From bbb74d4f60033899cd5cdd36aa70f157bc52209e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 1 Nov 2019 12:19:03 +0100 Subject: Fix bug in yesterdays release, add methods for BIC --- docs/reference/AIC.mmkin.html | 13 +- docs/reference/Extract.mmkin.html | 8 +- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 16 +- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 16 +- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 16 +- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 16 +- docs/reference/FOCUS_2006_datasets.html | 16 +- docs/reference/NAFTA_2015_datasets-1.png | Bin 41450 -> 0 bytes docs/reference/NAFTA_2015_datasets.html | 218 ----------------------- docs/reference/NAFTA_SOP_2015.html | 16 +- docs/reference/NAFTA_SOP_Attachment.html | 16 +- docs/reference/confint.mkinfit.html | 2 +- docs/reference/experimental_data_for_UBA.html | 16 +- docs/reference/index.html | 12 +- docs/reference/mccall81_245T-1.png | Bin 58349 -> 58310 bytes docs/reference/mccall81_245T.html | 16 +- docs/reference/mkinfit.html | 28 +-- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 4 +- docs/reference/mmkin.html | 4 +- docs/reference/nobs.mkinfit.html | 189 ++++++++++++++++++++ docs/reference/plot.mkinfit-6.png | Bin 65273 -> 0 bytes docs/reference/plot.mmkin-4.png | Bin 37076 -> 38129 bytes docs/reference/print.nafta.html | 197 --------------------- docs/reference/schaefer07_complex_case.html | 16 +- docs/reference/summary.mkinfit.html | 6 +- docs/reference/synthetic_data_for_UBA.html | 225 ------------------------ docs/reference/synthetic_data_for_UBA_2014.html | 6 +- docs/reference/test_data_from_UBA_2014-1.png | Bin 53086 -> 52908 bytes docs/reference/test_data_from_UBA_2014-2.png | Bin 68670 -> 68111 bytes docs/reference/test_data_from_UBA_2014.html | 16 +- docs/reference/update.mkinfit.html | 12 +- 32 files changed, 308 insertions(+), 794 deletions(-) delete mode 100644 docs/reference/NAFTA_2015_datasets-1.png delete mode 100644 docs/reference/NAFTA_2015_datasets.html create mode 100644 docs/reference/nobs.mkinfit.html delete mode 100644 docs/reference/plot.mkinfit-6.png delete mode 100644 docs/reference/print.nafta.html delete mode 100644 docs/reference/synthetic_data_for_UBA.html (limited to 'docs/reference') diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index 103bcb4a..7ca12302 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -6,7 +6,7 @@ -Calculated the AIC for a column of an mmkin object — AIC.mmkin • mkin +Calculate the AIC for a column of an mmkin object — AIC.mmkin • mkin @@ -35,7 +35,7 @@ - + @@ -70,7 +70,7 @@ same dataset." /> mkin - 0.9.49.6 + 0.9.49.7 @@ -128,7 +128,7 @@ same dataset." />
-

Calculated the AIC for a column of an mmkin object

+

Calculate the AIC for a column of an mmkin object

@@ -139,7 +139,10 @@ same dataset.

# S3 method for mmkin
-AIC(object, ..., k = 2)
+AIC(object, ..., k = 2) + +# S3 method for mmkin +BIC(object, ...)

Arguments

diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 879c1444..7273b5de 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -176,16 +176,16 @@ either a list of mkinfit objects or a single mkinfit object.

cores=1, quiet=TRUE) fits["FOMC", ]
#> dataset #> model B C -#> FOMC List,40 List,40 +#> FOMC List,41 List,41 #> attr(,"class") #> [1] "mmkin"
fits[, "B"]
#> dataset #> model B -#> SFO List,40 -#> FOMC List,40 +#> SFO List,41 +#> FOMC List,41 #> attr(,"class") #> [1] "mmkin"
fits["SFO", "B"]
#> dataset #> model B -#> SFO List,40 +#> SFO List,41 #> attr(,"class") #> [1] "mmkin"
head( diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index 8f418b75..83d624bb 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -8,11 +8,13 @@ Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin + + @@ -32,8 +34,8 @@ - + + @@ -113,7 +116,6 @@ in this fit." /> News -
@@ -135,17 +137,16 @@ in this fit." />
-

A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit.

