitted using 222 model solutions performed in 0.046 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -515,9 +515,9 @@ Degradation Data. Environments 6(12) 124
 FOCUS_D <- subset(FOCUS_2006_D, value != 0)
 # Use mkinsub for convenience in model formulation. Pathway to sink included per default.
 SFO_SFO <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
-
    #> Successfully compiled differential equation model from auto-generated C code.
    
+  parent = mkinsub("SFO", "m1"),
+  m1 = mkinsub("SFO"))
+
    #> Temporary DLL for differentials generated and loaded
    
 # Fit the model quietly to the FOCUS example dataset D using defaults
 fit <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE)
 plot_sep(fit)
@@ -574,16 +574,16 @@ Degradation Data. Environments 6(12) 124
       solution_type = "analytical"))
 }
 
    #>               test relative elapsed
-#> 3       analytical    1.000   0.534
-#> 1 deSolve_compiled    1.908   1.019
-#> 2            eigen    2.238   1.195
    # }
+#> 3       analytical    1.000   0.532
+#> 1 deSolve_compiled    1.831   0.974
+#> 2            eigen    2.235   1.189
    # }
 
 # Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO
 # \dontrun{
 FOMC_SFO <- mkinmod(
-  parent = mkinsub("FOMC", "m1"),
-  m1 = mkinsub("SFO"))
-
    #> Successfully compiled differential equation model from auto-generated C code.
    fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE)
+  parent = mkinsub("FOMC", "m1"),
+  m1 = mkinsub("SFO"))
+
    #> Temporary DLL for differentials generated and loaded
    fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE)
 # Again, we get a warning and try a more sophisticated error model
 fit.FOMC_SFO.tc <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE, error_model = "tc")
 
    #> Warning: Optimisation did not converge:
@@ -600,8 +600,8 @@ Degradation Data. Environments 6(12) 124
 summary(fit.FOMC_SFO.tc, data = FALSE)
 
    #> Warning: NaNs produced
    #> Warning: NaNs produced
    #> Warning: NaNs produced
    #> Warning: diag(.) had 0 or NA entries; non-finite result is doubtful
    #> mkin version used for fitting:    0.9.50.4 
 #> R version used for fitting:       4.0.3 
-#> Date of fit:     Thu Nov 19 14:49:49 2020 
-#> Date of summary: Thu Nov 19 14:49:49 2020 
+#> Date of fit:     Mon Nov 30 15:48:45 2020 
+#> Date of summary: Mon Nov 30 15:48:45 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -610,7 +610,7 @@ Degradation Data. Environments 6(12) 124
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 4273 model solutions performed in 3.1 s
+#> Fitted using 4273 model solutions performed in 3.191 s
 #> 
 #> Error model: Two-component variance function 
 #> 
diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html
index 803be90d..9e37e664 100644
--- a/docs/dev/reference/mkinmod.html
+++ b/docs/dev/reference/mkinmod.html
@@ -162,9 +162,13 @@ components.
    
     
    mkinmod(
   ...,
   use_of_ff = "max",
+  name = NULL,
   speclist = NULL,
   quiet = FALSE,
-  verbose = FALSE
+  verbose = FALSE,
+  dll_dir = NULL,
+  unload = FALSE,
+  overwrite = FALSE
 )
 
 # S3 method for mkinmod
@@ -200,6 +204,10 @@ formation fractions are always used (default).  If "min", a minimum use of
 formation fractions is made, i.e. each pathway to a metabolite has its
 own rate constant.
    
     
+
    + + + + + + + + + + + + + + + @@ -299,18 +324,37 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

    SFO_SFO<-mkinmod( parent =mkinsub("SFO", "m1"), m1 =mkinsub("SFO")) -
    #> Successfully compiled differential equation model from auto-generated C code.
    +
    #> Temporary DLL for differentials generated and loaded
    print(SFO_SFO) +
    #> <mkinmod> model generated with +#> Use of formation fractions $use_of_ff: max +#> Specification $spec: +#> $parent +#> $type: SFO; $to: m1; $sink: TRUE +#> $m1 +#> $type: SFO; $sink: TRUE +#> Coefficient matrix $coefmat available +#> Compiled model $cf available +#> Differential equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
    # \dontrun{ -# Now supplying full names used for plotting + fit_sfo_sfo <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve") +
    #> Warning: Observations with value of zero were removed from the data
    + # Now supplying compound names used for plotting, and write to user defined location + # We need to choose a path outside the session tempdir because this gets removed + DLL_dir <- "~/.local/share/mkin" + if (!dir.exists(DLL_dir)) dir.create(DLL_dir) SFO_SFO.2 <- mkinmod( parent = mkinsub("SFO", "m1", full_name = "Test compound"), - m1 = mkinsub("SFO", full_name = "Metabolite M1")) -
    #> Successfully compiled differential equation model from auto-generated C code.
    -# The above model used to be specified like this, before the advent of mkinsub() -SFO_SFO <- mkinmod( - parent = list(type = "SFO", to = "m1"), - m1 = list(type = "SFO")) -
    #> Successfully compiled differential equation model from auto-generated C code.
    + m1 = mkinsub("SFO", full_name = "Metabolite M1"), + name = "SFO_SFO", dll_dir = DLL_dir, unload = TRUE, overwrite = TRUE) +
    #> Copied DLL from /tmp/RtmpX9Xf3y/file6d622f3b7e08.so to /home/jranke/.local/share/mkin/SFO_SFO.so
    # Now we can save the model and restore it in a new session +saveRDS(SFO_SFO.2, file = "~/SFO_SFO.rds") +# Terminate the R session here if you would like to check, and then do +library(mkin) +SFO_SFO.3 <- readRDS("~/SFO_SFO.rds") +fit_sfo_sfo <- mkinfit(SFO_SFO.3, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve") +
    #> Warning: Observations with value of zero were removed from the data
    # Show details of creating the C function SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), @@ -330,11 +374,11 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

    #> 12: } #> 13: #> 14: -#> 15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) { +#> 15: void diffs ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) { #> 16: #> 17: f[0] = - k_parent * y[0]; #> 18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1]; -#> 19: }
    #> Successfully compiled differential equation model from auto-generated C code.
    +#> 19: }
    #> Temporary DLL for differentials generated and loaded
    # The symbolic solution which is available in this case is not # made for human reading but for speed of computation SFO_SFO$deg_func @@ -353,7 +397,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

    #> }) #> return(predicted) #> } -#> <environment: 0x55555c97f8d8>
    +#> <environment: 0x55555c5b8d68>
    # If we have several parallel metabolites # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R) m_synth_DFOP_par <- mkinmod( @@ -367,27 +411,6 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

    quiet = TRUE) # } - - m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"), - M1 = list(type = "SFO", to = "M2"), - M2 = list(type = "SFO"), use_of_ff = "max") -
    #> Successfully compiled differential equation model from auto-generated C code.
    - print(m_synth_SFO_lin) -
    #> <mkinmod> model generated with -#> Use of formation fractions $use_of_ff: max -#> Specification $spec: -#> $parent -#> $type: SFO; $to: M1; $sink: TRUE -#> $M1 -#> $type: SFO; $to: M2; $sink: TRUE -#> $M2 -#> $type: SFO; $sink: TRUE -#> Coefficient matrix $coefmat available -#> Compiled model $cf available -#> Differential equations: -#> d_parent/dt = - k_parent * parent -#> d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1 -#> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2
    @@ -121,7 +121,7 @@ plot.mkinfit." />
    • - + @@ -140,7 +140,7 @@ plot.mkinfit." />

      Plot the observed data and the fitted model of an mkinfit object

      - Source: R/plot.mkinfit.R + Source: R/plot.mkinfit.R
      @@ -149,7 +149,7 @@ plot.mkinfit." /> plot.mkinfit.

      - 
      mkinplot(fit, ...)
      + 
      mkinplot(fit, ...)

      Arguments

    name

    A name for the model. Should be a valid R object name.

    speclist

    The specification of the observed variables and their @@ -214,6 +222,23 @@ argument. Default is NULL.

    		 verbose

    If TRUE, passed to inline::cfunction() if applicable to give detailed information about the C function being built.

    dll_dir

    Directory where an DLL object, if generated internally by +inline::cfunction(), should be saved. The DLL will only be stored in a +permanent location for use in future sessions, if 'dll_dir' and 'name' +are specified.

    unload

    If a DLL from the target location in 'dll_dir' is already +loaded, should that be unloaded first?

    overwrite

    If a file exists at the target DLL location in 'dll_dir', +should this be overwritten?
    x
    @@ -167,6 +167,9 @@ plot.mkinfit." />

    Value

    The function is called for its side effect.

    +

    Author

    + +

    Johannes Ranke

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.6.1.

    diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html index d3a86276..3221fc23 100644 --- a/docs/dev/reference/mkinpredict.html +++ b/docs/dev/reference/mkinpredict.html @@ -266,7 +266,7 @@ as these always return mapped output.

    Examples

    
-SFO <- mkinmod(degradinol = mkinsub("SFO"))
+SFO <- mkinmod(degradinol = mkinsub("SFO"))
 # Compare solution types
 mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
       solution_type = "analytical")
@@ -388,7 +388,7 @@ as these always return mapped output.
    
 # Comparison of the performance of solution types
 SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),
                   m1 = list(type = "SFO"), use_of_ff = "max")
-
    #> Successfully compiled differential equation model from auto-generated C code.
    if(require(rbenchmark)) {
+
    #> Temporary DLL for differentials generated and loaded
    if(require(rbenchmark)) {
   benchmark(replications = 10, order = "relative", columns = c("test", "relative", "elapsed"),
     eigen = mkinpredict(SFO_SFO,
       c(k_parent = 0.15, f_parent_to_m1 = 0.5, k_m1 = 0.01),
@@ -408,10 +408,10 @@ as these always return mapped output.
    
       solution_type = "analytical", use_compiled = FALSE)[201,])
 }
 
    #>               test relative elapsed
-#> 2 deSolve_compiled      1.0   0.005
 #> 4       analytical      1.0   0.005
+#> 2 deSolve_compiled      1.2   0.006
 #> 1            eigen      4.0   0.020
-#> 3          deSolve     44.6   0.223
    
+#> 3          deSolve     44.2   0.221
    
 # \dontrun{
   # Predict from a fitted model
   f <- mkinfit(SFO_SFO, FOCUS_2006_C, quiet = TRUE)
diff --git a/docs/dev/reference/mkinresplot.html b/docs/dev/reference/mkinresplot.html
index 38c52425..4b2f6bea 100644
--- a/docs/dev/reference/mkinresplot.html
+++ b/docs/dev/reference/mkinresplot.html
@@ -246,8 +246,8 @@ combining the plot of the fit and the residual plot.
    
 
     
    Examples
    
     
    
-model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
-
    #> Successfully compiled differential equation model from auto-generated C code.
    fit <- mkinfit(model, FOCUS_2006_D, quiet = TRUE)
+model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
+
    #> Temporary DLL for differentials generated and loaded
    fit <- mkinfit(model, FOCUS_2006_D, quiet = TRUE)
 
    #> Warning: Observations with value of zero were removed from the data
    mkinresplot(fit, "m1")
 
    
 
    
diff --git a/docs/dev/reference/mkinsub.html b/docs/dev/reference/mkinsub.html
deleted file mode 100644
index 68fd6268..00000000
--- a/docs/dev/reference/mkinsub.html
+++ /dev/null
@@ -1,234 +0,0 @@
-
-
-
-  
-  
-
-
-
-Function to set up a kinetic submodel for one state variable — mkinsub • mkin
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-  
-
-  
-    
    
-      
    
-      
-
-      
-
-      
    
-
-
    
-  
    
-    
    
-    
    Function to set up a kinetic submodel for one state variable
    
-    Source: R/mkinsub.R
-    
-    
    
-
-    
    
-    
    This is a convenience function to set up the lists used as arguments for
-mkinmod.
    
-    
    
-
-    
    mkinsub(submodel, to = NULL, sink = TRUE, full_name = NA)
    
-
-    
    Arguments
    
-
    - - - - - - - - - - - - - - - - - -
    submodel

    Character vector of length one to specify the submodel type. -See mkinmod for the list of allowed submodel names.

    to

    Vector of the names of the state variable to which a -transformation shall be included in the model.

    sink

    Should a pathway to sink be included in the model in addition to -the pathways to other state variables?

    full_name

    An optional name to be used e.g. for plotting fits -performed with the model. You can use non-ASCII characters here, but then -your R code will not be portable, i.e. may produce unintended plot -results on other operating systems or system configurations.

    - -

    Value

    - -

    A list for use with mkinmod.

    -

    Author

    - -

    Johannes Ranke

    - -

    Examples

    - 
    
-# One parent compound, one metabolite, both single first order.
-SFO_SFO <- mkinmod(
-  parent = list(type = "SFO", to = "m1"),
-  m1 = list(type = "SFO"))
-
    #> Successfully compiled differential equation model from auto-generated C code.
    
-# The same model using mkinsub
-SFO_SFO.2 <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
-
    #> Successfully compiled differential equation model from auto-generated C code.
    
-# \dontrun{
-  # Now supplying full names
-  SFO_SFO.2 <- mkinmod(
-    parent = mkinsub("SFO", "m1", full_name = "Test compound"),
-    m1 = mkinsub("SFO", full_name = "Metabolite M1"))
-
    #> Successfully compiled differential equation model from auto-generated C code.
     # }
-
    - - - - - -
    -
    -

    Developed by Johannes Ranke.

    -
    - -
    -

    Site built with pkgdown 1.6.1.

    -
    - -
    - - - - - - - - - diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html index 4786b02e..651eb9a6 100644 --- a/docs/dev/reference/mmkin.html +++ b/docs/dev/reference/mmkin.html @@ -210,14 +210,14 @@ plotting.

