From e05656d57668688b971c28e32b4cfd4d3eac4662 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 Sep 2019 13:03:50 +0200 Subject: Correct and rebuild docs - Reconcile docs and code for max_twa_parent - Correct links to docs in twa vignette - Static documentation rebuilt by pkgdown --- R/max_twa_parent.R | 30 +++-- build.log | 9 -- docs/404.html | 154 +++++++++++++++++++++++++ docs/articles/FOCUS_D.html | 31 ++--- docs/articles/FOCUS_L.html | 133 +++++++++++---------- docs/articles/index.html | 16 ++- docs/articles/mkin.html | 27 +++-- docs/articles/twa.html | 23 +++- docs/articles/web_only/FOCUS_Z.html | 39 ++++--- docs/articles/web_only/NAFTA_examples.html | 79 +++++++------ docs/articles/web_only/benchmarks.html | 75 ++++++------ docs/articles/web_only/compiled_models.html | 49 ++++---- docs/authors.html | 18 ++- docs/index.html | 19 +-- docs/news/index.html | 27 +++-- docs/pkgdown.css | 46 +++++--- docs/pkgdown.js | 14 +-- docs/pkgdown.yml | 2 +- docs/reference/AIC.mmkin.html | 37 +++--- docs/reference/CAKE_export.html | 20 +++- docs/reference/DFOP.solution.html | 18 ++- docs/reference/Extract.mmkin.html | 20 +++- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 22 +++- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 22 +++- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 22 +++- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 22 +++- docs/reference/FOCUS_2006_datasets.html | 27 ++++- docs/reference/FOMC.solution.html | 18 ++- docs/reference/HS.solution.html | 18 ++- docs/reference/IORE.solution.html | 28 +++-- docs/reference/NAFTA_SOP_2015.html | 27 +++-- docs/reference/NAFTA_SOP_Attachment.html | 20 +++- docs/reference/SFO.solution.html | 18 ++- docs/reference/SFORB.solution.html | 18 ++- docs/reference/add_err.html | 39 ++++--- docs/reference/endpoints.html | 16 ++- docs/reference/experimental_data_for_UBA.html | 36 ++++-- docs/reference/geometric_mean.html | 18 ++- docs/reference/ilr.html | 32 +++-- docs/reference/index.html | 22 ++-- docs/reference/logLik.mkinfit.html | 32 +++-- docs/reference/logistic.solution.html | 42 ++++--- docs/reference/max_twa_parent.html | 67 +++++++++-- docs/reference/mccall81_245T.html | 36 ++++-- docs/reference/mkin_long_to_wide.html | 16 ++- docs/reference/mkin_wide_to_long.html | 18 ++- docs/reference/mkinds.html | 38 ++++-- docs/reference/mkinerrmin.html | 26 +++-- docs/reference/mkinerrplot.html | 35 ++++-- docs/reference/mkinfit.html | 106 +++++++++-------- docs/reference/mkinmod.html | 32 +++-- docs/reference/mkinparplot.html | 25 ++-- docs/reference/mkinplot.html | 18 ++- docs/reference/mkinpredict.html | 74 +++++++----- docs/reference/mkinresplot.html | 26 +++-- docs/reference/mkinsub.html | 20 +++- docs/reference/mmkin.html | 44 ++++--- docs/reference/nafta.html | 24 ++-- docs/reference/plot.mkinfit.html | 82 +++++++------ docs/reference/plot.mmkin.html | 46 +++++--- docs/reference/plot.nafta.html | 22 ++-- docs/reference/print.mkinds.html | 20 +++- docs/reference/print.mkinmod.html | 28 +++-- docs/reference/print.nafta.html | 20 +++- docs/reference/schaefer07_complex_case.html | 37 +++--- docs/reference/sigma_twocomp.html | 16 ++- docs/reference/summary.mkinfit.html | 32 +++-- docs/reference/synthetic_data_for_UBA.html | 124 +++----------------- docs/reference/test_data_from_UBA_2014.html | 32 +++-- docs/reference/transform_odeparms.html | 70 ++++++----- man/max_twa_parent.Rd | 44 ++++++- vignettes/mkin_benchmarks.rda | Bin 874 -> 877 bytes vignettes/twa.Rmd | 7 +- 73 files changed, 1657 insertions(+), 913 deletions(-) create mode 100644 docs/404.html diff --git a/R/max_twa_parent.R b/R/max_twa_parent.R index 946a9b3d..5129e369 100644 --- a/R/max_twa_parent.R +++ b/R/max_twa_parent.R @@ -1,4 +1,4 @@ -# Copyright (C) 2016,2017,2018 Johannes Ranke +# Copyright (C) 2016-2019 Johannes Ranke # Contact: jranke@uni-bremen.de # This file is part of the R package mkin @@ -37,14 +37,14 @@ max_twa_parent <- function(fit, windows) { } k <- parms.all[k_name] twafunc <- function(t) { - M0 * (1 - exp(- k * t)) / (k * t) + max_twa_sfo(M0, k, t) } } if (type == "FOMC") { alpha <- parms.all["alpha"] beta <- parms.all["beta"] twafunc <- function(t) { - M0 * (beta)/(t * (1 - alpha)) * ((t/beta + 1)^(1 - alpha) - 1) + max_twa_fomc(M0, alpha, beta, t) } } if (type == "DFOP") { @@ -52,7 +52,7 @@ max_twa_parent <- function(fit, windows) { k2 <- parms.all["k2"] g <- parms.all["g"] twafunc <- function(t) { - M0/t * ((g/k1) * (1 - exp(- k1 * t)) + ((1 - g)/k2) * (1 - exp(- k2 * t))) + max_twa_dfop(M0, k1, k2, g, t) } } if (type == "HS") { @@ -61,11 +61,8 @@ max_twa_parent <- function(fit, windows) { tb <- parms.all["tb"] twafunc <- function(t) { ifelse(t <= tb, - M0 * (1 - exp(- k1 * t)) / (k1 * t), - (M0 / t) * ( - (1/k1) * (1 - exp(- k1 * tb)) + - (exp(- k1 * tb) / k2) * (1 - exp(- k2 * (t - tb))) - ) + max_twa_sfo(M0, k1, t), + max_twa_hs(M0, k1, k2, tb, t) ) } } @@ -77,3 +74,18 @@ max_twa_parent <- function(fit, windows) { names(res) <- windows return(res) } +max_twa_sfo <- function(M0 = 1, k, t) { + M0 * (1 - exp(- k * t)) / (k * t) +} +max_twa_fomc <- function(M0 = 1, alpha, beta, t) { + M0 * (beta)/(t * (1 - alpha)) * ((t/beta + 1)^(1 - alpha) - 1) +} +max_twa_dfop <- function(M0 = 1, k1, k2, g, t) { + M0/t * ((g/k1) * (1 - exp(- k1 * t)) + ((1 - g)/k2) * (1 - exp(- k2 * t))) +} +max_twa_hs <- function(M0 = 1, k1, k2, tb, t) { + (M0 / t) * ( + (1/k1) * (1 - exp(- k1 * tb)) + + (exp(- k1 * tb) / k2) * (1 - exp(- k2 * (t - tb))) + ) +} diff --git a/build.log b/build.log index 65e585da..976d27d4 100644 --- a/build.log +++ b/build.log @@ -1,10 +1 @@ * checking for file ‘./DESCRIPTION’ ... OK -* preparing ‘mkin’: -* checking DESCRIPTION meta-information ... OK -* installing the package to build vignettes -* creating vignettes ... OK -* checking for LF line-endings in source and make files and shell scripts -* checking for empty or unneeded directories -* looking to see if a ‘data/datalist’ file should be added -* building ‘mkin_0.9.49.6.tar.gz’ - diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 00000000..bdc5053f --- /dev/null +++ b/docs/404.html @@ -0,0 +1,154 @@ + + + + + + + + +Page not found (404) • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + +
+ +
+
+
+

Page not found (404)

+
+ +Content not found. Please use links in the navbar. + +
+ +
+ + + +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown 1.4.1.

+
+ +
+
+ + + + + + + + diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 00c3cabe..70739ae6 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -7,8 +7,9 @@ Example evaluation of FOCUS Example Dataset D • mkin - - + + + @@ -82,13 +83,14 @@ +

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2019-07-09

+

2019-09-18

@@ -98,8 +100,8 @@

This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using mkin. After loading the library we look at the data. We have observed concentrations in the column named value at the times specified in column time for the two observed variables named parent and m1.

-
library(mkin, quietly = TRUE)
-print(FOCUS_2006_D)
+
library(mkin, quietly = TRUE)
+print(FOCUS_2006_D)
##      name time  value
 ## 1  parent    0  99.46
 ## 2  parent    0 102.04
@@ -149,7 +151,7 @@
 
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.

-
print(SFO_SFO$diffs)

+
print(SFO_SFO$diffs)

 
##                                                       parent 
 ## "d_parent = - k_parent_sink * parent - k_parent_m1 * parent" 
 ##                                                           m1 
@@ -159,17 +161,17 @@
 
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
 ## value of zero were removed from the data

 
A plot of the fit including a residual plot for both observed variables is obtained using the plot_sep method for mkinfit objects, which shows separate graphs for all compounds and their residuals.

-
plot_sep(fit, lpos = c("topright", "bottomright"))

+
plot_sep(fit, lpos = c("topright", "bottomright"))

 

 
Confidence intervals for the parameter estimates are obtained using the mkinparplot function.

 
 

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

-
summary(fit)

+
summary(fit)

 
## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jul  9 09:00:18 2019 
-## Date of summary: Tue Jul  9 09:00:18 2019 
+## R version used for fitting:       3.6.1 
+## Date of fit:     Wed Sep 18 12:57:33 2019 
+## Date of summary: Wed Sep 18 12:57:33 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -177,7 +179,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted using 389 model solutions performed in 1.003 s
+## Fitted using 389 model solutions performed in 1.01 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -301,17 +303,20 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 779635cd..81659030 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -7,8 +7,9 @@ Example evaluation of FOCUS Laboratory Data L1 to L3 • mkin - - + + + @@ -82,13 +83,14 @@ +

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2019-07-09

+

2019-09-18

@@ -101,28 +103,28 @@

Laboratory Data L1

The following code defines example dataset L1 from the FOCUS kinetics report, p. 284:

-
library("mkin", quietly = TRUE)
-FOCUS_2006_L1 = data.frame(
-  t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
-  parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6,
+
library("mkin", quietly = TRUE)
+FOCUS_2006_L1 = data.frame(
+  t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
+  parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6,
              72.0, 71.9, 50.3, 59.4, 47.0, 45.1,
              27.7, 27.3, 10.0, 10.4, 2.9, 4.0))
 FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)

 
Here we use the assumptions of simple first order (SFO), the case of declining rate constant over time (FOMC) and the case of two different phases of the kinetics (DFOP). For a more detailed discussion of the models, please see the FOCUS kinetics report.

 
Since mkin version 0.9-32 (July 2014), we can use shorthand notation like "SFO" for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.

 
m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
-summary(m.L1.SFO)

+summary(m.L1.SFO)
## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jul  9 09:00:20 2019 
-## Date of summary: Tue Jul  9 09:00:20 2019 
+## R version used for fitting:       3.6.1 
+## Date of fit:     Wed Sep 18 12:57:35 2019 
+## Date of summary: Wed Sep 18 12:57:35 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.282 s
+## Fitted using 133 model solutions performed in 0.287 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -198,7 +200,7 @@
 ##    30   parent      2.9     5.251  -2.3513
 ##    30   parent      4.0     5.251  -1.2513

A plot of the fit is obtained with the plot function for mkinfit objects.

-
plot(m.L1.SFO, show_errmin = TRUE, main = "FOCUS L1 - SFO")
+
plot(m.L1.SFO, show_errmin = TRUE, main = "FOCUS L1 - SFO")

The residual plot can be easily obtained by

mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")
@@ -207,17 +209,17 @@ 
m.L1.FOMC <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE)
## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation did not converge:
 ## false convergence (8)
-
plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")
+
plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")

-
summary(m.L1.FOMC, data = FALSE)
+
summary(m.L1.FOMC, data = FALSE)
## Warning in sqrt(diag(covar)): NaNs wurden erzeugt
## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt
## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
 ## finite result is doubtful
## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jul  9 09:00:22 2019 
-## Date of summary: Tue Jul  9 09:00:22 2019 
+## R version used for fitting:       3.6.1 
+## Date of fit:     Wed Sep 18 12:57:37 2019 
+## Date of summary: Wed Sep 18 12:57:37 2019 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -229,7 +231,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 899 model solutions performed in 1.881 s
+## Fitted using 899 model solutions performed in 1.921 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -292,9 +294,9 @@
 

 Laboratory Data L2

 
The following code defines example dataset L2 from the FOCUS kinetics report, p. 287:

-
FOCUS_2006_L2 = data.frame(
-  t = rep(c(0, 1, 3, 7, 14, 28), each = 2),
-  parent = c(96.1, 91.8, 41.4, 38.7,
+
@@ -303,7 +305,7 @@
 SFO fit for L2
 
Again, the SFO model is fitted and the result is plotted. The residual plot can be obtained simply by adding the argument show_residuals to the plot command.

 
m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE)
-plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE,
+plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - SFO")

 

 
The \(\chi^2\) error level of 14% suggests that the model does not fit very well. This is also obvious from the plots of the fit, in which we have included the residual plot.

@@ -315,21 +317,21 @@
 FOMC fit for L2
 
For comparison, the FOMC model is fitted as well, and the \(\chi^2\) error level is checked.

 
m.L2.FOMC <- mkinfit("FOMC", FOCUS_2006_L2_mkin, quiet = TRUE)
-plot(m.L2.FOMC, show_residuals = TRUE,
+plot(m.L2.FOMC, show_residuals = TRUE,
      main = "FOCUS L2 - FOMC")

 

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

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

 
## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jul  9 09:00:23 2019 
-## Date of summary: Tue Jul  9 09:00:23 2019 
+## R version used for fitting:       3.6.1 
+## Date of fit:     Wed Sep 18 12:57:38 2019 
+## Date of summary: Wed Sep 18 12:57:38 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 239 model solutions performed in 0.495 s
+## Fitted using 239 model solutions performed in 0.49 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -391,14 +393,14 @@
 DFOP fit for L2
 
Fitting the four parameter DFOP model further reduces the \(\chi^2\) error level.

 
m.L2.DFOP <- mkinfit("DFOP", FOCUS_2006_L2_mkin, quiet = TRUE)
-plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
+plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - DFOP")

 

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

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

 
## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jul  9 09:00:24 2019 
-## Date of summary: Tue Jul  9 09:00:25 2019 
+## R version used for fitting:       3.6.1 
+## Date of fit:     Wed Sep 18 12:57:40 2019 
+## Date of summary: Wed Sep 18 12:57:40 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -407,7 +409,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 572 model solutions performed in 1.193 s
+## Fitted using 572 model solutions performed in 1.209 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -474,18 +476,18 @@
 

 Laboratory Data L3

 
The following code defines example dataset L3 from the FOCUS kinetics report, p. 290.

-
FOCUS_2006_L3 = data.frame(
-  t = c(0, 3, 7, 14, 30, 60, 91, 120),
-  parent = c(97.8, 60, 51, 43, 35, 22, 15, 12))
+
FOCUS_2006_L3 = data.frame(
+  t = c(0, 3, 7, 14, 30, 60, 91, 120),
+  parent = c(97.8, 60, 51, 43, 35, 22, 15, 12))
 FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)

 

 

 Fit multiple models

 
As of mkin version 0.9-39 (June 2015), we can fit several models to one or more datasets in one call to the function mmkin. The datasets have to be passed in a list, in this case a named list holding only the L3 dataset prepared above.