- 
FOCUS_2006_DFOP_ref_A_to_B
- + +

Format

A data frame containing the following variables.

@@ -160,7 +161,6 @@ in this fit.

-

Source

FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -168,7 +168,6 @@ in this fit.

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

data(FOCUS_2006_DFOP_ref_A_to_B)
@@ -176,11 +175,8 @@ in this fit.

-

A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit.

- 
FOCUS_2006_FOMC_ref_A_to_F
- + +

Format

A data frame containing the following variables.

@@ -159,7 +160,6 @@ in this fit.

-

Source

FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -167,7 +167,6 @@ in this fit.

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

data(FOCUS_2006_FOMC_ref_A_to_F)
@@ -175,11 +174,8 @@ in this fit.

-

A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit.

- 
FOCUS_2006_HS_ref_A_to_F
- + +

Format

A data frame containing the following variables.

@@ -160,7 +161,6 @@ in this fit.

-

Source

FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -168,7 +168,6 @@ in this fit.

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

data(FOCUS_2006_HS_ref_A_to_F)
@@ -176,11 +175,8 @@ in this fit.

-

A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit.

- 
FOCUS_2006_SFO_ref_A_to_F
- + +

Format

A data frame containing the following variables.

@@ -158,7 +159,6 @@ in this fit.

-

Source

FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -166,7 +166,6 @@ in this fit.

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

data(FOCUS_2006_SFO_ref_A_to_F)
@@ -174,11 +173,8 @@ in this fit.

-

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

- 
FOCUS_2006_A
@@ -142,7 +142,8 @@
   FOCUS_2006_D
   FOCUS_2006_E
   FOCUS_2006_F
- + +

Format

6 datasets with observations on the following variables.

@@ -152,7 +153,6 @@
-

Source

FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -160,7 +160,6 @@ 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

FOCUS_2006_C
#>     name time value
@@ -177,11 +176,8 @@
   
 
     

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

-    
     

 
     
NAFTA_SOP_Appendix_B
   NAFTA_SOP_Appendix_D

-        
+
+
     
Format

 
     
2 datasets with observations on the following variables.

@@ -148,7 +149,6 @@
   
 

 
-    
     
Source

 
     
NAFTA (2011) Guidance for evaluating and calculating degradation kinetics
@@ -159,7 +159,6 @@
   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

-    
 
     
Examples

     
  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
@@ -204,11 +203,8 @@
   
 
     

-    
     
Data taken from from Attachment 1 of the SOP.

-    
     

 
     
NAFTA_SOP_Attachment

-        
+
+
     
Format

 
     
A list (NAFTA_SOP_Attachment) containing 16 datasets suitable
   for the evaluation with nafta

-    
     
Source

 
     
NAFTA (2011) Guidance for evaluating and calculating degradation kinetics
@@ -153,7 +153,6 @@
   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

-    
 
     
Examples

     
  nafta_att_p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]], cores = 1)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The half-life obtained from the IORE model may be used
  print(nafta_att_p5a)
#> Sums of squares:
@@ -198,11 +197,8 @@
   
#>        User      System verstrichen 
-#>      50.987       0.008      51.023 
# The following does not save much time, as parent_0 takes up most of the time
+#>      51.646       0.000      51.673 
# The following does not save much time, as parent_0 takes up most of the time
 # system.time(ci_profile <- confint(f_d_1, cores = 5))
 # system.time(ci_profile <- confint(f_d_1,
 #   c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = 1))
diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html
index f35aee5f..18e11261 100644
--- a/docs/reference/experimental_data_for_UBA.html
+++ b/docs/reference/experimental_data_for_UBA.html
@@ -8,11 +8,13 @@
 
 Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019 • mkin
 
+
 
 
 
 
 
+
 
 
 
@@ -32,8 +34,8 @@
 
 
 
-
 
+
 
 
@@ -137,7 +140,6 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
   News
 
       
-      
       
    
         
       

@@ -159,7 +161,6 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
     

 
     

-    
     
The 12 datasets were extracted from active substance evaluation dossiers published
  by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate
  and advance error model specifications. The fact that these data and some
@@ -189,11 +190,11 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
  to one half of the LOD reported to be 1% AR.

 
Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
  (United Kingdom, 2014, p. 81).