    Examples

    
 # \dontrun{
-m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
-                           M1 = mkinsub("SFO", "M2"),
-                           M2 = mkinsub("SFO"), use_of_ff = "max")
-
    #> Successfully compiled differential equation model from auto-generated C code.
    
-m_synth_FOMC_lin <- mkinmod(parent = mkinsub("FOMC", "M1"),
-                            M1 = mkinsub("SFO", "M2"),
-                            M2 = mkinsub("SFO"), use_of_ff = "max")
-
    #> Successfully compiled differential equation model from auto-generated C code.
    
+m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
+                           M1 = mkinsub("SFO", "M2"),
+                           M2 = mkinsub("SFO"), use_of_ff = "max")
+
    #> Temporary DLL for differentials generated and loaded
    
+m_synth_FOMC_lin <- mkinmod(parent = mkinsub("FOMC", "M1"),
+                            M1 = mkinsub("SFO", "M2"),
+                            M2 = mkinsub("SFO"), use_of_ff = "max")
+
    #> Temporary DLL for differentials generated and loaded
    
 models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)
 datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)
 names(datasets) <- paste("Dataset", 1:3)
@@ -227,9 +227,9 @@ plotting.
    
 
 time_default
 
    #>    user  system elapsed 
-#>   4.664   0.433   1.317 
    time_1
+#>   4.968   0.427   1.342 
    time_1
 
    #>    user  system elapsed 
-#>   5.326   0.001   5.330 
    
+#>   5.365   0.000   5.368 
    
 endpoints(fits.0[["SFO_lin", 2]])
 
    #> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
diff --git a/docs/dev/reference/nlme-2.png b/docs/dev/reference/nlme-2.png
index 7129c580..c0fb6dcf 100644
Binary files a/docs/dev/reference/nlme-2.png and b/docs/dev/reference/nlme-2.png differ
diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html
index e109b34e..b3e88428 100644
--- a/docs/dev/reference/nlme.html
+++ b/docs/dev/reference/nlme.html
@@ -186,7 +186,7 @@ nlme for the case of a single grouping variable ds.
    
 
     
    Examples
    
     
    sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
-m_SFO <- mkinmod(parent = mkinsub("SFO"))
+m_SFO <- mkinmod(parent = mkinsub("SFO"))
 d_SFO_1 <- mkinpredict(m_SFO,
   c(k_parent = 0.1),
   c(parent = 98), sampling_times)
@@ -254,9 +254,8 @@ nlme for the case of a single grouping variable ds.
    
 #
 # The procedure is greatly simplified by the nlme.mmkin function
 f_nlme <- nlme(f)
-plot(f_nlme)
-
    
-
    
+
    #> Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    plot(f_nlme)
+
    #> df AIC -#> f_nlme_sfo 5 625.0539 -#> f_nlme_dfop 9 495.1270
    print(f_nlme_dfop) +
    #> Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    +# \dontrun{ + + f_nlme_dfop <- nlme(f["DFOP", ]) + anova(f_nlme_sfo, f_nlme_dfop) +
    #> Model df AIC BIC logLik Test L.Ratio p-value +#> f_nlme_sfo 1 6 622.0677 637.0666 -305.0338 +#> f_nlme_dfop 2 15 487.0134 524.5105 -228.5067 1 vs 2 153.0543 <.0001
    print(f_nlme_dfop)
    #> Kinetic nonlinear mixed-effects model fit by maximum likelihood #> #> Structural model: @@ -289,48 +294,30 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Data: #> 90 observations of 1 variable(s) grouped in 5 datasets #> -#> Log-likelihood: -238.5635 +#> Log-likelihood: -228.5067 #> #> Fixed effects: #> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> parent_0 log_k1 log_k2 g_qlogis -#> 94.1702 -1.8002 -4.1474 0.0324 +#> 94.18273 -1.82135 -4.16872 0.08949 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> Level: ds -#> Structure: Diagonal -#> parent_0 log_k1 log_k2 g_qlogis Residual -#> StdDev: 2.488 0.8447 1.33 0.4652 2.321 -#>
    plot(f_nlme_dfop) -
    endpoints(f_nlme_dfop) +#> Structure: General positive-definite, Log-Cholesky parametrization +#> StdDev Corr +#> parent_0 2.4656397 prnt_0 log_k1 log_k2 +#> log_k1 0.7950788 0.240 +#> log_k2 1.2605419 0.150 0.984 +#> g_qlogis 0.5013272 -0.075 0.843 0.834 +#> Residual 2.3308100 +#>
    plot(f_nlme_dfop) +
    endpoints(f_nlme_dfop)
    #> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 10.79857 100.7937 30.34192 4.193937 43.85442 +#> parent 10.57119 101.0652 30.42366 4.283776 44.80015 #>
    -# \dontrun{ - f_nlme_2 <- nlme(f["SFO", ], start = c(parent_0 = 100, log_k_parent = 0.1)) - update(f_nlme_2, random = parent_0 ~ 1) -
    #> Kinetic nonlinear mixed-effects model fit by maximum likelihood -#> -#> Structural model: -#> d_parent/dt = - k_parent * parent -#> -#> Data: -#> observations of 0 variable(s) grouped in 0 datasets -#> -#> Log-likelihood: -404.3729 -#> -#> Fixed effects: -#> list(parent_0 ~ 1, log_k_parent ~ 1) -#> parent_0 log_k_parent -#> 75.933 -3.556 -#> -#> Random effects: -#> Formula: parent_0 ~ 1 | ds -#> parent_0 Residual -#> StdDev: 0.002417 21.63 -#>
    ds_2 <- lapply(experimental_data_for_UBA_2019[6:10], + ds_2 <- lapply(experimental_data_for_UBA_2019[6:10], function(x) x$data[c("name", "time", "value")]) m_sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), A1 = mkinsub("SFO"), use_of_ff = "min", quiet = TRUE) @@ -345,66 +332,42 @@ methods that will automatically work on 'nlme.mmkin' objects, such as ds_2, quiet = TRUE) f_nlme_sfo_sfo <- nlme(f_2["SFO-SFO", ]) - plot(f_nlme_sfo_sfo) +
    #> Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    #> Warning: Iteration 2, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    plot(f_nlme_sfo_sfo)
    - # With formation fractions - f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ]) - plot(f_nlme_sfo_sfo_ff) -
    - # For the following fit we need to increase pnlsMaxIter and the tolerance - # to get convergence - f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ], - control = list(pnlsMaxIter = 120, tolerance = 5e-4), verbose = TRUE) -
    #> -#> **Iteration 1 -#> LME step: Loglik: -404.9583, nlminb iterations: 1 -#> reStruct parameters: -#> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.4114356 0.9798646 1.3524300 0.7293315 0.3354323 1.3647313 -#> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.3633 -#> fixed effects: 93.82269 -5.455993 -0.9601037 -1.862196 -4.199671 0.07824609 -#> iterations: 120 -#> Convergence crit. (must all become <= tolerance = 0.0005): -#> fixed reStruct -#> 0.7897284 0.5822782 -#> -#> **Iteration 2 -#> LME step: Loglik: -407.7755, nlminb iterations: 11 -#> reStruct parameters: -#> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.37122411 0.00305562 1.44336560 0.72467122 0.30160310 1.40762692 -#> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.3637 -#> fixed effects: 93.82269 -5.455992 -0.9601036 -1.862196 -4.199671 0.0782462 -#> iterations: 120 -#> Convergence crit. (must all become <= tolerance = 0.0005): -#> fixed reStruct -#> 1.375673e-06 9.758294e-06
    + # With formation fractions this does not coverge with defaults + # f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ]) + #plot(f_nlme_sfo_sfo_ff) + + # With the log-Cholesky parameterization, this converges in 11 + # iterations and around 100 seconds, but without tweaking control + # parameters (with pdDiag, increasing the tolerance and pnlsMaxIter was + # necessary) + f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ]) +
    #> Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    #> Warning: Iteration 2, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    #> Warning: Iteration 3, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    #> Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    plot(f_nlme_dfop_sfo) -
    +
    anova(f_nlme_dfop_sfo, f_nlme_sfo_sfo)
    #> Model df AIC BIC logLik Test L.Ratio p-value -#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 -#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001
    +#> f_nlme_dfop_sfo 1 28 811.7199 899.5222 -377.8599 +#> f_nlme_sfo_sfo 2 15 1075.1934 1122.2304 -522.5967 1 vs 2 289.4736 <.0001
    endpoints(f_nlme_sfo_sfo)
    #> $ff #> parent_sink parent_A1 A1_sink -#> 0.5912432 0.4087568 1.0000000 +#> 0.6512742 0.3487258 1.0000000 #> #> $distimes -#> DT50 DT90 -#> parent 19.13518 63.5657 -#> A1 66.02155 219.3189 +#> DT50 DT90 +#> parent 18.03144 59.89916 +#> A1 102.72949 341.25997 #>
    endpoints(f_nlme_dfop_sfo)
    #> $ff #> parent_A1 parent_sink -#> 0.2768574 0.7231426 +#> 0.2762167 0.7237833 #> #> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 11.07091 104.6320 31.49738 4.462384 46.20825 -#> A1 162.30523 539.1663 NA NA NA +#> parent 11.15024 133.9652 40.32755 4.688015 62.16017 +#> A1 235.83191 783.4167 NA NA NA #>
    if (length(findFunction("varConstProp")) > 0) { # tc error model for nlme available # Attempts to fit metabolite kinetics with the tc error model are possible, @@ -416,7 +379,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as AIC(f_nlme_sfo, f_nlme_sfo_tc, f_nlme_dfop, f_nlme_dfop_tc) print(f_nlme_dfop_tc) } -
    #> Kinetic nonlinear mixed-effects model fit by maximum likelihood +
    #> Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    #> Warning: Iteration 14, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    #> Warning: Iteration 2, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    #> Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 5, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 6, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 7, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 8, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 9, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 10, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 11, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 12, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 14, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 15, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 16, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 17, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 18, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Kinetic nonlinear mixed-effects model fit by maximum likelihood #> #> Structural model: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -426,31 +389,35 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Data: #> 90 observations of 1 variable(s) grouped in 5 datasets #> -#> Log-likelihood: -238.4298 +#> Log-likelihood: -228.3575 #> #> Fixed effects: #> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> parent_0 log_k1 log_k2 g_qlogis -#> 94.04775 -1.82340 -4.16715 0.05685 +#> 93.6695 -1.9187 -4.4253 0.2215 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> Level: ds -#> Structure: Diagonal -#> parent_0 log_k1 log_k2 g_qlogis Residual -#> StdDev: 2.474 0.85 1.337 0.4659 1 +#> Structure: General positive-definite, Log-Cholesky parametrization +#> StdDev Corr +#> parent_0 2.8574651 prnt_0 log_k1 log_k2 +#> log_k1 0.9689083 0.506 +#> log_k2 1.5798002 0.446 0.997 +#> g_qlogis 0.5761569 -0.457 0.247 0.263 +#> Residual 1.0000000 #> #> Variance function: #> Structure: Constant plus proportion of variance covariate #> Formula: ~fitted(.) #> Parameter estimates: -#> const prop -#> 2.23224114 0.01262341
    +#> const prop +#> 2.0376990 0.0221686
    f_2_obs <- mmkin(list("SFO-SFO" = m_sfo_sfo, "DFOP-SFO" = m_dfop_sfo), ds_2, quiet = TRUE, error_model = "obs") f_nlme_sfo_sfo_obs <- nlme(f_2_obs["SFO-SFO", ]) - print(f_nlme_sfo_sfo_obs) +
    #> Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    print(f_nlme_sfo_sfo_obs)
    #> Kinetic nonlinear mixed-effects model fit by maximum likelihood #> #> Structural model: @@ -460,29 +427,44 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Data: #> 170 observations of 2 variable(s) grouped in 5 datasets #> -#> Log-likelihood: -472.976 +#> Log-likelihood: -462.2203 #> #> Fixed effects: #> list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1) #> parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink -#> 87.976 -3.670 -4.164 -4.645 +#> 88.682 -3.664 -4.164 -4.665 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1) #> Level: ds -#> Structure: Diagonal -#> parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink Residual -#> StdDev: 3.992 1.777 1.055 0.4821 6.483 +#> Structure: General positive-definite, Log-Cholesky parametrization +#> StdDev Corr +#> parent_0 4.9153305 prnt_0 lg_k__ l___A1 +#> log_k_parent_sink 1.8158570 0.956 +#> log_k_parent_A1 1.0514548 0.821 0.907 +#> log_k_A1_sink 0.4924122 0.035 0.315 0.533 +#> Residual 6.3987599 #> #> Variance function: #> Structure: Different standard deviations per stratum #> Formula: ~1 | name #> Parameter estimates: #> parent A1 -#> 1.0000000 0.2050003
    # The same with DFOP-SFO does not converge, apparently the variances of - # parent and A1 are too similar in this case, so that the model is - # overparameterised - #f_nlme_dfop_sfo_obs <- nlme(f_2_obs["DFOP-SFO", ], control = list(maxIter = 100)) +#> 1.0000000 0.2040647
    f_nlme_dfop_sfo_obs <- nlme(f_2_obs["DFOP-SFO", ]) +
    #> Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    #> Warning: Iteration 2, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    #> Warning: Iteration 3, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    #> Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    + f_2_tc <- mmkin(list("SFO-SFO" = m_sfo_sfo, + "DFOP-SFO" = m_dfop_sfo), + ds_2, quiet = TRUE, error_model = "tc") + # f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # stops with error message + f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ]) +
    #> Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    #> Warning: Iteration 2, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    #> Warning: Iteration 3, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    #> Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    #> Warning: Iteration 6, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 7, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 8, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 9, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 11, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 12, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 15, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    #> Warning: Iteration 25, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
    # We get warnings about false convergence in the LME step in several iterations + # but as the last such warning occurs in iteration 25 and we have 28 iterations + # we can ignore these + anova(f_nlme_dfop_sfo, f_nlme_dfop_sfo_obs, f_nlme_dfop_sfo_tc) +
    #> Model df AIC BIC logLik Test L.Ratio p-value +#> f_nlme_dfop_sfo 1 28 811.7199 899.5222 -377.8599 +#> f_nlme_dfop_sfo_obs 2 29 784.1304 875.0685 -363.0652 1 vs 2 29.5895 <.0001 +#> f_nlme_dfop_sfo_tc 3 29 791.9981 882.9362 -366.9990
    # }
    diff --git a/docs/dev/reference/nobs.mkinfit.html b/docs/dev/reference/nobs.mkinfit.html index 06575d54..621eb622 100644 --- a/docs/dev/reference/nobs.mkinfit.html +++ b/docs/dev/reference/nobs.mkinfit.html @@ -72,7 +72,7 @@ mkin - 0.9.50.3 + 0.9.50.4 @@ -120,7 +120,7 @@
  • - + @@ -139,7 +139,7 @@

    Number of observations on which an mkinfit object was fitted

    - Source: R/nobs.mkinfit.R + Source: R/nobs.mkinfit.R
    @@ -148,7 +148,7 @@ 
    # S3 method for mkinfit
-nobs(object, ...)
    +nobs(object, ...)