 
# Only use one core here, not to offend the CRAN checks
-mm.L3 <- mmkin(c("SFO", "FOMC", "DFOP"), cores = 1,
-               list("FOCUS L3" = FOCUS_2006_L3_mkin), quiet = TRUE)
-plot(mm.L3)

+mm.L3 <- mmkin(c("SFO", "FOMC", "DFOP"), cores = 1,
+               list("FOCUS L3" = FOCUS_2006_L3_mkin), quiet = TRUE)
+plot(mm.L3)

 

 
The \(\chi^2\) error level of 21% as well as the plot suggest that the SFO model does not fit very well. The FOMC model performs better, with an error level at which the \(\chi^2\) test passes of 7%. Fitting the four parameter DFOP model further reduces the \(\chi^2\) error level considerably.

 

@@ -494,11 +496,11 @@
 Accessing mmkin objects
 
The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.

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

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

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

 
## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jul  9 09:00:26 2019 
-## Date of summary: Tue Jul  9 09:00:27 2019 
+## R version used for fitting:       3.6.1 
+## Date of fit:     Wed Sep 18 12:57:42 2019 
+## Date of summary: Wed Sep 18 12:57:42 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -507,7 +509,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 373 model solutions performed in 0.797 s
+## Fitted using 373 model solutions performed in 0.783 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -578,7 +580,7 @@
 ##    60   parent     22.0     23.26 -1.25919
 ##    91   parent     15.0     15.18 -0.18181
 ##   120   parent     12.0     10.19  1.81395

-
plot(mm.L3[["DFOP", 1]], show_errmin = TRUE)

+
plot(mm.L3[["DFOP", 1]], show_errmin = TRUE)

 

 
Here, a look to the model plot, the confidence intervals of the parameters and the correlation matrix suggest that the parameter estimates are reliable, and the DFOP model can be used as the best-fit model based on the \(\chi^2\) error level criterion for laboratory data L3.

 
This is also an example where the standard t-test for the parameter g_ilr is misleading, as it tests for a significant difference from zero. In this case, zero appears to be the correct value for this parameter, and the confidence interval for the backtransformed parameter g is quite narrow.

@@ -588,30 +590,30 @@
 

 Laboratory Data L4

 
The following code defines example dataset L4 from the FOCUS kinetics report, p. 293:

-
FOCUS_2006_L4 = data.frame(
-  t = c(0, 3, 7, 14, 30, 60, 91, 120),
-  parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0))
+
FOCUS_2006_L4 = data.frame(
+  t = c(0, 3, 7, 14, 30, 60, 91, 120),
+  parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0))
 FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)

 
Fits of the SFO and FOMC models, plots and summaries are produced below:

 
# Only use one core here, not to offend the CRAN checks
-mm.L4 <- mmkin(c("SFO", "FOMC"), cores = 1,
-               list("FOCUS L4" = FOCUS_2006_L4_mkin),
+mm.L4 <- mmkin(c("SFO", "FOMC"), cores = 1,
+               list("FOCUS L4" = FOCUS_2006_L4_mkin),
                quiet = TRUE)
-plot(mm.L4)

+plot(mm.L4)

 

 
The \(\chi^2\) error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the \(\chi^2\) test passes is slightly lower for the FOMC model. However, the difference appears negligible.

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

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

 
## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jul  9 09:00:27 2019 
-## Date of summary: Tue Jul  9 09:00:28 2019 
+## R version used for fitting:       3.6.1 
+## Date of fit:     Wed Sep 18 12:57:42 2019 
+## Date of summary: Wed Sep 18 12:57:43 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 142 model solutions performed in 0.299 s
+## Fitted using 142 model solutions performed in 0.288 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -665,18 +667,18 @@
 ## Estimated disappearance times:
 ##        DT50 DT90
 ## parent  106  352

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

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

 
## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Tue Jul  9 09:00:28 2019 
-## Date of summary: Tue Jul  9 09:00:28 2019 
+## R version used for fitting:       3.6.1 
+## Date of fit:     Wed Sep 18 12:57:43 2019 
+## Date of summary: Wed Sep 18 12:57:43 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 224 model solutions performed in 0.478 s
+## Fitted using 224 model solutions performed in 0.463 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -771,17 +773,20 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ diff --git a/docs/articles/index.html b/docs/articles/index.html index 95828a82..cc136fdc 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -44,6 +46,7 @@ + @@ -113,6 +116,7 @@
+
@@ -139,19 +143,23 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 926bd907..90549b0f 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -7,8 +7,9 @@ Introduction to mkin • mkin - - + + + @@ -82,13 +83,14 @@ +

Introduction to mkin

Johannes Ranke

-

2019-07-09

+

2019-09-18

@@ -102,7 +104,7 @@

Abstract

In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance has been developed, based on nonlinear optimisation. The R add-on package mkin implements fitting some of the models recommended in this guidance from within R and calculates some statistical measures for data series within one or more compartments, for parent and metabolites.

-
library("mkin", quietly = TRUE)
+
library("mkin", quietly = TRUE)
 # Define the kinetic model
 m_SFO_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
                          M1 = mkinsub("SFO", "M2"),
@@ -111,12 +113,12 @@
 
 
 # Produce model predictions using some arbitrary parameters
-sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
 d_SFO_SFO_SFO <- mkinpredict(m_SFO_SFO_SFO,
-  c(k_parent = 0.03,
-    f_parent_to_M1 = 0.5, k_M1 = log(2)/100,
-    f_M1_to_M2 = 0.9, k_M2 = log(2)/50),
-  c(parent = 100, M1 = 0, M2 = 0),
+  c(k_parent = 0.03,
+    f_parent_to_M1 = 0.5, k_M1 = log(2)/100,
+    f_M1_to_M2 = 0.9, k_M2 = log(2)/50),
+  c(parent = 100, M1 = 0, M2 = 0),
   sampling_times)
 
 # Generate a dataset by adding normally distributed errors with
@@ -129,7 +131,7 @@
 f_SFO_SFO_SFO <- mkinfit(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[1]], quiet = TRUE)
 
 # Plot the results separately for parent and metabolites
-plot_sep(f_SFO_SFO_SFO, lpos = c("topright", "bottomright", "bottomright"))

+plot_sep(f_SFO_SFO_SFO, lpos = c("topright", "bottomright", "bottomright"))

@@ -246,17 +248,20 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ diff --git a/docs/articles/twa.html b/docs/articles/twa.html index 30d54f9e..b15f1522 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -7,8 +7,9 @@ Calculation of time weighted average concentrations with mkin • mkin - - + + + @@ -82,13 +83,14 @@ +

Calculation of time weighted average concentrations with mkin

Johannes Ranke

-

2019-07-09

+

2019-09-18

@@ -108,6 +110,10 @@

\[c_\textrm{twa} = \frac{c_0}{t} \left( \frac{g}{k_1} \left( 1 - e^{- k_1 t} \right) + \frac{1-g}{k_2} \left( 1 - e^{- k_2 t} \right) \right) \]

+

HS for \(t > t_b\):

+

\[c_\textrm{twa} = \frac{c_0}{t} \left( + \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) + + \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right) \right) \]

Often, the ratio between the time weighted average concentration \(c_\textrm{twa}\) and the initial concentration \(c_0\)

\[f_\textrm{twa} = \frac{c_\textrm{twa}}{c_0}\]

is needed. This can be calculated from the fitted initial concentration \(c_0\) and the time weighted average concentration \(c_\textrm{twa}\), or directly from the model parameters using the following formulas:

@@ -120,7 +126,11 @@

\[f_\textrm{twa} = \frac{1}{t} \left( \frac{g}{k_1} \left( 1 - e^{- k_1 t} \right) + \frac{1-g}{k_2} \left( 1 - e^{- k_2 t} \right) \right) \]

-

Note that a method for calculating maximum moving window time weighted average concentrations for any model fitted by ‘mkinfit’, and also for metabolites in such models, can be found in the ‘pfm’ package, which is currently not published on CRAN, but available from github and documented at my website.

+

HS for \(t > t_b\):

+

\[f_\textrm{twa} = \frac{1}{t} \left( + \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) + + \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right) \right) \]

+

Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ is include in the ‘mkin’ package (‘max_twa_parent’. If the same is needed for metabolites, the function ‘max_twa’ can be used.

FOCUS Work Group on Degradation Kinetics. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics.

@@ -134,17 +144,20 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 8f3fe97e..aed1debc 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -7,8 +7,9 @@ Example evaluation of FOCUS dataset Z • mkin - - + + + @@ -82,13 +83,14 @@ +

Example evaluation of FOCUS dataset Z

Johannes Ranke

-

2019-07-09

+

2019-09-18

@@ -102,18 +104,18 @@

The data

The following code defines the example dataset from Appendix 7 to the FOCUS kinetics report (FOCUS Work Group on Degradation Kinetics 2014, 354).

-
library(mkin, quietly = TRUE)
+
library(mkin, quietly = TRUE)
 LOD = 0.5
-FOCUS_2006_Z = data.frame(
-  t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21,
+FOCUS_2006_Z = data.frame(
+  t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21,
         42, 61, 96, 124),
-  Z0 = c(100, 81.7, 70.4, 51.1, 41.2, 6.6, 4.6, 3.9, 4.6, 4.3, 6.8,
+  Z0 = c(100, 81.7, 70.4, 51.1, 41.2, 6.6, 4.6, 3.9, 4.6, 4.3, 6.8,
          2.9, 3.5, 5.3, 4.4, 1.2, 0.7),
-  Z1 = c(0, 18.3, 29.6, 46.3, 55.1, 65.7, 39.1, 36, 15.3, 5.6, 1.1,
+  Z1 = c(0, 18.3, 29.6, 46.3, 55.1, 65.7, 39.1, 36, 15.3, 5.6, 1.1,
          1.6, 0.6, 0.5 * LOD, NA, NA, NA),
-  Z2 = c(0, NA, 0.5 * LOD, 2.6, 3.8, 15.3, 37.2, 31.7, 35.6, 14.5,
+  Z2 = c(0, NA, 0.5 * LOD, 2.6, 3.8, 15.3, 37.2, 31.7, 35.6, 14.5,
          0.8, 2.1, 1.9, 0.5 * LOD, NA, NA, NA),
-  Z3 = c(0, NA, NA, NA, NA, 0.5 * LOD, 9.2, 13.1, 22.3, 28.4, 32.5,
+  Z3 = c(0, NA, NA, NA, NA, 0.5 * LOD, 9.2, 13.1, 22.3, 28.4, 32.5,
          25.2, 17.2, 4.8, 4.5, 2.8, 4.4))
 
 FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z)

@@ -130,7 +132,7 @@
 ## with value of zero were removed from the data
plot_sep(m.Z.2a)

-
summary(m.Z.2a, data = FALSE)$bpar
+
summary(m.Z.2a, data = FALSE)$bpar
##             Estimate se_notrans    t value     Pr(>t)    Lower    Upper
 ## Z0_0      9.7015e+01   3.393176 2.8591e+01 6.4352e-21 91.66556 102.3642
 ## k_Z0_sink 7.2231e-10   0.225254 3.2067e-09 5.0000e-01  0.00000      Inf
@@ -148,7 +150,7 @@
 ## with value of zero were removed from the data
plot_sep(m.Z.2a.ff)

-
summary(m.Z.2a.ff, data = FALSE)$bpar
+
summary(m.Z.2a.ff, data = FALSE)$bpar
##            Estimate se_notrans t value     Pr(>t)    Lower    Upper
 ## Z0_0       97.01488   3.301084 29.3888 3.2971e-21 91.66556 102.3642
 ## k_Z0        2.23601   0.207078 10.7979 3.3309e-11  1.95303   2.5600
@@ -166,7 +168,7 @@
 ## value of zero were removed from the data
plot_sep(m.Z.3)

-
summary(m.Z.3, data = FALSE)$bpar
+
summary(m.Z.3, data = FALSE)$bpar
##       Estimate se_notrans t value     Pr(>t)    Lower    Upper
 ## Z0_0  97.01488   2.597342  37.352 2.0106e-24 91.67597 102.3538
 ## k_Z0   2.23601   0.146904  15.221 9.1477e-15  1.95354   2.5593
@@ -201,7 +203,7 @@
 ## 5$bparms.ode, : Observations with value of zero were removed from the data
plot_sep(m.Z.FOCUS)

-
summary(m.Z.FOCUS, data = FALSE)$bpar
+
summary(m.Z.FOCUS, data = FALSE)$bpar
##             Estimate se_notrans t value     Pr(>t)     Lower      Upper
 ## Z0_0       96.838607   1.994273 48.5584 4.0283e-42 92.826626 100.850589
 ## k_Z0        2.215405   0.118459 18.7018 1.0415e-23  1.989465   2.467003
@@ -241,7 +243,7 @@
 ## with value of zero were removed from the data
plot_sep(m.Z.mkin.1)

-
summary(m.Z.mkin.1, data = FALSE)$cov.unscaled
+
summary(m.Z.mkin.1, data = FALSE)$cov.unscaled
##                            Z0_0 log_k_Z0_Z1 log_k_Z1_Z2 log_k_Z2_sink
 ## Z0_0                 3.8375e+00  5.4918e-03  3.0584e-02    1.2969e-01
 ## log_k_Z0_Z1          5.4918e-03  2.7613e-03 -1.8820e-04    2.6634e-04
@@ -312,7 +314,7 @@
 

 
The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized  is excessively small, it seems reasonable to fix it to zero.

 
m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
-                       parms.ini = c(m.Z.mkin.5$bparms.ode[1:7],
+                       parms.ini = c(m.Z.mkin.5$bparms.ode[1:7],
                                      k_Z3_bound_free = 0),
                        fixed_parms = "k_Z3_bound_free",
                        quiet = TRUE)

@@ -372,17 +374,20 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index b8a5215d..3ca93667 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -7,8 +7,9 @@ Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance • mkin - - + + + @@ -82,13 +83,14 @@ +

Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance

Johannes Ranke

-

2019-07-09

+

2019-09-18

@@ -113,9 +115,9 @@ 
p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]])
## 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
-
plot(p5a)
+
plot(p5a)

-
print(p5a)
+
print(p5a)
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 465.21753  56.27506  32.06401 
@@ -161,9 +163,9 @@
 
p5b <- nafta(NAFTA_SOP_Attachment[["p5b"]])

 
## 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

-
plot(p5b)

+
plot(p5b)

 

-
print(p5b)

+
print(p5b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 94.81123 10.10936  7.55871 
@@ -209,9 +211,9 @@
 
p6 <- nafta(NAFTA_SOP_Attachment[["p6"]])

 
## 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

-
plot(p6)

+
plot(p6)

 

-
print(p6)

+
print(p6)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 188.45361  51.00699  42.46931 
@@ -257,9 +259,9 @@
 
p7 <- nafta(NAFTA_SOP_Attachment[["p7"]])

 
## 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

-
plot(p7)

+
plot(p7)

 

-
print(p7)

+
print(p7)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 3661.661 3195.030 3174.145 
@@ -307,12 +309,12 @@
 

 Example on page 8

 
For this dataset, the IORE fit does not converge when the default starting values used by mkin for the IORE model are used. Therefore, a lower value for the rate constant is used here.