-    
     

 
     
experimental_data_for_UBA_2019

-        
+
+
     
Format

 
     
A list containing twelve datasets as an R6 class defined by mkinds,
@@ -203,7 +204,6 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
   
 
 
-    
     
Source

 
     
@@ -225,7 +225,6 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
 
United Kingdom (2014). Thifensulfuron-methyl - Annex B.8 (Volume 3) to the Report and Proposed
   Decision of the United Kingdom made to the European Commission under Regulation (EC) No.
   1141/2010 for renewal of an active substance

-    
 
     
Examples

     
# \dontrun{
@@ -264,11 +263,8 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
   
 
@@ -255,9 +255,9 @@ of an mmkin object
- + @@ -447,6 +447,12 @@ kinetic models fitted with mkinfit

+ + + + diff --git a/docs/reference/mccall81_245T-1.png b/docs/reference/mccall81_245T-1.png index b9a42571..5b70455c 100644 Binary files a/docs/reference/mccall81_245T-1.png and b/docs/reference/mccall81_245T-1.png differ diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 91c55a6a..ce2d40cd 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -8,11 +8,13 @@ Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin + + @@ -32,8 +34,8 @@ - + @@ -41,6 +43,7 @@ + @@ -111,7 +114,6 @@ News - @@ -133,15 +135,14 @@
-

Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether extracts.

- 
mccall81_245T
- + +

Format

A dataframe containing the following variables.

@@ -156,12 +157,10 @@
-

Source

McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 http://dx.doi.org/10.1021/jf00103a026

-

Examples

  SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"),
@@ -228,11 +227,8 @@
   
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.1 
-#> Date of fit:     Thu Oct 31 01:48:29 2019 
-#> Date of summary: Thu Oct 31 01:48:29 2019 
+#> Date of fit:     Fri Nov  1 10:08:21 2019 
+#> Date of summary: Fri Nov  1 10:08:21 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.455 s
+#> Fitted using 222 model solutions performed in 0.456 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -482,7 +482,7 @@ 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 
-#>       1.464       0.000       1.465 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
+#>       1.488       0.000       1.491 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -555,7 +555,7 @@ estimators.

 #> Sum of squared residuals at call 126: 371.2134
 #> Sum of squared residuals at call 135: 371.2134
 #> Negative log-likelihood at call 145: 97.22429
#> Optimisation successfully terminated.
#>        User      System verstrichen 
-#>       1.047       0.000       1.047 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
+#>       1.058       0.000       1.059 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -591,8 +591,8 @@ estimators.

 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
                       m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.1 
-#> Date of fit:     Thu Oct 31 01:48:44 2019 
-#> Date of summary: Thu Oct 31 01:48:44 2019 
+#> Date of fit:     Fri Nov  1 10:08:36 2019 
+#> Date of summary: Fri Nov  1 10:08:36 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -600,7 +600,7 @@ estimators.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 421 model solutions performed in 1.136 s
+#> Fitted using 421 model solutions performed in 1.083 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -708,8 +708,8 @@ estimators.

 #>   120       m1    25.15  28.78984 -3.640e+00
 #>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.1 
-#> Date of fit:     Thu Oct 31 01:48:47 2019 
-#> Date of summary: Thu Oct 31 01:48:47 2019 
+#> Date of fit:     Fri Nov  1 10:08:39 2019 
+#> Date of summary: Fri Nov  1 10:08:39 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -717,7 +717,7 @@ estimators.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 978 model solutions performed in 2.512 s
+#> Fitted using 978 model solutions performed in 2.553 s
 #> 
 #> Error model: Variance unique to each observed variable 
 #> 
@@ -840,8 +840,8 @@ estimators.

 #>   120       m1    25.15  28.80429 -3.654e+00
 #>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.1 
-#> Date of fit:     Thu Oct 31 01:48:56 2019 
-#> Date of summary: Thu Oct 31 01:48:56 2019 
+#> Date of fit:     Fri Nov  1 10:08:48 2019 
+#> Date of summary: Fri Nov  1 10:08:48 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -849,7 +849,7 @@ estimators.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 2289 model solutions performed in 9.124 s
+#> Fitted using 2289 model solutions performed in 9.253 s
 #> 
 #> Error model: Two-component variance function 
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 2eefdc2e..317ffe5f 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -239,7 +239,7 @@ 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 file59d942b9ac06.c 2> file59d942b9ac06.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file12cd48616f1.c 2> file12cd48616f1.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index f7d543ad..0eca973c 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -350,7 +350,7 @@ solver is used.