    Arguments

    @@ -182,7 +182,7 @@
    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.6.1.

    diff --git a/docs/dev/reference/plot.mixed.mmkin-2.png b/docs/dev/reference/plot.mixed.mmkin-2.png index c0d67204..0821dcca 100644 Binary files a/docs/dev/reference/plot.mixed.mmkin-2.png and b/docs/dev/reference/plot.mixed.mmkin-2.png differ diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html index 6ed7cbba..492e289c 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -264,8 +264,8 @@ corresponding model prediction lines for the different datasets.

    ds <- lapply(experimental_data_for_UBA_2019[6:10],
  function(x) x$data[c("name", "time", "value")])
 names(ds) <- paste0("ds ", 6:10)
-dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
-  A1 = mkinsub("SFO"), quiet = TRUE)
+dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
+  A1 = mkinsub("SFO"), quiet = TRUE)
 # \dontrun{
 f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE)
 plot(f[, 3:4], standardized = TRUE)
@@ -273,14 +273,14 @@ corresponding model prediction lines for the different datasets.
    
 # For this fit we need to increase pnlsMaxiter, and we increase the
 # tolerance in order to speed up the fit for this example evaluation
 f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3))
-plot(f_nlme)
+
    #> Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    #> Warning: Iteration 2, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
    plot(f_nlme)
 
    
 f_saem <- saem(f)
 
    #> Running main SAEM algorithm
-#> [1] "Thu Nov 19 14:51:14 2020"
+#> [1] "Mon Nov 30 15:52:45 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Thu Nov 19 14:51:24 2020"
    plot(f_saem)
+#> [1] "Mon Nov 30 15:52:54 2020"
    plot(f_saem)
 
    # }
    diff --git a/docs/dev/reference/plot.mkinfit.html b/docs/dev/reference/plot.mkinfit.html index 3a05a02d..c7eda78f 100644 --- a/docs/dev/reference/plot.mkinfit.html +++ b/docs/dev/reference/plot.mkinfit.html @@ -340,9 +340,9 @@ latex is being used for the formatting of the chi2 error level, if # One parent compound, one metabolite, both single first order, path from# parent to sink included# \dontrun{ -SFO_SFO<-mkinmod(parent =mkinsub("SFO", "m1", full ="Parent"), - m1 =mkinsub("SFO", full ="Metabolite M1")) -
    #> Successfully compiled differential equation model from auto-generated C code.
    fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) +SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"), + m1 = mkinsub("SFO", full = "Metabolite M1" )) +
    #> Temporary DLL for differentials generated and loaded
    fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
    #> Warning: Observations with value of zero were removed from the data
    fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc")
    #> Warning: Observations with value of zero were removed from the data
    plot(fit)
    plot_res(fit) diff --git a/docs/dev/reference/plot.nafta.html b/docs/dev/reference/plot.nafta.html index dab84955..9fc59f94 100644 --- a/docs/dev/reference/plot.nafta.html +++ b/docs/dev/reference/plot.nafta.html @@ -73,7 +73,7 @@ function (SFO, then IORE, then DFOP)." /> mkin - 0.9.50.3 + 0.9.50.4
    @@ -121,7 +121,7 @@ function (SFO, then IORE, then DFOP)." />
    • - + @@ -140,7 +140,7 @@ function (SFO, then IORE, then DFOP)." />

      Plot the results of the three models used in the NAFTA scheme.

      - Source: R/nafta.R + Source: R/nafta.R
      @@ -150,7 +150,7 @@ function (SFO, then IORE, then DFOP).

      # S3 method for nafta
-plot(x, legend = FALSE, main = "auto", ...)
      +plot(x, legend = FALSE, main = "auto", ...)

      Arguments

    @@ -179,6 +179,9 @@ function (SFO, then IORE, then DFOP).

    Details

    Calls plot.mmkin.

    +

    Author

    + +

    Johannes Ranke

    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.6.1.

    diff --git a/docs/dev/reference/plot.nlme.mmkin-1.png b/docs/dev/reference/plot.nlme.mmkin-1.png deleted file mode 100644 index 5cb33214..00000000 Binary files a/docs/dev/reference/plot.nlme.mmkin-1.png and /dev/null differ diff --git a/docs/dev/reference/plot.nlme.mmkin-2.png b/docs/dev/reference/plot.nlme.mmkin-2.png deleted file mode 100644 index c0d67204..00000000 Binary files a/docs/dev/reference/plot.nlme.mmkin-2.png and /dev/null differ diff --git a/docs/dev/reference/plot.nlme.mmkin.html b/docs/dev/reference/plot.nlme.mmkin.html deleted file mode 100644 index 8f5f85f7..00000000 --- a/docs/dev/reference/plot.nlme.mmkin.html +++ /dev/null @@ -1,302 +0,0 @@ - - - - - - - - -Plot a fitted nonlinear mixed model obtained via an mmkin row object — plot.nlme.mmkin • mkin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -
    - - - - -
    - -
    -
    -
    -

    Plot a fitted nonlinear mixed model obtained via an mmkin row object

    - Source: R/plot.nlme.mmkin.R - -
    - -
    -

    Plot a fitted nonlinear mixed model obtained via an mmkin row object

    -
    - - 
    # S3 method for nlme.mmkin
-plot(
-  x,
-  i = 1:ncol(x$mmkin),
-  obs_vars = names(x$mkinmod$map),
-  standardized = TRUE,
-  xlab = "Time",
-  xlim = range(x$data$time),
-  resplot = c("predicted", "time"),
-  ymax = "auto",
-  maxabs = "auto",
-  ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
-  nrow.legend = ceiling((length(i) + 1)/ncol.legend),
-  rel.height.legend = 0.03 + 0.08 * nrow.legend,
-  rel.height.bottom = 1.1,
-  pch_ds = 1:length(i),
-  col_ds = pch_ds + 1,
-  lty_ds = col_ds,
-  frame = TRUE
-)
    - -

    Arguments

    -
    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    x

    An object of class nlme.mmkin

    i

    A numeric index to select datasets for which to plot the nlme fit, -in case plots get too large

    obs_vars

    A character vector of names of the observed variables for -which the data and the model should be plotted. Defauls to all observed -variables in the model.

    standardized

    Should the residuals be standardized? Only takes effect if -resplot = "time".

    xlab

    Label for the x axis.

    xlim

    Plot range in x direction.

    resplot

    Should the residuals plotted against time or against -predicted values?

    ymax

    Vector of maximum y axis values

    maxabs

    Maximum absolute value of the residuals. This is used for the -scaling of the y axis and defaults to "auto".

    ncol.legend

    Number of columns to use in the legend

    nrow.legend

    Number of rows to use in the legend

    rel.height.legend

    The relative height of the legend shown on top

    rel.height.bottom

    The relative height of the bottom plot row

    pch_ds

    Symbols to be used for plotting the data.

    col_ds

    Colors used for plotting the observed data and the -corresponding model prediction lines for the different datasets.

    lty_ds

    Line types to be used for the model predictions.

    frame

    Should a frame be drawn around the plots?

    - -

    Value

    - -

    The function is called for its side effect.

    -

    Author

    - -

    Johannes Ranke

    - -

    Examples

    - 
    ds <- lapply(experimental_data_for_UBA_2019[6:10],
- function(x) x$data[c("name", "time", "value")])
-names(ds) <- paste0("ds ", 6:10)
-dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
-  A1 = mkinsub("SFO"), quiet = TRUE)
-# \dontrun{
-f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE)
-plot(f[, 3:4], standardized = TRUE)
-
    
-library(nlme)
-# For this fit we need to increase pnlsMaxiter, and we increase the
-# tolerance in order to speed up the fit for this example evaluation
-f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3))
-plot(f_nlme)
-
    # }
-
    - - - - - -
    -
    -

    Developed by Johannes Ranke.

    -
    - -
    -

    Site built with pkgdown 1.6.1.

    -
    - -
    - - - - - - - - - diff --git a/docs/dev/reference/plot.saem.mmkin-1.png b/docs/dev/reference/plot.saem.mmkin-1.png deleted file mode 100644 index 5cb33214..00000000 Binary files a/docs/dev/reference/plot.saem.mmkin-1.png and /dev/null differ diff --git a/docs/dev/reference/plot.saem.mmkin-2.png b/docs/dev/reference/plot.saem.mmkin-2.png deleted file mode 100644 index 67058e6c..00000000 Binary files a/docs/dev/reference/plot.saem.mmkin-2.png and /dev/null differ diff --git a/docs/dev/reference/plot.saem.mmkin.html b/docs/dev/reference/plot.saem.mmkin.html deleted file mode 100644 index d0790a98..00000000 --- a/docs/dev/reference/plot.saem.mmkin.html +++ /dev/null @@ -1,308 +0,0 @@ - - - - - - - - -Plot an saem fitted nonlinear mixed model obtained via an mmkin row object — plot.saem.mmkin • mkin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -
    - - - - -
    - -
    -
    -
    -

    Plot an saem fitted nonlinear mixed model obtained via an mmkin row object

    - Source: R/plot.saem.mmkin.R - -
    - -
    -

    Plot an saem fitted nonlinear mixed model obtained via an mmkin row object

    -
    - - 
    # S3 method for saem.mmkin
-plot(
-  x,
-  i = 1:ncol(x$mmkin),
-  obs_vars = names(x$mkinmod$map),
-  standardized = TRUE,
-  xlab = "Time",
-  xlim = range(x$data$time),
-  resplot = c("predicted", "time"),
-  ymax = "auto",
-  maxabs = "auto",
-  ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
-  nrow.legend = ceiling((length(i) + 1)/ncol.legend),
-  rel.height.legend = 0.03 + 0.08 * nrow.legend,
-  rel.height.bottom = 1.1,
-  pch_ds = 1:length(i),
-  col_ds = pch_ds + 1,
-  lty_ds = col_ds,
-  frame = TRUE,
-  ...
-)
    - -

    Arguments

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    x

    An object of class saem.mmkin

    i

    A numeric index to select datasets for which to plot the saem fit, -in case plots get too large

    obs_vars

    A character vector of names of the observed variables for -which the data and the model should be plotted. Defauls to all observed -variables in the model.

    standardized

    Should the residuals be standardized? Only takes effect if -resplot = "time".

    xlab

    Label for the x axis.

    xlim

    Plot range in x direction.

    resplot

    Should the residuals plotted against time or against -predicted values?

    ymax

    Vector of maximum y axis values

    maxabs

    Maximum absolute value of the residuals. This is used for the -scaling of the y axis and defaults to "auto".

    ncol.legend

    Number of columns to use in the legend

    nrow.legend

    Number of rows to use in the legend

    rel.height.legend

    The relative height of the legend shown on top

    rel.height.bottom

    The relative height of the bottom plot row

    pch_ds

    Symbols to be used for plotting the data.

    col_ds

    Colors used for plotting the observed data and the -corresponding model prediction lines for the different datasets.

    lty_ds

    Line types to be used for the model predictions.

    frame

    Should a frame be drawn around the plots?

    ...

    Further arguments passed to plot.

    - -

    Value

    - -

    The function is called for its side effect.

    -

    Author

    - -

    Johannes Ranke

    - -

    Examples

    - 
    ds <- lapply(experimental_data_for_UBA_2019[6:10],
- function(x) x$data[c("name", "time", "value")])
-names(ds) <- paste0("ds ", 6:10)
-dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
-  A1 = mkinsub("SFO"), quiet = TRUE)
-# \dontrun{
-f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE)
-plot(f[, 3:4], standardized = TRUE)
-
    
-f_saem <- saem(f)
-
    #> Running main SAEM algorithm
-#> [1] "Mon Nov  9 14:21:22 2020"
-#> ....
-#>     Minimisation finished
-#> [1] "Mon Nov  9 14:21:31 2020"
    plot(f_saem)
-
    # }
-
    -
    - -
    - - -
    -
    -

    Developed by Johannes Ranke.

    -
    - -
    -

    Site built with pkgdown 1.6.1.