-
p8 <- nafta(NAFTA_SOP_Attachment[["p8"]], parms.ini = c(k__iore_parent_sink = 1e-3))

+
p8 <- nafta(NAFTA_SOP_Attachment[["p8"]], parms.ini = c(k__iore_parent_sink = 1e-3))

 
## 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

-
plot(p8)

+
plot(p8)

 

-
print(p8)

+
print(p8)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 1996.9408  444.9237  547.5616 
@@ -362,9 +364,9 @@
 
p9a <- nafta(NAFTA_SOP_Attachment[["p9a"]])

 
## 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

-
plot(p9a)

+
plot(p9a)

 

-
print(p9a)

+
print(p9a)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 839.35238  88.57064   9.93363 
@@ -416,9 +418,9 @@
 ## finite result is doubtful

 
## 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

-
plot(p9b)

+
plot(p9b)

 

-
print(p9b)

+
print(p9b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 35.64867 23.22334 35.64867 
@@ -465,9 +467,9 @@
 
p10 <- nafta(NAFTA_SOP_Attachment[["p10"]])

 
## 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

-
plot(p10)

+
plot(p10)

 

-
print(p10)

+
print(p10)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 899.4089 336.4348 899.4089 
@@ -518,9 +520,9 @@
 
p11 <- nafta(NAFTA_SOP_Attachment[["p11"]])

 
## 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

-
plot(p11)

+
plot(p11)

 

-
print(p11)

+
print(p11)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 579.6805 204.7932 144.7783 
@@ -574,9 +576,9 @@
 ## covariance matrix

 
## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c

 
## The half-life obtained from the IORE model may be used

-
plot(p12a)

+
plot(p12a)

 

-
print(p12a)

+
print(p12a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 695.4440 220.0685 695.4440 
@@ -630,9 +632,9 @@
 ## finite result is doubtful

 
## 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

-
plot(p12b)

+
plot(p12b)

 

-
print(p12b)

+
print(p12b)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 58.90242 19.06353 58.90242 
@@ -682,9 +684,9 @@
 ## finite result is doubtful

 
## 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

-
plot(p13)

+
plot(p13)

 

-
print(p13)

+
print(p13)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 174.5971 142.3951 174.5971 
@@ -735,9 +737,9 @@
 ## finite result is doubtful

 
## 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

-
plot(p14)

+
plot(p14)

 

-
print(p14)

+
print(p14)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 48.43249 28.67746 27.26248 
@@ -789,9 +791,9 @@
 ## finite result is doubtful

 
## 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

-
plot(p15a)

+
plot(p15a)

 

-
print(p15a)

+
print(p15a)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 245.5248 135.0132 245.5248 
@@ -837,9 +839,9 @@
 ## finite result is doubtful

 
## 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

-
plot(p15b)

+
plot(p15b)

 

-
print(p15b)

+
print(p15b)

 
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 106.91629  68.55574 106.91629 
@@ -888,9 +890,9 @@
 
## 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

-
plot(p16)

+
plot(p16)

 

-
print(p16)

+
print(p16)

 
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 3831.804 2062.008 1550.980 
@@ -998,17 +1000,20 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index f71659be..f1ed1f96 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -7,8 +7,9 @@ Benchmark timings for mkin on various systems • mkin - - + + + @@ -82,13 +83,14 @@ +

Benchmark timings for mkin on various systems

Johannes Ranke

-

2019-07-09

+

2019-09-18

@@ -101,12 +103,12 @@

Systems

Each system is characterized by its CPU type, the operating system type and the mkin version.

-
cpu_model <- benchmarkme::get_cpu()$model_name
-operating_system <- Sys.info()[["sysname"]]
-mkin_version <- as.character(packageVersion("mkin"))
-system_string <- paste0(operating_system, ", ", cpu_model, ", mkin version ", mkin_version)
-load("~/git/mkin/vignettes/web_only/mkin_benchmarks.rda")
-mkin_benchmarks[system_string, c("CPU", "OS", "mkin")] <- c(cpu_model, operating_system, mkin_version)
+
cpu_model <- benchmarkme::get_cpu()$model_name
+operating_system <- Sys.info()[["sysname"]]
+mkin_version <- as.character(packageVersion("mkin"))
+system_string <- paste0(operating_system, ", ", cpu_model, ", mkin version ", mkin_version)
+load("~/git/mkin/vignettes/web_only/mkin_benchmarks.rda")
+mkin_benchmarks[system_string, c("CPU", "OS", "mkin")] <- c(cpu_model, operating_system, mkin_version)
 
 if (mkin_version > "0.9.48.1") {
   mmkin_bench <- function(models, datasets, error_model = "const") mmkin(models, datasets, error_model = error_model, cores = 1, quiet = TRUE)
@@ -114,8 +116,8 @@
   mmkin_bench <- function(models, datasets, error_model = NULL) mmkin(models, datasets, reweight.method = error_model, cores = 1, quiet = TRUE)
 }

 
# Parent only
-t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D)))[["elapsed"]]
-t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D), error_model = "tc"))[["elapsed"]]

+t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D)))[["elapsed"]]
+t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D), error_model = "tc"))[["elapsed"]]
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
 ## iteration limit reached without convergence (10)
# One metabolite
@@ -131,7 +133,7 @@
   parent = mkinsub("FOMC", "m1"),
   m1 = mkinsub("SFO"))
## Successfully compiled differential equation model from auto-generated C code.
-
t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D)))[["elapsed"]]
+
t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D)))[["elapsed"]]
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
 ## Observations with value of zero were removed from the data
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
@@ -139,8 +141,8 @@
 
 ## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
 ## Observations with value of zero were removed from the data
-
t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(subset(FOCUS_2006_D, value != 0)), error_model = "tc"))[["elapsed"]]
-t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D), error_model = "obs"))[["elapsed"]]
+
t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(subset(FOCUS_2006_D, value != 0)), error_model = "tc"))[["elapsed"]]
+t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D), error_model = "obs"))[["elapsed"]]
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
 ## Observations with value of zero were removed from the data
 
@@ -155,7 +157,7 @@
                            M2 = mkinsub("SFO"),
                            use_of_ff = "max", quiet = TRUE)
 
-m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
+m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
                            M1 = mkinsub("SFO"),
                            M2 = mkinsub("SFO"),
                            use_of_ff = "max", quiet = TRUE)
@@ -164,16 +166,16 @@
 
 DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
 
-t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))["elapsed"]
-t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))["elapsed"]
+t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))["elapsed"]
+t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))["elapsed"]
 
-t8 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = "tc"))["elapsed"]
-t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "tc"))["elapsed"]
+t8 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = "tc"))["elapsed"]
+t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "tc"))["elapsed"]
 
-t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = "obs"))["elapsed"]
-t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "obs"))["elapsed"]
+t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = "obs"))["elapsed"]
+t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "obs"))["elapsed"]
 
-mkin_benchmarks[system_string, paste0("t", 1:11)] <- c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
+mkin_benchmarks[system_string, paste0("t", 1:11)] <- c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
 mkin_benchmarks
##                                                                                                       CPU
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 AMD Ryzen 7 1700 Eight-Core Processor
@@ -202,78 +204,78 @@
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 5.826
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 5.920
 ##                                                                         t2
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 36.053
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 36.932
 ##                                                                        t3
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.452
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.519
 ##                                                                         t4
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  8.461
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 30.603
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 31.518
 ##                                                                         t5
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1  9.495
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  6.395
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.675
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.386
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  6.002
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.465
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.619
 ##                                                                        t6
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.595
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6  2.61
 ##                                                                        t7
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.202
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.312
 ##                                                                        t8
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.02
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 7.726
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6  8.07
 ##                                                                         t9
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  8.171
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  7.618
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  7.763
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 23.042
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.102
 ##                                                                       t10
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 18.26
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.013
 ##                                                                        t11
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  5.636
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.574
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.365
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  5.626
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 12.106
-
save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.805 +
save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")
@@ -290,17 +292,20 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 0bb564ad..89977591 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -7,8 +7,9 @@ Performance benefit by using compiled model definitions in mkin • mkin - - + + + @@ -82,13 +83,14 @@ +

Performance benefit by using compiled model definitions in mkin

Johannes Ranke

-

2019-07-09

+

2019-09-18

@@ -101,18 +103,18 @@

Model that can also be solved with Eigenvalues

This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The mkinmod() function checks for presence of the gcc compiler using

-
Sys.which("gcc")
+
Sys.which("gcc")
##            gcc 
 ## "/usr/bin/gcc"

First, we build a simple degradation model for a parent compound with one metabolite.

-
library("mkin", quietly = TRUE)
+
library("mkin", quietly = TRUE)
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))

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

 
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.

-
if (require(rbenchmark)) {
-  b.1 <- benchmark(
+
if (require(rbenchmark)) {
+  b.1 <- benchmark(
     "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
                                       solution_type = "deSolve",
                                       use_compiled = FALSE, quiet = TRUE),
@@ -121,11 +123,11 @@
     "deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_2006_D,
                                   solution_type = "deSolve", quiet = TRUE),
     replications = 3)
-  print(b.1)
-  factor_SFO_SFO <- round(b.1["1", "relative"])
+  print(b.1)
+  factor_SFO_SFO <- round(b.1["1", "relative"])
 } else {
   factor_SFO_SFO <- NA
-  print("R package rbenchmark is not available")
+  print("R package rbenchmark is not available")
 }

 
## Lade nötiges Paket: rbenchmark

 
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve",
@@ -163,9 +165,9 @@
 ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
 ## = TRUE): Observations with value of zero were removed from the data

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   3.127    1.000     3.125        0
-## 1 deSolve, not compiled            3  28.337    9.062    28.322        0
-## 2      Eigenvalue based            3   4.320    1.382     4.317        0
+## 3     deSolve, compiled            3   3.124    1.000     3.122        0
+## 1 deSolve, not compiled            3  28.822    9.226    28.807        0
+## 2      Eigenvalue based            3   4.416    1.414     4.413        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -176,21 +178,21 @@
 

 Model that can not be solved with Eigenvalues

 
This evaluation is also taken from the example section of mkinfit.

-
if (require(rbenchmark)) {
+
if (require(rbenchmark)) {
   FOMC_SFO <- mkinmod(
     parent = mkinsub("FOMC", "m1"),
     m1 = mkinsub( "SFO"))
 
-  b.2 <- benchmark(
+  b.2 <- benchmark(
     "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D,
                                       use_compiled = FALSE, quiet = TRUE),
     "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
     replications = 3)
-  print(b.2)
-  factor_FOMC_SFO <- round(b.2["1", "relative"])
+  print(b.2)
+  factor_FOMC_SFO <- round(b.2["1", "relative"])
 } else {
   factor_FOMC_SFO <- NA
-  print("R package benchmark is not available")
+  print("R package benchmark is not available")
 }

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

 
## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet =
@@ -214,14 +216,14 @@
 ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
 ## value of zero were removed from the data

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.783    1.000     4.780        0
-## 1 deSolve, not compiled            3  52.761   11.031    52.733        0
+## 2     deSolve, compiled            3   4.878    1.000     4.875        0
+## 1 deSolve, not compiled            3  53.602   10.989    53.568        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

 
Here we get a performance benefit of a factor of 11 using the version of the differential equation model compiled from C code!

 
This vignette was built with mkin 0.9.49.6 on

-
## R version 3.6.0 (2019-04-26)
+
## R version 3.6.1 (2019-07-05)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 10 (buster)

 
## CPU model: AMD Ryzen 7 1700 Eight-Core Processor

@@ -242,17 +244,20 @@
 

 
 
+
       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

 

 
   
 
+
   
 
diff --git a/docs/authors.html b/docs/authors.html
index 70336977..6e113c82 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -44,6 +46,7 @@
 
 
 
+
   
 
   
@@ -113,6 +116,7 @@
+
@@ -123,7 +127,7 @@
  • -

    Johannes Ranke. Author, maintainer, copyright holder. ORCID +

    Johannes Ranke. Author, maintainer, copyright holder. ORCID

  • @@ -145,19 +149,23 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/index.html b/docs/index.html index b4f5eead..2b8e0303 100644 --- a/docs/index.html +++ b/docs/index.html @@ -7,14 +7,15 @@ Kinetic Evaluation of Chemical Degradation Data • mkin - - + + + @@ -89,6 +90,7 @@ +
@@ -100,7 +102,7 @@

Installation

You can install the latest released version from CRAN from within R:

- +

@@ -185,7 +187,7 @@

Developers

    -
  • Johannes Ranke
    Author, maintainer, copyright holder ORCID
    • +
  • Johannes Ranke
    Author, maintainer, copyright holder ORCID
  • All authors...
@@ -201,17 +203,20 @@

+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ diff --git a/docs/news/index.html b/docs/news/index.html index a49f4b08..058205de 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -44,6 +46,7 @@ + @@ -113,6 +116,7 @@
+
@@ -122,11 +126,14 @@
-
+

-mkin 0.9.49.6 (2019-07-08) Unreleased +mkin 0.9.49.6 (unreleased) Unreleased

    +

  • Vignette ‘twa.html’: Add the maximum time weighted average formulas for the hockey stick model

    • +

  • Support frameless plots (‘frame = FALSE’)

    • +

  • Support to suppress the chi2 error level (‘show_errmin = FALSE’) in ‘plot.mmkin’

  • Update README and the introductory vignette

  • Report ‘OLS’ as error_model_algorithm in the summary in the case that the default error_model (‘const’) is used

  • Support summarizing ‘mkinfit’ objects generated with versions < 0.9.49.5

    • @@ -386,7 +393,7 @@ Bug fixes
    • -endpoints(): For DFOP and SFORB models, where optimize() is used, make use of the fact that the DT50 must be between DT50_k1 and DT50_k2 (DFOP) or DT50_b1 and DT50_b2 (SFORB), as optimize() sometimes did not find the minimum. Likewise for finding DT90 values. Also fit on the log scale to make the function more efficient.
      • +endpoints(): For DFOP and SFORB models, where optimize() is used, make use of the fact that the DT50 must be between DT50_k1 and DT50_k2 (DFOP) or DT50_b1 and DT50_b2 (SFORB), as optimize() sometimes did not find the minimum. Likewise for finding DT90 values. Also fit on the log scale to make the function more efficient.
@@ -709,7 +716,7 @@

Contents

+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/pkgdown.css b/docs/pkgdown.css index c03fb08d..91459581 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -21,8 +21,6 @@ body > .container { display: flex; height: 100%; flex-direction: column; - - padding-top: 60px; } body > .container .row { @@ -102,21 +100,13 @@ a.anchor { margin-top: -40px; } -/* Static header placement on mobile devices */ -@media (max-width: 767px) { - .navbar-fixed-top { - position: absolute; - } - .navbar { - padding: 0; - } -} - - /* Sidebar --------------------------*/ #sidebar { margin-top: 30px; + position: -webkit-sticky; + position: sticky; + top: 70px; } #sidebar h2 { font-size: 1.5em; @@ -133,6 +123,9 @@ a.anchor { .orcid { height: 16px; + /* margins are required by official ORCID trademark and display guidelines */ + margin-left:4px; + margin-right:4px; vertical-align: middle; } @@ -222,6 +215,19 @@ a.sourceLine:hover { visibility: visible; } +/* headroom.js ------------------------ */ + +.headroom { + will-change: transform; + transition: transform 200ms linear; +} +.headroom--pinned { + transform: translateY(0%); +} +.headroom--unpinned { + transform: translateY(-100%); +} + /* mark.js ----------------------------*/ mark { @@ -234,3 +240,17 @@ mark { .html-widget { margin-bottom: 10px; } + +/* fontawesome ------------------------ */ + +.fab { + font-family: "Font Awesome 5 Brands" !important; +} + +/* don't display links in code chunks when printing */ +/* source: https://stackoverflow.com/a/10781533 */ +@media print { + code a:link:after, code a:visited:after { + content: ""; + } +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index eb7e83d2..087a7622 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -2,14 +2,12 @@ (function($) { $(function() { - $("#sidebar") - .stick_in_parent({offset_top: 40}) - .on('sticky_kit:bottom', function(e) { - $(this).parent().css('position', 'static'); - }) - .on('sticky_kit:unbottom', function(e) { - $(this).parent().css('position', 'relative'); - }); + $('.navbar-fixed-top').headroom(); + + $('body').css('padding-top', $('.navbar').height() + 10); + $(window).resize(function(){ + $('body').css('padding-top', $('.navbar').height() + 10); + }); $('body').scrollspy({ target: '#sidebar', diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index db7859c8..76c7efa6 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ pandoc: 2.2.1 -pkgdown: 1.3.0 +pkgdown: 1.4.1 pkgdown_sha: ~ articles: FOCUS_D: FOCUS_D.html diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index 881af6b3..2fe02c97 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -48,6 +50,7 @@ + @@ -117,6 +120,7 @@
+
@@ -135,7 +139,7 @@ 
# S3 method for mmkin
-AIC(object, ..., k = 2)
+AIC(object, ..., k = 2)

