From 9ac853c7ceece333099021974025d07e75be2b33 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 12 May 2020 08:07:07 +0200 Subject: Documentation improvements, rebuild static docs --- DESCRIPTION | 1 + GNUmakefile | 1 - R/mkinfit.R | 10 +- R/mkinmod.R | 7 +- docs/news/index.html | 2 +- docs/pkgdown.yml | 2 +- docs/reference/AIC.mmkin.html | 58 ++++++------ docs/reference/DFOP.solution.html | 18 ++-- docs/reference/FOMC.solution.html | 26 +++--- docs/reference/HS.solution.html | 18 ++-- docs/reference/IORE.solution.html | 10 +- docs/reference/SFO.solution.html | 18 ++-- docs/reference/SFORB.solution.html | 20 ++-- docs/reference/add_err-1.png | Bin 89498 -> 111278 bytes docs/reference/add_err-2.png | Bin 50582 -> 63031 bytes docs/reference/add_err-3.png | Bin 52523 -> 60608 bytes docs/reference/add_err.html | 59 ++++++------ docs/reference/confint.mkinfit.html | 164 +++++++++++++++++++-------------- docs/reference/endpoints.html | 57 ++++++------ docs/reference/get_deg_func.html | 48 +++++----- docs/reference/ilr.html | 60 ++++++------ docs/reference/logLik.mkinfit.html | 58 ++++++------ docs/reference/logistic.solution.html | 20 ++-- docs/reference/max_twa_parent.html | 63 ++++++------- docs/reference/mkinerrplot-1.png | Bin 35440 -> 41458 bytes docs/reference/mkinerrplot.html | 57 ++++++------ docs/reference/mkinfit.html | 133 +++++++++++++------------- docs/reference/mkinmod.html | 37 ++++---- docs/reference/mkinparplot-1.png | Bin 16467 -> 16468 bytes docs/reference/mkinparplot.html | 52 ++++++----- docs/reference/mkinresplot-1.png | Bin 14863 -> 14861 bytes docs/reference/mkinresplot.html | 59 ++++++------ docs/reference/mmkin-1.png | Bin 97412 -> 115683 bytes docs/reference/mmkin-2.png | Bin 88002 -> 113464 bytes docs/reference/mmkin-3.png | Bin 85375 -> 100799 bytes docs/reference/mmkin-4.png | Bin 62550 -> 70430 bytes docs/reference/mmkin-5.png | Bin 57465 -> 66958 bytes docs/reference/mmkin.html | 79 ++++++++-------- docs/reference/nafta.html | 73 +++++++-------- docs/reference/nlme.html | 8 +- docs/reference/nlme.mmkin-1.png | Bin 69863 -> 81816 bytes docs/reference/nlme.mmkin-2.png | Bin 70426 -> 82384 bytes docs/reference/nlme.mmkin-3.png | Bin 70519 -> 82591 bytes docs/reference/nlme.mmkin-4.png | Bin 72803 -> 86006 bytes docs/reference/nlme.mmkin-5.png | Bin 72587 -> 85418 bytes docs/reference/nlme.mmkin-6.png | Bin 71892 -> 84796 bytes docs/reference/nlme.mmkin-7.png | Bin 72316 -> 84926 bytes docs/reference/nlme.mmkin.html | 152 ++++++++++++++---------------- docs/reference/plot.mkinfit.html | 4 +- docs/reference/plot.mmkin.html | 61 ++++++------ docs/reference/plot.nlme.mmkin-2.png | Bin 35313 -> 35346 bytes docs/reference/plot.nlme.mmkin.html | 58 ++++++------ docs/reference/sigma_twocomp.html | 55 +++++------ docs/reference/summary.mkinfit.html | 156 +++++++++++++++---------------- docs/reference/transform_odeparms.html | 95 +++++++++---------- dumpdata.R | 7 ++ man/AIC.mmkin.Rd | 2 +- man/DFOP.solution.Rd | 16 ++-- man/FOMC.solution.Rd | 26 +++--- man/HS.solution.Rd | 16 ++-- man/IORE.solution.Rd | 8 +- man/SFO.solution.Rd | 16 ++-- man/SFORB.solution.Rd | 18 ++-- man/add_err.Rd | 2 +- man/confint.mkinfit.Rd | 14 +-- man/endpoints.Rd | 6 +- man/get_deg_func.Rd | 2 +- man/ilr.Rd | 8 +- man/logLik.mkinfit.Rd | 6 +- man/logistic.solution.Rd | 18 ++-- man/max_twa_parent.Rd | 12 +-- man/mkinerrplot.Rd | 4 +- man/mkinfit.Rd | 118 +++++++++++++----------- man/mkinmod.Rd | 59 ++++++------ man/mkinparplot.Rd | 2 +- man/mkinresplot.Rd | 6 +- man/mmkin.Rd | 6 +- man/nafta.Rd | 22 ++--- man/nlme.Rd | 6 +- man/nlme.mmkin.Rd | 2 +- man/plot.mkinfit.Rd | 2 +- man/plot.mmkin.Rd | 2 +- man/plot.nlme.mmkin.Rd | 2 +- man/sigma_twocomp.Rd | 8 +- man/summary.mkinfit.Rd | 50 +++++----- man/transform_odeparms.Rd | 2 +- 86 files changed, 1165 insertions(+), 1102 deletions(-) create mode 100644 dumpdata.R diff --git a/DESCRIPTION b/DESCRIPTION index 0facf77e..760d8207 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -27,4 +27,5 @@ Encoding: UTF-8 VignetteBuilder: knitr BugReports: http://github.com/jranke/mkin/issues URL: https://pkgdown.jrwb.de/mkin +Roxygen: list(markdown = TRUE) RoxygenNote: 7.1.0 diff --git a/GNUmakefile b/GNUmakefile index 58d40e52..830b998d 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -100,7 +100,6 @@ articles: vignettes/web_only/FOCUS_Z.html vignettes/web_only/compiled_models.htm pd: roxygen "$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE, lazy = TRUE)" git add -A - git commit -m 'Static documentation rebuilt by pkgdown' -e r-forge: git archive master > $(HOME)/git/mkin/mkin.tar;\ diff --git a/R/mkinfit.R b/R/mkinfit.R index 683a6b3d..c796f06f 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -165,8 +165,12 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value")) #' #' Fitting of several models to several datasets in a single call to #' \code{\link{mmkin}}. -#' @source Rocke, David M. und Lorenzato, Stefan (1995) A two-component model -#' for measurement error in analytical chemistry. Technometrics 37(2), 176-184. +#' @references Rocke DM and Lorenzato S (1995) A two-component model +#' for measurement error in analytical chemistry. *Technometrics* 37(2), 176-184. +#' +#' Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical +#' Degradation Data. *Environments* 6(12) 124 +#' [doi:10.3390/environments6120124](https://doi.org/10.3390/environments6120124). #' @examples #' #' # Use shorthand notation for parent only degradation @@ -217,7 +221,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value")) #' } #' #' \dontrun{ -#' # Weighted fits, including IRLS +#' # Weighted fits, including IRLS (error_model = "obs") #' SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), #' m1 = mkinsub("SFO"), use_of_ff = "max") #' f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) diff --git a/R/mkinmod.R b/R/mkinmod.R index 7e9e9248..e58d1e22 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -48,12 +48,17 @@ #' \item{use_of_ff}{ #' The content of \code{use_of_ff} is passed on in this list component. #' } +#' \item{deg_func}{ +#' If generated, a function containing the solution of the degradation +#' model. +#' } #' \item{coefmat}{ #' The coefficient matrix, if the system of differential equations can be #' represented by one. #' } #' \item{cf}{ -#' If generated, the compiled function as returned by cfunction. +#' If generated, a compiled function calculating the derivatives as +#' returned by cfunction. #' } #' @note The IORE submodel is not well tested for metabolites. When using this #' model for metabolites, you may want to read the second note in the help diff --git a/docs/news/index.html b/docs/news/index.html index 3965df70..2874175c 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -140,7 +140,7 @@

-mkin 0.9.50.1 (unreleased) Unreleased +mkin 0.9.50.1 (unreleased) 2020-05-11

@@ -129,7 +137,7 @@ same dataset." />

Calculate the AIC for a column of an mmkin object

- + Source: R/AIC.mmkin.R
@@ -165,7 +173,7 @@ column.

Value

As in the generic method (a numeric value for single fits, or a - dataframe if there are several fits in the column).

+dataframe if there are several fits in the column).

Examples


@@ -181,13 +189,13 @@ column.

   # of parameters, the higher (worse) the AIC
   AIC(f[, "FOCUS A"])
#>      df      AIC
 #> SFO   3 55.28197
-#> FOMC  4 57.28202
+#> FOMC  4 57.28211
 #> 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
+#> FOMC  4 49.28211
 #> DFOP  5 49.28197
  BIC(f[, "FOCUS A"])        # Comparing the BIC gives a very similar picture
#>      df      BIC
 #> SFO   3 55.52030
-#> FOMC  4 57.59979
+#> FOMC  4 57.59987
 #> DFOP  5 59.67918

   # For FOCUS C, the more complex models fit better
   AIC(f[, "FOCUS C"])
#>      df      AIC
@@ -200,16 +208,10 @@ column.
- @@ -220,7 +222,7 @@ column.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 84e33f9e..e0094738 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -73,7 +73,7 @@ two exponential decline functions." /> mkin - 0.9.50 + 0.9.50.1 @@ -180,15 +180,15 @@ kinetic constant.

References

FOCUS (2006) “Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics FOCUS (2014) “Generic guidance for Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, - Version 1.1, 18 December 2014 - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

+and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

See also

Other parent solutions: diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 369398d5..f8fbd2ba 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -73,7 +73,7 @@ a decreasing rate constant." /> mkin - 0.9.50 + 0.9.50.1

@@ -181,23 +181,23 @@ in the original equation.

Note

The solution of the FOMC kinetic model reduces to the - SFO.solution for large values of alpha and - beta with \(k = \frac{\beta}{\alpha}\).

+SFO.solution for large values of alpha and +beta with \(k = \frac{\beta}{\alpha}\).

References

FOCUS (2006) “Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

+and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

FOCUS (2014) “Generic guidance for Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, - Version 1.1, 18 December 2014 - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

+and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: - A new model based on spatial variability. Environmental Science and - Technology 24, 1032-1038

+A new model based on spatial variability. Environmental Science and +Technology 24, 1032-1038

See also

Other parent solutions: diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 2684ee60..9404893c 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -73,7 +73,7 @@ between them." /> mkin - 0.9.50 + 0.9.50.1

@@ -181,15 +181,15 @@ according to k2.

References

FOCUS (2006) “Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics FOCUS (2014) “Generic guidance for Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, - Version 1.1, 18 December 2014 - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

+and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

See also

Other parent solutions: diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index f197cb08..194d11aa 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -73,7 +73,7 @@ a concentration dependent rate constant." /> mkin - 0.9.49.11 + 0.9.50.1

@@ -176,13 +176,13 @@ units used.

Note

The solution of the IORE kinetic model reduces to the - SFO.solution if N = 1. The parameters of the IORE model can - be transformed to equivalent parameters of the FOMC mode - see the NAFTA - guidance for details.

+SFO.solution if N = 1. The parameters of the IORE model can +be transformed to equivalent parameters of the FOMC mode - see the NAFTA +guidance for details.

References

NAFTA Technical Working Group on Pesticides (not dated) Guidance - for Evaluating and Calculating Degradation Kinetics in Environmental Media

+for Evaluating and Calculating Degradation Kinetics in Environmental Media

See also

Other parent solutions: diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 9664deb3..b263f2f3 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -72,7 +72,7 @@ mkin - 0.9.50 + 0.9.50.1

@@ -169,15 +169,15 @@

References

FOCUS (2006) “Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics FOCUS (2014) “Generic guidance for Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, - Version 1.1, 18 December 2014 - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

+and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

See also

Other parent solutions: diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 504f209f..4ef85274 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -76,7 +76,7 @@ and no substance in the bound fraction." /> mkin - 0.9.50 + 0.9.50.1

@@ -183,19 +183,19 @@ fraction.

Value

The value of the response variable, which is the sum of free and - bound fractions at time t.

+bound fractions at time t.

References

FOCUS (2006) “Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics FOCUS (2014) “Generic guidance for Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, - Version 1.1, 18 December 2014 - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

+and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

See also

Other parent solutions: diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png index 3018ff7f..88806d7b 100644 Binary files a/docs/reference/add_err-1.png and b/docs/reference/add_err-1.png differ diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png index d476bba1..6a806c2d 100644 Binary files a/docs/reference/add_err-2.png and b/docs/reference/add_err-2.png differ diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png index 298f2ebd..1919a566 100644 Binary files a/docs/reference/add_err-3.png and b/docs/reference/add_err-3.png differ diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index ab499a19..c25bbe17 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -39,7 +43,6 @@ - @@ -57,7 +60,7 @@ may depend on the predicted value and is specified as a standard deviation." /> - +

@@ -115,7 +118,12 @@ may depend on the predicted value and is specified as a standard deviation." />
@@ -130,7 +138,7 @@ may depend on the predicted value and is specified as a standard deviation." />

Add normally distributed errors to simulated kinetic degradation data

- + Source: R/add_err.R
@@ -197,7 +205,7 @@ seed is not set.

Value

A list of datasets compatible with mmkin, i.e. the - components of the list are datasets compatible with mkinfit.

+components of the list are datasets compatible with mkinfit.