    -
    - -
    -
    - - - - - - - - diff --git a/docs/dev/reference/plot_mixed-1.png b/docs/dev/reference/plot_mixed-1.png deleted file mode 100644 index 5cb33214..00000000 Binary files a/docs/dev/reference/plot_mixed-1.png and /dev/null differ diff --git a/docs/dev/reference/plot_mixed-2.png b/docs/dev/reference/plot_mixed-2.png deleted file mode 100644 index c0d67204..00000000 Binary files a/docs/dev/reference/plot_mixed-2.png and /dev/null differ diff --git a/docs/dev/reference/plot_mixed-3.png b/docs/dev/reference/plot_mixed-3.png deleted file mode 100644 index 67058e6c..00000000 Binary files a/docs/dev/reference/plot_mixed-3.png and /dev/null differ diff --git a/docs/dev/reference/plot_mixed.html b/docs/dev/reference/plot_mixed.html deleted file mode 100644 index b5b3ba49..00000000 --- a/docs/dev/reference/plot_mixed.html +++ /dev/null @@ -1,336 +0,0 @@ - - - - - - - - -Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot_mixed • mkin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -
    - - - - -
    - -
    -
    -
    -

    Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object

    - Source: R/plot_mixed.R - -
    - -
    -

    Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object

    -
    - - 
    # S3 method for saem.mmkin
-plot(
-  x,
-  i = 1:ncol(x$mmkin),
-  obs_vars = names(x$mkinmod$map),
-  standardized = TRUE,
-  xlab = "Time",
-  xlim = range(x$data$time),
-  resplot = c("predicted", "time"),
-  ymax = "auto",
-  maxabs = "auto",
-  ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
-  nrow.legend = ceiling((length(i) + 1)/ncol.legend),
-  rel.height.legend = 0.03 + 0.08 * nrow.legend,
-  rel.height.bottom = 1.1,
-  pch_ds = 1:length(i),
-  col_ds = pch_ds + 1,
-  lty_ds = col_ds,
-  frame = TRUE,
-  ...
-)
-
-# S3 method for nlme.mmkin
-plot(
-  x,
-  i = 1:ncol(x$mmkin),
-  obs_vars = names(x$mkinmod$map),
-  standardized = TRUE,
-  xlab = "Time",
-  xlim = range(x$data$time),
-  resplot = c("predicted", "time"),
-  ymax = "auto",
-  maxabs = "auto",
-  ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),
-  nrow.legend = ceiling((length(i) + 1)/ncol.legend),
-  rel.height.legend = 0.03 + 0.08 * nrow.legend,
-  rel.height.bottom = 1.1,
-  pch_ds = 1:length(i),
-  col_ds = pch_ds + 1,
-  lty_ds = col_ds,
-  frame = TRUE,
-  ...
-)
    - -

    Arguments

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    x

    An object of class saem.mmkin or nlme.mmkin

    i

    A numeric index to select datasets for which to plot the individual predictions, -in case plots get too large

    obs_vars

    A character vector of names of the observed variables for -which the data and the model should be plotted. Defauls to all observed -variables in the model.

    standardized

    Should the residuals be standardized? Only takes effect if -resplot = "time".

    xlab

    Label for the x axis.

    xlim

    Plot range in x direction.

    resplot

    Should the residuals plotted against time or against -predicted values?

    ymax

    Vector of maximum y axis values

    maxabs

    Maximum absolute value of the residuals. This is used for the -scaling of the y axis and defaults to "auto".

    ncol.legend

    Number of columns to use in the legend

    nrow.legend

    Number of rows to use in the legend

    rel.height.legend

    The relative height of the legend shown on top

    rel.height.bottom

    The relative height of the bottom plot row

    pch_ds

    Symbols to be used for plotting the data.

    col_ds

    Colors used for plotting the observed data and the -corresponding model prediction lines for the different datasets.

    lty_ds

    Line types to be used for the model predictions.

    frame

    Should a frame be drawn around the plots?

    ...

    Further arguments passed to plot.

    - -

    Value

    - -

    The functions are called for their side effect.

    -

    Author

    - -

    Johannes Ranke

    - -

    Examples

    - 
    ds <- lapply(experimental_data_for_UBA_2019[6:10],
- function(x) x$data[c("name", "time", "value")])
-names(ds) <- paste0("ds ", 6:10)
-dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
-  A1 = mkinsub("SFO"), quiet = TRUE)
-# \dontrun{
-f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE)
-plot(f[, 3:4], standardized = TRUE)
-
    
-library(nlme)
-# For this fit we need to increase pnlsMaxiter, and we increase the
-# tolerance in order to speed up the fit for this example evaluation
-f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3))
-plot(f_nlme)
-
    
-f_saem <- saem(f)
-
    #> Running main SAEM algorithm
-#> [1] "Mon Nov  9 16:07:05 2020"
-#> ....
-#>     Minimisation finished
-#> [1] "Mon Nov  9 16:07:14 2020"
    plot(f_saem)
-
    # }
-
    -
    - -
    - - -
    -
    -

    Developed by Johannes Ranke.

    -
    - -
    -

    Site built with pkgdown 1.6.1.

    -
    - -
    -
    - - - - - - - - diff --git a/docs/dev/reference/print.mkinds.html b/docs/dev/reference/print.mkinds.html deleted file mode 100644 index a8c0d808..00000000 --- a/docs/dev/reference/print.mkinds.html +++ /dev/null @@ -1,194 +0,0 @@ - - - - - - - - -Print mkinds objects — print.mkinds • mkin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -
    - - - - -
    - -
    -
    -
    -

    Print mkinds objects

    - Source: R/mkinds.R - -
    - -
    -

    Print mkinds objects

    -
    - - 
    # S3 method for mkinds
-print(x, ...)
    - -

    Arguments

    - - - - - - - - - - -
    x

    An mkinds object.

    ...

    Not used.

    - - -
    - -
    - - -
    -
    -

    Developed by Johannes Ranke.

    -
    - -
    -

    Site built with pkgdown 1.5.1.

    -
    - -
    -
    - - - - - - - - diff --git a/docs/dev/reference/print.mkinmod.html b/docs/dev/reference/print.mkinmod.html deleted file mode 100644 index fd0f624a..00000000 --- a/docs/dev/reference/print.mkinmod.html +++ /dev/null @@ -1,217 +0,0 @@ - - - - - - - - -Print mkinmod objects — print.mkinmod • mkin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    -
    - - - - -
    - -
    -
    -
    -

    Print mkinmod objects

    - Source: R/mkinmod.R - -
    - -
    -

    Print mkinmod objects in a way that the user finds his way to get to its -components.

    -
    - - 
    # S3 method for mkinmod
-print(x, ...)
    - -

    Arguments

    - - - - - - - - - - -
    x

    An mkinmod object.

    ...

    Not used.

    - - -

    Examples

    - 
    
-  m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
-                             M1 = list(type = "SFO", to = "M2"),
-                             M2 = list(type = "SFO"), use_of_ff = "max")
    #> Successfully compiled differential equation model from auto-generated C code.
    
-  print(m_synth_SFO_lin)
    #> <mkinmod> model generated with
-#> Use of formation fractions $use_of_ff: max 
-#> Specification $spec:
-#> $parent
-#> $type: SFO; $to: M1; $sink: TRUE
-#> $M1
-#> $type: SFO; $to: M2; $sink: TRUE
-#> $M2
-#> $type: SFO; $sink: TRUE
-#> Coefficient matrix $coefmat available
-#> Compiled model $cf available
-#> Differential equations:
-#> d_parent/dt = - k_parent * parent
-#> d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1
-#> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2
    
-
    -
    - -
    - - -
    -
    -

    Developed by Johannes Ranke.

    -
    - -
    -

    Site built with pkgdown 1.5.1.

    -
    - -
    -
    - - - - - - - - diff --git a/docs/dev/reference/residuals.mkinfit.html b/docs/dev/reference/residuals.mkinfit.html index 89552630..95114dae 100644 --- a/docs/dev/reference/residuals.mkinfit.html +++ b/docs/dev/reference/residuals.mkinfit.html @@ -72,7 +72,7 @@ mkin - 0.9.50.3 + 0.9.50.4 @@ -120,7 +120,7 @@
  • - + @@ -139,7 +139,7 @@

    Extract residuals from an mkinfit model

    - Source: R/residuals.mkinfit.R + Source: R/residuals.mkinfit.R
    @@ -148,7 +148,7 @@ 
    # S3 method for mkinfit
-residuals(object, standardized = FALSE, ...)
    +residuals(object, standardized = FALSE, ...)

    Arguments

    @@ -170,10 +170,12 @@ standard deviation obtained from the fitted error model?

    Examples

    - 
    f <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE)
-residuals(f)
    #> [1]  0.09726306 -0.13912135 -0.15351176  0.73388319 -0.08657030 -0.93204730
-#> [7] -0.03269102  1.45347805 -0.88423710
    residuals(f, standardized = TRUE)
    #> [1]  0.13969820 -0.19981894 -0.22048777  1.05407086 -0.12434027 -1.33869248
-#> [7] -0.04695387  2.08761953 -1.27002305
    + 
    f <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE)
+residuals(f)
+
    #> [1]  0.09726374 -0.13912142 -0.15351210  0.73388322 -0.08657004 -0.93204702
+#> [7] -0.03269080  1.45347823 -0.88423697
    residuals(f, standardized = TRUE)
+
    #> [1]  0.13969917 -0.19981904 -0.22048826  1.05407091 -0.12433989 -1.33869208
+#> [7] -0.04695354  2.08761977 -1.27002287
    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.6.1.

    diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 948e1378..e4ebf5d9 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -247,27 +247,27 @@ using mmkin.

    state.ini =c(parent =100), fixed_initials ="parent", quiet =TRUE)f_saem_p0_fixed<-saem(f_mmkin_parent_p0_fixed)
    #> Running main SAEM algorithm -#> [1] "Thu Nov 19 14:51:31 2020" +#> [1] "Mon Nov 30 15:53:02 2020" #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:51:33 2020"
    +#> [1] "Mon Nov 30 15:53:04 2020"
    f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE) f_saem_sfo <- saem(f_mmkin_parent["SFO", ])
    #> Running main SAEM algorithm -#> [1] "Thu Nov 19 14:51:34 2020" +#> [1] "Mon Nov 30 15:53:05 2020" #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:51:36 2020"
    f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) +#> [1] "Mon Nov 30 15:53:07 2020"
    f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
    #> Running main SAEM algorithm -#> [1] "Thu Nov 19 14:51:36 2020" +#> [1] "Mon Nov 30 15:53:07 2020" #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:51:38 2020"
    f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) +#> [1] "Mon Nov 30 15:53:09 2020"
    f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
    #> Running main SAEM algorithm -#> [1] "Thu Nov 19 14:51:39 2020" +#> [1] "Mon Nov 30 15:53:10 2020" #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:51:42 2020"
    +#> [1] "Mon Nov 30 15:53:13 2020"
    # The returned saem.mmkin object contains an SaemixObject, therefore we can use # functions from saemix library(saemix) @@ -313,20 +313,20 @@ using mmkin.

    f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc") f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ])
    #> Running main SAEM algorithm -#> [1] "Thu Nov 19 14:51:44 2020" +#> [1] "Mon Nov 30 15:53:15 2020" #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:51:49 2020"
    compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)) +#> [1] "Mon Nov 30 15:53:20 2020"
    compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so))
    #> Likelihoods computed by importance sampling
    #> AIC BIC #> 1 467.7096 464.9757 #> 2 469.5208 466.3963
    -sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), - A1 = mkinsub("SFO")) -
    #> Successfully compiled differential equation model from auto-generated C code.
    fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"), - A1 = mkinsub("SFO")) -
    #> Successfully compiled differential equation model from auto-generated C code.
    dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), - A1 = mkinsub("SFO")) -
    #> Successfully compiled differential equation model from auto-generated C code.
    # The following fit uses analytical solutions for SFO-SFO and DFOP-SFO, +sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), + A1 = mkinsub("SFO")) +
    #> Temporary DLL for differentials generated and loaded
    fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"), + A1 = mkinsub("SFO")) +
    #> Temporary DLL for differentials generated and loaded
    dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), + A1 = mkinsub("SFO")) +
    #> Temporary DLL for differentials generated and loaded
    # The following fit uses analytical solutions for SFO-SFO and DFOP-SFO, # and compiled ODEs for FOMC that are much slower f_mmkin <- mmkin(list( "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo), @@ -336,15 +336,15 @@ using mmkin.

    # solutions written for mkin this took around four minutes f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ])
    #> Running main SAEM algorithm -#> [1] "Thu Nov 19 14:51:52 2020" +#> [1] "Mon Nov 30 15:53:23 2020" #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:51:57 2020"
    f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ]) +#> [1] "Mon Nov 30 15:53:28 2020"
    f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])
    #> Running main SAEM algorithm -#> [1] "Thu Nov 19 14:51:57 2020" +#> [1] "Mon Nov 30 15:53:29 2020" #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:52:06 2020"
    # We can use print, plot and summary methods to check the results +#> [1] "Mon Nov 30 15:53:38 2020"
    # We can use print, plot and summary methods to check the results print(f_saem_dfop_sfo)
    #> Kinetic nonlinear mixed-effects model fit by SAEM #> Structural model: @@ -387,8 +387,8 @@ using mmkin.

    #> saemix version used for fitting: 3.1.9000 #> mkin version used for pre-fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Thu Nov 19 14:52:07 2020 -#> Date of summary: Thu Nov 19 14:52:07 2020 +#> Date of fit: Mon Nov 30 15:53:38 2020 +#> Date of summary: Mon Nov 30 15:53:39 2020 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -403,7 +403,7 @@ using mmkin.

    #> #> Model predictions using solution type analytical #> -#> Fitted in 10.034 s using 300, 100 iterations +#> Fitted in 9.963 s using 300, 100 iterations #> #> Variance model: Constant variance #> @@ -647,7 +647,7 @@ using mmkin.

    # analytical solution. Using 10 cores it is slower instead of faster f_saem_fomc <- saem(f_mmkin["FOMC-SFO", ], cores = 1)
    #> Running main SAEM algorithm -#> [1] "Thu Nov 19 14:52:08 2020" +#> [1] "Mon Nov 30 15:53:39 2020" #> DLSODA- At current T (=R1), MXSTEP (=I1) steps #> taken on this call before reaching TOUT #> In above message, I1 = 5000 @@ -667,7 +667,7 @@ using mmkin.