Arguments

@@ -145,7 +149,7 @@ - + @@ -161,25 +165,26 @@

Examples

- 
  
 # skip, as it takes > 10 s on winbuilder
-  f <- mmkin(c("SFO", "FOMC", "DFOP"),
-    list("FOCUS A" = FOCUS_2006_A,
+    
   # skip, as it takes > 10 s on winbuilder
+  f <- mmkin(c("SFO", "FOMC", "DFOP"),
+    list("FOCUS A" = FOCUS_2006_A,
          "FOCUS C" = FOCUS_2006_C), cores = 1, quiet = TRUE)
#> Warning: Optimisation did not converge:
-#> false convergence (8)
  AIC(f[1, "FOCUS A"]) # We get a single number for a single fit
#> [1] 55.28197

+#> false convergence (8)
  AIC(f[1, "FOCUS A"]) # We get a single number for a single fit
#> [1] 55.28197

   # For FOCUS A, the models fit almost equally well, so the higher the number
   # of parameters, the higher (worse) the AIC
-  AIC(f[, "FOCUS A"])
#>      df      AIC
+  AIC(f[, "FOCUS A"])
#>      df      AIC
 #> SFO   3 55.28197
 #> FOMC  4 57.28202
-#> DFOP  5 59.28197
  AIC(f[, "FOCUS A"], k = 0) # If we do not penalize additional parameters, we get nearly the same
#>      df      AIC
+#> DFOP  5 59.28197
  AIC(f[, "FOCUS A"], k = 0) # If we do not penalize additional parameters, we get nearly the same
#>      df      AIC
 #> SFO   3 49.28197
 #> FOMC  4 49.28202
 #> DFOP  5 49.28197

   # For FOCUS C, the more complex models fit better
-  AIC(f[, "FOCUS C"])
#>      df      AIC
+  AIC(f[, "FOCUS C"])
#>      df      AIC
 #> SFO   3 59.29336
 #> FOMC  4 44.68652
-#> DFOP  5 29.02372
  

+#> DFOP  5 29.02372
  
+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index b9684490..52d00ac2 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -48,6 +50,7 @@ + @@ -117,6 +120,7 @@ +
@@ -134,7 +138,7 @@
- 
CAKE_export(ds, map = c(parent = "Parent"),
+    
CAKE_export(ds, map = c(parent = "Parent"),
   links = NA,
   filename = "CAKE_export.csf", path = ".", overwrite = FALSE,
   study = "Codlemone aerobic soil degradation",
@@ -142,7 +146,7 @@
   time_unit = "days",
   res_unit = "% AR",
   comment = "Created using mkin::CAKE_export",
-  date = Sys.Date(),
+  date = Sys.Date(),
   optimiser = "IRLS")

     
     
Arguments

@@ -226,19 +230,23 @@
   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index 4a0432e0..b34d00a1 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -48,6 +50,7 @@
 
 
 
+
   
 
   
@@ -117,6 +120,7 @@
 
 
       
+
       
 
 

@@ -176,7 +180,7 @@
     
 
     
Examples

-    
  plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim=c(0,100))

+    
  plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim=c(0,100))

   

   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 62f4a23f..ae120587 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -47,6 +49,7 @@
 
 
 
+
   
 
   
@@ -116,6 +119,7 @@
 
 
       
+
       
 
 

@@ -168,7 +172,7 @@
 
     
Examples

     
  # Only use one core, to pass R CMD check --as-cran
-  fits <- mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C),
+  fits <- mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C),
                 cores = 1, quiet = TRUE)
   fits["FOMC", ]
#>       dataset
 #> model  B       C      
@@ -184,7 +188,7 @@
 #>   SFO List,39
 #> attr(,"class")
 #> [1] "mmkin"

-  head(
+  head(
     # This extracts an mkinfit object with lots of components
     fits[["FOMC", "B"]]
   )
#> $par
@@ -223,19 +227,23 @@
   

 

 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
index 6da112f3..8f418b75 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -51,6 +53,7 @@ in this fit." />
 
 
 
+
   
 
   
@@ -120,6 +123,7 @@ in this fit." />
 
 
       
+
       
 
 

@@ -153,7 +157,9 @@ in this fit.

     
DT50
The resulting half-life of the parent compound

     
DT90
The resulting DT90 of the parent compound

     
dataset
The FOCUS dataset that was used

-  
+  
+
+
     
     
Source

 
@@ -165,7 +171,7 @@ in this fit.

     
 
     
Examples

-    
data(FOCUS_2006_DFOP_ref_A_to_B)

+    
data(FOCUS_2006_DFOP_ref_A_to_B)

   

   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
index 729e23b2..a457a4a2 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -51,6 +53,7 @@ in this fit." />
 
 
 
+
   
 
   
@@ -120,6 +123,7 @@ in this fit." />
 
 
       
+
       
 
 

@@ -152,7 +156,9 @@ in this fit.

     
DT50
The resulting half-life of the parent compound

     
DT90
The resulting DT90 of the parent compound

     
dataset
The FOCUS dataset that was used

-  
+  
+
+
     
     
Source

 
@@ -164,7 +170,7 @@ in this fit.

     
 
     
Examples

-    
data(FOCUS_2006_FOMC_ref_A_to_F)

+    
data(FOCUS_2006_FOMC_ref_A_to_F)

   

   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
index a0bdd522..4285c70c 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -51,6 +53,7 @@ in this fit." />
 
 
 
+
   
 
   
@@ -120,6 +123,7 @@ in this fit." />
 
 
       
+
       
 
 

@@ -153,7 +157,9 @@ in this fit.

     
DT50
The resulting half-life of the parent compound

     
DT90
The resulting DT90 of the parent compound

     
dataset
The FOCUS dataset that was used

-  
+  
+
+
     
     
Source

 
@@ -165,7 +171,7 @@ in this fit.

     
 
     
Examples

-    
data(FOCUS_2006_HS_ref_A_to_F)

+    
data(FOCUS_2006_HS_ref_A_to_F)

   

   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
index d92d7d6a..d1dab9a9 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -51,6 +53,7 @@ in this fit." />
 
 
 
+
   
 
   
@@ -120,6 +123,7 @@ in this fit." />
 
 
       
+
       
 
 

@@ -151,7 +155,9 @@ in this fit.

     
DT50
The resulting half-life of the parent compound

     
DT90
The resulting DT90 of the parent compound

     
dataset
The FOCUS dataset that was used

-  
+  
+
+
     
     
Source

 
@@ -163,7 +169,7 @@ in this fit.

     
 
     
Examples

-    
data(FOCUS_2006_SFO_ref_A_to_F)

+    
data(FOCUS_2006_SFO_ref_A_to_F)

   

   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 86721dd2..2f183654 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -47,6 +49,7 @@
 
 
 
+
   
 
   
@@ -116,6 +119,7 @@
 
 
       
+
       
 
 

@@ -132,7 +136,12 @@
     
     

 
-    
FOCUS_2006_datasets

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

         
     
Format

 
@@ -140,7 +149,9 @@
     
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

-  
+  
+
+
     
     
Source

 
@@ -177,19 +188,23 @@
   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index 072ec4c3..df05afbd 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -51,6 +53,7 @@ The form given here differs slightly from the original reference by Gustafson
 
 
 
+
   
 
   
@@ -120,6 +123,7 @@ The form given here differs slightly from the original reference by Gustafson
 
 
       
+
       
 
 

@@ -188,7 +192,7 @@ The form given here differs slightly from the original reference by Gustafson
     
 
     
Examples

-    
  plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100))

+    
  plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100))

   

   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index a3dee0f4..b46902c5 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -48,6 +50,7 @@
 
 
 
+
   
 
   
@@ -117,6 +120,7 @@
 
 
       
+
       
 
 

@@ -177,7 +181,7 @@
     
 
     
Examples

-    
  plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))

+    
  plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))

   

   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index 99467f51..082c2f41 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -48,6 +50,7 @@
 
 
 
+
   
 
   
@@ -117,6 +120,7 @@
 
 
       
+
       
 
 

@@ -176,20 +180,22 @@
     
 
     
Examples

-    
  plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2, ylim = c(0, 100))
  
    fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
+    
  plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2, ylim = c(0, 100))
  # \dontrun{
+    fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
     fit.iore <- mkinfit("IORE", FOCUS_2006_C, quiet = TRUE)
     fit.iore.deS <- mkinfit("IORE", FOCUS_2006_C, solution_type = "deSolve", quiet = TRUE)
 
-    print(data.frame(fit.fomc$par, fit.iore$par, fit.iore.deS$par,
-                     row.names = paste("model par", 1:4)))
#>             fit.fomc.par fit.iore.par fit.iore.deS.par
+    print(data.frame(fit.fomc$par, fit.iore$par, fit.iore.deS$par,
+                     row.names = paste("model par", 1:4)))
#>             fit.fomc.par fit.iore.par fit.iore.deS.par
 #> model par 1  85.87489063    85.874890        85.874890
 #> model par 2   0.05192238    -4.826631        -4.826631
 #> model par 3   0.65096665     1.949403         1.949403
-#> model par 4   1.85744396     1.857444         1.857444
    print(rbind(fomc = endpoints(fit.fomc)$distimes, iore = endpoints(fit.iore)$distimes,
+#> model par 4   1.85744396     1.857444         1.857444
    print(rbind(fomc = endpoints(fit.fomc)$distimes, iore = endpoints(fit.iore)$distimes,
                 iore.deS = endpoints(fit.iore)$distimes))
#>              DT50    DT90 DT50back
 #> fomc     1.785233 15.1479 4.559973
 #> iore     1.785233 15.1479 4.559973
-#> iore.deS 1.785233 15.1479 4.559973
  

+#> iore.deS 1.785233 15.1479 4.559973
  # }
+

   

   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html
index cc760dd7..84d5508a 100644
--- a/docs/reference/NAFTA_SOP_2015.html
+++ b/docs/reference/NAFTA_SOP_2015.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -47,6 +49,7 @@
 
 
 
+
   
 
   
@@ -116,6 +119,7 @@
 
 
       
+
       
 
 

@@ -132,7 +136,8 @@
     
     

 
-    
NAFTA_SOP_2015

+    
NAFTA_SOP_Appendix_B
+  NAFTA_SOP_Appendix_D

         
     
Format

 
@@ -140,7 +145,9 @@
     
name
a factor containing the name of the observed variable

     
time
a numeric vector containing time points

     
value
a numeric vector containing concentrations

-  
+  
+
+
     
     
Source

 
@@ -155,7 +162,7 @@
     
 
     
Examples

-    
  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
+    
  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#> 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 
 #> 
@@ -192,7 +199,7 @@
 #> DFOP  429    2380      841
 #> 
 #> Representative half-life:
-#> [1] 841.41
  plot(nafta_evaluation)

+#> [1] 841.41
  plot(nafta_evaluation)

   
   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html
index 6bb19a4b..a0498a31 100644
--- a/docs/reference/NAFTA_SOP_Attachment.html
+++ b/docs/reference/NAFTA_SOP_Attachment.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -47,6 +49,7 @@
 
 
 
+
   
 
   
@@ -116,6 +119,7 @@
 
 
       
+
       
 
 

@@ -152,7 +156,7 @@
     
 
     
Examples

-    
  nafta_att_p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]], cores = 1)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The half-life obtained from the IORE model may be used
  print(nafta_att_p5a)
#> Sums of squares:
+    
  nafta_att_p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]], cores = 1)
#> 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 
 #> 
@@ -189,7 +193,7 @@
 #> DFOP 55.5 4.42e+11 2.42e+11
 #> 
 #> Representative half-life:
-#> [1] 321.51
  plot(nafta_att_p5a)

+#> [1] 321.51
  plot(nafta_att_p5a)

   

   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index c0d849e6..cb0870a8 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -47,6 +49,7 @@
 
 
 
+
   
 
   
@@ -116,6 +119,7 @@
 
 
       
+
       
 
 

@@ -165,7 +169,7 @@
     
 
     
Examples

-    
  
plot(function(x) SFO.solution(x, 100, 3), 0, 2)

+    
  plot(function(x) SFO.solution(x, 100, 3), 0, 2)

   

   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index 91b153a7..398f787f 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -51,6 +53,7 @@
 
 
 
+
   
 
   
@@ -120,6 +123,7 @@
 
 
       
+
       
 
 

@@ -182,7 +186,7 @@
     
 
     
Examples

-    
  
plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)

+    
  plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)

   

   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index cf873540..eeaf9e5b 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -49,6 +51,7 @@
 
 
 
+
   
 
   
@@ -118,6 +121,7 @@
 
 
       
+
       
 
 

@@ -136,7 +140,7 @@
     
     

 
-    
add_err(prediction, sdfunc, secondary = c("M1", "M2"),
+    
add_err(prediction, sdfunc, secondary = c("M1", "M2"),
           n = 1000, LOD = 0.1, reps = 2,
           digits = 1, seed = NA)

     
@@ -198,14 +202,14 @@
 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.

 # Generate a prediction for a specific set of parameters
-sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
 
 # This is the prediction used for the "Type 2 datasets" on the Piacenza poster
 # from 2015
 d_SFO_SFO <- mkinpredict(m_SFO_SFO,
-                         c(k_parent = 0.1, f_parent_to_M1 = 0.5,
-                           k_M1 = log(2)/1000),
-                         c(parent = 100, M1 = 0),
+                         c(k_parent = 0.1, f_parent_to_M1 = 0.5,
+                           k_M1 = log(2)/1000),
+                         c(parent = 100, M1 = 0),
                          sampling_times)
 
 # Add an error term with a constant (independent of the value) standard deviation
@@ -213,22 +217,25 @@
 d_SFO_SFO_err <- add_err(d_SFO_SFO, function(x) 10, n = 3, seed = 123456789 )
 
 # Name the datasets for nicer plotting
-names(d_SFO_SFO_err) <- paste("Dataset", 1:3)
+names(d_SFO_SFO_err) <- paste("Dataset", 1:3)
 
 # Name the model in the list of models (with only one member in this case) for
 # nicer plotting later on.  Be quiet and use only one core not to offend CRAN
-# checks
f_SFO_SFO <- mmkin(list("SFO-SFO" = m_SFO_SFO),
+# checks
+# \dontrun{
+f_SFO_SFO <- mmkin(list("SFO-SFO" = m_SFO_SFO),
                    d_SFO_SFO_err, cores = 1,
                    quiet = TRUE)
 
-plot(f_SFO_SFO)

+plot(f_SFO_SFO)

 # We would like to inspect the fit for dataset 3 more closely
 # Using double brackets makes the returned object an mkinfit object
 # instead of a list of mkinfit objects, so plot.mkinfit is used
-plot(f_SFO_SFO[[3]], show_residuals = TRUE)

+plot(f_SFO_SFO[[3]], show_residuals = TRUE)

 # If we use single brackets, we should give two indices (model and dataset),
 # and plot.mmkin is used
-plot(f_SFO_SFO[1, 3])

+plot(f_SFO_SFO[1, 3])
# }
+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 4c4c6f45..f0abb0b6 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -50,6 +52,7 @@ with the advantage that the SFORB model can also be used for metabolites." /> + @@ -119,6 +122,7 @@ with the advantage that the SFORB model can also be used for metabolites." /> +
@@ -188,19 +192,23 @@ with the advantage that the SFORB model can also be used for metabolites.