                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "eigen")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.004       0.000       0.004 
  system.time(
+#>       0.004       0.000       0.003 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
#>     time   parent       m1
@@ -360,7 +360,7 @@ solver is used.

                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve", use_compiled = FALSE)[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>        User      System verstrichen 
-#>       0.021       0.000       0.021 

+#>       0.021       0.000       0.022 

   # \dontrun{
     # Predict from a fitted model
     f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Ordinary least squares optimisation
#> Sum of squared residuals at call 1: 552.5739
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 8312c17c..d1ea7a52 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -202,8 +202,8 @@ for parallel execution.

 time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
#>        User      System verstrichen 
-#>       0.011       0.032       4.774 
time_1
#>        User      System verstrichen 
-#>      18.676       0.000      18.687 

+#>       0.014       0.024       4.895 
time_1
#>        User      System verstrichen 
+#>      19.047       0.004      19.063 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
 #>   0.7340481   0.2659519   0.7505684   0.2494316 
diff --git a/docs/reference/nobs.mkinfit.html b/docs/reference/nobs.mkinfit.html
new file mode 100644
index 00000000..1bd97732
--- /dev/null
+++ b/docs/reference/nobs.mkinfit.html
@@ -0,0 +1,189 @@
+
+
+
+  
+  
+
+
+
+Number of observations on which an mkinfit object was fitted — nobs.mkinfit • mkin
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+  
+
+  
+    

+      

+      
+
+      
+
+      

+
+

+  

+    

+    
Number of observations on which an mkinfit object was fitted

+    
+    
+    

+
+    

+    
Number of observations on which an mkinfit object was fitted

+    

+
+    
# S3 method for mkinfit
+nobs(object, ...)

+
+    
Arguments

+
-

AIC(<mmkin>)

+

AIC(<mmkin>) BIC(<mmkin>)

Calculated the AIC for a column of an mmkin object

Calculate the AIC for a column of an mmkin object

Extract residuals from an mkinfit model
+

nobs(<mkinfit>)

+

Number of observations on which an mkinfit object was fitted

mkinresplot()

+ + + + + + + + + +
object

An mkinfit object

...

For compatibility with the generic method

+ +

Value

+ +

The number of rows in the data included in the mkinfit object

+ +
+ + + + + + + + + + + + + + diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png deleted file mode 100644 index ad2ffa8c..00000000 Binary files a/docs/reference/plot.mkinfit-6.png and /dev/null differ diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png index 13d96256..44037bb4 100644 Binary files a/docs/reference/plot.mmkin-4.png and b/docs/reference/plot.mmkin-4.png differ diff --git a/docs/reference/print.nafta.html b/docs/reference/print.nafta.html deleted file mode 100644 index fa8223ad..00000000 --- a/docs/reference/print.nafta.html +++ /dev/null @@ -1,197 +0,0 @@ - - - - - - - - -Print nafta objects — print.nafta • mkin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-
- - - - -
- -
-
-
-

Print nafta objects

- - -
- -
- -

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.

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

Arguments

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

An nafta object.

quiet

Should the evaluation text be shown?

digits

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

...

Not used.

- - -
- -
- - -
-
-

Developed by Johannes Ranke.

-
- -
-

Site built with pkgdown 1.4.1.

-
- -
-
- - - - - - - - diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index c6635409..27b19430 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -8,11 +8,13 @@ Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • mkin + + @@ -32,8 +34,8 @@ - + @@ -41,6 +43,7 @@ + @@ -111,7 +114,6 @@ News - @@ -133,15 +135,14 @@
-

This dataset was used for a comparison of KinGUI and ModelMaker to check the software quality of KinGUI in the original publication (Schäfer et al., 2007). The results from the fitting are also included.

- 
schaefer07_complex_case
- + +

Format

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

@@ -153,14 +154,12 @@
A2

a numeric vector

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

-

References

Schäfer D, Mikolasch B, Rainbird P and Harvey B (2007). KinGUI: a new kinetic software tool for evaluations according to FOCUS degradation kinetics. In: Del Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.

-

Examples

data <- mkin_wide_to_long(schaefer07_complex_case, time = "time")
@@ -206,11 +205,8 @@