    #> #> .... #> Minimisation finished -#> [1] "Thu Nov 19 14:59:05 2020"
    plot(f_saem_fomc) +#> [1] "Mon Nov 30 16:00:45 2020"
    plot(f_saem_fomc)
    # }
    diff --git a/docs/dev/reference/saemix-1.png b/docs/dev/reference/saemix-1.png deleted file mode 100644 index e5e01249..00000000 Binary files a/docs/dev/reference/saemix-1.png and /dev/null differ diff --git a/docs/dev/reference/saemix-10.png b/docs/dev/reference/saemix-10.png deleted file mode 100644 index 19aa6cfb..00000000 Binary files a/docs/dev/reference/saemix-10.png and /dev/null differ diff --git a/docs/dev/reference/saemix-11.png b/docs/dev/reference/saemix-11.png deleted file mode 100644 index 454b9be0..00000000 Binary files a/docs/dev/reference/saemix-11.png and /dev/null differ diff --git a/docs/dev/reference/saemix-12.png b/docs/dev/reference/saemix-12.png deleted file mode 100644 index c8b0fd71..00000000 Binary files a/docs/dev/reference/saemix-12.png and /dev/null differ diff --git a/docs/dev/reference/saemix-13.png b/docs/dev/reference/saemix-13.png deleted file mode 100644 index e3538cb6..00000000 Binary files a/docs/dev/reference/saemix-13.png and /dev/null differ diff --git a/docs/dev/reference/saemix-2.png b/docs/dev/reference/saemix-2.png deleted file mode 100644 index 4bc3d0bc..00000000 Binary files a/docs/dev/reference/saemix-2.png and /dev/null differ diff --git a/docs/dev/reference/saemix-3.png b/docs/dev/reference/saemix-3.png deleted file mode 100644 index be6b0acb..00000000 Binary files a/docs/dev/reference/saemix-3.png and /dev/null differ diff --git a/docs/dev/reference/saemix-4.png b/docs/dev/reference/saemix-4.png deleted file mode 100644 index fa4db812..00000000 Binary files a/docs/dev/reference/saemix-4.png and /dev/null differ diff --git a/docs/dev/reference/saemix-5.png b/docs/dev/reference/saemix-5.png deleted file mode 100644 index 2b7b8f46..00000000 Binary files a/docs/dev/reference/saemix-5.png and /dev/null differ diff --git a/docs/dev/reference/saemix-6.png b/docs/dev/reference/saemix-6.png deleted file mode 100644 index af14b43b..00000000 Binary files a/docs/dev/reference/saemix-6.png and /dev/null differ diff --git a/docs/dev/reference/saemix-7.png b/docs/dev/reference/saemix-7.png deleted file mode 100644 index e3538cb6..00000000 Binary files a/docs/dev/reference/saemix-7.png and /dev/null differ diff --git a/docs/dev/reference/saemix-8.png b/docs/dev/reference/saemix-8.png deleted file mode 100644 index 35cc6c6e..00000000 Binary files a/docs/dev/reference/saemix-8.png and /dev/null differ diff --git a/docs/dev/reference/saemix-9.png b/docs/dev/reference/saemix-9.png deleted file mode 100644 index e3538cb6..00000000 Binary files a/docs/dev/reference/saemix-9.png and /dev/null differ diff --git a/docs/dev/reference/schaefer07_complex_case-1.png b/docs/dev/reference/schaefer07_complex_case-1.png index 7cf7484d..16e657dd 100644 Binary files a/docs/dev/reference/schaefer07_complex_case-1.png and b/docs/dev/reference/schaefer07_complex_case-1.png differ diff --git a/docs/dev/reference/schaefer07_complex_case.html b/docs/dev/reference/schaefer07_complex_case.html index 308db2db..83555b99 100644 --- a/docs/dev/reference/schaefer07_complex_case.html +++ b/docs/dev/reference/schaefer07_complex_case.html @@ -74,7 +74,7 @@ mkin - 0.9.50.3 + 0.9.50.4 @@ -122,7 +122,7 @@
    • - + @@ -151,12 +151,12 @@ The results from the fitting are also included.

      - 
      schaefer07_complex_case
      + 
      schaefer07_complex_case

      Format

      -

      The data set is a data frame with 8 observations on the following 6 variables.

      +

      The data set is a data frame with 8 observations on the following 6 variables.

      time

      a numeric vector

      parent

      a numeric vector

      A1

      a numeric vector

      @@ -173,28 +173,32 @@ Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.

      Examples

      - 
      data <- mkin_wide_to_long(schaefer07_complex_case, time = "time")
-model <- mkinmod(
-  parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),
-  A1 = list(type = "SFO", to = "A2"),
-  B1 = list(type = "SFO"),
-  C1 = list(type = "SFO"),
-  A2 = list(type = "SFO"), use_of_ff = "max")
      #> Successfully compiled differential equation model from auto-generated C code.
        # \dontrun{
-    fit <- mkinfit(model, data, quiet = TRUE)
-    plot(fit)
          endpoints(fit)
      #> $ff
+    
      data <- mkin_wide_to_long(schaefer07_complex_case, time = "time")
+model <- mkinmod(
+  parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),
+  A1 = list(type = "SFO", to = "A2"),
+  B1 = list(type = "SFO"),
+  C1 = list(type = "SFO"),
+  A2 = list(type = "SFO"), use_of_ff = "max")
+
      #> Temporary DLL for differentials generated and loaded
        # \dontrun{
+    fit <- mkinfit(model, data, quiet = TRUE)
+    plot(fit)
+
          endpoints(fit)
+
      #> $ff
 #>   parent_A1   parent_B1   parent_C1 parent_sink       A1_A2     A1_sink 
-#>   0.3809619   0.1954667   0.4235714   0.0000000   0.4479609   0.5520391 
+#>   0.3809620   0.1954665   0.4235715   0.0000000   0.4479662   0.5520338 
 #> 
 #> $distimes
 #>            DT50      DT90
 #> parent 13.95078  46.34350
-#> A1     49.75343 165.27733
-#> B1     37.26907 123.80517
+#> A1     49.75343 165.27731
+#> B1     37.26912 123.80533
 #> C1     11.23131  37.30959
-#> A2     28.50638  94.69614
+#> A2     28.50569  94.69386
 #> 
        # }
  # Compare with the results obtained in the original publication
- print(schaefer07_complex_results)
      #>         compound          parameter  KinGUI ModelMaker deviation
+ print(schaefer07_complex_results)
+
      #>         compound          parameter  KinGUI ModelMaker deviation
 #> 1         parent   degradation rate  0.0496     0.0506       2.0
 #> 2         parent               DT50 13.9900    13.6900       2.2
 #> 3  metabolite A1 formation fraction  0.3803     0.3696       2.9
@@ -224,7 +228,7 @@
 
      
 
 
      
-  
      Site built with pkgdown 1.5.1.
      
+  
      Site built with pkgdown 1.6.1.
      
 
      
 
       
diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html
index cd183cbc..f314dfa8 100644
--- a/docs/dev/reference/summary.mkinfit.html
+++ b/docs/dev/reference/summary.mkinfit.html
@@ -235,18 +235,18 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
 
     
      Examples
      
     
      
-  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
+  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
 
      #> mkin version used for fitting:    0.9.50.4 
 #> R version used for fitting:       4.0.3 
-#> Date of fit:     Thu Nov 19 14:59:41 2020 
-#> Date of summary: Thu Nov 19 14:59:41 2020 
+#> Date of fit:     Mon Nov 30 16:01:20 2020 
+#> Date of summary: Mon Nov 30 16:01:20 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 131 model solutions performed in 0.033 s
+#> Fitted using 131 model solutions performed in 0.028 s
 #> 
 #> Error model: Constant variance 
 #> 
diff --git a/docs/dev/reference/summary.nlme.mmkin.html b/docs/dev/reference/summary.nlme.mmkin.html
index d016796e..2aeadc46 100644
--- a/docs/dev/reference/summary.nlme.mmkin.html
+++ b/docs/dev/reference/summary.nlme.mmkin.html
@@ -239,7 +239,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
      
 k_in_pop <- log(2) / dt50_sfo_in_pop
 set.seed(1234)
 k_in <- rlnorm(5, log(k_in_pop), 0.5)
-SFO <- mkinmod(parent = mkinsub("SFO"))
+SFO <- mkinmod(parent = mkinsub("SFO"))
 
 pred_sfo <- function(k) {
   mkinpredict(SFO,
@@ -251,6 +251,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
      
 ds_sfo_mean <- lapply(k_in, pred_sfo)
 names(ds_sfo_mean) <- paste("ds", 1:5)
 
+set.seed(12345)
 ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) {
   add_err(ds,
     sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2),
@@ -260,13 +261,14 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
      
 # Evaluate using mmkin and nlme
 library(nlme)
 f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1)
-f_nlme <- nlme(f_mmkin)
-
      #> Warning: Iteration 3, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
      summary(f_nlme, data = TRUE)
+
      #> Warning: Optimisation did not converge:
+#> iteration limit reached without convergence (10)
      f_nlme <- nlme(f_mmkin)
+
      #> Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
      summary(f_nlme, data = TRUE)
 
      #> nlme version used for fitting:      3.1.150.1 
 #> mkin version used for pre-fitting:  0.9.50.4 
 #> R version used for fitting:         4.0.3 
-#> Date of fit:     Thu Nov 19 14:59:43 2020 
-#> Date of summary: Thu Nov 19 14:59:43 2020 
+#> Date of fit:     Mon Nov 30 16:01:23 2020 
+#> Date of summary: Mon Nov 30 16:01:23 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -276,146 +278,148 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
      