+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index 512cb6e4..f35aee5f 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -75,6 +77,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl + @@ -144,6 +147,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl +
@@ -196,12 +200,15 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl each containing, among others, the following components

title

The name of the dataset, e.g. Soil 1

data

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

-
+ + +

Source

-

Austria (2015). Ethofumesate Renewal Assessment Report Volume 3 Annex B.8 (AS)

+ +

Austria (2015). Ethofumesate Renewal Assessment Report Volume 3 Annex B.8 (AS)

Belgium (2014). Isofetamid (IKF-5411) Draft Assessment Report Volume 3 Annex B.8 (AS)

France (2015). Imazamox Draft Renewal Assessment Report Volume 3 Annex B.8 (AS)

FOCUS (2014) “Generic guidance for Estimating Persistence and @@ -221,7 +228,8 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl

Examples

- 

+    
# \dontrun{
+
 # Model definitions
 sfo_sfo <- mkinmod(
   parent = mkinsub("SFO", to = "A1"),
@@ -244,14 +252,14 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
   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$data)
-names(d_1_2) <- paste("Soil", 1:2)
+)
#> Successfully compiled differential equation model from auto-generated C code.
d_1_2 <- lapply(experimental_data_for_UBA_2019[1:2], function(x) x$data)
+names(d_1_2) <- paste("Soil", 1:2)
 
 
-f_1_2_tc <- mmkin(list("DFOP-SFO-SFO" = dfop_sfo_sfo), d_1_2, error_model = "tc")
+f_1_2_tc <- mmkin(list("DFOP-SFO-SFO" = dfop_sfo_sfo), d_1_2, error_model = "tc")
 
-plot(f_1_2_tc, resplot = "errmod")

-

+plot(f_1_2_tc, resplot = "errmod")

+# }
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 2626e08b..3f9241b4 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -47,6 +49,7 @@ + @@ -116,6 +119,7 @@ +
@@ -153,7 +157,7 @@

Examples

- 
  geometric_mean(c(1,3, 9))
#> [1] 3
  geometric_mean(c(1,3, NA))
#> [1] NA
  geometric_mean(c(1,3, NA), na.rm = TRUE)
#> [1] 1.732051
+ 
  geometric_mean(c(1,3, 9))
#> [1] 3
  geometric_mean(c(1,3, NA))
#> [1] NA
  geometric_mean(c(1,3, NA), na.rm = TRUE)
#> [1] 1.732051
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index d6bd247f..925698d9 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -47,6 +49,7 @@ + @@ -116,6 +119,7 @@ +
@@ -161,15 +165,15 @@

Examples

# Order matters
-ilr(c(0.1, 1, 10))
#> [1] -1.628174 -2.820079
ilr(c(10, 1, 0.1))
#> [1] 1.628174 2.820079
# Equal entries give ilr transformations with zeros as elements
-ilr(c(3, 3, 3))
#> [1] 0 0
# Almost equal entries give small numbers
-ilr(c(0.3, 0.4, 0.3))
#> [1] -0.2034219  0.1174457
# Only the ratio between the numbers counts, not their sum
-invilr(ilr(c(0.7, 0.29, 0.01)))
#> [1] 0.70 0.29 0.01
invilr(ilr(2.1 * c(0.7, 0.29, 0.01)))
#> [1] 0.70 0.29 0.01
# Inverse transformation of larger numbers gives unequal elements
-invilr(-10)
#> [1] 7.213536e-07 9.999993e-01
invilr(c(-10, 0))
#> [1] 7.207415e-07 9.991507e-01 8.486044e-04
# The sum of the elements of the inverse ilr is 1
-sum(invilr(c(-10, 0)))
#> [1] 1
# This is why we do not need all elements of the inverse transformation to go back:
-a <- c(0.1, 0.3, 0.5)
+ilr(c(0.1, 1, 10))
#> [1] -1.628174 -2.820079
ilr(c(10, 1, 0.1))
#> [1] 1.628174 2.820079
# Equal entries give ilr transformations with zeros as elements
+ilr(c(3, 3, 3))
#> [1] 0 0
# Almost equal entries give small numbers
+ilr(c(0.3, 0.4, 0.3))
#> [1] -0.2034219  0.1174457
# Only the ratio between the numbers counts, not their sum
+invilr(ilr(c(0.7, 0.29, 0.01)))
#> [1] 0.70 0.29 0.01
invilr(ilr(2.1 * c(0.7, 0.29, 0.01)))
#> [1] 0.70 0.29 0.01
# Inverse transformation of larger numbers gives unequal elements
+invilr(-10)
#> [1] 7.213536e-07 9.999993e-01
invilr(c(-10, 0))
#> [1] 7.207415e-07 9.991507e-01 8.486044e-04
# The sum of the elements of the inverse ilr is 1
+sum(invilr(c(-10, 0)))
#> [1] 1
# This is why we do not need all elements of the inverse transformation to go back:
+a <- c(0.1, 0.3, 0.5)
 b <- invilr(a)
-length(b) # Four elements
#> [1] 4
ilr(c(b[1:3], 1 - sum(b[1:3]))) # Gives c(0.1, 0.3, 0.5)
#> [1] 0.1 0.3 0.5
+length(b) # Four elements
#> [1] 4
ilr(c(b[1:3], 1 - sum(b[1:3]))) # Gives c(0.1, 0.3, 0.5)
#> [1] 0.1 0.3 0.5
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/index.html b/docs/reference/index.html index 1f0a7327..b86df636 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -44,6 +46,7 @@ + @@ -113,6 +116,7 @@ +
@@ -253,7 +257,7 @@
@@ -283,7 +287,7 @@ @@ -385,7 +389,7 @@ @@ -535,19 +539,23 @@ +

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 6c914dd4..dbe0c116 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -53,6 +55,7 @@ The total number of estimated parameters returned with the value + @@ -122,6 +125,7 @@ The total number of estimated parameters returned with the value +
@@ -135,7 +139,7 @@ The total number of estimated parameters returned with the value

This function simply calculates the product of the likelihood densities - calculated using dnorm, i.e. assuming normal distribution, + calculated using dnorm, i.e. assuming normal distribution, with of the mean predicted by the degradation model, and the standard deviation predicted by the error model.

The total number of estimated parameters returned with the value @@ -145,7 +149,7 @@ The total number of estimated parameters returned with the value 

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

Arguments

An object of class mmkin, containing only one column.
…...

For compatibility with the generic method
-

FOCUS_2006_datasets

+

FOCUS_2006_A FOCUS_2006_B FOCUS_2006_C FOCUS_2006_D FOCUS_2006_E FOCUS_2006_F

Datasets A to F from the FOCUS Kinetics report from 2006
-

NAFTA_SOP_2015

+

NAFTA_SOP_Appendix_B NAFTA_SOP_Appendix_D

Example datasets from the NAFTA SOP published 2015
-

max_twa_parent()

+

max_twa_parent() max_twa_sfo() max_twa_fomc() max_twa_dfop() max_twa_hs()

Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
@@ -155,14 +159,14 @@ The total number of estimated parameters returned with the value - +

An object of class mkinfit.
…...

For compatibility with the generic method

Value

-

An object of class logLik with the number of +

An object of class logLik with the number of estimated parameters (degradation model parameters plus variance model parameters) as attribute.

@@ -173,14 +177,16 @@ The total number of estimated parameters returned with the value

Examples

- 
  
  sfo_sfo <- mkinmod(
+    
  # \dontrun{
+  sfo_sfo <- mkinmod(
     parent = mkinsub("SFO", to = "m1"),
     m1 = mkinsub("SFO")
   )
#> Successfully compiled differential equation model from auto-generated C code.
  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)
#> Warning: Observations with value of zero were removed from the data
  AIC(f_nw, f_obs, f_tc)
#>       df      AIC
+  f_nw <- mkinfit(sfo_sfo, d_t, quiet = TRUE) # no weighting (weights are unity)
#> Warning: Observations with value of zero were removed from the data
  f_obs <- mkinfit(sfo_sfo, d_t, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
  f_tc <- mkinfit(sfo_sfo, d_t, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
  AIC(f_nw, f_obs, f_tc)
#>       df      AIC
 #> f_nw   5 204.4486
 #> f_obs  6 205.8727
-#> f_tc   6 141.9656
  

+#> f_tc   6 141.9656
  # }
+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index eb4b0de0..91fe035e 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -48,6 +50,7 @@ + @@ -117,6 +120,7 @@
+
@@ -182,30 +186,30 @@

Examples

  # Reproduce the plot on page 57 of FOCUS (2014)
-  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.2),
-       from = 0, to = 100, ylim = c(0, 100),
-       xlab = "Time", ylab = "Residue")
  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.4),
-       from = 0, to = 100, add = TRUE, lty = 2, col = 2)
  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.8),
-       from = 0, to = 100, add = TRUE, lty = 3, col = 3)
  plot(function(x) logistic.solution(x, 100, 0.08, 0.001, 0.2),
-       from = 0, to = 100, add = TRUE, lty = 4, col = 4)
  plot(function(x) logistic.solution(x, 100, 0.08, 0.08, 0.2),
-       from = 0, to = 100, add = TRUE, lty = 5, col = 5)
  legend("topright", inset = 0.05,
-         legend = paste0("k0 = ", c(0.0001, 0.0001, 0.0001, 0.001, 0.08),
-                         ", r = ", c(0.2, 0.4, 0.8, 0.2, 0.2)),
+  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.2),
+       from = 0, to = 100, ylim = c(0, 100),
+       xlab = "Time", ylab = "Residue")
  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.4),
+       from = 0, to = 100, add = TRUE, lty = 2, col = 2)
  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.8),
+       from = 0, to = 100, add = TRUE, lty = 3, col = 3)
  plot(function(x) logistic.solution(x, 100, 0.08, 0.001, 0.2),
+       from = 0, to = 100, add = TRUE, lty = 4, col = 4)
  plot(function(x) logistic.solution(x, 100, 0.08, 0.08, 0.2),
+       from = 0, to = 100, add = TRUE, lty = 5, col = 5)
  legend("topright", inset = 0.05,
+         legend = paste0("k0 = ", c(0.0001, 0.0001, 0.0001, 0.001, 0.08),
+                         ", r = ", c(0.2, 0.4, 0.8, 0.2, 0.2)),
          lty = 1:5, col = 1:5)

   # Fit with synthetic data
   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)
+  sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+  parms_logistic <- c(kmax = 0.08, k0 = 0.0001, r = 0.2)
   d_logistic <- mkinpredict(logistic,
-    parms_logistic, c(parent = 100),
+    parms_logistic, c(parent = 100),
     sampling_times)
   d_2_1 <- add_err(d_logistic,
     sdfunc = function(x) sigma_twocomp(x, 0.5, 0.07),
     n = 1, reps = 2, digits = 5, LOD = 0.1, seed = 123456)[[1]]
 
   m <- mkinfit("logistic", d_2_1, quiet = TRUE)
-  plot_sep(m)
  summary(m)$bpar
#>              Estimate   se_notrans   t value       Pr(>t)        Lower
+  plot_sep(m)
  summary(m)$bpar
#>              Estimate   se_notrans   t value       Pr(>t)        Lower
 #> parent_0 1.057896e+02 1.9023449649 55.610120 3.768361e-16 1.016451e+02
 #> kmax     6.398190e-02 0.0143201029  4.467978 3.841828e-04 3.929235e-02
 #> k0       1.612775e-04 0.0005866813  0.274898 3.940351e-01 5.846685e-08
@@ -236,19 +240,23 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 596e51ec..d1c2a805 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -51,6 +53,7 @@ guidance." /> + @@ -120,6 +123,7 @@ guidance." />
+
@@ -140,7 +144,11 @@ guidance.

- 
max_twa_parent(fit, windows)
+ 
max_twa_parent(fit, windows)
+  max_twa_sfo(M0 = 1, k, t)
+  max_twa_fomc(M0 = 1, alpha, beta, t)
+  max_twa_dfop(M0 = 1, k1, k2, g, t)
+  max_twa_hs(M0 = 1, k1, k2, tb, t)

Arguments

@@ -153,11 +161,52 @@ guidance.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
windows

The width of the time windows for which the TWAs should be calculated.
M0

The initial concentration for which the maximum time weighted + average over the decline curve should be calculated. The default + is to use a value of 1, which means that a relative maximum time + weighted average factor (f_twa) is calculated.

k

The rate constant in the case of SFO kinetics.

t

The width of the time window.

alpha

Parameter of the FOMC model.

beta

Parameter of the FOMC model.

k1

The first rate constant of the DFOP or the HS kinetics.

k2

The second rate constant of the DFOP or the HS kinetics.

g

Parameter of the DFOP model.

tb

Parameter of the HS model.

Value

-

A numeric vector, named using the windows argument.

+

For max_twa_parent, a numeric vector, named using the windows argument. + For the other functions, a numeric vector of length one (also known as 'a + number').

References

@@ -170,7 +219,7 @@ guidance.

Examples

  fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-  max_twa_parent(fit, c(7, 21))
#>        7       21 
+  max_twa_parent(fit, c(7, 21))
#>        7       21 
 #> 34.71343 18.22124
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index aa888f0f..91c55a6a 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -49,6 +51,7 @@ + @@ -118,6 +121,7 @@ +
@@ -149,7 +153,9 @@ treatment

value

a numeric vector containing concentrations in percent of applied radioactivity

soil

a factor containing the name of the soil

- + + +

Source

@@ -158,9 +164,10 @@

Examples

- 
  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.
  
    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)$bpar
#> Warning: NaNs wurden erzeugt
#>                      Estimate   se_notrans   t value       Pr(>t)        Lower
+    
  SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"),
+                         phenol = list(type = "SFO", to = "anisole"),
+                         anisole = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  # \dontrun{
+    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
    summary(fit.1)$bpar
#> Warning: NaNs wurden erzeugt
#>                      Estimate   se_notrans   t value       Pr(>t)        Lower
 #> T245_0           1.038550e+02 2.1508110557 48.286452 3.542232e-18 99.246062215
 #> k_T245_sink      1.636106e-02          NaN       NaN          NaN  0.012661558
 #> k_T245_phenol    2.700936e-02          NaN       NaN          NaN  0.024487315
@@ -188,9 +195,9 @@
 #> phenol    1.711229   5.68458
 #> anisole 103.784092 344.76329
 #> 
    # k_phenol_sink is really small, therefore fix it to zero
-    fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),
-                   parms.ini = c(k_phenol_sink = 0),
-                   fixed_parms = "k_phenol_sink", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
    summary(fit.2)$bpar
#>                      Estimate   se_notrans   t value       Pr(>t)        Lower
+    fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),
+                   parms.ini = c(k_phenol_sink = 0),
+                   fixed_parms = "k_phenol_sink", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
    summary(fit.2)$bpar
#>                      Estimate   se_notrans   t value       Pr(>t)        Lower
 #> T245_0           1.038550e+02 2.1623653063 48.028441 4.993105e-19 99.271025146
 #> k_T245_sink      1.636106e-02 0.0019676255  8.315130 1.673674e-07  0.012679148
 #> k_T245_phenol    2.700936e-02 0.0012421966 21.743224 1.314080e-13  0.024500319
@@ -215,7 +222,8 @@
 #> T245     15.982025  53.09114
 #> phenol    1.711229   5.68458
 #> anisole 103.784092 344.76329
-#> 
    plot_sep(fit.2)
  

+#> 
    plot_sep(fit.2)
  # }
+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 479bc5dd..169aefd4 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -49,6 +51,7 @@ + @@ -118,6 +121,7 @@ +
@@ -202,19 +206,23 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index c95fe952..d8ae913f 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -48,6 +50,7 @@ + @@ -117,6 +120,7 @@ +
@@ -156,7 +160,7 @@

Examples

- 
wide <- data.frame(t = c(1,2,3), x = c(1,4,7), y = c(3,4,5))
+    
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
@@ -180,19 +184,23 @@
   

 

 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
+ + diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 2a34173c..e0f4fbb6 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -47,6 +49,7 @@ + @@ -116,6 +119,7 @@ +
@@ -141,15 +145,23 @@

Fields

-
+ +
title

A full title for the dataset

-
sampling

times The sampling times

-
time_unit

The time unit

-
observed

Names of the observed compounds

-
unit

The unit of the observations

-
replicates

The number of replicates

-
data

A dataframe with at least the columns name, time and value + +

sampling

times The sampling times

+ +
time_unit

The time unit

+ +
observed

Names of the observed compounds

+ +
unit

The unit of the observations

+ +
replicates

The number of replicates

+ +
data

A dataframe with at least the columns name, time and value in order to be compatible with mkinfit

+
@@ -170,19 +182,23 @@ in order to be compatible with mkinfit

+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 359ce5f5..941e30f5 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -48,6 +50,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> + @@ -117,6 +120,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> +
@@ -179,14 +183,16 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.