References

Ranke J and Lehmann R (2015) To t-test or not to t-test, that is @@ -236,28 +244,21 @@ http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf

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])
# }
- @@ -268,7 +269,7 @@ http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 1dd6288b..7658a572 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -44,7 +48,6 @@ parameter. The 'profile' method uses two nested optimisations and can take a very long time, even if parallelized by specifying 'cores' on unixoid platforms. The speed of the method could likely be improved by using the method of Venzon and Moolgavkar (1988)." /> - @@ -62,7 +65,7 @@ method of Venzon and Moolgavkar (1988)." /> - +
@@ -120,7 +123,12 @@ method of Venzon and Moolgavkar (1988)." />
@@ -135,7 +143,7 @@ method of Venzon and Moolgavkar (1988)." />

Confidence intervals for parameters of mkinfit objects

- + Source: R/confint.mkinfit.R
@@ -212,7 +220,7 @@ their confidence intervals?

cores -

The number of cores to be used for multicore processing. +

The number of cores to be used for multicore processing. On Windows machines, cores > 1 is currently not supported.

@@ -228,15 +236,15 @@ On Windows machines, cores > 1 is currently not supported.

Value

A matrix with columns giving lower and upper confidence limits for - each parameter.

+each parameter.

References

Bates DM and Watts GW (1988) Nonlinear regression analysis & its applications

Pawitan Y (2013) In all likelihood - Statistical modelling and - inference using likelihood. Clarendon Press, Oxford.

+inference using likelihood. Clarendon Press, Oxford.

Venzon DJ and Moolgavkar SH (1988) A Method for Computing - Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, - 87–94.

+Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, +87–94.

Examples

f <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE)
@@ -262,50 +270,71 @@ On Windows machines, cores > 1 is currently not supported.

 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"),
   use_of_ff = "max", quiet = TRUE)
 f_d_1 <- mkinfit(SFO_SFO, subset(FOCUS_2006_D, value != 0), quiet = TRUE)
-system.time(ci_profile <- confint(f_d_1, method = "profile", cores = 1, quiet = TRUE))
#> Error in mkinpredict.mkinmod(mkinmod, parms, odeini, outtimes, solution_type = solution_type,     use_compiled = use_compiled, method.ode = method.ode, atol = atol,     rtol = rtol, ...): Differential equations were not integrated for all output times because
-#> NaN values occurred in output from ode()
#> Timing stopped at: 11.39 0 11.4
# Using more cores does not save much time here, as parent_0 takes up most of the time
+system.time(ci_profile <- confint(f_d_1, method = "profile", cores = 1, quiet = TRUE))
#>        User      System verstrichen 
+#>       3.362       0.000       3.364 
# Using more cores does not save much time here, as parent_0 takes up most of the time
 # If we additionally exclude parent_0 (the confidence of which is often of
 # minor interest), we get a nice performance improvement from about 50
 # seconds to about 12 seconds if we use at least four cores
 system.time(ci_profile_no_parent_0 <- confint(f_d_1, method = "profile",
-  c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores))
#> Profiling the likelihood
#>        User      System verstrichen 
-#>      20.058       0.122      11.784 
ci_profile
#> Error in eval(expr, envir, enclos): Objekt 'ci_profile' nicht gefunden
ci_quadratic_transformed <- confint(f_d_1, method = "quadratic")
-ci_quadratic_transformed
#>                       2.5%        97.5%
-#> parent_0      96.403841641 1.027931e+02
-#> k_parent_sink  0.041033378 5.596269e-02
-#> k_parent_m1    0.046777902 5.511931e-02
-#> k_m1_sink      0.004012217 6.897547e-03
-#> sigma          2.396089689 3.854918e+00
ci_quadratic_untransformed <- confint(f_d_1, method = "quadratic", transformed = FALSE)
-ci_quadratic_untransformed
#>                       2.5%        97.5%
-#> parent_0      96.403841648 102.79312450
-#> k_parent_sink  0.040485331   0.05535491
-#> k_parent_m1    0.046611582   0.05494364
-#> k_m1_sink      0.003835483   0.00668582
-#> sigma          2.396089689   3.85491806
# Against the expectation based on Bates and Watts (1988), the confidence
+  c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores))
#> Profiling the likelihood
#> Warning: scheduled cores 1, 2, 3 encountered errors in user code, all values of the jobs will be affected
#> Error in dimnames(x) <- dn: Länge von 'dimnames' [2] ungleich der Arrayausdehnung
#> Timing stopped at: 0.011 0.045 0.201
ci_profile
#>                        2.5%        97.5%
+#> parent_0       96.456003640 1.027703e+02
+#> k_parent        0.090911032 1.071578e-01
+#> k_m1            0.003892605 6.702778e-03
+#> f_parent_to_m1  0.471328495 5.611550e-01
+#> sigma           2.535612399 3.985263e+00
ci_quadratic_transformed <- confint(f_d_1, method = "quadratic")
+ci_quadratic_transformed
#>                        2.5%        97.5%
+#> parent_0       96.403839460 1.027931e+02
+#> k_parent        0.090823790 1.072543e-01
+#> k_m1            0.004012216 6.897547e-03
+#> f_parent_to_m1  0.469118713 5.595960e-01
+#> sigma           2.396089689 3.854918e+00
ci_quadratic_untransformed <- confint(f_d_1, method = "quadratic", transformed = FALSE)
+ci_quadratic_untransformed
#>                        2.5%        97.5%
+#> parent_0       96.403839413 1.027931e+02
+#> k_parent        0.090491931 1.069035e-01
+#> k_m1            0.003835483 6.685819e-03
+#> f_parent_to_m1  0.469113365 5.598386e-01
+#> sigma           2.396089689 3.854918e+00
# Against the expectation based on Bates and Watts (1988), the confidence
 # intervals based on the internal parameter transformation are less
 # congruent with the likelihood based intervals. Note the superiority of the
 # interval based on the untransformed fit for k_m1_sink
-rel_diffs_transformed <- abs((ci_quadratic_transformed - ci_profile)/ci_profile)
#> Error in eval(expr, envir, enclos): Objekt 'ci_profile' nicht gefunden
rel_diffs_untransformed <- abs((ci_quadratic_untransformed - ci_profile)/ci_profile)
#> Error in eval(expr, envir, enclos): Objekt 'ci_profile' nicht gefunden
rel_diffs_transformed < rel_diffs_untransformed
#> Error in eval(expr, envir, enclos): Objekt 'rel_diffs_transformed' nicht gefunden
signif(rel_diffs_transformed, 3)
#> Error in eval(expr, envir, enclos): Objekt 'rel_diffs_transformed' nicht gefunden
signif(rel_diffs_untransformed, 3)
#> Error in eval(expr, envir, enclos): Objekt 'rel_diffs_untransformed' nicht gefunden

+rel_diffs_transformed <- abs((ci_quadratic_transformed - ci_profile)/ci_profile)
+rel_diffs_untransformed <- abs((ci_quadratic_untransformed - ci_profile)/ci_profile)
+rel_diffs_transformed < rel_diffs_untransformed
#>                 2.5% 97.5%
+#> parent_0        TRUE  TRUE
+#> k_parent        TRUE  TRUE
+#> k_m1           FALSE FALSE
+#> f_parent_to_m1  TRUE FALSE
+#> sigma          FALSE FALSE
signif(rel_diffs_transformed, 3)
#>                    2.5%    97.5%
+#> parent_0       0.000541 0.000222
+#> k_parent       0.000960 0.000900
+#> k_m1           0.030700 0.029100
+#> f_parent_to_m1 0.004690 0.002780
+#> sigma          0.055000 0.032700
signif(rel_diffs_untransformed, 3)
#>                    2.5%    97.5%
+#> parent_0       0.000541 0.000222
+#> k_parent       0.004610 0.002370
+#> k_m1           0.014700 0.002530
+#> f_parent_to_m1 0.004700 0.002350
+#> sigma          0.055000 0.032700

 
 # Investigate a case with formation fractions
 f_d_2 <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), quiet = TRUE)
 ci_profile_ff <- confint(f_d_2, method = "profile", cores = n_cores)
#> Profiling the likelihood
ci_profile_ff
#>                        2.5%        97.5%
-#> parent_0       96.456003650 1.027703e+02
+#> parent_0       96.456003640 1.027703e+02
 #> k_parent        0.090911032 1.071578e-01
 #> k_m1            0.003892605 6.702778e-03
 #> f_parent_to_m1  0.471328495 5.611550e-01
 #> sigma           2.535612399 3.985263e+00
ci_quadratic_transformed_ff <- confint(f_d_2, method = "quadratic")
 ci_quadratic_transformed_ff
#>                        2.5%        97.5%
-#> parent_0       96.403839992 1.027931e+02
+#> parent_0       96.403839460 1.027931e+02
 #> k_parent        0.090823790 1.072543e-01
 #> k_m1            0.004012216 6.897547e-03
-#> f_parent_to_m1  0.469118711 5.595960e-01
+#> f_parent_to_m1  0.469118713 5.595960e-01
 #> sigma           2.396089689 3.854918e+00
ci_quadratic_untransformed_ff <- confint(f_d_2, method = "quadratic", transformed = FALSE)
 ci_quadratic_untransformed_ff
#>                        2.5%        97.5%
-#> parent_0       96.403839944 1.027931e+02
+#> parent_0       96.403839413 1.027931e+02
 #> k_parent        0.090491931 1.069035e-01
 #> k_m1            0.003835483 6.685819e-03
-#> f_parent_to_m1  0.469113362 5.598386e-01
+#> f_parent_to_m1  0.469113365 5.598386e-01
 #> sigma           2.396089689 3.854918e+00
rel_diffs_transformed_ff <- abs((ci_quadratic_transformed_ff - ci_profile_ff)/ci_profile_ff)
 rel_diffs_untransformed_ff <- abs((ci_quadratic_untransformed_ff - ci_profile_ff)/ci_profile_ff)
 # While the confidence interval for the parent rate constant is closer to
@@ -318,15 +347,15 @@ On Windows machines, cores > 1 is currently not supported.

 #> k_m1           FALSE FALSE
 #> f_parent_to_m1  TRUE FALSE
 #> sigma          FALSE FALSE
rel_diffs_transformed_ff
#>                        2.5%        97.5%
-#> parent_0       0.0005408026 0.0002217846
-#> k_parent       0.0009596414 0.0009003877
-#> k_m1           0.0307277403 0.0290579212
-#> f_parent_to_m1 0.0046884168 0.0027782604
+#> parent_0       0.0005408080 0.0002217794
+#> k_parent       0.0009596417 0.0009003876
+#> k_m1           0.0307277370 0.0290579182
+#> f_parent_to_m1 0.0046884130 0.0027782556
 #> sigma          0.0550252516 0.0327066836
rel_diffs_untransformed_ff
#>                        2.5%        97.5%
-#> parent_0       0.0005408031 0.0002217851
-#> k_parent       0.0046100089 0.0023730230
-#> k_m1           0.0146746442 0.0025300972
-#> f_parent_to_m1 0.0046997642 0.0023460268
+#> parent_0       0.0005408085 0.0002217799
+#> k_parent       0.0046100096 0.0023730229
+#> k_m1           0.0146746469 0.0025301011
+#> f_parent_to_m1 0.0046997599 0.0023460223
 #> sigma          0.0550252516 0.0327066836

 # The profiling for the following fit does not finish in a reasonable time,
 # therefore we use the quadratic approximation
@@ -337,29 +366,24 @@ On Windows machines, cores > 1 is currently not supported.

 DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
 f_tc_2 <- mkinfit(m_synth_DFOP_par, DFOP_par_c, error_model = "tc",
   error_model_algorithm = "direct", quiet = TRUE)
-confint(f_tc_2, method = "quadratic")
#>                        2.5%        97.5%
-#> parent_0       94.596218141 106.19934683
-#> k_M1            0.037605440   0.04490756
-#> k_M2            0.008568747   0.01087674
-#> f_parent_to_M1  0.021466788   0.62023878
-#> f_parent_to_M2  0.015168650   0.37975352
-#> k1              0.273897581   0.33388066
-#> k2              0.018614556   0.02250379
-#> g               0.671943831   0.73583255
-#> sigma_low       0.251283700   0.83992071
-#> rsd_high        0.040411017   0.07662005
confint(f_tc_2, "parent_0", method = "quadratic")
#>              2.5%    97.5%
-#> parent_0 94.59622 106.1993
# }
+confint(f_tc_2, method = "quadratic")
#>                       2.5%        97.5%
+#> parent_0       94.59613833 106.19939215
+#> k_M1            0.03760542   0.04490759
+#> k_M2            0.00856874   0.01087675
+#> f_parent_to_M1  0.02146166   0.62023888
+#> f_parent_to_M2  0.01516502   0.37975343
+#> k1              0.27389751   0.33388078
+#> k2              0.01861456   0.02250379
+#> g               0.67194349   0.73583256
+#> sigma_low       0.25128383   0.83992146
+#> rsd_high        0.04041100   0.07662001
confint(f_tc_2, "parent_0", method = "quadratic")
#>              2.5%    97.5%
+#> parent_0 94.59614 106.1994
# }
- @@ -370,7 +394,7 @@ On Windows machines, cores > 1 is currently not supported.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index ef38c521..05d65191 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -11,23 +11,27 @@ with mkinfit — endpoints • mkin - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,6 @@ from kinetic models fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but with the advantage that the SFORB model can also be used for metabolites." /> - @@ -61,7 +64,7 @@ advantage that the SFORB model can also be used for metabolites." /> - +
@@ -119,7 +122,12 @@ advantage that the SFORB model can also be used for metabolites." />
@@ -135,7 +143,7 @@ advantage that the SFORB model can also be used for metabolites." />

Function to calculate endpoints for further use from kinetic models fitted with mkinfit

- + Source: R/endpoints.R
@@ -162,9 +170,9 @@ advantage that the SFORB model can also be used for metabolites.

Value

A list with a matrix of dissipation times named distimes, - and, if applicable, a vector of formation fractions named ff - and, if the SFORB model was in use, a vector of eigenvalues - of these SFORB models, equivalent to DFOP rate constants

+and, if applicable, a vector of formation fractions named ff +and, if the SFORB model was in use, a vector of eigenvalues +of these SFORB models, equivalent to DFOP rate constants

Note

The function is used internally by summary.mkinfit.