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted in 0.681 s using 5 iterations
+#> Fitted in 0.996 s using 6 iterations
 #> 
 #> Variance model: Two-component variance function 
 #> 
 #> Mean of starting values for individual parameters:
 #>     parent_0 log_k_parent 
-#>    97.849556    -4.455036 
+#>   101.568773    -4.454103 
 #> 
 #> Fixed degradation parameter values:
 #> None
 #> 
 #> Results:
 #> 
-#>       AIC      BIC   logLik
-#>   555.792 570.7908 -271.896
+#>        AIC      BIC    logLik
+#>   586.4159 603.9145 -286.2079
 #> 
 #> Optimised, transformed parameters with symmetric confidence intervals:
-#>               lower   est.   upper
-#> parent_0     94.701 97.763 100.826
-#> log_k_parent -5.008 -4.462  -3.916
+#>               lower    est.   upper
+#> parent_0     99.360 101.593 103.825
+#> log_k_parent -4.979  -4.451  -3.924
 #> 
 #> Correlation: 
 #>              prnt_0
-#> log_k_parent 0.024 
+#> log_k_parent 0.155 
 #> 
 #> Random effects:
 #>  Formula: list(parent_0 ~ 1, log_k_parent ~ 1)
 #>  Level: ds
-#>  Structure: Diagonal
-#>         parent_0 log_k_parent Residual
-#> StdDev:    2.898       0.6119        1
+#>  Structure: General positive-definite, Log-Cholesky parametrization
+#>              StdDev    Corr  
+#> parent_0     0.2624248 prnt_0
+#> log_k_parent 0.5907146 0.999 
+#> Residual     1.0000000       
 #> 
 #> Variance function:
 #>  Structure: Constant plus proportion of variance covariate
 #>  Formula: ~fitted(.) 
 #>  Parameter estimates:
-#>      const       prop 
-#> 1.55075176 0.05680853 
+#>       const        prop 
+#> 6.56706e-24 7.89583e-02 
 #> 
 #> Backtransformed parameters with asymmetric confidence intervals:
-#>              lower     est.     upper
-#> parent_0 94.701336 97.76345 100.82556
-#> k_parent  0.006687  0.01154   0.01992
+#>              lower      est.     upper
+#> parent_0 99.360213 101.59280 103.82539
+#> k_parent  0.006883   0.01166   0.01976
 #> 
 #> Estimated disappearance times:
 #>         DT50  DT90
-#> parent 60.05 199.5
+#> parent 59.44 197.4
 #> 
 #> Data:
-#>    ds   name time observed predicted residual   std standardized
-#>  ds 1 parent    0    103.6     97.42  6.17540 5.748     1.074413
-#>  ds 1 parent    0     95.9     97.42 -1.52460 5.748    -0.265253
-#>  ds 1 parent    1     95.4     96.72 -1.31719 5.709    -0.230721
-#>  ds 1 parent    1     95.3     96.72 -1.41719 5.709    -0.248237
-#>  ds 1 parent    3     91.6     95.32 -3.71774 5.633    -0.660046
-#>  ds 1 parent    3     94.5     95.32 -0.81774 5.633    -0.145181
-#>  ds 1 parent    7     88.1     92.58 -4.47930 5.483    -0.816920
-#>  ds 1 parent    7     89.6     92.58 -2.97930 5.483    -0.543355
-#>  ds 1 parent   14     90.3     87.97  2.32502 5.233     0.444318
-#>  ds 1 parent   14     96.0     87.97  8.02502 5.233     1.533602
-#>  ds 1 parent   28     80.2     79.44  0.75809 4.772     0.158862
-#>  ds 1 parent   28     77.9     79.44 -1.54191 4.772    -0.323118
-#>  ds 1 parent   60     59.3     62.92 -3.61742 3.896    -0.928458
-#>  ds 1 parent   60     59.6     62.92 -3.31742 3.896    -0.851459
-#>  ds 1 parent   90     59.4     50.56  8.83825 3.264     2.707613
-#>  ds 1 parent   90     51.0     50.56  0.43825 3.264     0.134260
-#>  ds 1 parent  120     38.8     40.63 -1.83247 2.781    -0.658968
-#>  ds 1 parent  120     38.9     40.63 -1.73247 2.781    -0.623007
-#>  ds 2 parent    0    103.2     97.17  6.02995 5.734     1.051655
-#>  ds 2 parent    0     95.1     97.17 -2.07005 5.734    -0.361027
-#>  ds 2 parent    1     88.3     95.59 -7.28901 5.647    -1.290694
-#>  ds 2 parent    1    102.4     95.59  6.81099 5.647     1.206048
-#>  ds 2 parent    3     88.4     92.50 -4.10371 5.479    -0.748984
-#>  ds 2 parent    3     95.2     92.50  2.69629 5.479     0.492110
-#>  ds 2 parent    7     83.5     86.63 -3.12863 5.160    -0.606349
-#>  ds 2 parent    7     96.4     86.63  9.77137 5.160     1.893751
-#>  ds 2 parent   14     77.3     77.23  0.06920 4.653     0.014871
-#>  ds 2 parent   14     76.0     77.23 -1.23080 4.653    -0.264497
-#>  ds 2 parent   28     61.7     61.38  0.31692 3.816     0.083043
-#>  ds 2 parent   28     56.5     61.38 -4.88308 3.816    -1.279513
-#>  ds 2 parent   60     35.1     36.31 -1.21343 2.581    -0.470178
-#>  ds 2 parent   60     32.2     36.31 -4.11343 2.581    -1.593868
-#>  ds 2 parent   90     21.2     22.20 -0.99906 1.999    -0.499832
-#>  ds 2 parent   90     23.3     22.20  1.10094 1.999     0.550800
-#>  ds 2 parent  120     14.1     13.57  0.52931 1.732     0.305638
-#>  ds 2 parent  120     16.9     13.57  3.32931 1.732     1.922443
-#>  ds 3 parent    0     92.4     94.12 -1.71979 5.567    -0.308917
-#>  ds 3 parent    0     94.0     94.12 -0.11979 5.567    -0.021517
-#>  ds 3 parent    1     95.7     91.97  3.72634 5.450     0.683712
-#>  ds 3 parent    1     90.8     91.97 -1.17366 5.450    -0.215343
-#>  ds 3 parent    3     86.7     87.83 -1.12709 5.225    -0.215720
-#>  ds 3 parent    3     85.8     87.83 -2.02709 5.225    -0.387976
-#>  ds 3 parent    7     77.1     80.09 -2.98635 4.807    -0.621300
-#>  ds 3 parent    7     81.5     80.09  1.41365 4.807     0.294104
-#>  ds 3 parent   14     69.1     68.15  0.95467 4.170     0.228922
-#>  ds 3 parent   14     62.4     68.15 -5.74533 4.170    -1.377682
-#>  ds 3 parent   28     49.1     49.34 -0.23911 3.203    -0.074644
-#>  ds 3 parent   28     47.2     49.34 -2.13911 3.203    -0.667787
-#>  ds 3 parent   60     21.9     23.58 -1.68477 2.049    -0.822090
-#>  ds 3 parent   60     23.6     23.58  0.01523 2.049     0.007431
-#>  ds 3 parent   90     12.4     11.81  0.59388 1.690     0.351500
-#>  ds 3 parent   90     13.8     11.81  1.99388 1.690     1.180112
-#>  ds 3 parent  120      4.9      5.91 -1.00993 1.587    -0.636506
-#>  ds 3 parent  120      7.5      5.91  1.59007 1.587     1.002137
-#>  ds 4 parent    0     91.8    101.72 -9.92097 5.983    -1.658171
-#>  ds 4 parent    0    104.6    101.72  2.87903 5.983     0.481194
-#>  ds 4 parent    1    117.5    101.27 16.23017 5.958     2.723944
-#>  ds 4 parent    1     99.3    101.27 -1.96983 5.958    -0.330602
-#>  ds 4 parent    3     94.0    100.37 -6.37355 5.909    -1.078583
-#>  ds 4 parent    3     98.7    100.37 -1.67355 5.909    -0.283212
-#>  ds 4 parent    7    109.2     98.60 10.59529 5.812     1.822915
-#>  ds 4 parent    7     89.2     98.60 -9.40471 5.812    -1.618075
-#>  ds 4 parent   14    103.3     95.58  7.71609 5.647     1.366386
-#>  ds 4 parent   14    103.0     95.58  7.41609 5.647     1.313261
-#>  ds 4 parent   28     90.8     89.82  0.98290 5.333     0.184310
-#>  ds 4 parent   28     88.7     89.82 -1.11710 5.333    -0.209477
-#>  ds 4 parent   60     74.8     77.91 -3.10870 4.690    -0.662879
-#>  ds 4 parent   60     75.3     77.91 -2.60870 4.690    -0.556262
-#>  ds 4 parent   90     71.1     68.18  2.91738 4.172     0.699234
-#>  ds 4 parent   90     78.0     68.18  9.81738 4.172     2.353017
-#>  ds 4 parent  120     59.1     59.67 -0.57073 3.728    -0.153107
-#>  ds 4 parent  120     53.8     59.67 -5.87073 3.728    -1.574902
-#>  ds 5 parent    0     94.9     98.38 -3.48183 5.800    -0.600307
-#>  ds 5 parent    0    101.8     98.38  3.41817 5.800     0.589332
-#>  ds 5 parent    1     96.1     96.75 -0.65141 5.711    -0.114065
-#>  ds 5 parent    1     97.1     96.75  0.34859 5.711     0.061040
-#>  ds 5 parent    3     93.8     93.57  0.22881 5.537     0.041323
-#>  ds 5 parent    3     85.8     93.57 -7.77119 5.537    -1.403444
-#>  ds 5 parent    7     87.6     87.52  0.07909 5.208     0.015186
-#>  ds 5 parent    7     94.0     87.52  6.47909 5.208     1.244026
-#>  ds 5 parent   14     82.5     77.86  4.64101 4.687     0.990182
-#>  ds 5 parent   14     81.7     77.86  3.84101 4.687     0.819498
-#>  ds 5 parent   28     60.0     61.62 -1.61729 3.829    -0.422433
-#>  ds 5 parent   28     61.0     61.62 -0.61729 3.829    -0.161236
-#>  ds 5 parent   60     32.5     36.10 -3.59608 2.571    -1.398750
-#>  ds 5 parent   60     35.5     36.10 -0.59608 2.571    -0.231854
-#>  ds 5 parent   90     21.8     21.86 -0.06415 1.987    -0.032287
-#>  ds 5 parent   90     24.4     21.86  2.53585 1.987     1.276317
-#>  ds 5 parent  120     14.1     13.24  0.85643 1.724     0.496877
-#>  ds 5 parent  120     12.1     13.24 -1.14357 1.724    -0.663473
      
+#>    ds   name time observed predicted  residual    std standardized
+#>  ds 1 parent    0    104.1   101.417   2.68283 8.0077     0.335030
+#>  ds 1 parent    0    105.0   101.417   3.58283 8.0077     0.447422
+#>  ds 1 parent    1     98.5   100.624  -2.12400 7.9451    -0.267334
+#>  ds 1 parent    1     96.1   100.624  -4.52400 7.9451    -0.569407
+#>  ds 1 parent    3    101.9    99.056   2.84379 7.8213     0.363595
+#>  ds 1 parent    3     85.2    99.056 -13.85621 7.8213    -1.771597
+#>  ds 1 parent    7     99.1    95.994   3.10646 7.5795     0.409850
+#>  ds 1 parent    7     93.0    95.994  -2.99354 7.5795    -0.394953
+#>  ds 1 parent   14     88.1    90.860  -2.75997 7.1741    -0.384710
+#>  ds 1 parent   14     84.1    90.860  -6.75997 7.1741    -0.942268
+#>  ds 1 parent   28     80.2    81.402  -1.20174 6.4273    -0.186973
+#>  ds 1 parent   28     91.3    81.402   9.89826 6.4273     1.540024
+#>  ds 1 parent   60     65.1    63.316   1.78361 4.9994     0.356767
+#>  ds 1 parent   60     65.8    63.316   2.48361 4.9994     0.496785
+#>  ds 1 parent   90     47.8    50.029  -2.22862 3.9502    -0.564182
+#>  ds 1 parent   90     53.5    50.029   3.47138 3.9502     0.878792
+#>  ds 1 parent  120     37.6    39.529  -1.92946 3.1212    -0.618182
+#>  ds 1 parent  120     39.3    39.529  -0.22946 3.1212    -0.073516
+#>  ds 2 parent    0    107.9   101.711   6.18875 8.0309     0.770613
+#>  ds 2 parent    0    102.1   101.711   0.38875 8.0309     0.048406
+#>  ds 2 parent    1    103.8   100.174   3.62597 7.9096     0.458428
+#>  ds 2 parent    1    108.6   100.174   8.42597 7.9096     1.065287
+#>  ds 2 parent    3     91.0    97.169  -6.16895 7.6723    -0.804055
+#>  ds 2 parent    3     84.9    97.169 -12.26895 7.6723    -1.599124
+#>  ds 2 parent    7     79.3    91.427 -12.12652 7.2189    -1.679833
+#>  ds 2 parent    7    100.9    91.427   9.47348 7.2189     1.312320
+#>  ds 2 parent   14     77.3    82.182  -4.88174 6.4889    -0.752318
+#>  ds 2 parent   14     83.5    82.182   1.31826 6.4889     0.203155
+#>  ds 2 parent   28     66.8    66.402   0.39792 5.2430     0.075895
+#>  ds 2 parent   28     63.3    66.402  -3.10208 5.2430    -0.591662
+#>  ds 2 parent   60     40.8    40.789   0.01138 3.2206     0.003532
+#>  ds 2 parent   60     44.8    40.789   4.01138 3.2206     1.245537
+#>  ds 2 parent   90     27.8    25.830   1.97002 2.0395     0.965937
+#>  ds 2 parent   90     27.0    25.830   1.17002 2.0395     0.573682
+#>  ds 2 parent  120     15.2    16.357  -1.15721 1.2915    -0.895991
+#>  ds 2 parent  120     15.5    16.357  -0.85721 1.2915    -0.663710
+#>  ds 3 parent    0     97.7   101.907  -4.20726 8.0464    -0.522873
+#>  ds 3 parent    0     88.2   101.907 -13.70726 8.0464    -1.703521
+#>  ds 3 parent    1    109.9    99.522  10.37805 7.8581     1.320685
+#>  ds 3 parent    1     97.8    99.522  -1.72195 7.8581    -0.219130
+#>  ds 3 parent    3    100.5    94.918   5.58248 7.4945     0.744875
+#>  ds 3 parent    3     77.4    94.918 -17.51752 7.4945    -2.337375
+#>  ds 3 parent    7     78.3    86.338  -8.03788 6.8171    -1.179077
+#>  ds 3 parent    7     90.3    86.338   3.96212 6.8171     0.581204
+#>  ds 3 parent   14     76.0    73.147   2.85281 5.7756     0.493944
+#>  ds 3 parent   14     79.1    73.147   5.95281 5.7756     1.030687
+#>  ds 3 parent   28     46.0    52.504  -6.50373 4.1456    -1.568826
+#>  ds 3 parent   28     53.4    52.504   0.89627 4.1456     0.216197
+#>  ds 3 parent   60     25.1    24.605   0.49461 1.9428     0.254586
+#>  ds 3 parent   60     21.4    24.605  -3.20539 1.9428    -1.649882
+#>  ds 3 parent   90     11.0    12.090  -1.09046 0.9546    -1.142271
+#>  ds 3 parent   90     14.2    12.090   2.10954 0.9546     2.209770
+#>  ds 3 parent  120      5.8     5.941  -0.14094 0.4691    -0.300464
+#>  ds 3 parent  120      6.1     5.941   0.15906 0.4691     0.339077
+#>  ds 4 parent    0     95.3   101.177  -5.87672 7.9887    -0.735625
+#>  ds 4 parent    0    102.0   101.177   0.82328 7.9887     0.103056
+#>  ds 4 parent    1    104.4   100.716   3.68438 7.9523     0.463307
+#>  ds 4 parent    1    105.4   100.716   4.68438 7.9523     0.589057
+#>  ds 4 parent    3    113.7    99.800  13.90026 7.8800     1.763989
+#>  ds 4 parent    3     82.3    99.800 -17.49974 7.8800    -2.220774
+#>  ds 4 parent    7     98.1    97.993   0.10713 7.7374     0.013846
+#>  ds 4 parent    7     87.8    97.993 -10.19287 7.7374    -1.317359
+#>  ds 4 parent   14     97.9    94.909   2.99079 7.4939     0.399098
+#>  ds 4 parent   14    104.8    94.909   9.89079 7.4939     1.319851
+#>  ds 4 parent   28     85.0    89.030  -4.02995 7.0297    -0.573279
+#>  ds 4 parent   28     77.2    89.030 -11.82995 7.0297    -1.682864
+#>  ds 4 parent   60     82.2    76.923   5.27690 6.0737     0.868808
+#>  ds 4 parent   60     86.1    76.923   9.17690 6.0737     1.510919
+#>  ds 4 parent   90     70.5    67.073   3.42743 5.2959     0.647182
+#>  ds 4 parent   90     61.7    67.073  -5.37257 5.2959    -1.014470
+#>  ds 4 parent  120     60.0    58.483   1.51654 4.6178     0.328416
+#>  ds 4 parent  120     56.4    58.483  -2.08346 4.6178    -0.451184
+#>  ds 5 parent    0     92.6   101.752  -9.15161 8.0341    -1.139091
+#>  ds 5 parent    0    116.5   101.752  14.74839 8.0341     1.835716
+#>  ds 5 parent    1    108.0   100.069   7.93112 7.9013     1.003778
+#>  ds 5 parent    1    104.9   100.069   4.83112 7.9013     0.611436
+#>  ds 5 parent    3    100.5    96.786   3.71355 7.6421     0.485934
+#>  ds 5 parent    3     89.5    96.786  -7.28645 7.6421    -0.953462
+#>  ds 5 parent    7     91.7    90.541   1.15895 7.1490     0.162114
+#>  ds 5 parent    7     95.1    90.541   4.55895 7.1490     0.637707
+#>  ds 5 parent   14     82.2    80.566   1.63437 6.3613     0.256923
+#>  ds 5 parent   14     84.5    80.566   3.93437 6.3613     0.618483
+#>  ds 5 parent   28     60.5    63.791  -3.29084 5.0368    -0.653357
+#>  ds 5 parent   28     72.8    63.791   9.00916 5.0368     1.788662
+#>  ds 5 parent   60     38.3    37.412   0.88840 2.9540     0.300748
+#>  ds 5 parent   60     40.7    37.412   3.28840 2.9540     1.113217
+#>  ds 5 parent   90     22.5    22.685  -0.18500 1.7912    -0.103287
+#>  ds 5 parent   90     20.8    22.685  -1.88500 1.7912    -1.052387
+#>  ds 5 parent  120     13.4    13.755  -0.35534 1.0861    -0.327173
+#>  ds 5 parent  120     13.8    13.755   0.04466 1.0861     0.041118
    • - + @@ -177,13 +177,13 @@ Compare also the code in the example section to see the degradation models." />

      Compare also the code in the example section to see the degradation models.