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
+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
  fit_FOCUS_E = mkinfit(SFO_SFO, FOCUS_2006_E, quiet = TRUE)
-  round(mkinerrmin(fit_FOCUS_E), 4)
#>          err.min n.optim df
+#> 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
 #> All data  0.1544       4 13
 #> parent    0.1659       2  7
-#> m1        0.1095       2  6
+#> m1 0.1095 2 6
# } +
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 80f0abf5..be2f7614 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -52,6 +54,7 @@ + @@ -121,6 +124,7 @@ +
@@ -143,11 +147,12 @@ 
mkinerrplot(object,
-    obs_vars = names(object$mkinmod$map),
-    xlim = c(0, 1.1 * max(object$data$predicted)),
+    obs_vars = names(object$mkinmod$map),
+    xlim = c(0, 1.1 * max(object$data$predicted)),
     xlab = "Predicted", ylab = "Squared residual",
     maxy = "auto", legend= TRUE, lpos = "topright",
     col_obs = "auto", pch_obs = "auto",
+    frame = TRUE,
     ...)

Arguments

@@ -186,7 +191,7 @@ lpos

Where should the legend be placed? Default is "topright". Will be passed on to - legend.

+ legend.

col_obs @@ -197,8 +202,12 @@

Symbols to be used for the observed variables.

- … -

further arguments passed to plot.

+ frame +

Should a frame be drawn around the plots?

+ + + ... +

further arguments passed to plot.

@@ -213,7 +222,9 @@

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, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
mkinerrplot(fit)
+ 
# \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)
#> Warning: Observations with value of zero were removed from the data
mkinerrplot(fit)
# }
+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 2ba4cc0c..b620f364 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -55,6 +57,7 @@ Per default, parameters in the kinetic models are internally transformed in + @@ -124,6 +127,7 @@ Per default, parameters in the kinetic models are internally transformed in +
@@ -137,7 +141,7 @@ Per default, parameters in the kinetic models are internally transformed in

This function maximises the likelihood of the observed data using - the Port algorithm nlminb, and the specified initial or fixed + the Port algorithm nlminb, and the specified initial or fixed parameters and starting values. In each step of the optimsation, the kinetic model is solved using the function mkinpredict. The parameters of the selected error model are fitted simultaneously with the degradation @@ -152,18 +156,18 @@ Per default, parameters in the kinetic models are internally transformed in parms.ini = "auto", state.ini = "auto", err.ini = "auto", - fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], + fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], from_max_mean = FALSE, - solution_type = c("auto", "analytical", "eigen", "deSolve"), + solution_type = c("auto", "analytical", "eigen", "deSolve"), method.ode = "lsoda", use_compiled = "auto", - control = list(eval.max = 300, iter.max = 200), + control = list(eval.max = 300, iter.max = 200), transform_rates = TRUE, transform_fractions = TRUE, quiet = FALSE, atol = 1e-8, rtol = 1e-10, n.outtimes = 100, - error_model = c("const", "obs", "tc"), - error_model_algorithm = c("d_3", "direct", "twostep", "threestep", "fourstep", "IRLS", + error_model = c("const", "obs", "tc"), + error_model_algorithm = c("d_3", "direct", "twostep", "threestep", "fourstep", "IRLS", "OLS"), reweight.tol = 1e-8, reweight.max.iter = 10, trace_parms = FALSE, ...) @@ -267,7 +271,7 @@ Per default, parameters in the kinetic models are internally transformed in control -

A list of control arguments passed to nlminb.

+

A list of control arguments passed to nlminb.

transform_rates @@ -368,7 +372,7 @@ Per default, parameters in the kinetic models are internally transformed in

Should a trace of the parameter values be listed?

- … + ...

Further arguments that will be passed on to deSolve.

@@ -381,7 +385,7 @@ Per default, parameters in the kinetic models are internally transformed in

See also

Plotting methods plot.mkinfit and mkinparplot.

-

Comparisons of models fitted to the same data can be made using AIC +

Comparisons of models fitted to the same data can be made using AIC by virtue of the method logLik.mkinfit.

Fitting of several models to several datasets in a single call to mmkin.

@@ -402,17 +406,17 @@ Per default, parameters in the kinetic models are internally transformed in

Examples

# Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version used for fitting:    0.9.49.6 
-#> R version used for fitting:       3.6.0 
-#> Date of fit:     Tue Jul  9 08:58:09 2019 
-#> Date of summary: Tue Jul  9 08:58:09 2019 
+summary(fit)
#> mkin version used for fitting:    0.9.49.6 
+#> R version used for fitting:       3.6.1 
+#> Date of fit:     Wed Sep 18 12:55:32 2019 
+#> Date of summary: Wed Sep 18 12:55:32 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.475 s
+#> Fitted using 222 model solutions performed in 0.459 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -484,9 +488,9 @@ Per default, parameters in the kinetic models are internally transformed in
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
-print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
+print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#> Warning: Observations with value of zero were removed from the data
#>        User      System verstrichen 
-#>       1.581       0.000       1.582 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
+#>       1.480       0.000       1.482 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -497,8 +501,9 @@ Per default, parameters in the kinetic models are internally transformed in
 #>              DT50      DT90
 #> parent   7.022929  23.32967
 #> m1     131.760712 437.69961
-#> 
# deSolve is slower when no C compiler (gcc) was available during model generation
-print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D,
+#> 
# \dontrun{
+# deSolve is slower when no C compiler (gcc) was available during model generation
+print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "deSolve")))
#> Warning: Observations with value of zero were removed from the data
#> Ordinary least squares optimisation
#> Sum of squared residuals at call 1: 18915.53
 #> Sum of squared residuals at call 2: 18915.53
 #> Sum of squared residuals at call 6: 11424.02
@@ -558,7 +563,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> Sum of squared residuals at call 126: 371.2134
 #> Sum of squared residuals at call 135: 371.2134
 #> Negative log-likelihood at call 145: 97.22429
#> Optimisation successfully terminated.
#>        User      System verstrichen 
-#>       1.109       0.000       1.109 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
+#>       1.045       0.000       1.046 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -569,9 +574,11 @@ Per default, parameters in the kinetic models are internally transformed in
 #>              DT50      DT90
 #> parent   7.022929  23.32967
 #> m1     131.760712 437.69961
-#> 

-# Use stepwise fitting, using optimised parameters from parent only fit, FOMC
-
FOMC_SFO <- mkinmod(
+#> 
# }
+
+# Use stepwise fitting, using optimised parameters from parent only fit, FOMC
+# \dontrun{
+FOMC_SFO <- mkinmod(
   parent = mkinsub("FOMC", "m1"),
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
# Use starting parameters from parent only FOMC fit
@@ -580,18 +587,20 @@ Per default, parameters in the kinetic models are internally transformed in
   parms.ini = fit.FOMC$bparms.ode)
#> Warning: Observations with value of zero were removed from the data

 # Use stepwise fitting, using optimised parameters from parent only fit, SFORB
 SFORB_SFO <- mkinmod(
-  parent = list(type = "SFORB", 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
+  parent = list(type = "SFORB", to = "m1", sink = TRUE),
+  m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve",
                                  quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
# Use starting parameters from parent only SFORB fit (not really needed in this case)
 fit.SFORB = mkinfit("SFORB", FOCUS_2006_D, quiet = TRUE)
-fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data

-
# Weighted fits, including IRLS
+fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
# }
+
+# \dontrun{
+# Weighted fits, including IRLS
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
-                      m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.6 
-#> R version used for fitting:       3.6.0 
-#> Date of fit:     Tue Jul  9 08:58:26 2019 
-#> Date of summary: Tue Jul  9 08:58:26 2019 
+                      m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.6 
+#> R version used for fitting:       3.6.1 
+#> Date of fit:     Wed Sep 18 12:55:47 2019 
+#> Date of summary: Wed Sep 18 12:55:47 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -599,7 +608,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 421 model solutions performed in 1.136 s
+#> Fitted using 421 model solutions performed in 1.077 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -707,10 +716,10 @@ Per default, parameters in the kinetic models are internally transformed in
 #>   100       m1    31.04  31.98163 -9.416e-01
 #>   100       m1    33.13  31.98163  1.148e+00
 #>   120       m1    25.15  28.78984 -3.640e+00
-#>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.6 
-#> R version used for fitting:       3.6.0 
-#> Date of fit:     Tue Jul  9 08:58:29 2019 
-#> Date of summary: Tue Jul  9 08:58:29 2019 
+#>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.6 
+#> R version used for fitting:       3.6.1 
+#> Date of fit:     Wed Sep 18 12:55:50 2019 
+#> Date of summary: Wed Sep 18 12:55:50 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -718,7 +727,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 979 model solutions performed in 2.836 s
+#> Fitted using 979 model solutions performed in 2.624 s
 #> 
 #> Error model: Variance unique to each observed variable 
 #> 
@@ -839,10 +848,10 @@ Per default, parameters in the kinetic models are internally transformed in
 #>   100       m1    31.04  31.98773 -9.477e-01
 #>   100       m1    33.13  31.98773  1.142e+00
 #>   120       m1    25.15  28.80429 -3.654e+00
-#>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.6 
-#> R version used for fitting:       3.6.0 
-#> Date of fit:     Tue Jul  9 08:58:39 2019 
-#> Date of summary: Tue Jul  9 08:58:39 2019 
+#>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.6 
+#> R version used for fitting:       3.6.1 
+#> Date of fit:     Wed Sep 18 12:55:59 2019 
+#> Date of summary: Wed Sep 18 12:55:59 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -850,7 +859,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 2289 model solutions performed in 9.908 s
+#> Fitted using 2289 model solutions performed in 9.376 s
 #> 
 #> Error model: Two-component variance function 
 #> 
@@ -964,7 +973,8 @@ Per default, parameters in the kinetic models are internally transformed in
 #>   100       m1    31.04  32.20082  -1.160823
 #>   100       m1    33.13  32.20082   0.929177
 #>   120       m1    25.15  29.04130  -3.891304
-#>   120       m1    33.31  29.04130   4.268696

+#>   120       m1    33.31  29.04130   4.268696
# }
+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 16f80fe0..81fed454 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -52,6 +54,7 @@ For the definition of model types and their parameters, the equations given + @@ -121,6 +124,7 @@ For the definition of model types and their parameters, the equations given +
@@ -220,21 +224,22 @@ For the definition of model types and their parameters, the equations given

Examples

# Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)
-SFO <- mkinmod(parent = list(type = "SFO"))
+SFO <- mkinmod(parent = list(type = "SFO"))
 
 # One parent compound, one metabolite, both single first order
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.

-
# The above model used to be specified like this, before the advent of mkinsub()
+# \dontrun{
+# 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.

+  parent = list(type = "SFO", to = "m1"),
+  m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.

 # Show details of creating the C function
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file37c428e02a2c.c 2> file37c428e02a2c.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file419a1fa6c394.c 2> file419a1fa6c394.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
@@ -257,14 +262,15 @@ For the definition of model types and their parameters, the equations given
 #>  19: }
#> Successfully compiled differential equation model from auto-generated C code.

 # If we have several parallel metabolites 
 # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
-m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
+m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
                            M1 = mkinsub("SFO"),
                            M2 = mkinsub("SFO"),
                            use_of_ff = "max", quiet = TRUE)
 
 fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par,
                           synthetic_data_for_UBA_2014[[12]]$data,
-                          quiet = TRUE)
+ quiet = TRUE) +# }
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 05a597a1..79a4cc2b 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -48,6 +50,7 @@ + @@ -117,6 +120,7 @@ +
@@ -151,10 +155,11 @@

Examples

- 
model <- mkinmod(
-  T245 = mkinsub("SFO", to = c("phenol"), sink = FALSE),
-  phenol = mkinsub("SFO", to = c("anisole")),
-  anisole = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
mkinparplot(fit)
+ 
# \dontrun{
+model <- mkinmod(
+  T245 = mkinsub("SFO", to = c("phenol"), sink = FALSE),
+  phenol = mkinsub("SFO", to = c("anisole")),
+  anisole = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
mkinparplot(fit)
# }
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index f32e0758..33d69b6d 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -47,6 +49,7 @@ + @@ -116,6 +119,7 @@ +
@@ -142,7 +146,7 @@

an object of class mkinfit.

- … + ...

further arguments passed to plot.mkinfit.

@@ -166,19 +170,23 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index fc3e8512..d162135a 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -49,6 +51,7 @@ + @@ -118,6 +121,7 @@ +
@@ -136,7 +140,7 @@
- 
mkinpredict(x, odeparms, odeini, outtimes = seq(0, 120, by = 0.1),
+    
mkinpredict(x, odeparms, odeini, outtimes = seq(0, 120, by = 0.1),
     solution_type = "deSolve", use_compiled = "auto", method.ode = "lsoda",
     atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...)

     
@@ -200,7 +204,7 @@
     variables (default) or for all state variables (if set to FALSE).

     
     
-      …
+      ...
       
Further arguments passed to the ode solver in case such a solver is used.