@@ -192,17 +200,10 @@ advantage that the SFORB model can also be used for metabolites.

- @@ -213,7 +214,7 @@ advantage that the SFORB model can also be used for metabolites.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index c5b8e38c..598a25c0 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -37,7 +41,6 @@ - @@ -55,7 +58,7 @@ - +
@@ -113,7 +116,12 @@
@@ -128,7 +136,7 @@

Retrieve a degradation function from the mmkin namespace

- + Source: R/nlme.mmkin.R
@@ -142,15 +150,13 @@

Value

A function that was likely previously assigned from within - nlme.mmkin

+nlme.mmkin

- @@ -161,7 +167,7 @@
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 76ce2233..8410e499 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -38,7 +42,6 @@ - @@ -56,7 +59,7 @@ transformations." /> - +
@@ -114,7 +117,12 @@ transformations." />
@@ -129,7 +137,7 @@ transformations." />

Function to perform isometric log-ratio transformation

- + Source: R/ilr.R
@@ -155,16 +163,16 @@ sensible for vectors with all elements being greater than zero.

Value

The result of the forward or backward transformation. The returned - components always sum to 1 for the case of the inverse log-ratio - transformation.

+components always sum to 1 for the case of the inverse log-ratio +transformation.

References

Peter Filzmoser, Karel Hron (2008) Outlier Detection for - Compositional Data Using Robust Methods. Math Geosci 40 233-248

+Compositional Data Using Robust Methods. Math Geosci 40 233-248

See also

Another implementation can be found in R package - robCompositions.

+robCompositions.

Examples


@@ -180,18 +188,10 @@ sensible for vectors with all elements being greater than zero.

 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
- @@ -202,7 +202,7 @@ sensible for vectors with all elements being greater than zero.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 9a54496e..8e33c28f 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -41,7 +45,6 @@ observed value, as calculated as part of the fitting procedure using dnorm, i.e. assuming normal distribution, and with the means predicted by the degradation model, and the standard deviations predicted by the error model." /> - @@ -59,7 +62,7 @@ the error model." /> - +
@@ -117,7 +120,12 @@ the error model." />
@@ -132,7 +140,7 @@ the error model." />

Calculated the log-likelihood of a fitted mkinfit object

- + Source: R/logLik.mkinfit.R
@@ -163,8 +171,8 @@ the error model.

Value

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

+parameters (degradation model parameters plus variance model parameters) +as attribute.

Details

The total number of estimated parameters returned with the value of the @@ -173,7 +181,7 @@ and the fitted error model parameters.

See also

Compare the AIC of columns of mmkin objects using - AIC.mmkin.

+AIC.mmkin.

Examples


@@ -189,18 +197,10 @@ and the fitted error model parameters.
- @@ -211,7 +211,7 @@ and the fitted error model parameters.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index b0ec77b1..9907297c 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -73,7 +73,7 @@ an increasing rate constant, supposedly caused by microbial growth" /> mkin - 0.9.50 + 0.9.50.1 @@ -179,19 +179,19 @@ an increasing rate constant, supposedly caused by microbial growth

Note

The solution of the logistic model reduces to the - SFO.solution if k0 is equal to kmax.

+SFO.solution if k0 is equal to kmax.

References

FOCUS (2006) “Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics FOCUS (2014) “Generic guidance for Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, - Version 1.1, 18 December 2014 - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

+and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

See also

Other parent solutions: diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index ef2a55bf..b8ce5397 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -11,23 +11,27 @@ kinetic models fitted with mkinfit — max_twa_parent • mkin - + - + - + + + + + - - + + - + - - + + @@ -43,7 +47,6 @@ concentrations (TWAs) for kinetic models fitted with mkinfit. Currently, only calculations for the parent are implemented for the SFO, FOMC, DFOP and HS models, using the analytical formulas given in the PEC soil section of the FOCUS guidance." /> - @@ -61,7 +64,7 @@ soil section of the FOCUS guidance." /> - +

@@ -119,7 +122,12 @@ soil section of the FOCUS guidance." />
@@ -135,7 +143,7 @@ soil section of the FOCUS guidance." />

Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit

- + Source: R/max_twa_parent.R
@@ -213,15 +221,15 @@ factor (f_twa) is calculated.

Value

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').

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

References

FOCUS (2006) “Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

+and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

Examples


@@ -230,17 +238,10 @@ factor (f_twa) is calculated.

 #> 34.71343 18.22124
- @@ -251,7 +252,7 @@ factor (f_twa) is calculated.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/mkinerrplot-1.png b/docs/reference/mkinerrplot-1.png index 46a80308..c5d3495f 100644 Binary files a/docs/reference/mkinerrplot-1.png and b/docs/reference/mkinerrplot-1.png differ diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 47f48b72..7e5a00f2 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -41,7 +45,6 @@ observed variables from an mkinfit object. In addition, one or more dashed line(s) show the fitted error model. A combined plot of the fitted model and this error model plot can be obtained with plot.mkinfit using the argument show_errplot = TRUE." /> - @@ -59,7 +62,7 @@ using the argument show_errplot = TRUE." /> - +
@@ -117,7 +120,12 @@ using the argument show_errplot = TRUE." />
@@ -132,7 +140,7 @@ using the argument show_errplot = TRUE." />

Function to plot squared residuals and the error model for an mkin object

- + Source: R/mkinerrplot.R
@@ -212,18 +220,18 @@ be passed on to legend ... -

further arguments passed to plot.

+

further arguments passed to plot.

Value

Nothing is returned by this function, as it is called for its side - effect, namely to produce a plot.

+effect, namely to produce a plot.

See also

mkinplot, for a way to plot the data and the fitted - lines of the mkinfit object.

+lines of the mkinfit object.

Examples


@@ -232,17 +240,10 @@ be passed on to legend
- @@ -253,7 +254,7 @@ be passed on to legend
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 9974b66b..ceac59bf 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -78,7 +78,7 @@ likelihood function." /> mkin - 0.9.50 + 0.9.50.1 @@ -209,15 +209,15 @@ detection.

parms.ini

A named vector of initial values for the parameters, - including parameters to be optimised and potentially also fixed parameters - as indicated by fixed_parms. If set to "auto", initial values for - rate constants are set to default values. Using parameter names that are - not in the model gives an error.

+including parameters to be optimised and potentially also fixed parameters +as indicated by fixed_parms. If set to "auto", initial values for +rate constants are set to default values. Using parameter names that are +not in the model gives an error.

It is possible to only specify a subset of the parameters that the model - needs. You can use the parameter lists "bparms.ode" from a previously - fitted model, which contains the differential equation parameters from - this model. This works nicely if the models are nested. An example is - given below.

+needs. You can use the parameter lists "bparms.ode" from a previously +fitted model, which contains the differential equation parameters from +this model. This works nicely if the models are nested. An example is +given below.

state.ini @@ -326,42 +326,44 @@ is 1e-10, much lower than in lsoda.

error_model

If the error model is "const", a constant standard - deviation is assumed.

+deviation is assumed.

If the error model is "obs", each observed variable is assumed to have its - own variance.

+own variance.

If the error model is "tc" (two-component error model), a two component - error model similar to the one described by Rocke and Lorenzato (1995) is - used for setting up the likelihood function. Note that this model - deviates from the model by Rocke and Lorenzato, as their model implies - that the errors follow a lognormal distribution for large values, not a - normal distribution as assumed by this method.

+error model similar to the one described by Rocke and Lorenzato (1995) is +used for setting up the likelihood function. Note that this model +deviates from the model by Rocke and Lorenzato, as their model implies +that the errors follow a lognormal distribution for large values, not a +normal distribution as assumed by this method.

error_model_algorithm

If "auto", the selected algorithm depends on - the error model. If the error model is "const", unweighted nonlinear - least squares fitting ("OLS") is selected. If the error model is "obs", or - "tc", the "d_3" algorithm is selected.

-

The algorithm "d_3" will directly minimize the negative log-likelihood and - - independently - also use the three step algorithm described below. The - fit with the higher likelihood is returned.

+the error model. If the error model is "const", unweighted nonlinear +least squares fitting ("OLS") is selected. If the error model is "obs", or +"tc", the "d_3" algorithm is selected.

+

The algorithm "d_3" will directly minimize the negative log-likelihood and

    +

  • independently - also use the three step algorithm described below. The +fit with the higher likelihood is returned.

    • +
+

The algorithm "direct" will directly minimize the negative log-likelihood.

The algorithm "twostep" will minimize the negative log-likelihood after an - initial unweighted least squares optimisation step.

+initial unweighted least squares optimisation step.

The algorithm "threestep" starts with unweighted least squares, then - optimizes only the error model using the degradation model parameters - found, and then minimizes the negative log-likelihood with free - degradation and error model parameters.

+optimizes only the error model using the degradation model parameters +found, and then minimizes the negative log-likelihood with free +degradation and error model parameters.

The algorithm "fourstep" starts with unweighted least squares, then - optimizes only the error model using the degradation model parameters - found, then optimizes the degradation model again with fixed error model - parameters, and finally minimizes the negative log-likelihood with free - degradation and error model parameters.

+optimizes only the error model using the degradation model parameters +found, then optimizes the degradation model again with fixed error model +parameters, and finally minimizes the negative log-likelihood with free +degradation and error model parameters.

The algorithm "IRLS" (Iteratively Reweighted Least Squares) starts with - unweighted least squares, and then iterates optimization of the error - model parameters and subsequent optimization of the degradation model - using those error model parameters, until the error model parameters - converge.

+unweighted least squares, and then iterates optimization of the error +model parameters and subsequent optimization of the degradation model +using those error model parameters, until the error model parameters +converge.

reweight.tol @@ -383,14 +385,10 @@ the error model parameters in IRLS fits.

-

Source

- -

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

Value

A list with "mkinfit" in the class attribute. A summary can be - obtained by summary.mkinfit.

+obtained by summary.mkinfit.

Details

Per default, parameters in the kinetic models are internally transformed in @@ -399,33 +397,40 @@ estimators.

Note

When using the "IORE" submodel for metabolites, fitting with - "transform_rates = TRUE" (the default) often leads to failures of the - numerical ODE solver. In this situation it may help to switch off the - internal rate transformation.

+"transform_rates = TRUE" (the default) often leads to failures of the +numerical ODE solver. In this situation it may help to switch off the +internal rate transformation.

+

References

+ +

Rocke DM and Lorenzato S (1995) A two-component model +for measurement error in analytical chemistry. Technometrics 37(2), 176-184.

+

Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical +Degradation Data. Environments 6(12) 124 +doi:10.3390/environments6120124.

See also

Plotting methods plot.mkinfit and - mkinparplot.

+mkinparplot.

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

+AIC by virtue of the method logLik.mkinfit.

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

+mmkin.

Examples


 # Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version used for fitting:    0.9.50 
+summary(fit)
#> mkin version used for fitting:    0.9.50.1 
 #> R version used for fitting:       4.0.0 
-#> Date of fit:     Mon May 11 05:14:26 2020 
-#> Date of summary: Mon May 11 05:14:26 2020 
+#> Date of fit:     Tue May 12 08:36:07 2020 
+#> Date of summary: Tue May 12 08:36:07 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.043 s
+#> Fitted using 222 model solutions performed in 0.047 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -502,7 +507,7 @@ estimators.

   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#> Warning: Observations with value of zero were removed from the data
#>        User      System verstrichen 
-#>       0.407       0.002       0.409 
parms(fit)
#>       parent_0       k_parent           k_m1 f_parent_to_m1          sigma 
+#>       0.408       0.008       0.416 
parms(fit)
#>       parent_0       k_parent           k_m1 f_parent_to_m1          sigma 
 #>   99.598483222    0.098697734    0.005260651    0.514475962    3.125503875 
endpoints(fit)
#> $ff
 #>   parent_m1 parent_sink 
 #>    0.514476    0.485524 
@@ -592,7 +597,7 @@ estimators.

 #> Sum of squared residuals at call 166: 371.2134
 #> Sum of squared residuals at call 168: 371.2134
 #> Negative log-likelihood at call 178: 97.22429
#> Optimisation successfully terminated.
#>        User      System verstrichen 
-#>       0.349       0.000       0.350 
parms(fit.deSolve)
#>       parent_0       k_parent           k_m1 f_parent_to_m1          sigma 
+#>       0.350       0.001       0.351 
parms(fit.deSolve)
#>       parent_0       k_parent           k_m1 f_parent_to_m1          sigma 
 #>   99.598480759    0.098697739    0.005260651    0.514475958    3.125503874 
endpoints(fit.deSolve)
#> $ff
 #>   parent_m1 parent_sink 
 #>    0.514476    0.485524 
@@ -622,12 +627,12 @@ estimators.

 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
#> Warning: Initial parameter(s) k_parent_free_sink not used in the model
# }
 
 # \dontrun{
-# Weighted fits, including IRLS
+# Weighted fits, including IRLS (error_model = "obs")
 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:    0.9.50 
+                      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:    0.9.50.1 
 #> R version used for fitting:       4.0.0 
-#> Date of fit:     Mon May 11 05:14:31 2020 
-#> Date of summary: Mon May 11 05:14:31 2020 
+#> Date of fit:     Tue May 12 08:36:12 2020 
+#> Date of summary: Tue May 12 08:36:12 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -635,7 +640,7 @@ estimators.

 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 421 model solutions performed in 0.124 s
+#> Fitted using 421 model solutions performed in 0.146 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -746,10 +751,10 @@ estimators.

 #>   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:    0.9.50 
+#>   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:    0.9.50.1 
 #> R version used for fitting:       4.0.0 
-#> Date of fit:     Mon May 11 05:14:32 2020 
-#> Date of summary: Mon May 11 05:14:32 2020 
+#> Date of fit:     Tue May 12 08:36:13 2020 
+#> Date of summary: Tue May 12 08:36:13 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -757,7 +762,7 @@ estimators.