      - 
      synthetic_data_for_UBA_2014
      + 
      synthetic_data_for_UBA_2014

      Format

      A list containing twelve datasets as an R6 class defined by mkinds, - each containing, among others, the following components

      + each containing, among others, the following components

      title

      The name of the dataset, e.g. SFO_lin_a

      data

      A data frame with the data in the form expected by mkinfit

      @@ -199,55 +199,59 @@ Compare also the code in the example section to see the degradation models." />

      Examples

      # \dontrun{
 # The data have been generated using the following kinetic models
-m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
-                           M1 = list(type = "SFO", to = "M2"),
-                           M2 = list(type = "SFO"), use_of_ff = "max")
      #> Successfully compiled differential equation model from auto-generated C code.
      
-
-m_synth_SFO_par <- mkinmod(parent = list(type = "SFO", to = c("M1", "M2"),
-                                         sink = FALSE),
-                           M1 = list(type = "SFO"),
-                           M2 = list(type = "SFO"), use_of_ff = "max")
      #> Successfully compiled differential equation model from auto-generated C code.
      
-m_synth_DFOP_lin <- mkinmod(parent = list(type = "DFOP", to = "M1"),
-                            M1 = list(type = "SFO", to = "M2"),
-                            M2 = list(type = "SFO"), use_of_ff = "max")
      #> Successfully compiled differential equation model from auto-generated C code.
      
-m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"),
-                                          sink = FALSE),
-                            M1 = list(type = "SFO"),
-                            M2 = list(type = "SFO"), use_of_ff = "max")
      #> Successfully compiled differential equation model from auto-generated C code.
      
+m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
+                           M1 = list(type = "SFO", to = "M2"),
+                           M2 = list(type = "SFO"), use_of_ff = "max")
+
      #> Temporary DLL for differentials generated and loaded
      
+
+m_synth_SFO_par <- mkinmod(parent = list(type = "SFO", to = c("M1", "M2"),
+                                         sink = FALSE),
+                           M1 = list(type = "SFO"),
+                           M2 = list(type = "SFO"), use_of_ff = "max")
+
      #> Temporary DLL for differentials generated and loaded
      
+m_synth_DFOP_lin <- mkinmod(parent = list(type = "DFOP", to = "M1"),
+                            M1 = list(type = "SFO", to = "M2"),
+                            M2 = list(type = "SFO"), use_of_ff = "max")
+
      #> Temporary DLL for differentials generated and loaded
      
+m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"),
+                                          sink = FALSE),
+                            M1 = list(type = "SFO"),
+                            M2 = list(type = "SFO"), use_of_ff = "max")
+
      #> Temporary DLL for differentials generated and loaded
      
 # The model predictions without intentional error were generated as follows
-sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
-
-d_synth_SFO_lin <- mkinpredict(m_synth_SFO_lin,
-                               c(k_parent = 0.7, f_parent_to_M1 = 0.8,
-                                 k_M1 = 0.3, f_M1_to_M2 = 0.7,
-                                 k_M2 = 0.02),
-                               c(parent = 100, M1 = 0, M2 = 0),
-                               sampling_times)
-
-d_synth_DFOP_lin <- mkinpredict(m_synth_DFOP_lin,
-                                c(k1 = 0.2, k2 = 0.02, g = 0.5,
-                                  f_parent_to_M1 = 0.5, k_M1 = 0.3,
-                                  f_M1_to_M2 = 0.7, k_M2 = 0.02),
-                                 c(parent = 100, M1 = 0, M2 = 0),
-                                 sampling_times)
-
-d_synth_SFO_par <- mkinpredict(m_synth_SFO_par,
-                               c(k_parent = 0.2,
-                                 f_parent_to_M1 = 0.8, k_M1 = 0.01,
-                                 f_parent_to_M2 = 0.2, k_M2 = 0.02),
-                                 c(parent = 100, M1 = 0, M2 = 0),
-                                 sampling_times)
-
-d_synth_DFOP_par <- mkinpredict(m_synth_DFOP_par,
-                               c(k1 = 0.3, k2 = 0.02, g = 0.7,
-                                 f_parent_to_M1 = 0.6, k_M1 = 0.04,
-                                 f_parent_to_M2 = 0.4, k_M2 = 0.01),
-                                 c(parent = 100, M1 = 0, M2 = 0),
-                                 sampling_times)
+sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+
+d_synth_SFO_lin <- mkinpredict(m_synth_SFO_lin,
+                               c(k_parent = 0.7, f_parent_to_M1 = 0.8,
+                                 k_M1 = 0.3, f_M1_to_M2 = 0.7,
+                                 k_M2 = 0.02),
+                               c(parent = 100, M1 = 0, M2 = 0),
+                               sampling_times)
+
+d_synth_DFOP_lin <- mkinpredict(m_synth_DFOP_lin,
+                                c(k1 = 0.2, k2 = 0.02, g = 0.5,
+                                  f_parent_to_M1 = 0.5, k_M1 = 0.3,
+                                  f_M1_to_M2 = 0.7, k_M2 = 0.02),
+                                 c(parent = 100, M1 = 0, M2 = 0),
+                                 sampling_times)
+
+d_synth_SFO_par <- mkinpredict(m_synth_SFO_par,
+                               c(k_parent = 0.2,
+                                 f_parent_to_M1 = 0.8, k_M1 = 0.01,
+                                 f_parent_to_M2 = 0.2, k_M2 = 0.02),
+                                 c(parent = 100, M1 = 0, M2 = 0),
+                                 sampling_times)
+
+d_synth_DFOP_par <- mkinpredict(m_synth_DFOP_par,
+                               c(k1 = 0.3, k2 = 0.02, g = 0.7,
+                                 f_parent_to_M1 = 0.6, k_M1 = 0.04,
+                                 f_parent_to_M2 = 0.4, k_M2 = 0.01),
+                                 c(parent = 100, M1 = 0, M2 = 0),
+                                 sampling_times)
 
 # Construct names for datasets with errors
-d_synth_names = paste0("d_synth_", c("SFO_lin", "SFO_par",
-                                     "DFOP_lin", "DFOP_par"))
+d_synth_names = paste0("d_synth_", c("SFO_lin", "SFO_par",
+                                     "DFOP_lin", "DFOP_par"))
 
 # Original function used or adding errors. The add_err function now published
 # with this package is a slightly generalised version where the names of
@@ -268,33 +272,35 @@ Compare also the code in the example section to see the degradation models." />
 
 # The following is the simplified version of the two-component model of Rocke
 # and Lorenzato (1995)
-sdfunc_twocomp = function(value, sd_low, rsd_high) {
-  sqrt(sd_low^2 + value^2 * rsd_high^2)
-}
+sdfunc_twocomp = function(value, sd_low, rsd_high) {
+  sqrt(sd_low^2 + value^2 * rsd_high^2)
+}
 
 # Add the errors.
-for (d_synth_name in d_synth_names)
-{
-  d_synth = get(d_synth_name)
-  assign(paste0(d_synth_name, "_a"), add_err(d_synth, function(value) 3))
-  assign(paste0(d_synth_name, "_b"), add_err(d_synth, function(value) 7))
-  assign(paste0(d_synth_name, "_c"), add_err(d_synth,
-                           function(value) sdfunc_twocomp(value, 0.5, 0.07)))
+for (d_synth_name in d_synth_names)
+{
+  d_synth = get(d_synth_name)
+  assign(paste0(d_synth_name, "_a"), add_err(d_synth, function(value) 3))
+  assign(paste0(d_synth_name, "_b"), add_err(d_synth, function(value) 7))
+  assign(paste0(d_synth_name, "_c"), add_err(d_synth,
+                           function(value) sdfunc_twocomp(value, 0.5, 0.07)))
 
-}
+}
 
-d_synth_err_names = c(
-  paste(rep(d_synth_names, each = 3), letters[1:3], sep = "_")
-)
+d_synth_err_names = c(
+  paste(rep(d_synth_names, each = 3), letters[1:3], sep = "_")
+)
 
 # This is just one example of an evaluation using the kinetic model used for
 # the generation of the data
-  fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data,
-                 quiet = TRUE)
-  plot_sep(fit)
        summary(fit)
      #> mkin version used for fitting:    0.9.50.3 
-#> R version used for fitting:       4.0.0 
-#> Date of fit:     Wed May 27 06:02:14 2020 
-#> Date of summary: Wed May 27 06:02:14 2020 
+  fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data,
+                 quiet = TRUE)
+  plot_sep(fit)
+
        summary(fit)
+
      #> mkin version used for fitting:    0.9.50.4 
+#> R version used for fitting:       4.0.3 
+#> Date of fit:     Mon Nov 30 16:01:42 2020 
+#> Date of summary: Mon Nov 30 16:01:42 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -303,7 +309,7 @@ Compare also the code in the example section to see the degradation models." />
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 817 model solutions performed in 0.623 s
+#> Fitted using 822 model solutions performed in 0.652 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -319,13 +325,13 @@ Compare also the code in the example section to see the degradation models." />
 #> f_M1_to_M2       0.5000 deparm
 #> 
 #> Starting values for the transformed parameters actually optimised:
-#>                     value lower upper
-#> parent_0       101.350000  -Inf   Inf
-#> log_k_parent    -2.302585  -Inf   Inf
-#> log_k_M1        -2.301586  -Inf   Inf
-#> log_k_M2        -2.300587  -Inf   Inf
-#> f_parent_ilr_1   0.000000  -Inf   Inf
-#> f_M1_ilr_1       0.000000  -Inf   Inf
+#>                      value lower upper
+#> parent_0        101.350000  -Inf   Inf
+#> log_k_parent     -2.302585  -Inf   Inf
+#> log_k_M1         -2.301586  -Inf   Inf
+#> log_k_M2         -2.300587  -Inf   Inf
+#> f_parent_qlogis   0.000000  -Inf   Inf
+#> f_M1_qlogis       0.000000  -Inf   Inf
 #> 
 #> Fixed parameter values:
 #>      value  type
@@ -338,32 +344,32 @@ Compare also the code in the example section to see the degradation models." />
 #>   188.7274 200.3723 -87.36368
 #> 
 #> Optimised, transformed parameters with symmetric confidence intervals:
-#>                Estimate Std. Error   Lower    Upper
-#> parent_0       102.1000    1.57000 98.8600 105.3000
-#> log_k_parent    -0.3020    0.03885 -0.3812  -0.2229
-#> log_k_M1        -1.2070    0.07123 -1.3520  -1.0620
-#> log_k_M2        -3.9010    0.06571 -4.0350  -3.7670
-#> f_parent_ilr_1   0.8492    0.16640  0.5103   1.1880
-#> f_M1_ilr_1       0.6780    0.17600  0.3196   1.0360
-#> sigma            2.2730    0.25740  1.7490   2.7970
+#>                 Estimate Std. Error   Lower    Upper
+#> parent_0        102.1000    1.57000 98.8600 105.3000
+#> log_k_parent     -0.3020    0.03885 -0.3812  -0.2229
+#> log_k_M1         -1.2070    0.07123 -1.3520  -1.0620
+#> log_k_M2         -3.9010    0.06571 -4.0350  -3.7670
+#> f_parent_qlogis   1.2010    0.23530  0.7216   1.6800
+#> f_M1_qlogis       0.9589    0.24890  0.4520   1.4660
+#> sigma             2.2730    0.25740  1.7490   2.7970
 #> 
 #> Parameter correlation:
-#>                  parent_0 log_k_parent   log_k_M1   log_k_M2 f_parent_ilr_1
-#> parent_0        1.000e+00    3.933e-01 -1.605e-01  2.819e-02     -4.624e-01
-#> log_k_parent    3.933e-01    1.000e+00 -4.082e-01  7.166e-02     -5.682e-01
-#> log_k_M1       -1.605e-01   -4.082e-01  1.000e+00 -3.929e-01      7.478e-01
-#> log_k_M2        2.819e-02    7.166e-02 -3.929e-01  1.000e+00     -2.658e-01
-#> f_parent_ilr_1 -4.624e-01   -5.682e-01  7.478e-01 -2.658e-01      1.000e+00
-#> f_M1_ilr_1      1.614e-01    4.102e-01 -8.109e-01  5.419e-01     -8.605e-01
-#> sigma          -1.384e-07   -2.581e-07  9.499e-08  1.518e-07      1.236e-07
-#>                f_M1_ilr_1      sigma
-#> parent_0        1.614e-01 -1.384e-07
-#> log_k_parent    4.102e-01 -2.581e-07
-#> log_k_M1       -8.109e-01  9.499e-08
-#> log_k_M2        5.419e-01  1.518e-07
-#> f_parent_ilr_1 -8.605e-01  1.236e-07
-#> f_M1_ilr_1      1.000e+00  8.795e-09
-#> sigma           8.795e-09  1.000e+00
+#>                   parent_0 log_k_parent   log_k_M1   log_k_M2 f_parent_qlogis
+#> parent_0         1.000e+00    3.933e-01 -1.605e-01  2.819e-02      -4.624e-01
+#> log_k_parent     3.933e-01    1.000e+00 -4.082e-01  7.166e-02      -5.682e-01
+#> log_k_M1        -1.605e-01   -4.082e-01  1.000e+00 -3.929e-01       7.478e-01
+#> log_k_M2         2.819e-02    7.166e-02 -3.929e-01  1.000e+00      -2.658e-01
+#> f_parent_qlogis -4.624e-01   -5.682e-01  7.478e-01 -2.658e-01       1.000e+00
+#> f_M1_qlogis      1.614e-01    4.102e-01 -8.109e-01  5.419e-01      -8.605e-01
+#> sigma           -7.941e-08   -9.143e-09 -1.268e-08  5.947e-08       5.657e-08
+#>                 f_M1_qlogis      sigma
+#> parent_0          1.614e-01 -7.941e-08
+#> log_k_parent      4.102e-01 -9.143e-09
+#> log_k_M1         -8.109e-01 -1.268e-08
+#> log_k_M2          5.419e-01  5.947e-08
+#> f_parent_qlogis  -8.605e-01  5.657e-08
+#> f_M1_qlogis       1.000e+00 -2.382e-10
+#> sigma            -2.382e-10  1.000e+00
 #> 
 #> Backtransformed parameters:
 #> Confidence intervals for internally transformed parameters are asymmetric.
@@ -410,8 +416,8 @@ Compare also the code in the example section to see the degradation models." />
 #>     7   parent      0.3  5.772e-01 -0.27717
 #>    14   parent      3.5  3.264e-03  3.49674
 #>    28   parent      3.2  1.045e-07  3.20000
-#>    90   parent      0.6  9.535e-10  0.60000
-#>   120   parent      3.5 -5.941e-10  3.50000
+#>    90   parent      0.6  9.532e-10  0.60000
+#>   120   parent      3.5 -5.940e-10  3.50000
 #>     1       M1     36.4  3.479e+01  1.61088
 #>     1       M1     37.4  3.479e+01  2.61088
 #>     3       M1     34.3  3.937e+01 -5.07027
@@ -421,9 +427,9 @@ Compare also the code in the example section to see the degradation models." />
 #>    14       M1      5.8  1.995e+00  3.80469
 #>    14       M1      1.2  1.995e+00 -0.79531
 #>    60       M1      0.5  2.111e-06  0.50000
-#>    90       M1      3.2 -9.676e-10  3.20000
-#>   120       M1      1.5  7.671e-10  1.50000
-#>   120       M1      0.6  7.671e-10  0.60000
+#>    90       M1      3.2 -9.671e-10  3.20000
+#>   120       M1      1.5  7.670e-10  1.50000
+#>   120       M1      0.6  7.670e-10  0.60000
 #>     1       M2      4.8  4.455e+00  0.34517
 #>     3       M2     20.9  2.153e+01 -0.62527
 #>     3       M2     19.3  2.153e+01 -2.22527
@@ -438,7 +444,7 @@ Compare also the code in the example section to see the degradation models." />
 #>    90       M2     10.6  1.013e+01  0.47130
 #>    90       M2     10.8  1.013e+01  0.67130
 #>   120       M2      9.8  5.521e+00  4.27893
-#>   120       M2      3.3  5.521e+00 -2.22107
      # }
+#>   120       M2      3.3  5.521e+00 -2.22107
      # }
      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/dev/reference/test_data_from_UBA_2014-1.png b/docs/dev/reference/test_data_from_UBA_2014-1.png index 431181cf..9e0afad2 100644 Binary files a/docs/dev/reference/test_data_from_UBA_2014-1.png and b/docs/dev/reference/test_data_from_UBA_2014-1.png differ diff --git a/docs/dev/reference/test_data_from_UBA_2014-2.png b/docs/dev/reference/test_data_from_UBA_2014-2.png index 4a064163..e889efde 100644 Binary files a/docs/dev/reference/test_data_from_UBA_2014-2.png and b/docs/dev/reference/test_data_from_UBA_2014-2.png differ diff --git a/docs/dev/reference/test_data_from_UBA_2014.html b/docs/dev/reference/test_data_from_UBA_2014.html index 291e3959..89ec3480 100644 --- a/docs/dev/reference/test_data_from_UBA_2014.html +++ b/docs/dev/reference/test_data_from_UBA_2014.html @@ -73,7 +73,7 @@ mkin - 0.9.50.3 + 0.9.50.4 @@ -121,7 +121,7 @@
    • - + @@ -149,13 +149,13 @@ software packages (Ranke, 2014).