     
     
@@ -213,7 +217,7 @@
     
Examples

     
  SFO <- mkinmod(degradinol = mkinsub("SFO"))
   # Compare solution types
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
         solution_type = "analytical")
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
@@ -235,7 +239,7 @@
 #> 18   17   0.6096747
 #> 19   18   0.4516581
 #> 20   19   0.3345965
-#> 21   20   0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#> 21   20   0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
         solution_type = "deSolve")
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
@@ -257,7 +261,7 @@
 #> 18   17   0.6096747
 #> 19   18   0.4516581
 #> 20   19   0.3345965
-#> 21   20   0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#> 21   20   0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
         solution_type = "deSolve", use_compiled = FALSE)
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
@@ -279,7 +283,7 @@
 #> 18   17   0.6096747
 #> 19   18   0.4516581
 #> 20   19   0.3345965
-#> 21   20   0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#> 21   20   0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
         solution_type = "eigen")
#>    time  degradinol
 #> 1     0 100.0000000
 #> 2     1  74.0818221
@@ -304,42 +308,43 @@
 #> 21   20   0.2478752

 
   # Compare integration methods to analytical solution
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
         solution_type = "analytical")[21,]
#>    time degradinol
-#> 21   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#> 21   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
         method = "lsoda")[21,]
#>    time degradinol
-#> 21   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#> 21   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
         method = "ode45")[21,]
#>    time degradinol
-#> 21   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#> 21   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
         method = "rk4")[21,]
#>    time degradinol
 #> 21   20  0.2480043
 # rk4 is not as precise here
 
   # The number of output times used to make a lot of difference until the
   # default for atol was adjusted
-  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
-        seq(0, 20, by = 0.1))[201,]
#>     time degradinol
-#> 201   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
-        seq(0, 20, by = 0.01))[2001,]
#>      time degradinol
+  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
+        seq(0, 20, by = 0.1))[201,]
#>     time degradinol
+#> 201   20  0.2478752
  mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
+        seq(0, 20, by = 0.01))[2001,]
#>      time degradinol
 #> 2001   20  0.2478752

   # Check compiled model versions - they are faster than the eigenvalue based solutions!
-  SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),
-                    m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  system.time(
-    print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
-                c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
+  SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),
+                    m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  system.time(
+    print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
+                c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "eigen")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.003       0.000       0.003 
  system.time(
-    print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
-                c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
+#>       0.004       0.000       0.003 
  system.time(
+    print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
+                c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.001       0.000       0.002 
  system.time(
-    print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
-                c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
+#>       0.002       0.000       0.001 
  system.time(
+    print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
+                c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve", use_compiled = FALSE)[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.022       0.000       0.021 

-  
    # Predict from a fitted model
+#>       0.021       0.000       0.021 

+  # \dontrun{
+    # Predict from a fitted model
     f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Ordinary least squares optimisation
#> Sum of squared residuals at call 1: 552.5739
 #> Sum of squared residuals at call 3: 552.5739
 #> Sum of squared residuals at call 4: 552.5739
@@ -368,13 +373,14 @@
 #> Sum of squared residuals at call 59: 196.5334
 #> Sum of squared residuals at call 65: 196.5334
 #> Sum of squared residuals at call 73: 196.5334
-#> Negative log-likelihood at call 75: 26.64668
#> Optimisation successfully terminated.
    head(mkinpredict(f))
#>   time   parent       m1
+#> Negative log-likelihood at call 75: 26.64668
#> Optimisation successfully terminated.
    head(mkinpredict(f))
#>   time   parent       m1
 #> 1  0.0 82.49216 0.000000
 #> 2  0.1 80.00563 1.179955
 #> 3  0.2 77.59404 2.312580
 #> 4  0.3 75.25515 3.399419
 #> 5  0.4 72.98675 4.441969
-#> 6  0.5 70.78673 5.441679
  

+#> 6  0.5 70.78673 5.441679
  # }
+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 1c485c93..d841909f 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -50,6 +52,7 @@ + @@ -119,6 +122,7 @@ +
@@ -139,8 +143,8 @@ 
mkinresplot(object,
-    obs_vars = names(object$mkinmod$map),
-    xlim = c(0, 1.1 * max(object$data$time)),
+    obs_vars = names(object$mkinmod$map),
+    xlim = c(0, 1.1 * max(object$data$time)),
     xlab = "Time", ylab = "Residual",
     maxabs = "auto", legend = TRUE, lpos = "topright", ...)
@@ -180,11 +184,11 @@ lpos

Where should the legend be placed? Default is "topright". Will be passed on to - legend.

+ legend.

- … -

further arguments passed to plot.

+ ... +

further arguments passed to plot.

@@ -218,19 +222,23 @@ +

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index e3035247..1523138c 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -48,6 +50,7 @@ + @@ -117,6 +120,7 @@ +
@@ -171,8 +175,8 @@

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.

+  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"),
@@ -197,19 +201,23 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 49860cbe..9bb7926b 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -48,6 +50,7 @@ + @@ -117,6 +120,7 @@ +
@@ -135,7 +139,7 @@ 
mmkin(models, datasets,
-      cores = round(detectCores()/2), cluster = NULL, ...)
+ cores = round(detectCores()/2), cluster = NULL, ...)

Arguments

@@ -164,7 +168,7 @@ execution.

- +
…...

Further arguments that will be passed to mkinfit.
@@ -180,22 +184,23 @@

Examples

- 
m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
+    
# \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.

-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$data)
-names(datasets) <- paste("Dataset", 1:3)
+models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)
+datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)
+names(datasets) <- paste("Dataset", 1:3)
 
-time_default <- system.time(fits.0 <- mmkin(models, datasets, quiet = TRUE))
-time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
+time_default <- system.time(fits.0 <- mmkin(models, datasets, quiet = TRUE))
+time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
#>        User      System verstrichen 
-#>       0.045       0.038       5.672 
time_1
#>        User      System verstrichen 
-#>      20.914       0.000      20.928 

+#>       0.012       0.024       5.064 
time_1
#>        User      System verstrichen 
+#>      19.094       0.000      19.104 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
 #>   0.7340481   0.2659519   0.7505684   0.2494316 
@@ -210,12 +215,13 @@
 #> M2     33.7200958 112.015734
 #> 

 # plot.mkinfit handles rows or columns of mmkin result objects
-plot(fits.0[1, ])
plot(fits.0[1, ], obs_var = c("M1", "M2"))
plot(fits.0[, 1])
# Use double brackets to extract a single mkinfit object, which will be plotted
+plot(fits.0[1, ])
plot(fits.0[1, ], obs_var = c("M1", "M2"))
plot(fits.0[, 1])
# Use double brackets to extract a single mkinfit object, which will be plotted
 # by plot.mkinfit and can be plotted using plot_sep
-plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)
plot_sep(fits.0[[1, 1]])
+plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)
plot_sep(fits.0[[1, 1]])
 # Plotting with mmkin (single brackets, extracting an mmkin object) does not
 # allow to plot the observed variables separately
-plot(fits.0[1, 1])

+plot(fits.0[1, 1])
# }
+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 1153f553..c5ea9a9a 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -49,6 +51,7 @@ + @@ -118,6 +121,7 @@ +
@@ -136,7 +140,7 @@
- 
nafta(ds, title = NA, quiet = FALSE, …)
+ 
nafta(ds, title = NA, quiet = FALSE, ...)

Arguments

@@ -157,7 +161,7 @@ - +

Should the evaluation text be shown?
…...

Further arguments passed to mmkin.
@@ -182,7 +186,7 @@

Examples

- 
  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
+    
  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#> 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 
 #> 
@@ -219,7 +223,7 @@
 #> DFOP  429    2380      841
 #> 
 #> Representative half-life:
-#> [1] 841.41
  plot(nafta_evaluation)

+#> [1] 841.41
  plot(nafta_evaluation)
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 7c6f2aac..795262f8 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -52,6 +54,7 @@ If the current plot device is a tikz device, + @@ -121,6 +124,7 @@ If the current plot device is a tikz device, +
@@ -136,28 +140,28 @@ If the current plot device is a tikz device,

Solves the differential equations with the optimised and fixed parameters from a previous successful call to mkinfit and plots the observed data together with the solution of the fitted model.

-

If the current plot device is a tikz device, +

If the current plot device is a tikz device, then latex is being used for the formatting of the chi2 error level, if show_errmin = TRUE.

- 
# S3 method for mkinfit
-plot(x, fit = x,
-  obs_vars = names(fit$mkinmod$map),
-  xlab = "Time", ylab = "Observed",
-  xlim = range(fit$data$time),
-  ylim = "default",
-  col_obs = 1:length(obs_vars), pch_obs = col_obs,
-  lty_obs = rep(1, length(obs_vars)),
-  add = FALSE, legend = !add,
-  show_residuals = FALSE,
-  show_errplot = FALSE,
-  maxabs = "auto",
-  sep_obs = FALSE, rel.height.middle = 0.9,
-  lpos = "topright", inset = c(0.05, 0.05),
-  show_errmin = FALSE, errmin_digits = 3, …)
-plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, …)
+ 
# S3 method for mkinfit
+plot(x, fit = x,
+  obs_vars = names(fit$mkinmod$map),
+  xlab = "Time", ylab = "Observed",
+  xlim = range(fit$data$time),
+  ylim = "default",
+  col_obs = 1:length(obs_vars), pch_obs = col_obs,
+  lty_obs = rep(1, length(obs_vars)),
+  add = FALSE, legend = !add,
+  show_residuals = FALSE,
+  show_errplot = FALSE,
+  maxabs = "auto",
+  sep_obs = FALSE, rel.height.middle = 0.9,
+  lpos = "topright", inset = c(0.05, 0.05),
+  show_errmin = FALSE, errmin_digits = 3, frame = TRUE, ...)
+plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, ...)

Arguments

@@ -242,12 +246,12 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … - - + @@ -258,8 +262,12 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … - - + + + + + +
lpos

Position(s) of the legend(s). Passed to legend as the first argument. +

Position(s) of the legend(s). Passed to legend as the first argument. If not length one, this should be of the same length as the obs_var argument.
inset

Passed to legend if applicable.

Passed to legend if applicable.
show_errmin

The number of significant digits for rounding the FOCUS chi2 error percentage.
…

Further arguments passed to plot.

frame

Should a frame be drawn around the plots?

...

Further arguments passed to plot.
@@ -269,21 +277,23 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …

Examples

- 
# One parent compound, one metabolite, both single first order, path from
-# parent to sink included
-
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, error_model = "tc")
#> Warning: Observations with value of zero were removed from the data
plot(fit)
plot(fit, show_residuals = TRUE)
plot(fit, show_errplot = TRUE)

+    
# 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, error_model = "tc")
#> Warning: Observations with value of zero were removed from the data
plot(fit)
plot(fit, show_residuals = TRUE)
plot(fit, show_errplot = TRUE)

 # Show the observed variables separately
-plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright"))

+plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright"))

 # Show the observed variables separately, with residuals
-plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"),
+plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"),
      show_errmin = TRUE)

 # The same can be obtained with less typing, using the convenience function plot_sep
-plot_sep(fit, lpos = c("topright", "bottomright"))
+plot_sep(fit, lpos = c("topright", "bottomright"))
 
 # Show the observed variables separately, with the error model
-plot(fit, sep_obs = TRUE, show_errplot = TRUE, lpos = c("topright", "bottomright"),
-     show_errmin = TRUE)

+plot(fit, sep_obs = TRUE, show_errplot = TRUE, lpos = c("topright", "bottomright"),
+     show_errmin = TRUE)
# }
+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index ef734bc8..9a11108f 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -51,6 +53,7 @@ If the current plot device is a tikz device, + @@ -120,6 +123,7 @@ If the current plot device is a tikz device, +
@@ -135,15 +139,15 @@ If the current plot device is a tikz device,

When x is a row selected from an mmkin object ([.mmkin), the same model fitted for at least one dataset is shown. When it is a column, the fit of at least one model to the same dataset is shown.

-

If the current plot device is a tikz device, +

If the current plot device is a tikz device, then latex is being used for the formatting of the chi2 error level.

# S3 method for mmkin
-plot(x, main = "auto", legends = 1,
-  resplot = c("time", "errmod"), errmin_var = "All data", errmin_digits = 3,
-  cex = 0.7, rel.height.middle = 0.9, ...)
+plot(x, main = "auto", legends = 1, + resplot = c("time", "errmod"), show_errmin = TRUE, errmin_var = "All data", + errmin_digits = 3, cex = 0.7, rel.height.middle = 0.9, ...)

Arguments

@@ -166,6 +170,10 @@ If the current plot device is a tikz device, or as squared residuals against predicted values, with the error model, using mkinerrplot.

+ + + + @@ -176,14 +184,14 @@ If the current plot device is a tikz device, - + - +
show_errmin

Should the chi2 error level be shown on top of the plots to the left?

errmin_var

The variable for which the FOCUS chi2 error value should be shown.

cex

Passed to the plot functions and mtext.

Passed to the plot functions and mtext.
rel.height.middle

The relative height of the middle plot, if more than two rows of plots are shown.
…...

Further arguments passed to plot.mkinfit and mkinresplot.
@@ -194,17 +202,19 @@ If the current plot device is a tikz device,

Examples

- 
  
  # Only use one core not to offend CRAN checks
-  fits <- mmkin(c("FOMC", "HS"),
-                list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C), # named list for titles
+    
  # \dontrun{
+  # Only use one core not to offend CRAN checks
+  fits <- mmkin(c("FOMC", "HS"),
+                list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C), # named list for titles
                 cores = 1, quiet = TRUE, error_model = "tc")
#> Warning: Optimisation did not converge:
-#> iteration limit reached without convergence (10)
  plot(fits[, "FOCUS C"])
  plot(fits["FOMC", ])

+#> iteration limit reached without convergence (10)
  plot(fits[, "FOCUS C"])
  plot(fits["FOMC", ])

   # We can also plot a single fit, if we like the way plot.mmkin works, but then the plot
   # height should be smaller than the plot width (this is not possible for the html pages
   # generated by pkgdown, as far as I know).
-  plot(fits["FOMC", "FOCUS C"]) # same as plot(fits[1, 2])

+  plot(fits["FOMC", "FOCUS C"]) # same as plot(fits[1, 2])

   # Show the error models
-  plot(fits["FOMC", ], resplot = "errmod")
  

+  plot(fits["FOMC", ], resplot = "errmod")
  # }
+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index 55fea47c..c5eed391 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -18,13 +18,15 @@ - + + - - + + + @@ -51,6 +53,7 @@ + @@ -120,6 +123,7 @@ +
@@ -138,8 +142,8 @@
- 
# S3 method for nafta
-plot(x, legend = FALSE, main = "auto", …)
+ 
# S3 method for nafta
+plot(x, legend = FALSE, main = "auto", ...)

Arguments

@@ -157,7 +161,7 @@ plot(x, legend = FALSE, main = "auto", …) - +

Possibility to override the main title of the plot.
…...

Further arguments passed to plot.mmkin.
@@ -181,19 +185,23 @@ plot(x, legend = FALSE, main = "auto", …) +

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 5eb42e68..810123b8 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -47,6 +49,7 @@ + @@ -116,6 +119,7 @@ +
@@ -133,7 +137,7 @@ 
# S3 method for mkinds
-print(x, ...)
+print(x, ...)

Arguments

@@ -143,7 +147,7 @@ - +

An mkinds object.
…...

Not used.
@@ -159,19 +163,23 @@ +

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 96279b89..5a8feab8 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -47,6 +49,7 @@ + @@ -116,6 +119,7 @@ +
@@ -133,7 +137,7 @@ 
# S3 method for mkinmod
-print(x, ...)
+print(x, ...)

Arguments

@@ -143,17 +147,17 @@ - +

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
+    
  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
@@ -180,19 +184,23 @@
   

 

 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/print.nafta.html b/docs/reference/print.nafta.html
index af0d9f65..fa8223ad 100644
--- a/docs/reference/print.nafta.html
+++ b/docs/reference/print.nafta.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -49,6 +51,7 @@
 
 
 
+
   
 
   
@@ -118,6 +121,7 @@
 
 
       
+
       
 
 

@@ -137,7 +141,7 @@
     

 
     
# S3 method for nafta
-print(x, quiet = TRUE, digits = 3, ...)

+print(x, quiet = TRUE, digits = 3, ...)

Arguments

@@ -155,7 +159,7 @@ - +

Number of digits to be used for printing parameters and dissipation times.
…...