 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 978 model solutions performed in 0.336 s
+#> Fitted using 978 model solutions performed in 0.337 s
 #> 
 #> Error model: Variance unique to each observed variable 
 #> 
@@ -883,10 +888,10 @@ estimators.

 #>   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:    0.9.50 
+#>   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:    0.9.50.1 
 #> R version used for fitting:       4.0.0 
-#> Date of fit:     Mon May 11 05:14:32 2020 
-#> Date of summary: Mon May 11 05:14:32 2020 
+#> Date of fit:     Tue May 12 08:36:14 2020 
+#> Date of summary: Tue May 12 08:36:14 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -894,7 +899,7 @@ estimators.

 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 1875 model solutions performed in 0.642 s
+#> Fitted using 1875 model solutions performed in 0.647 s
 #> 
 #> Error model: Two-component variance function 
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 81b62ae1..1c97048e 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -75,7 +75,7 @@ list of lists can be given in the speclist argument." />
       
       
         mkin
-        0.9.50
+        0.9.50.1
       
     

 
@@ -205,15 +205,18 @@ applicable to give detailed information about the C function being built.
Value
 
     
A list of class mkinmod for use with mkinfit,
-  containing, among others,

+containing, among others,

 
diffs
A vector of string representations of differential equations, one for
-    each modelling variable.

-  
map
A list containing named character vectors for each observed variable,
-    specifying the modelling variables by which it is represented.

-  
use_of_ff
The content of use_of_ff is passed on in this list component.

-  
coefmat
The coefficient matrix, if the system of differential equations can be
-    represented by one.

-  
cf
If generated, the compiled function as returned by cfunction.

+each modelling variable.

+
map
A list containing named character vectors for each observed variable,
+specifying the modelling variables by which it is represented.

+
use_of_ff
The content of use_of_ff is passed on in this list component.

+
deg_func
If generated, a function containing the solution of the degradation
+model.

+
coefmat
The coefficient matrix, if the system of differential equations can be
+represented by one.

+
cf
If generated, a compiled function calculating the derivatives as
+returned by cfunction.

 
     
Details

 
@@ -222,17 +225,17 @@ in the FOCUS and NAFTA guidance documents are used.

     
Note

 
     
The IORE submodel is not well tested for metabolites. When using this
-  model for metabolites, you may want to read the second note in the help
-  page to mkinfit.

+model for metabolites, you may want to read the second note in the help
+page to mkinfit.

     
References

 
     
FOCUS (2006) “Guidance Document on Estimating Persistence
-  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
-  EU Registration” Report of the FOCUS Work Group on Degradation Kinetics,
-  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

+and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+EU Registration” Report of the FOCUS Work Group on Degradation Kinetics,
+EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

 
NAFTA Technical Working Group on Pesticides (not dated) Guidance for
-  Evaluating and Calculating Degradation Kinetics in Environmental Media

+Evaluating and Calculating Degradation Kinetics in Environmental Media

 
     
Examples

     

@@ -252,7 +255,7 @@ in the FOCUS and NAFTA guidance documents are used.

 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file1a1abf38df.c 2> file1a1abf38df.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file15d32c282a7d.c 2> file15d32c282a7d.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png
index d4259579..6853a4ba 100644
Binary files a/docs/reference/mkinparplot-1.png and b/docs/reference/mkinparplot-1.png differ
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index af936795..dfe695d0 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -38,7 +42,6 @@
 
 
-
 
 
 
@@ -56,7 +59,7 @@ mkinfit." />
 
   
 
-  
+  
     

       

       
 
@@ -114,7 +117,12 @@ mkinfit." />
 
       
       
       
     

@@ -129,7 +137,7 @@ mkinfit." />
   

     

     
Function to plot the confidence intervals obtained using mkinfit

-    
+    Source: R/mkinparplot.R
     
     

 
@@ -152,7 +160,7 @@ mkinfit." />
     
Value

 
     
Nothing is returned by this function, as it is called for its side
-  effect, namely to produce a plot.

+effect, namely to produce a plot.

 
     
Examples

     

@@ -163,16 +171,10 @@ mkinfit." />
   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)
# }
 

   

-  
 
@@ -183,7 +185,7 @@ mkinfit." />
 

 
 

-  
Site built with pkgdown 1.4.1.

+  
Site built with pkgdown 1.5.1.

 

 
       
diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png
index d29181c3..bb9657b4 100644
Binary files a/docs/reference/mkinresplot-1.png and b/docs/reference/mkinresplot-1.png differ
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index 698af302..cd6bf4a1 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -40,7 +44,6 @@
 variables from an mkinfit object. A combined plot of the fitted model and
 the residuals can be obtained using plot.mkinfit using the
 argument show_residuals = TRUE." />
-
 
 
 
@@ -58,7 +61,7 @@ argument show_residuals = TRUE." />
 
   
 
-  
+  
     

       

       
 
@@ -116,7 +119,12 @@ argument show_residuals = TRUE." />
 
       
       
       
     

@@ -131,7 +139,7 @@ argument show_residuals = TRUE." />
   

     

     
Function to plot residuals stored in an mkin object

-    
+    Source: R/mkinresplot.R
     
     

 
@@ -216,36 +224,29 @@ be passed on to legend
     
       ...
-      
further arguments passed to plot.

+      
further arguments passed to plot.

     
     
 
     
Value

 
     
Nothing is returned by this function, as it is called for its side
-  effect, namely to produce a plot.

+effect, namely to produce a plot.

     
See also

 
     
mkinplot, for a way to plot the data and the fitted
-  lines of the mkinfit object, and plot_res for a function
-  combining the plot of the fit and the residual plot.

+lines of the mkinfit object, and plot_res for a function
+combining the plot of the fit and the residual plot.

 
     
Examples

     

 model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
fit <- mkinfit(model, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
mkinresplot(fit, "m1")

 

   
-  
 
@@ -256,7 +257,7 @@ be passed on to legend
 
 

-  
Site built with pkgdown 1.4.1.

+  
Site built with pkgdown 1.5.1.

 

 
       
diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png
index 328cec9b..135d5446 100644
Binary files a/docs/reference/mmkin-1.png and b/docs/reference/mmkin-1.png differ
diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png
index 7b1d73d5..40109afc 100644
Binary files a/docs/reference/mmkin-2.png and b/docs/reference/mmkin-2.png differ
diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png
index 4c412abc..bce34531 100644
Binary files a/docs/reference/mmkin-3.png and b/docs/reference/mmkin-3.png differ
diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png
index 201ef0fd..02976ced 100644
Binary files a/docs/reference/mmkin-4.png and b/docs/reference/mmkin-4.png differ
diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png
index 29206932..56750342 100644
Binary files a/docs/reference/mmkin-5.png and b/docs/reference/mmkin-5.png differ
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index c1f62be7..db359f48 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -11,23 +11,27 @@ more datasets — mmkin • mkin
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -40,7 +44,6 @@ more datasets — mmkin • mkin
 more datasets — mmkin" />
 
-
 
 
 
@@ -58,7 +61,7 @@ datasets specified in its first two arguments." />
 
   
 
-  
+  
     

       

       
 
@@ -116,7 +119,12 @@ datasets specified in its first two arguments." />
 
       
       
       
     

@@ -132,7 +140,7 @@ datasets specified in its first two arguments." />
     

     
Fit one or more kinetic models with one or more state variables to one or
 more datasets

-    
+    Source: R/mmkin.R
     
     

 
@@ -184,12 +192,12 @@ for parallel execution.

     
Value

 
     
A two-dimensional array of mkinfit
-  objects that can be indexed using the model names for the first index (row index) 
-  and the dataset names for the second index (column index).

+objects that can be indexed using the model names for the first index (row index)
+and the dataset names for the second index (column index).

     
See also

 
     
[.mmkin for subsetting, plot.mmkin for
-  plotting.

+plotting.

 
     
Examples

     

@@ -205,42 +213,35 @@ for parallel execution.

 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_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
#> Warning: Optimisation did not converge:
+#> false convergence (8)

 time_default
#>        User      System verstrichen 
-#>      16.471       0.352       5.654 
time_1
#>        User      System verstrichen 
-#>      19.578       0.000      19.590 

+#>       4.370       0.401       1.265 
time_1
#>        User      System verstrichen 
+#>       5.000       0.008       5.011 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
-#>   0.7340480   0.2659520   0.7505686   0.2494314 
+#>   0.7340478   0.2659522   0.7505691   0.2494309 
 #> 
 #> $distimes
 #>              DT50       DT90
-#> parent  0.8777689   2.915885
-#> M1      2.3257452   7.725958
-#> M2     33.7200890 112.015711
+#> parent  0.8777688   2.915885
+#> M1      2.3257466   7.725963
+#> M2     33.7200800 112.015681
 #> 

 # 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])
# }
 
 

   
-  
 
@@ -251,7 +252,7 @@ for parallel execution.

 
 
 

-  
Site built with pkgdown 1.4.1.

+  
Site built with pkgdown 1.5.1.

 

 
       
diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html
index 60917ff4..02c44737 100644
--- a/docs/reference/nafta.html
+++ b/docs/reference/nafta.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -41,7 +45,6 @@ and returns an object of class nafta that has methods for printing
 and plotting.
 Print nafta objects. The results for the three models are printed in the
 order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." />
-
 
 
 
@@ -59,7 +62,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." />
 
   
 
-  
+  
     

       

       
 
@@ -117,7 +120,12 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." />
 
       
       
       
     

@@ -132,7 +140,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." />
   

     

     
Evaluate parent kinetics using the NAFTA guidance

-    
+    Source: R/nafta.R
     
     

 
@@ -186,20 +194,20 @@ dissipation times.

     
Source

 
     
NAFTA (2011) Guidance for evaluating and calculating degradation
-  kinetics in environmental media. NAFTA Technical Working Group on
-  Pesticides
-  https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation
-  accessed 2019-02-22

+kinetics in environmental media. NAFTA Technical Working Group on
+Pesticides
+https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation
+accessed 2019-02-22

 
US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to
-  Calculate Representative Half-life Values and Characterizing Pesticide
-  Degradation
-  https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance

+Calculate Representative Half-life Values and Characterizing Pesticide
+Degradation
+https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance

     
Value

 
     
An list of class nafta. The list element named "mmkin" is the
-  mmkin object containing the fits of the three models. The
-  list element named "title" contains the title of the dataset used. The
-  list element "data" contains the dataset used in the fits.

+mmkin object containing the fits of the three models. The
+list element named "title" contains the title of the dataset used. The
+list element "data" contains the dataset used in the fits.

 
     
Examples

     

@@ -240,20 +248,13 @@ dissipation times.

 #> DFOP  429    2380      841
 #> 
 #> Representative half-life:
-#> [1] 841.41
  plot(nafta_evaluation)

+#> [1] 841.41
  plot(nafta_evaluation)

 

   

-  
 
@@ -264,7 +265,7 @@ dissipation times.

 
 
 

-  
Site built with pkgdown 1.4.1.

+  
Site built with pkgdown 1.5.1.

 

 
       
diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html
index b92d2141..78489ee7 100644
--- a/docs/reference/nlme.html
+++ b/docs/reference/nlme.html
@@ -75,7 +75,7 @@ datasets." />
       
       
         mkin
-        0.9.50
+        0.9.50.1
       
     
 
@@ -173,9 +173,9 @@ datasets.

 
     
A function that can be used with nlme

 
If random is FALSE (default), a named vector containing mean values
-  of the fitted degradation model parameters. If random is TRUE, a list with
-  fixed and random effects, in the format required by the start argument of
-  nlme for the case of a single grouping variable ds?

+of the fitted degradation model parameters. If random is TRUE, a list with
+fixed and random effects, in the format required by the start argument of
+nlme for the case of a single grouping variable ds?

 
A groupedData object

     
See also

 
diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png
index 67bd07de..67f279da 100644
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index ee6bb2e4..16a5d7bd 100644
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index 5f5a759a..7b663991 100644
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diff --git a/docs/reference/nlme.mmkin-7.png b/docs/reference/nlme.mmkin-7.png
index 1d4fa8ea..d2c38a63 100644
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diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html
index 33cc9164..4e5a86cb 100644
--- a/docs/reference/nlme.mmkin.html
+++ b/docs/reference/nlme.mmkin.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -39,7 +43,6 @@
 
-
 
 
 
@@ -57,7 +60,7 @@ have been obtained by fitting the same model to a list of datasets." />
 
   
 
-  
+  
     

       

       
 
@@ -115,7 +118,12 @@ have been obtained by fitting the same model to a list of datasets." />
 
       
       
       
     

@@ -130,7 +138,7 @@ have been obtained by fitting the same model to a list of datasets." />
   

     

     
Create an nlme model for an mmkin row object

-    
+    Source: R/nlme.mmkin.R
     
     

 
@@ -243,7 +251,7 @@ parameters taken from the mmkin object are used

     
Value

 
     
Upon success, a fitted nlme.mmkin object, which is an nlme object
-  with additional elements

+with additional elements

     
See also

 
     
nlme_function

@@ -309,142 +317,124 @@ parameters taken from the mmkin object are used

    "FOMC-SFO" = m_fomc_sfo,
    "DFOP-SFO" = m_dfop_sfo),
     ds_2, quiet = TRUE)
-  plot(f_2["SFO-SFO", 3:4]) # Separate fits for datasets 3 and 4

+  plot(f_2["SFO-SFO", 3:4]) # Separate fits for datasets 3 and 4

   f_nlme_sfo_sfo <- nlme(f_2["SFO-SFO", ])
   # plot(f_nlme_sfo_sfo) # not feasible with pkgdown figures
-  plot(f_nlme_sfo_sfo, 3:4) # Global mixed model: Fits for datasets 3 and 4

+  plot(f_nlme_sfo_sfo, 3:4) # Global mixed model: Fits for datasets 3 and 4

   # With formation fractions
   f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ])
-  plot(f_nlme_sfo_sfo_ff, 3:4) # chi2 different due to different df attribution