      - 
      test_data_from_UBA_2014
      + 
      test_data_from_UBA_2014

      Format

      A list containing three datasets as an R6 class defined by mkinds. - Each dataset has, among others, the following components

      + Each dataset has, among others, the following components

      title

      The name of the dataset, e.g. UBA_2014_WS_river

      data

      A data frame with the data in the form expected by mkinfit

      @@ -174,52 +174,62 @@ # generally considered deprecated due to the frequent occurrence of such # large parameter correlations, among other reasons (e.g. the adequacy of the # 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
      #> Warning: Could not calculate correlation; no covariance matrix
      #> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_w_0 95.91998116 NA NA NA NA NA + m_ws <- mkinmod(parent_w = mkinsub("SFO", "parent_s"), + parent_s = mkinsub("SFO", "parent_w")) +
      #> Temporary DLL for differentials generated and loaded
      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 +
      #> Warning: Could not calculate correlation; no covariance matrix
      #> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_w_0 95.91998118 NA NA NA NA NA #> k_parent_w 0.41145375 NA NA NA NA NA #> k_parent_s 0.04663944 NA NA NA NA NA #> f_parent_w_to_parent_s 0.12467894 NA NA NA NA NA #> f_parent_s_to_parent_w 0.50000000 NA NA NA NA NA -#> sigma 3.13612618 NA NA NA NA NA
      mkinerrmin(f_river)
      #> err.min n.optim df +#> sigma 3.13612618 NA NA NA NA NA
      mkinerrmin(f_river) +
      #> err.min n.optim df #> All data 0.1090929 5 6 #> parent_w 0.0817436 3 3 #> parent_s 0.1619965 2 3
      # This is the evaluation used for the validation of software packages # in the expertise from 2014 - m_soil <- mkinmod(parent = mkinsub("SFO", c("M1", "M2")), - M1 = mkinsub("SFO", "M3"), - 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 0.859186419 89.1008681 1.113862e-26 74.755958720 -#> k_parent 0.12081956 0.004601919 26.2541703 1.077361e-16 0.111561576 -#> k_M1 0.84258629 0.806165149 1.0451783 1.545282e-01 0.113778910 -#> k_M2 0.04210878 0.017083049 2.4649452 1.170195e-02 0.018013823 -#> k_M3 0.01122919 0.007245870 1.5497364 6.885076e-02 0.002909418 -#> f_parent_to_M1 0.32240193 0.240785518 1.3389590 9.819221e-02 NA -#> f_parent_to_M2 0.16099854 0.033691991 4.7785404 6.531224e-05 NA -#> f_M1_to_M3 0.27921506 0.269425582 1.0363346 1.565282e-01 0.022977955 -#> f_M2_to_M3 0.55641331 0.595121774 0.9349571 1.807710e-01 0.008002320 + m_soil <- mkinmod(parent = mkinsub("SFO", c("M1", "M2")), + M1 = mkinsub("SFO", "M3"), + M2 = mkinsub("SFO", "M3"), + M3 = mkinsub("SFO"), + use_of_ff = "max") +
      #> Temporary DLL for differentials generated and loaded
      + 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 76.55425649 0.859186399 89.1008710 1.113861e-26 74.755959406 +#> k_parent 0.12081956 0.004601918 26.2541722 1.077359e-16 0.111561575 +#> k_M1 0.84258614 0.806159820 1.0451850 1.545267e-01 0.113779670 +#> k_M2 0.04210880 0.017083035 2.4649483 1.170188e-02 0.018013857 +#> k_M3 0.01122918 0.007245855 1.5497385 6.885052e-02 0.002909431 +#> f_parent_to_M1 0.32240200 0.240783909 1.3389682 9.819073e-02 NA +#> f_parent_to_M2 0.16099855 0.033691953 4.7785463 6.531137e-05 NA +#> f_M1_to_M3 0.27921507 0.269423745 1.0363417 1.565266e-01 0.022978220 +#> f_M2_to_M3 0.55641253 0.595119954 0.9349586 1.807707e-01 0.008002509 #> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778 #> Upper -#> parent_0 78.35255297 +#> parent_0 78.35255357 #> k_parent 0.13084582 -#> k_M1 6.23974738 -#> k_M2 0.09843271 -#> k_M3 0.04334017 +#> k_M1 6.23970352 +#> k_M2 0.09843260 +#> k_M3 0.04333992 #> f_parent_to_M1 NA #> f_parent_to_M2 NA -#> f_M1_to_M3 0.86450905 -#> f_M2_to_M3 0.99489911 -#> sigma 1.45337221
      mkinerrmin(f_soil)
      #> err.min n.optim df +#> f_M1_to_M3 0.86450768 +#> f_M2_to_M3 0.99489895 +#> sigma 1.45337221
      mkinerrmin(f_soil) +
      #> err.min n.optim df #> All data 0.09649963 9 20 #> parent 0.04721283 2 6 #> M1 0.26551208 2 5 #> M2 0.20327575 2 5 -#> M3 0.05196550 3 4
      # } +#> M3 0.05196550 3 4
      # }
      -

      Site built with pkgdown 1.5.1.

      +

      Site built with pkgdown 1.6.1.

      diff --git a/docs/dev/reference/transform_odeparms.html b/docs/dev/reference/transform_odeparms.html index 0845d478..46b66073 100644 --- a/docs/dev/reference/transform_odeparms.html +++ b/docs/dev/reference/transform_odeparms.html @@ -232,7 +232,7 @@ This is no problem for the internal use in mkinfit.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 +
      #> Temporary DLL for differentials generated and loaded
      # 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 @@ -252,7 +252,7 @@ This is no problem for the internal use in mkinfit.# \dontrun{ # 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
      #> Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", signif(cost.current, 6), "\n", sep = "")}: missing value where TRUE/FALSE needed
      #> Timing stopped at: 0.002 0 0.003
      fit.2.s <- summary(fit.2) +
      #> Warning: Observations with value of zero were removed from the data
      #> Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", signif(cost.current, 6), "\n", sep = "")}: missing value where TRUE/FALSE needed
      #> Timing stopped at: 0.006 0 0.005
      fit.2.s <- summary(fit.2)
      #> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'summary': object 'fit.2' not found
      print(fit.2.s$par, 3)
      #> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'fit.2.s' not found
      print(fit.2.s$bpar, 3)
      #> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'fit.2.s' not found
      # } @@ -272,7 +272,7 @@ This is no problem for the internal use in mkinfit.= 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.
      +
      #> Temporary DLL for differentials generated and loaded
      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) @@ -297,7 +297,7 @@ This is no problem for the internal use in mkinfit.= list(type = "SFO", to = "m1", sink = FALSE), m1 = list(type = "SFO"), use_of_ff = "max") -
      #> Successfully compiled differential equation model from auto-generated C code.
      +
      #> Temporary DLL for differentials generated and loaded
      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) diff --git a/docs/dev/reference/update.mkinfit-1.png b/docs/dev/reference/update.mkinfit-1.png index 4cbefa56..7d2f1bdb 100644 Binary files a/docs/dev/reference/update.mkinfit-1.png and b/docs/dev/reference/update.mkinfit-1.png differ diff --git a/docs/dev/reference/update.mkinfit-2.png b/docs/dev/reference/update.mkinfit-2.png index f432f6f8..8dcabcdc 100644 Binary files a/docs/dev/reference/update.mkinfit-2.png and b/docs/dev/reference/update.mkinfit-2.png differ diff --git a/docs/dev/reference/update.mkinfit.html b/docs/dev/reference/update.mkinfit.html index d6363edf..10a93373 100644 --- a/docs/dev/reference/update.mkinfit.html +++ b/docs/dev/reference/update.mkinfit.html @@ -75,7 +75,7 @@ override these starting values." /> mkin - 0.9.50.3 + 0.9.50.4
      @@ -123,7 +123,7 @@ override these starting values." />
    • - + @@ -142,7 +142,7 @@ override these starting values." />

      Update an mkinfit model with different arguments

      - Source: R/update.mkinfit.R + Source: R/update.mkinfit.R
      @@ -154,7 +154,7 @@ override these starting values.

      # S3 method for mkinfit
-update(object, ..., evaluate = TRUE)
      +update(object, ..., evaluate = TRUE)

      Arguments

    @@ -178,11 +178,15 @@ remove arguments given in the original call

    Examples

    # \dontrun{
-fit <- mkinfit("SFO", subset(FOCUS_2006_D, value != 0), quiet = TRUE)
-parms(fit)
    #>      parent_0 k_parent_sink         sigma 
-#>   99.44423886    0.09793574    3.39632469 
    plot_err(fit)
    fit_2 <- update(fit, error_model = "tc")
-parms(fit_2)
    #>      parent_0 k_parent_sink     sigma_low      rsd_high 
-#>  1.008549e+02  1.005665e-01  3.752222e-03  6.763434e-02 
    plot_err(fit_2)
    # }
+fit <- mkinfit("SFO", subset(FOCUS_2006_D, value != 0), quiet = TRUE)
+parms(fit)
+
    #>    parent_0    k_parent       sigma 
+#> 99.44423885  0.09793574  3.39632469 
    plot_err(fit)
+
    fit_2 <- update(fit, error_model = "tc")
+parms(fit_2)
+
    #>     parent_0     k_parent    sigma_low     rsd_high 
+#> 1.008549e+02 1.005665e-01 3.752222e-03 6.763434e-02 
    plot_err(fit_2)
+
    # }
    -

    Site built with pkgdown 1.5.1.

    +

    Site built with pkgdown 1.6.1.

    -- cgit v1.2.1