Not used.
@@ -171,19 +175,23 @@ +

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index a9c64362..c6635409 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -49,6 +51,7 @@ + @@ -118,6 +121,7 @@ +
@@ -147,7 +151,8 @@
B1

a numeric vector

C1

a numeric vector

A2

a numeric vector

-

The results are a data frame with 14 results for different parameter values

+ +

The results are a data frame with 14 results for different parameter values

References

@@ -160,12 +165,13 @@

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.
  
    fit <- mkinfit(model, data, quiet = TRUE)
-    plot(fit)
    endpoints(fit)
#> $ff
+  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
 #>   parent_A1   parent_B1   parent_C1 parent_sink       A1_A2     A1_sink 
 #>   0.3809619   0.1954667   0.4235714   0.0000000   0.4479620   0.5520380 
 #> 
@@ -179,8 +185,9 @@
 #> B1     37.26907 123.80517
 #> C1     11.23131  37.30960
 #> A2     28.50627  94.69577
-#> 
  
 # Compare with the results obtained in the original publication
- print(schaefer07_complex_results)
#>         compound          parameter  KinGUI ModelMaker deviation
+#> 
  # }
+ # Compare with the results obtained in the original publication
+ 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
@@ -210,19 +217,23 @@
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index cbf253f9..ee956f9f 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -52,6 +54,7 @@ This is the error model used for example by Werner et al. (1978). The model + @@ -121,6 +124,7 @@ This is the error model used for example by Werner et al. (1978). The model +
@@ -189,19 +193,23 @@ This is the error model used for example by Werner et al. (1978). The model
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.3.0.

+

Site built with pkgdown 1.4.1.

+
+ + diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 1eec5820..fafca9ce 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -16,13 +16,15 @@ - + + - - + + + @@ -50,6 +52,7 @@ + @@ -119,6 +122,7 @@ +
@@ -139,9 +143,9 @@ 
# S3 method for mkinfit
-summary(object, data = TRUE, distimes = TRUE, alpha = 0.05, ...)
+summary(object, data = TRUE, distimes = TRUE, alpha = 0.05, ...)
 # S3 method for summary.mkinfit
-print(x, digits = max(3, getOption("digits") - 3), ...)
+print(x, digits = max(3, getOption("digits") - 3), ...)

Arguments

@@ -171,7 +175,7 @@ - +

Number of digits to use for printing
…...

optional arguments passed to methods like print.
@@ -209,17 +213,17 @@

Examples

- 
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.6 
-#> R version used for fitting:       3.6.0 
-#> Date of fit:     Tue Jul  9 09:00:02 2019 
-#> Date of summary: Tue Jul  9 09:00:02 2019 
+    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.6 
+#> R version used for fitting:       3.6.1 
+#> Date of fit:     Wed Sep 18 12:57:18 2019 
+#> Date of summary: Wed Sep 18 12:57:18 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 131 model solutions performed in 0.278 s
+#> Fitted using 131 model solutions performed in 0.267 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -302,19 +306,23 @@
   

 

 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 1f8bc914..b3da0016 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -62,6 +64,7 @@ Compare also the code in the example section to see the degradation models." />
 
 
 
+
   
 
   
@@ -131,6 +134,7 @@ Compare also the code in the example section to see the degradation models." />
 
 
       
+
       
 
 

@@ -170,7 +174,9 @@ Compare also the code in the example section to see the degradation models." />
   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

-  

+  
+
+
     
     
Source

 
@@ -181,109 +187,7 @@ Compare also the code in the example section to see the degradation models." />
     
 
     
Examples

-    
# 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")
-
-
-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")
-
-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")
-
-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")
-
-# 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)
-
-# Construct names for datasets with errors
-d_synth_names = paste0("d_synth_", c("SFO_lin", "SFO_par",
-                                     "DFOP_lin", "DFOP_par"))
-
-# Function for adding errors. The add_err function now published with this
-# package is a slightly generalised version where the names of secondary
-# compartments that should have an initial value of zero (M1 and M2 in this
-# case) are not hardcoded any more.
-add_err = function(d, sdfunc, LOD = 0.1, reps = 2, seed = 123456789)
-{
-  set.seed(seed)
-  d_long = mkin_wide_to_long(d, time = "time")
-  d_rep = data.frame(lapply(d_long, rep, each = 2))
-  d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value))
-
-  d_rep[d_rep$time == 0 & d_rep$name 
-  d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value))
-  d_NA$value <- round(d_NA$value, 1)
-  return(d_NA)
-}
-
-# 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)
-}
-
-# 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)))
-
-}
-
-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]]$data,
-               quiet = TRUE)
-plot_sep(fit)
-summary(fit)
-
#> Error: <text>:67:43: Unerwartete(s) SPECIAL
-#> 66: 
-#> 67:   d_rep[d_rep$time == 0 & d_rep$name <!-- %in%
-#>                                               ^

+    

   

   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 8899ed11..5c1a3bed 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -48,6 +50,7 @@
 
 
 
+
   
 
   
@@ -117,6 +120,7 @@
 
 
       
+
       
 
 

@@ -142,7 +146,9 @@
   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

-  

+  
+
+
     
     
Source

 
@@ -151,7 +157,8 @@
     
 
     
Examples

-    
  
  # This is a level P-II evaluation of the dataset according to the FOCUS kinetics
+    
  # \dontrun{
+  # This is a level P-II evaluation of the dataset according to the FOCUS kinetics
   # guidance. Due to the strong correlation of the parameter estimates, the
   # covariance matrix is not returned. Note that level P-II evaluations are
   # generally considered deprecated due to the frequent occurrence of such
@@ -159,7 +166,7 @@
   # model).
   m_ws <- mkinmod(parent_w = mkinsub("SFO", "parent_s"),
                   parent_s = mkinsub("SFO", "parent_w"))
#> Successfully compiled differential equation model from auto-generated C code.
  f_river <- mkinfit(m_ws, test_data_from_UBA_2014[[1]]$data, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
  plot_sep(f_river)

-  summary(f_river)$bpar
#>                         Estimate se_notrans      t value       Pr(>t)
+  summary(f_river)$bpar
#>                         Estimate se_notrans      t value       Pr(>t)
 #> parent_w_0          9.598567e+01 2.12351789 4.520126e+01 9.476190e-18
 #> k_parent_w_sink     3.603743e-01 0.03149282 1.144306e+01 4.126593e-09
 #> k_parent_w_parent_s 6.031371e-02 0.01603582 3.761186e+00 9.436275e-04
@@ -178,12 +185,12 @@
 #> parent_s 0.20882325       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")),
+  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
+  f_soil <- mkinfit(m_soil, test_data_from_UBA_2014[[3]]$data, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
  plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright"))
  summary(f_soil)$bpar
#>                   Estimate  se_notrans    t value       Pr(>t)        Lower
 #> parent_0       76.55425584 0.859186619 89.1008474 1.113866e-26 74.755959756
 #> k_parent        0.12081956 0.004601922 26.2541544 1.077373e-16  0.111561582
 #> k_M1            0.84258649 0.806231419  1.0450926 1.545475e-01  0.113839803
@@ -209,7 +216,8 @@
 #> parent   0.04721283       2  6
 #> M1       0.26551209       2  5
 #> M2       0.20327575       2  5
-#> M3       0.05196549       3  4
  

+#> M3       0.05196549       3  4
  # }
+

   

   
 
 
+
       

       

   
Developed by Johannes Ranke.

 

 
 

-  
Site built with pkgdown 1.3.0.

+  
Site built with pkgdown 1.4.1.

 

+
       

    
 
   
 
+
   
 
 
+
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 72b4c2a7..b1a952d9 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -16,13 +16,15 @@
 
 
 
-
+
+
 
 
 
 
-
-
+
+
+
 
 
 
@@ -55,6 +57,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 
 
 
+
   
 
   
@@ -124,6 +127,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 
 
       
+
       
 
 

@@ -200,77 +204,81 @@ The transformation of sets of formation fractions is fragile, as it supposes
 
     
Examples

     
SFO_SFO <- mkinmod(
-  parent = list(type = "SFO", to = "m1", sink = TRUE),
-  m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.s <- summary(fit)
+  parent = list(type = "SFO", to = "m1", sink = TRUE),
+  m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.s <- summary(fit)
 # Transformed and backtransformed parameters
-print(fit.s$par, 3)
#>                   Estimate Std. Error Lower  Upper
+print(fit.s$par, 3)
#>                   Estimate Std. Error Lower  Upper
 #> parent_0             99.60     1.5702 96.40 102.79
 #> log_k_parent_sink    -3.04     0.0763 -3.19  -2.88
 #> log_k_parent_m1      -2.98     0.0403 -3.06  -2.90
 #> log_k_m1_sink        -5.25     0.1332 -5.52  -4.98
-#> sigma                 3.13     0.3585  2.40   3.85
print(fit.s$bpar, 3)
#>               Estimate se_notrans t value   Pr(>t)    Lower    Upper
+#> sigma                 3.13     0.3585  2.40   3.85
print(fit.s$bpar, 3)
#>               Estimate se_notrans t value   Pr(>t)    Lower    Upper
 #> parent_0      99.59848    1.57022   63.43 2.30e-36 96.40384 102.7931
 #> k_parent_sink  0.04792    0.00365   13.11 6.13e-15  0.04103   0.0560
 #> k_parent_m1    0.05078    0.00205   24.80 3.27e-23  0.04678   0.0551
 #> k_m1_sink      0.00526    0.00070    7.51 6.16e-09  0.00401   0.0069
 #> sigma          3.12550    0.35852    8.72 2.24e-10  2.39609   3.8549

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

+#> sigma          3.12550    0.35852    8.72 2.24e-10  2.39609 3.85e+00
# }
+
 initials <- fit$start$value
-names(initials) <- rownames(fit$start)
+names(initials) <- rownames(fit$start)
 transformed <- fit$start_transformed$value
-names(transformed) <- rownames(fit$start_transformed)
+names(transformed) <- rownames(fit$start_transformed)
 transform_odeparms(initials, SFO_SFO)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>        100.750000         -2.302585         -2.301586         -2.300587 
backtransform_odeparms(transformed, SFO_SFO)
#>      parent_0 k_parent_sink   k_parent_m1     k_m1_sink 
 #>      100.7500        0.1000        0.1001        0.1002 

-
# The case of formation fractions
+# \dontrun{
+# The case of formation fractions
 SFO_SFO.ff <- mkinmod(
-  parent = list(type = "SFO", to = "m1", sink = TRUE),
-  m1 = list(type = "SFO"),
+  parent = list(type = "SFO", to = "m1", sink = TRUE),
+  m1 = list(type = "SFO"),
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

-fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.ff.s <- summary(fit.ff)
-print(fit.ff.s$par, 3)
#>                Estimate Std. Error   Lower   Upper
+fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.ff.s <- summary(fit.ff)
+print(fit.ff.s$par, 3)
#>                Estimate Std. Error   Lower   Upper
 #> parent_0         99.598     1.5702 96.4038 102.793
 #> log_k_parent     -2.316     0.0409 -2.3988  -2.233
 #> log_k_m1         -5.248     0.1332 -5.5184  -4.977
 #> f_parent_ilr_1    0.041     0.0631 -0.0875   0.169
-#> sigma             3.126     0.3585  2.3961   3.855
print(fit.ff.s$bpar, 3)
#>                Estimate se_notrans t value   Pr(>t)    Lower    Upper
+#> sigma             3.126     0.3585  2.3961   3.855
print(fit.ff.s$bpar, 3)
#>                Estimate se_notrans t value   Pr(>t)    Lower    Upper
 #> parent_0       99.59848    1.57022   63.43 2.30e-36 96.40384 102.7931
 #> k_parent        0.09870    0.00403   24.47 4.96e-23  0.09082   0.1073
 #> k_m1            0.00526    0.00070    7.51 6.16e-09  0.00401   0.0069
 #> f_parent_to_m1  0.51448    0.02230   23.07 3.10e-22  0.46912   0.5596
-#> sigma           3.12550    0.35852    8.72 2.24e-10  2.39609   3.8549
initials <- c("f_parent_to_m1" = 0.5)
+#> sigma           3.12550    0.35852    8.72 2.24e-10  2.39609   3.8549
initials <- c("f_parent_to_m1" = 0.5)
 transformed <- transform_odeparms(initials, SFO_SFO.ff)
 backtransform_odeparms(transformed, SFO_SFO.ff)
#> f_parent_to_m1 
 #>            0.5 

 # And without sink
 SFO_SFO.ff.2 <- mkinmod(
-  parent = list(type = "SFO", to = "m1", sink = FALSE),
-  m1 = list(type = "SFO"),
+  parent = 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.

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

+#> sigma      8.2229    0.94323    8.72 1.73e-10  6.3060 10.140
# }
+

   
   
 
 
+
       
    
 
   
 
+
   
 
 
+
diff --git a/man/max_twa_parent.Rd b/man/max_twa_parent.Rd
index f599eb1c..c601b768 100644
--- a/man/max_twa_parent.Rd
+++ b/man/max_twa_parent.Rd
@@ -1,5 +1,9 @@
 \name{max_twa_parent}
 \alias{max_twa_parent}
+\alias{max_twa_sfo}
+\alias{max_twa_fomc}
+\alias{max_twa_dfop}
+\alias{max_twa_hs}
 \title{
   Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit
 }
@@ -11,6 +15,10 @@ using the analytical formulas given in the PEC soil section of the FOCUS
 guidance.}
 \usage{
   max_twa_parent(fit, windows)
+  max_twa_sfo(M0 = 1, k, t)
+  max_twa_fomc(M0 = 1, alpha, beta, t)
+  max_twa_dfop(M0 = 1, k1, k2, g, t)
+  max_twa_hs(M0 = 1, k1, k2, tb, t)
 }
 \arguments{
   \item{fit}{
@@ -19,13 +27,45 @@ guidance.}
   \item{windows}{
     The width of the time windows for which the TWAs should be calculated.
   }
+  \item{M0}{
+   The initial concentration for which the maximum time weighted
+   average over the decline curve should be calculated. The default
+   is to use a value of 1, which means that a relative maximum time
+   weighted average factor (f_twa) is calculated.
+  }
+  \item{k}{
+    The rate constant in the case of SFO kinetics.
+  }
+  \item{t}{
+    The width of the time window.
+  }
+  \item{alpha}{
+    Parameter of the FOMC model.
+  }
+  \item{beta}{
+    Parameter of the FOMC model.
+  }
+  \item{k1}{
+    The first rate constant of the DFOP or the HS kinetics.
+  }
+  \item{k2}{
+    The second rate constant of the DFOP or the HS kinetics.
+  }
+  \item{g}{
+    Parameter of the DFOP model.
+  }
+  \item{tb}{
+    Parameter of the HS model.
+  }
 }
 \value{
-  A numeric vector, named using the \code{windows} argument.
+  For \code{max_twa_parent}, a numeric vector, named using the \code{windows} argument.
+  For the other functions, a numeric vector of length one (also known as 'a
+  number').
 }
 \examples{
   fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-  max_twa_parent(fit, c(7, 21))  
+  max_twa_parent(fit, c(7, 21))
 }
 \references{
   FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and
diff --git a/vignettes/mkin_benchmarks.rda b/vignettes/mkin_benchmarks.rda
index fc996a73..b5132fa8 100644
Binary files a/vignettes/mkin_benchmarks.rda and b/vignettes/mkin_benchmarks.rda differ
diff --git a/vignettes/twa.Rmd b/vignettes/twa.Rmd
index 92a0cd4b..724775bc 100644
--- a/vignettes/twa.Rmd
+++ b/vignettes/twa.Rmd
@@ -73,6 +73,7 @@ $$f_\textrm{twa} = \frac{1}{t} \left(
   \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right)  \right) $$
 
 Note that a method for calculating maximum moving window time weighted average
-concentrations for any model fitted by 'mkinfit', and also for metabolites in
-such models, is integrated in the 'mkin' package, see the
-[documentation](https://pkgdown.jrwb.de/pfm/reference/max_twa_parent.html) at my website.
+concentrations for a model fitted by 'mkinfit' is include in the 
+'mkin' package (['max_twa_parent'](https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html).
+If the same is needed for metabolites, the function 
+['max_twa'](https://pkgdown.jrwb.de/pfm/reference/max_twa.html) can be used.
-- 
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