+  plot(f_nlme_sfo_sfo_ff, 3:4) # chi2 different due to different df attribution

   # For more parameters, we need to increase pnlsMaxIter and the tolerance
   # to get convergence
   f_nlme_fomc_sfo <- nlme(f_2["FOMC-SFO", ],
     control = list(pnlsMaxIter = 100, tolerance = 1e-4), verbose = TRUE)
#> 
 #> **Iteration 1
-#> LME step: Loglik: -394.1603, nlminb iterations: 2
+#> LME step: Loglik: -394.1603, nlminb iterations: 3
 #> reStruct  parameters:
 #>        ds1        ds2        ds3        ds4        ds5 
-#> -0.2079984  0.8563873  1.7454146  1.0917723  1.2756924 
+#> -0.2079793  0.8563830  1.7454105  1.0917354  1.2756825 
 #>  Beginning PNLS step: ..  completed fit_nlme() step.
-#> PNLS step: RSS =  643.8786 
-#>  fixed effects: 94.17379  -5.473199  -0.6970239  -0.2025094  2.103883  
+#> PNLS step: RSS =  643.8803 
+#>  fixed effects: 94.17379  -5.473193  -0.6970236  -0.2025091  2.103883  
 #>  iterations: 100 
 #> Convergence crit. (must all become <= tolerance = 0.0001):
 #>     fixed  reStruct 
-#> 0.7865373 0.1448077 
+#> 0.7960134 0.1447728 
 #> 
 #> **Iteration 2
 #> LME step: Loglik: -396.3824, nlminb iterations: 7
 #> reStruct  parameters:
 #>           ds1           ds2           ds3           ds4           ds5 
-#> -1.712408e-01 -2.680989e-05  1.842119e+00  1.073975e+00  1.322924e+00 
+#> -1.712404e-01 -2.432655e-05  1.842120e+00  1.073975e+00  1.322925e+00 
 #>  Beginning PNLS step: ..  completed fit_nlme() step.
-#> PNLS step: RSS =  643.8022 
-#>  fixed effects: 94.17385  -5.473491  -0.6970405  -0.202514  2.103871  
+#> PNLS step: RSS =  643.8035 
+#>  fixed effects: 94.17385  -5.473487  -0.6970404  -0.2025137  2.103871  
 #>  iterations: 100 
 #> Convergence crit. (must all become <= tolerance = 0.0001):
 #>        fixed     reStruct 
-#> 5.341904e-05 1.227073e-03 
+#> 5.382757e-05 1.236667e-03 
 #> 
 #> **Iteration 3
 #> LME step: Loglik: -396.3825, nlminb iterations: 7
 #> reStruct  parameters:
 #>           ds1           ds2           ds3           ds4           ds5 
-#> -0.1712484347 -0.0001513555  1.8420964843  1.0739800649  1.3229176990 
+#> -0.1712499044 -0.0001499831  1.8420971364  1.0739799123  1.3229167796 
 #>  Beginning PNLS step: ..  completed fit_nlme() step.
-#> PNLS step: RSS =  643.7947 
-#>  fixed effects: 94.17386  -5.473522  -0.6970423  -0.2025142  2.10387  
+#> PNLS step: RSS =  643.7948 
+#>  fixed effects: 94.17386  -5.473521  -0.6970422  -0.2025144  2.10387  
 #>  iterations: 100 
 #> Convergence crit. (must all become <= tolerance = 0.0001):
 #>        fixed     reStruct 
-#> 5.568186e-06 1.276609e-04 
+#> 6.072817e-06 1.400857e-04 
 #> 
 #> **Iteration 4
 #> LME step: Loglik: -396.3825, nlminb iterations: 7
 #> reStruct  parameters:
-#>          ds1          ds2          ds3          ds4          ds5 
-#> -0.171251200 -0.000164506  1.842095097  1.073980200  1.322916184 
+#>           ds1           ds2           ds3           ds4           ds5 
+#> -0.1712529502 -0.0001641277  1.8420957542  1.0739797181  1.3229173076 
 #>  Beginning PNLS step: ..  completed fit_nlme() step.
-#> PNLS step: RSS =  643.7934 
+#> PNLS step: RSS =  643.7936 
 #>  fixed effects: 94.17386  -5.473526  -0.6970426  -0.2025146  2.103869  
 #>  iterations: 100 
 #> Convergence crit. (must all become <= tolerance = 0.0001):
 #>        fixed     reStruct 
-#> 2.332100e-06 1.979007e-05 
  f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ],
+#> 1.027451e-06 2.275704e-05 
  f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ],
     control = list(pnlsMaxIter = 120, tolerance = 5e-4), verbose = TRUE)
#> 
 #> **Iteration 1
-#> LME step: Loglik: -404.9591, nlminb iterations: 1
+#> LME step: Loglik: -404.9582, nlminb iterations: 1
 #> reStruct  parameters:
 #>        ds1        ds2        ds3        ds4        ds5        ds6 
-#> -0.4114594  0.9798456  1.6990016  0.7293119  0.3353829  1.7112922 
+#> -0.4114355  0.9798697  1.6990037  0.7293315  0.3354323  1.7113046 
 #>  Beginning PNLS step: ..  completed fit_nlme() step.
-#> PNLS step: RSS =  630.391 
-#>  fixed effects: 93.82265  -5.455841  -0.6788837  -1.862191  -4.199654  0.05531046  
+#> PNLS step: RSS =  630.3644 
+#>  fixed effects: 93.82269  -5.455991  -0.6788957  -1.862196  -4.199671  0.05532828  
 #>  iterations: 120 
 #> Convergence crit. (must all become <= tolerance = 0.0005):
 #>     fixed  reStruct 
-#> 0.7872619 0.5811683 
+#> 0.7885368 0.5822683 
 #> 
 #> **Iteration 2
 #> LME step: Loglik: -407.7755, nlminb iterations: 11
 #> reStruct  parameters:
 #>          ds1          ds2          ds3          ds4          ds5          ds6 
-#> -0.371222832  0.003084754  1.789952290  0.724634064  0.301559136  1.754244638 
-#>  Beginning PNLS step: ..  completed fit_nlme() step.
-#> PNLS step: RSS =  630.359 
-#>  fixed effects: 93.82269  -5.456014  -0.6788967  -1.862202  -4.199678  0.05534118  
-#>  iterations: 120 
-#> Convergence crit. (must all become <= tolerance = 0.0005):
-#>        fixed     reStruct 
-#> 0.0005550885 0.0007749418 
-#> 
-#> **Iteration 3
-#> LME step: Loglik: -407.7756, nlminb iterations: 11
-#> reStruct  parameters:
-#>          ds1          ds2          ds3          ds4          ds5          ds6 
-#> -0.371217033  0.003064156  1.789935045  0.724683005  0.301622307  1.754234135 
+#> -0.371224133  0.003056179  1.789939402  0.724671158  0.301602977  1.754200729 
 #>  Beginning PNLS step: ..  completed fit_nlme() step.
-#> PNLS step: RSS =  630.358 
-#>  fixed effects: 93.82269  -5.456017  -0.6788969  -1.862197  -4.199677  0.05532978  
+#> PNLS step: RSS =  630.3633 
+#>  fixed effects: 93.82269  -5.455992  -0.6788958  -1.862196  -4.199671  0.05532831  
 #>  iterations: 120 
 #> Convergence crit. (must all become <= tolerance = 0.0005):
 #>        fixed     reStruct 
-#> 2.059533e-04 4.860085e-05 
  plot(f_2["FOMC-SFO", 3:4])
  plot(f_nlme_fomc_sfo, 3:4)

-  plot(f_2["DFOP-SFO", 3:4])
  plot(f_nlme_dfop_sfo, 3:4)

+#> 4.789774e-07 2.200661e-05 
  plot(f_2["FOMC-SFO", 3:4])
  plot(f_nlme_fomc_sfo, 3:4)

+  plot(f_2["DFOP-SFO", 3:4])
  plot(f_nlme_dfop_sfo, 3:4)

   anova(f_nlme_dfop_sfo, f_nlme_fomc_sfo, f_nlme_sfo_sfo)
#>                 Model df       AIC       BIC    logLik   Test   L.Ratio p-value
-#> f_nlme_dfop_sfo     1 13  843.8541  884.6194 -408.9270                         
-#> f_nlme_fomc_sfo     2 11  818.5149  853.0087 -398.2575 1 vs 2  21.33913  <.0001
-#> f_nlme_sfo_sfo      3  9 1085.1821 1113.4042 -533.5910 2 vs 3 270.66712  <.0001
  anova(f_nlme_dfop_sfo, f_nlme_sfo_sfo) # if we ignore FOMC
#>                 Model df       AIC       BIC   logLik   Test L.Ratio p-value
-#> f_nlme_dfop_sfo     1 13  843.8541  884.6194 -408.927                       
-#> f_nlme_sfo_sfo      2  9 1085.1821 1113.4042 -533.591 1 vs 2 249.328  <.0001

+#> f_nlme_dfop_sfo     1 13  843.8547  884.6201 -408.9273                         
+#> f_nlme_fomc_sfo     2 11  818.5149  853.0087 -398.2575 1 vs 2  21.33975  <.0001
+#> f_nlme_sfo_sfo      3  9 1085.1821 1113.4043 -533.5910 2 vs 3 270.66716  <.0001
  anova(f_nlme_dfop_sfo, f_nlme_sfo_sfo) # if we ignore FOMC
#>                 Model df       AIC       BIC    logLik   Test  L.Ratio p-value
+#> f_nlme_dfop_sfo     1 13  843.8547  884.6201 -408.9273                        
+#> f_nlme_sfo_sfo      2  9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274  <.0001

   endpoints(f_nlme_sfo_sfo)
#> $ff
 #> parent_sink   parent_A1     A1_sink 
-#>   0.5912435   0.4087565   1.0000000 
+#>   0.5912432   0.4087568   1.0000000 
 #> 
 #> $distimes
-#>            DT50      DT90
-#> parent 19.13517  63.56565
-#> A1     66.02149 219.31865
+#>            DT50     DT90
+#> parent 19.13518  63.5657
+#> A1     66.02155 219.3189
 #> 
  endpoints(f_nlme_dfop_sfo)
#> $ff
-#>   parent_A1 parent_sink     A1_sink 
-#>   0.2768571   0.7231429   1.0000000 
+#>   parent_A1 parent_sink 
+#>   0.2768574   0.7231426 
 #> 
 #> $distimes
-#>             DT50     DT90  DT50_k1 DT50_k2
-#> parent  11.07092 104.6325 4.462389 46.2085
-#> A1     162.30937 539.1801       NA      NA
+#>             DT50     DT90  DT50_k1  DT50_k2
+#> parent  11.07091 104.6320 4.462384 46.20825
+#> A1     162.30536 539.1667       NA       NA
 #> 
# }
 

   
-  
 
@@ -455,7 +445,7 @@ parameters taken from the mmkin object are used

 
 
 

-  
Site built with pkgdown 1.4.1.

+  
Site built with pkgdown 1.5.1.

 

 
       
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index 2ede2dec..284c30a6 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -74,7 +74,7 @@ observed data together with the solution of the fitted model." />
       
       
         mkin
-        0.9.50
+        0.9.50.1
       
     
 
@@ -255,7 +255,7 @@ fits is shown, the residual plot is in the lower third of the plot.
 Otherwise, i.e. if "sep_obs" is given, the residual plots will be located
 to the right of the plots of the fitted curves. If this is set to
 'standardized', a plot of the residuals divided by the standard deviation
- given by the fitted error model will be shown.

+given by the fitted error model will be shown.

     
     
       show_errplot
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index ef5718e5..4b893032 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -11,23 +11,27 @@ of an mmkin object — plot.mmkin • mkin
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -41,7 +45,6 @@ of an mmkin object — plot.mmkin" />
 
-
 
 
 
@@ -59,7 +62,7 @@ the fit of at least one model to the same dataset is shown." />
 
   
 
-  
+  
     

       

       
 
@@ -117,7 +120,12 @@ the fit of at least one model to the same dataset is shown." />
 
       
       
       
     

@@ -133,7 +141,7 @@ the fit of at least one model to the same dataset is shown." />
     

     
Plot model fits (observed and fitted) and the residuals for a row or column
 of an mmkin object

-    
+    Source: R/plot.mmkin.R
     
     

 
@@ -144,7 +152,7 @@ the fit of at least one model to the same dataset is shown.

     
 
     
# S3 method for mmkin
-plot(
+plot(
   x,
   main = "auto",
   legends = 1,
@@ -185,7 +193,7 @@ values, with the error model, using mkinerrplot
       standardized
       
Should the residuals be standardized? This option
 is passed to mkinresplot, it only takes effect if
-`resplot = "time"`.

+resplot = "time".

     
     
       show_errmin
@@ -237,27 +245,20 @@ latex is being used for the formatting of the chi2 error level.

   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", ])
  plot(fits["FOMC", ], show_errmin = FALSE)

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

   # 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")
  # }
 
 

   
-  
 
@@ -268,7 +269,7 @@ latex is being used for the formatting of the chi2 error level.

 
 
 

-  
Site built with pkgdown 1.4.1.

+  
Site built with pkgdown 1.5.1.

 

 
       
diff --git a/docs/reference/plot.nlme.mmkin-2.png b/docs/reference/plot.nlme.mmkin-2.png
index 27c09796..265fd2e0 100644
Binary files a/docs/reference/plot.nlme.mmkin-2.png and b/docs/reference/plot.nlme.mmkin-2.png differ
diff --git a/docs/reference/plot.nlme.mmkin.html b/docs/reference/plot.nlme.mmkin.html
index 256739eb..9c85fbf0 100644
--- a/docs/reference/plot.nlme.mmkin.html
+++ b/docs/reference/plot.nlme.mmkin.html
@@ -10,23 +10,27 @@
 
 
 
-
+
 
 
-
+
 
-
+
+
+
+
+
 
 
-
-
+
+
 
 
-
+
 
 
-
-
+
+
 
 
 
@@ -37,7 +41,6 @@
 
 
 
-
 
 
 
@@ -55,7 +58,7 @@
 
   
 
-  
+  
     

       

       
 
@@ -113,7 +116,12 @@
 
       
       
       
     

@@ -128,7 +136,7 @@
   

     

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

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

 
@@ -137,7 +145,7 @@
     

 
     
# S3 method for nlme.mmkin
-plot(
+plot(
   x,
   i = 1:ncol(x$mmkin_orig),
   main = "auto",
@@ -183,7 +191,7 @@ values, with the error model, using mkinerrplot
       standardized
       
Should the residuals be standardized? This option
 is passed to mkinresplot, it only takes effect if
-`resplot = "time"`.

+resplot = "time".

     
     
       show_errmin
@@ -229,22 +237,16 @@ than two rows of plots are shown.

  function(x) subset(x$data[c("name", "time", "value")], name == "parent"))
 f <- mmkin("SFO", ds, quiet = TRUE, cores = 1)
 #plot(f) # too many panels for pkgdown
-plot(f[, 3:4])
library(nlme)
+plot(f[, 3:4])
library(nlme)
 f_nlme <- nlme(f)
 
 #plot(f_nlme) # too many panels for pkgdown
-plot(f_nlme, 3:4)

+plot(f_nlme, 3:4)
- @@ -255,7 +257,7 @@ than two rows of plots are shown.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 1795e6c3..76e2eb8f 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -38,7 +42,6 @@ - @@ -56,7 +59,7 @@ dependence of the measured value \(y\):" /> - +
@@ -114,7 +117,12 @@ dependence of the measured value \(y\):" />
@@ -129,7 +137,7 @@ dependence of the measured value \(y\):" />

Two-component error model

- + Source: R/sigma_twocomp.R
@@ -173,21 +181,16 @@ y.

References

Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978) - Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry - 24(11), 1895-1898.

+Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry +24(11), 1895-1898.

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

+measurement error in analytical chemistry. Technometrics 37(2), 176-184.

- @@ -198,7 +201,7 @@ y.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index ec79c37d..84e65787 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -41,7 +45,6 @@ some uncertainty statistics, the chi2 error levels calculated according to FOCUS guidance (2006) as defined therein, formation fractions, DT50 values and optionally the data, consisting of observed, predicted and residual values." /> - @@ -59,7 +62,7 @@ values." /> - +
@@ -117,7 +120,12 @@ values." />
@@ -132,7 +140,7 @@ values." />

Summary method for class "mkinfit"

- + Source: R/summary.mkinfit.R
@@ -190,96 +198,97 @@ distribution

The summary function returns a list with components, among others

version, Rversion

The mkin and R versions used

-
date.fit, date.summary

The dates where the fit and the summary were - produced

-
diffs

The differential equations used in the model

-
use_of_ff

Was maximum or minimum use made of formation fractions

-
bpar

Optimised and backtransformed - parameters

-
data

The data (see Description above).

-
start

The starting values and bounds, if applicable, for optimised - parameters.

-
fixed

The values of fixed parameters.

-
errmin

The chi2 error levels for - each observed variable.

-
bparms.ode

All backtransformed ODE - parameters, for use as starting parameters for related models.

-
errparms

Error model parameters.

-
ff

The estimated formation fractions derived from the fitted - model.

-
distimes

The DT50 and DT90 values for each observed variable.

-
SFORB

If applicable, eigenvalues of SFORB components of the model.

- The print method is called for its side effect, i.e. printing the summary. +
date.fit, date.summary

The dates where the fit and the summary were +produced

+
diffs

The differential equations used in the model

+
use_of_ff

Was maximum or minimum use made of formation fractions

+
bpar

Optimised and backtransformed +parameters

+
data

The data (see Description above).

+
start

The starting values and bounds, if applicable, for optimised +parameters.

+
fixed

The values of fixed parameters.

+
errmin

The chi2 error levels for +each observed variable.

+
bparms.ode

All backtransformed ODE +parameters, for use as starting parameters for related models.

+
errparms

Error model parameters.

+
ff

The estimated formation fractions derived from the fitted +model.

+
distimes

The DT50 and DT90 values for each observed variable.

+
SFORB

If applicable, eigenvalues of SFORB components of the model.

+The print method is called for its side effect, i.e. printing the summary.

References

FOCUS (2006) “Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

+and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

Examples


-  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.9 
-#> R version used for fitting:       3.6.3 
-#> Date of fit:     Mon Mar 30 21:43:00 2020 
-#> Date of summary: Mon Mar 30 21:43:00 2020 
+  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.50.1 
+#> R version used for fitting:       4.0.0 
+#> Date of fit:     Tue May 12 08:07:03 2020 
+#> Date of summary: Tue May 12 08:07:03 2020 
 #> 
 #> Equations:
-#> d_parent/dt = - k_parent_sink * parent
+#> d_parent/dt = - k_parent * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 131 model solutions performed in 0.306 s
+#> Fitted using 131 model solutions performed in 0.026 s
 #> 
 #> Error model: Constant variance 
 #> 
 #> Error model algorithm: OLS 
 #> 
 #> Starting values for parameters to be optimised:
-#>                value   type
-#> parent_0      101.24  state
-#> k_parent_sink   0.10 deparm
+#>           value   type
+#> parent_0 101.24  state
+#> k_parent   0.10 deparm
 #> 
 #> Starting values for the transformed parameters actually optimised:
-#>                        value lower upper
-#> parent_0          101.240000  -Inf   Inf
-#> log_k_parent_sink  -2.302585  -Inf   Inf
+#>                   value lower upper
+#> parent_0     101.240000  -Inf   Inf
+#> log_k_parent  -2.302585  -Inf   Inf
 #> 
 #> Fixed parameter values:
 #> None
 #> 
+#> Results:
+#> 
+#>        AIC     BIC    logLik
+#>   55.28197 55.5203 -24.64099
+#> 
 #> Optimised, transformed parameters with symmetric confidence intervals:
-#>                   Estimate Std. Error  Lower   Upper
-#> parent_0           109.200    3.70400 99.630 118.700
-#> log_k_parent_sink   -3.291    0.09176 -3.527  -3.055
-#> sigma                5.266    1.31600  1.882   8.649
+#>              Estimate Std. Error  Lower   Upper
+#> parent_0      109.200    3.70400 99.630 118.700
+#> log_k_parent   -3.291    0.09176 -3.527  -3.055
+#> sigma           5.266    1.31600  1.882   8.649
 #> 
 #> Parameter correlation:
-#>                    parent_0 log_k_parent_sink     sigma
-#> parent_0          1.000e+00         5.428e-01 1.642e-07
-#> log_k_parent_sink 5.428e-01         1.000e+00 2.507e-07
-#> sigma             1.642e-07         2.507e-07 1.000e+00
+#>               parent_0 log_k_parent     sigma
+#> parent_0     1.000e+00    5.428e-01 1.642e-07
+#> log_k_parent 5.428e-01    1.000e+00 2.507e-07
+#> sigma        1.642e-07    2.507e-07 1.000e+00
 #> 
 #> Backtransformed parameters:
 #> Confidence intervals for internally transformed parameters are asymmetric.
 #> t-test (unrealistically) based on the assumption of normal distribution
 #> for estimators of untransformed parameters.
-#>                Estimate t value    Pr(>t)   Lower     Upper
-#> parent_0      109.20000   29.47 4.218e-07 99.6300 118.70000
-#> k_parent_sink   0.03722   10.90 5.650e-05  0.0294   0.04712
-#> sigma           5.26600    4.00 5.162e-03  1.8820   8.64900
+#>           Estimate t value    Pr(>t)   Lower     Upper
+#> parent_0 109.20000   29.47 4.218e-07 99.6300 118.70000
+#> k_parent   0.03722   10.90 5.650e-05  0.0294   0.04712
+#> sigma      5.26600    4.00 5.162e-03  1.8820   8.64900
 #> 
 #> FOCUS Chi2 error levels in percent:
 #>          err.min n.optim df
 #> All data   8.385       2  6
 #> parent     8.385       2  6
 #> 
-#> Resulting formation fractions:
-#>             ff
-#> parent_sink  1
-#> 
 #> Estimated disappearance times:
 #>         DT50  DT90
 #> parent 18.62 61.87
@@ -296,17 +305,10 @@ distribution

 #>   118   parent     0.39     1.351  -0.9613
- @@ -317,7 +319,7 @@ distribution

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 2a08228d..fc0ffef2 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -10,23 +10,27 @@ - + - + - + + + + + - - + + - + - - + + @@ -42,7 +46,6 @@ constants and other paramters that can only take on positive values, a simple log transformation is used. For compositional parameters, such as the formations fractions that should always sum up to 1 and can not be negative, the ilr transformation is used." /> - @@ -60,7 +63,7 @@ the ilr transformation is used." /> - +
@@ -118,7 +121,12 @@ the ilr transformation is used." />
@@ -133,7 +141,7 @@ the ilr transformation is used." />

Functions to transform and backtransform kinetic parameters for fitting

- + Source: R/transform_odeparms.R
@@ -204,7 +212,7 @@ fitting procedure.

Value

A vector of transformed or backtransformed parameters with the same - names as the original parameters.

+names as the original parameters.

Details

The transformation of sets of formation fractions is fragile, as it supposes @@ -224,39 +232,28 @@ This is no problem for the internal use in mkinfit< m1 = list(type = "SFO"))

#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
fit.s <- summary(fit) # Transformed and backtransformed parameters -print(fit.s$par, 3)
#> Estimate Std. Error Lower Upper -#> parent_0 99.60 1.5702 96.40 102.79 -#> log_k_parent_sink -3.04 0.0763 -3.19 -2.88 -#> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90 -#> log_k_m1_sink -5.25 0.1332 -5.52 -4.98 -#> sigma 3.13 0.3585 2.40 3.85
print(fit.s$bpar, 3)
#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931 -#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560 -#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551 -#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549
+print(fit.s$par, 3)
#> Estimate Std. Error Lower Upper +#> parent_0 99.598 1.5702 96.4038 102.793 +#> log_k_parent -2.316 0.0409 -2.3988 -2.233 +#> log_k_m1 -5.248 0.1332 -5.5184 -4.977 +#> f_parent_ilr_1 0.041 0.0631 -0.0875 0.169 +#> sigma 3.126 0.3585 2.3961 3.855
print(fit.s$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
# \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 -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02 -#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02 -#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02 -#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00
# } +fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
#> Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", cost.current, "\n", sep = "")}: Fehlender Wert, wo TRUE/FALSE nötig ist
#> Timing stopped at: 0.002 0 0.003
fit.2.s <- summary(fit.2)
#> Error in summary(fit.2): Objekt 'fit.2' nicht gefunden
print(fit.2.s$par, 3)
#> Error in print(fit.2.s$par, 3): Objekt 'fit.2.s' nicht gefunden
print(fit.2.s$bpar, 3)
#> Error in print(fit.2.s$bpar, 3): Objekt 'fit.2.s' nicht gefunden
# } initials <- fit$start$value names(initials) <- rownames(fit$start) transformed <- fit$start_transformed$value names(transformed) <- rownames(fit$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
+transform_odeparms(initials, SFO_SFO)
#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> 100.750000 -2.302585 -2.301586 0.000000
backtransform_odeparms(transformed, SFO_SFO)
#> parent_0 k_parent k_m1 f_parent_to_m1 +#> 100.7500 0.1000 0.1001 0.5000
# \dontrun{ # The case of formation fractions SFO_SFO.ff <- mkinmod( @@ -297,18 +294,10 @@ This is no problem for the internal use in mkinfit<
- @@ -319,7 +308,7 @@ This is no problem for the internal use in mkinfit<
-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 1.5.1.

diff --git a/dumpdata.R b/dumpdata.R new file mode 100644 index 00000000..881df526 --- /dev/null +++ b/dumpdata.R @@ -0,0 +1,7 @@ +mkinpredict <- +function (x, odeparms, odeini, outtimes = seq(0, 120, by = 0.10000000000000001), + solution_type = "deSolve", use_compiled = "auto", method.ode = "lsoda", + atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...) +{ + UseMethod("mkinpredict", x) +} diff --git a/man/AIC.mmkin.Rd b/man/AIC.mmkin.Rd index a10d0aeb..13081561 100644 --- a/man/AIC.mmkin.Rd +++ b/man/AIC.mmkin.Rd @@ -19,7 +19,7 @@ column.} } \value{ As in the generic method (a numeric value for single fits, or a - dataframe if there are several fits in the column). +dataframe if there are several fits in the column). } \description{ Provides a convenient way to compare different kinetic models fitted to the diff --git a/man/DFOP.solution.Rd b/man/DFOP.solution.Rd index 8ada60c5..d8c4553e 100644 --- a/man/DFOP.solution.Rd +++ b/man/DFOP.solution.Rd @@ -32,15 +32,15 @@ two exponential decline functions. } \references{ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, - Version 1.1, 18 December 2014 - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \seealso{ Other parent solutions: diff --git a/man/FOMC.solution.Rd b/man/FOMC.solution.Rd index e5e46c87..eeee85f9 100644 --- a/man/FOMC.solution.Rd +++ b/man/FOMC.solution.Rd @@ -30,8 +30,8 @@ in the original equation. } \note{ The solution of the FOMC kinetic model reduces to the - \code{\link{SFO.solution}} for large values of \code{alpha} and - \code{beta} with \eqn{k = \frac{\beta}{\alpha}}{k = beta/alpha}. +\code{\link{SFO.solution}} for large values of \code{alpha} and +\code{beta} with \eqn{k = \frac{\beta}{\alpha}}{k = beta/alpha}. } \examples{ @@ -40,20 +40,20 @@ The solution of the FOMC kinetic model reduces to the } \references{ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, - Version 1.1, 18 December 2014 - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} - Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: - A new model based on spatial variability. \emph{Environmental Science and - Technology} \bold{24}, 1032-1038 +Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: +A new model based on spatial variability. \emph{Environmental Science and +Technology} \bold{24}, 1032-1038 } \seealso{ Other parent solutions: diff --git a/man/HS.solution.Rd b/man/HS.solution.Rd index f72df23b..2940e949 100644 --- a/man/HS.solution.Rd +++ b/man/HS.solution.Rd @@ -33,15 +33,15 @@ between them. } \references{ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, - Version 1.1, 18 December 2014 - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \seealso{ Other parent solutions: diff --git a/man/IORE.solution.Rd b/man/IORE.solution.Rd index e1f1be1a..1150f023 100644 --- a/man/IORE.solution.Rd +++ b/man/IORE.solution.Rd @@ -25,9 +25,9 @@ a concentration dependent rate constant. } \note{ The solution of the IORE kinetic model reduces to the - \code{\link{SFO.solution}} if N = 1. The parameters of the IORE model can - be transformed to equivalent parameters of the FOMC mode - see the NAFTA - guidance for details. +\code{\link{SFO.solution}} if N = 1. The parameters of the IORE model can +be transformed to equivalent parameters of the FOMC mode - see the NAFTA +guidance for details. } \examples{ @@ -46,7 +46,7 @@ The solution of the IORE kinetic model reduces to the } \references{ NAFTA Technical Working Group on Pesticides (not dated) Guidance - for Evaluating and Calculating Degradation Kinetics in Environmental Media +for Evaluating and Calculating Degradation Kinetics in Environmental Media } \seealso{ Other parent solutions: diff --git a/man/SFO.solution.Rd b/man/SFO.solution.Rd index 6892cccc..c0aac237 100644 --- a/man/SFO.solution.Rd +++ b/man/SFO.solution.Rd @@ -26,15 +26,15 @@ Function describing exponential decline from a defined starting value. } \references{ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, - Version 1.1, 18 December 2014 - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \seealso{ Other parent solutions: diff --git a/man/SFORB.solution.Rd b/man/SFORB.solution.Rd index 98a8c684..dc78d1f1 100644 --- a/man/SFORB.solution.Rd +++ b/man/SFORB.solution.Rd @@ -20,7 +20,7 @@ fraction.} } \value{ The value of the response variable, which is the sum of free and - bound fractions at time \code{t}. +bound fractions at time \code{t}. } \description{ Function describing the solution of the differential equations describing @@ -36,15 +36,15 @@ and no substance in the bound fraction. } \references{ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, - Version 1.1, 18 December 2014 - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \seealso{ Other parent solutions: diff --git a/man/add_err.Rd b/man/add_err.Rd index 3452923e..1171e0fd 100644 --- a/man/add_err.Rd +++ b/man/add_err.Rd @@ -40,7 +40,7 @@ seed is not set.} } \value{ A list of datasets compatible with \code{\link{mmkin}}, i.e. the - components of the list are datasets compatible with \code{\link{mkinfit}}. +components of the list are datasets compatible with \code{\link{mkinfit}}. } \description{ Normally distributed errors are added to data predicted for a specific diff --git a/man/confint.mkinfit.Rd b/man/confint.mkinfit.Rd index 81d7a6e8..f295afc4 100644 --- a/man/confint.mkinfit.Rd +++ b/man/confint.mkinfit.Rd @@ -45,7 +45,7 @@ applied to the likelihood based on the transformed parameters?} transformed parameters, should we backtransform the parameters with their confidence intervals?} -\item{cores}{The number of cores to be used for multicore processing. +\item{cores}{The number of cores to be used for multicore processing. On Windows machines, cores > 1 is currently not supported.} \item{quiet}{Should we suppress the message "Profiling the likelihood"} @@ -54,7 +54,7 @@ On Windows machines, cores > 1 is currently not supported.} } \value{ A matrix with columns giving lower and upper confidence limits for - each parameter. +each parameter. } \description{ The default method 'quadratic' is based on the quadratic approximation of @@ -143,10 +143,10 @@ confint(f_tc_2, "parent_0", method = "quadratic") \references{ Bates DM and Watts GW (1988) Nonlinear regression analysis & its applications - Pawitan Y (2013) In all likelihood - Statistical modelling and - inference using likelihood. Clarendon Press, Oxford. +Pawitan Y (2013) In all likelihood - Statistical modelling and +inference using likelihood. Clarendon Press, Oxford. - Venzon DJ and Moolgavkar SH (1988) A Method for Computing - Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, - 87–94. +Venzon DJ and Moolgavkar SH (1988) A Method for Computing +Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, +87–94. } diff --git a/man/endpoints.Rd b/man/endpoints.Rd index 26b5ee08..49f44d74 100644 --- a/man/endpoints.Rd +++ b/man/endpoints.Rd @@ -13,9 +13,9 @@ endpoints(fit) } \value{ A list with a matrix of dissipation times named distimes, - and, if applicable, a vector of formation fractions named ff - and, if the SFORB model was in use, a vector of eigenvalues - of these SFORB models, equivalent to DFOP rate constants +and, if applicable, a vector of formation fractions named ff +and, if the SFORB model was in use, a vector of eigenvalues +of these SFORB models, equivalent to DFOP rate constants } \description{ This function calculates DT50 and DT90 values as well as formation fractions diff --git a/man/get_deg_func.Rd b/man/get_deg_func.Rd index 1d8a3de9..75743448 100644 --- a/man/get_deg_func.Rd +++ b/man/get_deg_func.Rd @@ -8,7 +8,7 @@ get_deg_func() } \value{ A function that was likely previously assigned from within - nlme.mmkin +nlme.mmkin } \description{ Retrieve a degradation function from the mmkin namespace diff --git a/man/ilr.Rd b/man/ilr.Rd index 0cbd7e2c..f691ec23 100644 --- a/man/ilr.Rd +++ b/man/ilr.Rd @@ -15,8 +15,8 @@ sensible for vectors with all elements being greater than zero.} } \value{ The result of the forward or backward transformation. The returned - components always sum to 1 for the case of the inverse log-ratio - transformation. +components always sum to 1 for the case of the inverse log-ratio +transformation. } \description{ This implementation is a special case of the class of isometric log-ratio @@ -48,11 +48,11 @@ ilr(c(b[1:3], 1 - sum(b[1:3]))) # Gives c(0.1, 0.3, 0.5) } \references{ Peter Filzmoser, Karel Hron (2008) Outlier Detection for - Compositional Data Using Robust Methods. Math Geosci 40 233-248 +Compositional Data Using Robust Methods. Math Geosci 40 233-248 } \seealso{ Another implementation can be found in R package - \code{robCompositions}. +\code{robCompositions}. } \author{ René Lehmann and Johannes Ranke diff --git a/man/logLik.mkinfit.Rd b/man/logLik.mkinfit.Rd index 502fb4d7..637570e4 100644 --- a/man/logLik.mkinfit.Rd +++ b/man/logLik.mkinfit.Rd @@ -13,8 +13,8 @@ } \value{ An object of class \code{\link{logLik}} with the number of estimated - parameters (degradation model parameters plus variance model parameters) - as attribute. +parameters (degradation model parameters plus variance model parameters) +as attribute. } \description{ This function returns the product of the likelihood densities of each @@ -45,7 +45,7 @@ and the fitted error model parameters. } \seealso{ Compare the AIC of columns of \code{\link{mmkin}} objects using - \code{\link{AIC.mmkin}}. +\code{\link{AIC.mmkin}}. } \author{ Johannes Ranke diff --git a/man/logistic.solution.Rd b/man/logistic.solution.Rd index 33b3d44a..efa12e7a 100644 --- a/man/logistic.solution.Rd +++ b/man/logistic.solution.Rd @@ -26,7 +26,7 @@ an increasing rate constant, supposedly caused by microbial growth } \note{ The solution of the logistic model reduces to the - \code{\link{SFO.solution}} if \code{k0} is equal to \code{kmax}. +\code{\link{SFO.solution}} if \code{k0} is equal to \code{kmax}. } \examples{ @@ -67,15 +67,15 @@ The solution of the logistic model reduces to the } \references{ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, - Version 1.1, 18 December 2014 - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \seealso{ Other parent solutions: diff --git a/man/max_twa_parent.Rd b/man/max_twa_parent.Rd index 7c9f4861..107eebd0 100644 --- a/man/max_twa_parent.Rd +++ b/man/max_twa_parent.Rd @@ -48,8 +48,8 @@ factor (f_twa) is calculated.} } \value{ 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'). +\code{windows} argument. For the other functions, a numeric vector of +length one (also known as 'a number'). } \description{ This function calculates maximum moving window time weighted average @@ -66,10 +66,10 @@ soil section of the FOCUS guidance. } \references{ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \author{ Johannes Ranke diff --git a/man/mkinerrplot.Rd b/man/mkinerrplot.Rd index 9564ec19..82178aa9 100644 --- a/man/mkinerrplot.Rd +++ b/man/mkinerrplot.Rd @@ -50,7 +50,7 @@ be passed on to \code{\link{legend}}.} } \value{ Nothing is returned by this function, as it is called for its side - effect, namely to produce a plot. +effect, namely to produce a plot. } \description{ This function plots the squared residuals for the specified subset of the @@ -70,7 +70,7 @@ mkinerrplot(fit) } \seealso{ \code{\link{mkinplot}}, for a way to plot the data and the fitted - lines of the mkinfit object. +lines of the mkinfit object. } \author{ Johannes Ranke diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index db3f5f3e..97dffef7 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -3,10 +3,6 @@ \name{mkinfit} \alias{mkinfit} \title{Fit a kinetic model to data with one or more state variables} -\source{ -Rocke, David M. und Lorenzato, Stefan (1995) A two-component model - for measurement error in analytical chemistry. Technometrics 37(2), 176-184. -} \usage{ mkinfit( mkinmod, @@ -53,16 +49,16 @@ not observed in degradation data, because there is a lower limit of detection.} \item{parms.ini}{A named vector of initial values for the parameters, - including parameters to be optimised and potentially also fixed parameters - as indicated by \code{fixed_parms}. If set to "auto", initial values for - rate constants are set to default values. Using parameter names that are - not in the model gives an error. +including parameters to be optimised and potentially also fixed parameters +as indicated by \code{fixed_parms}. If set to "auto", initial values for +rate constants are set to default values. Using parameter names that are +not in the model gives an error. - It is possible to only specify a subset of the parameters that the model - needs. You can use the parameter lists "bparms.ode" from a previously - fitted model, which contains the differential equation parameters from - this model. This works nicely if the models are nested. An example is - given below.} +It is possible to only specify a subset of the parameters that the model +needs. You can use the parameter lists "bparms.ode" from a previously +fitted model, which contains the differential equation parameters from +this model. This works nicely if the models are nested. An example is +given below.} \item{state.ini}{A named vector of initial values for the state variables of the model. In case the observed variables are represented by more than one @@ -141,48 +137,50 @@ is 1e-8, lower than in \code{\link{lsoda}}.} is 1e-10, much lower than in \code{\link{lsoda}}.} \item{error_model}{If the error model is "const", a constant standard - deviation is assumed. +deviation is assumed. - If the error model is "obs", each observed variable is assumed to have its - own variance. +If the error model is "obs", each observed variable is assumed to have its +own variance. - If the error model is "tc" (two-component error model), a two component - error model similar to the one described by Rocke and Lorenzato (1995) is - used for setting up the likelihood function. Note that this model - deviates from the model by Rocke and Lorenzato, as their model implies - that the errors follow a lognormal distribution for large values, not a - normal distribution as assumed by this method.} +If the error model is "tc" (two-component error model), a two component +error model similar to the one described by Rocke and Lorenzato (1995) is +used for setting up the likelihood function. Note that this model +deviates from the model by Rocke and Lorenzato, as their model implies +that the errors follow a lognormal distribution for large values, not a +normal distribution as assumed by this method.} \item{error_model_algorithm}{If "auto", the selected algorithm depends on - the error model. If the error model is "const", unweighted nonlinear - least squares fitting ("OLS") is selected. If the error model is "obs", or - "tc", the "d_3" algorithm is selected. - - The algorithm "d_3" will directly minimize the negative log-likelihood and - - independently - also use the three step algorithm described below. The - fit with the higher likelihood is returned. +the error model. If the error model is "const", unweighted nonlinear +least squares fitting ("OLS") is selected. If the error model is "obs", or +"tc", the "d_3" algorithm is selected. + +The algorithm "d_3" will directly minimize the negative log-likelihood and +\itemize{ +\item independently - also use the three step algorithm described below. The +fit with the higher likelihood is returned. +} - The algorithm "direct" will directly minimize the negative log-likelihood. +The algorithm "direct" will directly minimize the negative log-likelihood. - The algorithm "twostep" will minimize the negative log-likelihood after an - initial unweighted least squares optimisation step. +The algorithm "twostep" will minimize the negative log-likelihood after an +initial unweighted least squares optimisation step. - The algorithm "threestep" starts with unweighted least squares, then - optimizes only the error model using the degradation model parameters - found, and then minimizes the negative log-likelihood with free - degradation and error model parameters. +The algorithm "threestep" starts with unweighted least squares, then +optimizes only the error model using the degradation model parameters +found, and then minimizes the negative log-likelihood with free +degradation and error model parameters. - The algorithm "fourstep" starts with unweighted least squares, then - optimizes only the error model using the degradation model parameters - found, then optimizes the degradation model again with fixed error model - parameters, and finally minimizes the negative log-likelihood with free - degradation and error model parameters. +The algorithm "fourstep" starts with unweighted least squares, then +optimizes only the error model using the degradation model parameters +found, then optimizes the degradation model again with fixed error model +parameters, and finally minimizes the negative log-likelihood with free +degradation and error model parameters. - The algorithm "IRLS" (Iteratively Reweighted Least Squares) starts with - unweighted least squares, and then iterates optimization of the error - model parameters and subsequent optimization of the degradation model - using those error model parameters, until the error model parameters - converge.} +The algorithm "IRLS" (Iteratively Reweighted Least Squares) starts with +unweighted least squares, and then iterates optimization of the error +model parameters and subsequent optimization of the degradation model +using those error model parameters, until the error model parameters +converge.} \item{reweight.tol}{Tolerance for the convergence criterion calculated from the error model parameters in IRLS fits.} @@ -196,7 +194,7 @@ the error model parameters in IRLS fits.} } \value{ A list with "mkinfit" in the class attribute. A summary can be - obtained by \code{\link{summary.mkinfit}}. +obtained by \code{\link{summary.mkinfit}}. } \description{ This function maximises the likelihood of the observed data using the Port @@ -214,9 +212,9 @@ estimators. } \note{ When using the "IORE" submodel for metabolites, fitting with - "transform_rates = TRUE" (the default) often leads to failures of the - numerical ODE solver. In this situation it may help to switch off the - internal rate transformation. +"transform_rates = TRUE" (the default) often leads to failures of the +numerical ODE solver. In this situation it may help to switch off the +internal rate transformation. } \examples{ @@ -268,7 +266,7 @@ fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.o } \dontrun{ -# Weighted fits, including IRLS +# Weighted fits, including IRLS (error_model = "obs") SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), use_of_ff = "max") f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) @@ -280,16 +278,24 @@ summary(f.tc) } +} +\references{ +Rocke DM and Lorenzato S (1995) A two-component model +for measurement error in analytical chemistry. \emph{Technometrics} 37(2), 176-184. + +Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical +Degradation Data. \emph{Environments} 6(12) 124 +\href{https://doi.org/10.3390/environments6120124}{doi:10.3390/environments6120124}. } \seealso{ Plotting methods \code{\link{plot.mkinfit}} and - \code{\link{mkinparplot}}. +\code{\link{mkinparplot}}. - Comparisons of models fitted to the same data can be made using - \code{\link{AIC}} by virtue of the method \code{\link{logLik.mkinfit}}. +Comparisons of models fitted to the same data can be made using +\code{\link{AIC}} by virtue of the method \code{\link{logLik.mkinfit}}. - Fitting of several models to several datasets in a single call to - \code{\link{mmkin}}. +Fitting of several models to several datasets in a single call to +\code{\link{mmkin}}. } \author{ Johannes Ranke diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd index a5736be7..6a6d2027 100644 --- a/man/mkinmod.Rd +++ b/man/mkinmod.Rd @@ -44,25 +44,30 @@ applicable to give detailed information about the C function being built.} } \value{ A list of class \code{mkinmod} for use with \code{\link{mkinfit}}, - containing, among others, - \item{diffs}{ - A vector of string representations of differential equations, one for - each modelling variable. - } - \item{map}{ - A list containing named character vectors for each observed variable, - specifying the modelling variables by which it is represented. - } - \item{use_of_ff}{ - The content of \code{use_of_ff} is passed on in this list component. - } - \item{coefmat}{ - The coefficient matrix, if the system of differential equations can be - represented by one. - } - \item{cf}{ - If generated, the compiled function as returned by cfunction. - } +containing, among others, +\item{diffs}{ +A vector of string representations of differential equations, one for +each modelling variable. +} +\item{map}{ +A list containing named character vectors for each observed variable, +specifying the modelling variables by which it is represented. +} +\item{use_of_ff}{ +The content of \code{use_of_ff} is passed on in this list component. +} +\item{deg_func}{ +If generated, a function containing the solution of the degradation +model. +} +\item{coefmat}{ +The coefficient matrix, if the system of differential equations can be +represented by one. +} +\item{cf}{ +If generated, a compiled function calculating the derivatives as +returned by cfunction. +} } \description{ The function usually takes several expressions, each assigning a compound @@ -76,8 +81,8 @@ in the FOCUS and NAFTA guidance documents are used. } \note{ The IORE submodel is not well tested for metabolites. When using this - model for metabolites, you may want to read the second note in the help - page to \code{\link{mkinfit}}. +model for metabolites, you may want to read the second note in the help +page to \code{\link{mkinfit}}. } \examples{ @@ -115,13 +120,13 @@ fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, } \references{ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} - NAFTA Technical Working Group on Pesticides (not dated) Guidance for - Evaluating and Calculating Degradation Kinetics in Environmental Media +NAFTA Technical Working Group on Pesticides (not dated) Guidance for +Evaluating and Calculating Degradation Kinetics in Environmental Media } \author{ Johannes Ranke diff --git a/man/mkinparplot.Rd b/man/mkinparplot.Rd index 975a0203..07b25009 100644 --- a/man/mkinparplot.Rd +++ b/man/mkinparplot.Rd @@ -11,7 +11,7 @@ mkinparplot(object) } \value{ Nothing is returned by this function, as it is called for its side - effect, namely to produce a plot. +effect, namely to produce a plot. } \description{ This function plots the confidence intervals for the parameters fitted using diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd index 2a8b2d41..498d914d 100644 --- a/man/mkinresplot.Rd +++ b/man/mkinresplot.Rd @@ -54,7 +54,7 @@ be passed on to \code{\link{legend}}.} } \value{ Nothing is returned by this function, as it is called for its side - effect, namely to produce a plot. +effect, namely to produce a plot. } \description{ This function plots the residuals for the specified subset of the observed @@ -71,8 +71,8 @@ mkinresplot(fit, "m1") } \seealso{ \code{\link{mkinplot}}, for a way to plot the data and the fitted - lines of the mkinfit object, and \code{\link{plot_res}} for a function - combining the plot of the fit and the residual plot. +lines of the mkinfit object, and \code{\link{plot_res}} for a function +combining the plot of the fit and the residual plot. } \author{ Johannes Ranke diff --git a/man/mmkin.Rd b/man/mmkin.Rd index 99895400..eda0d837 100644 --- a/man/mmkin.Rd +++ b/man/mmkin.Rd @@ -33,8 +33,8 @@ for parallel execution.} } \value{ A two-dimensional \code{\link{array}} of \code{\link{mkinfit}} - objects that can be indexed using the model names for the first index (row index) - and the dataset names for the second index (column index). +objects that can be indexed using the model names for the first index (row index) +and the dataset names for the second index (column index). } \description{ This function calls \code{\link{mkinfit}} on all combinations of models and @@ -79,7 +79,7 @@ plot(fits.0[1, 1]) } \seealso{ \code{\link{[.mmkin}} for subsetting, \code{\link{plot.mmkin}} for - plotting. +plotting. } \author{ Johannes Ranke diff --git a/man/nafta.Rd b/man/nafta.Rd index 49c13afc..4f05324b 100644 --- a/man/nafta.Rd +++ b/man/nafta.Rd @@ -6,15 +6,15 @@ \title{Evaluate parent kinetics using the NAFTA guidance} \source{ NAFTA (2011) Guidance for evaluating and calculating degradation - kinetics in environmental media. NAFTA Technical Working Group on - Pesticides - \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation} - accessed 2019-02-22 +kinetics in environmental media. NAFTA Technical Working Group on +Pesticides +\url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation} +accessed 2019-02-22 - US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to - Calculate Representative Half-life Values and Characterizing Pesticide - Degradation - \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance} +US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to +Calculate Representative Half-life Values and Characterizing Pesticide +Degradation +\url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance} } \usage{ nafta(ds, title = NA, quiet = FALSE, ...) @@ -41,9 +41,9 @@ dissipation times.} } \value{ An list of class \code{nafta}. The list element named "mmkin" is the - \code{\link{mmkin}} object containing the fits of the three models. The - list element named "title" contains the title of the dataset used. The - list element "data" contains the dataset used in the fits. +\code{\link{mmkin}} object containing the fits of the three models. The +list element named "title" contains the title of the dataset used. The +list element "data" contains the dataset used in the fits. } \description{ The function fits the SFO, IORE and DFOP models using \code{\link{mmkin}} diff --git a/man/nlme.Rd b/man/nlme.Rd index a9e368dd..bf527320 100644 --- a/man/nlme.Rd +++ b/man/nlme.Rd @@ -21,9 +21,9 @@ nlme_data(object) A function that can be used with nlme If random is FALSE (default), a named vector containing mean values - of the fitted degradation model parameters. If random is TRUE, a list with - fixed and random effects, in the format required by the start argument of - nlme for the case of a single grouping variable ds? +of the fitted degradation model parameters. If random is TRUE, a list with +fixed and random effects, in the format required by the start argument of +nlme for the case of a single grouping variable ds? A \code{\link{groupedData}} object } diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd index 430dbda1..ae2b2d22 100644 --- a/man/nlme.mmkin.Rd +++ b/man/nlme.mmkin.Rd @@ -67,7 +67,7 @@ parameters taken from the mmkin object are used} } \value{ Upon success, a fitted nlme.mmkin object, which is an nlme object - with additional elements +with additional elements } \description{ This functions sets up a nonlinear mixed effects model for an mmkin row diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd index 4235557e..bf38c5a5 100644 --- a/man/plot.mkinfit.Rd +++ b/man/plot.mkinfit.Rd @@ -85,7 +85,7 @@ fits is shown, the residual plot is in the lower third of the plot. Otherwise, i.e. if "sep_obs" is given, the residual plots will be located to the right of the plots of the fitted curves. If this is set to 'standardized', a plot of the residuals divided by the standard deviation - given by the fitted error model will be shown.} +given by the fitted error model will be shown.} \item{show_errplot}{Should squared residuals and the error model be shown? If only one plot of the fits is shown, this plot is in the lower third of diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd index 600881ea..998e25e1 100644 --- a/man/plot.mmkin.Rd +++ b/man/plot.mmkin.Rd @@ -34,7 +34,7 @@ values, with the error model, using \code{\link{mkinerrplot}}.} \item{standardized}{Should the residuals be standardized? This option is passed to \code{\link{mkinresplot}}, it only takes effect if -`resplot = "time"`.} +\code{resplot = "time"}.} \item{show_errmin}{Should the chi2 error level be shown on top of the plots to the left?} diff --git a/man/plot.nlme.mmkin.Rd b/man/plot.nlme.mmkin.Rd index 9bea7013..91130402 100644 --- a/man/plot.nlme.mmkin.Rd +++ b/man/plot.nlme.mmkin.Rd @@ -36,7 +36,7 @@ values, with the error model, using \code{\link{mkinerrplot}}.} \item{standardized}{Should the residuals be standardized? This option is passed to \code{\link{mkinresplot}}, it only takes effect if -`resplot = "time"`.} +\code{resplot = "time"}.} \item{show_errmin}{Should the chi2 error level be shown on top of the plots to the left?} diff --git a/man/sigma_twocomp.Rd b/man/sigma_twocomp.Rd index 0004144f..4e1f7c38 100644 --- a/man/sigma_twocomp.Rd +++ b/man/sigma_twocomp.Rd @@ -33,9 +33,9 @@ y. } \references{ Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978) - Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry - 24(11), 1895-1898. +Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry +24(11), 1895-1898. - Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for - measurement error in analytical chemistry. Technometrics 37(2), 176-184. +Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for +measurement error in analytical chemistry. Technometrics 37(2), 176-184. } diff --git a/man/summary.mkinfit.Rd b/man/summary.mkinfit.Rd index fabe31d0..24991d71 100644 --- a/man/summary.mkinfit.Rd +++ b/man/summary.mkinfit.Rd @@ -29,27 +29,27 @@ distribution} } \value{ The summary function returns a list with components, among others - \item{version, Rversion}{The mkin and R versions used} - \item{date.fit, date.summary}{The dates where the fit and the summary were - produced} - \item{diffs}{The differential equations used in the model} - \item{use_of_ff}{Was maximum or minimum use made of formation fractions} - \item{bpar}{Optimised and backtransformed - parameters} - \item{data}{The data (see Description above).} - \item{start}{The starting values and bounds, if applicable, for optimised - parameters.} - \item{fixed}{The values of fixed parameters.} - \item{errmin }{The chi2 error levels for - each observed variable.} - \item{bparms.ode}{All backtransformed ODE - parameters, for use as starting parameters for related models.} - \item{errparms}{Error model parameters.} - \item{ff}{The estimated formation fractions derived from the fitted - model.} - \item{distimes}{The DT50 and DT90 values for each observed variable.} - \item{SFORB}{If applicable, eigenvalues of SFORB components of the model.} - The print method is called for its side effect, i.e. printing the summary. +\item{version, Rversion}{The mkin and R versions used} +\item{date.fit, date.summary}{The dates where the fit and the summary were +produced} +\item{diffs}{The differential equations used in the model} +\item{use_of_ff}{Was maximum or minimum use made of formation fractions} +\item{bpar}{Optimised and backtransformed +parameters} +\item{data}{The data (see Description above).} +\item{start}{The starting values and bounds, if applicable, for optimised +parameters.} +\item{fixed}{The values of fixed parameters.} +\item{errmin }{The chi2 error levels for +each observed variable.} +\item{bparms.ode}{All backtransformed ODE +parameters, for use as starting parameters for related models.} +\item{errparms}{Error model parameters.} +\item{ff}{The estimated formation fractions derived from the fitted +model.} +\item{distimes}{The DT50 and DT90 values for each observed variable.} +\item{SFORB}{If applicable, eigenvalues of SFORB components of the model.} +The print method is called for its side effect, i.e. printing the summary. } \description{ Lists model equations, initial parameter values, optimised parameters with @@ -65,10 +65,10 @@ values. } \references{ FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, - EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \author{ Johannes Ranke diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd index 5257fe12..e250483a 100644 --- a/man/transform_odeparms.Rd +++ b/man/transform_odeparms.Rd @@ -48,7 +48,7 @@ fitting procedure.} } \value{ A vector of transformed or backtransformed parameters with the same - names as the original parameters. +names as the original parameters. } \description{ The transformations are intended to map parameters that should only take on -- cgit v1.2.1