From 8f38147e145c66ebd27f5d9fcc6f00172c25872f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 26 Oct 2016 23:18:20 +0200 Subject: Static documentation rebuilt by pkgdown::build_site() --- docs/reference/DFOP.solution-2.png | Bin 0 -> 6375 bytes docs/reference/DFOP.solution.html | 70 ++++++++----- docs/reference/Extract.mmkin.html | 85 +++++++++------- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 65 ++++++++----- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 65 ++++++++----- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 65 ++++++++----- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 65 ++++++++----- docs/reference/FOCUS_2006_datasets.html | 65 ++++++++----- docs/reference/FOMC.solution-2.png | Bin 0 -> 6406 bytes docs/reference/FOMC.solution.html | 83 ++++++++++------ docs/reference/HS.solution-2.png | Bin 0 -> 6153 bytes docs/reference/HS.solution.html | 69 ++++++++----- docs/reference/IORE.solution-2.png | Bin 0 -> 6168 bytes docs/reference/IORE.solution.html | 89 ++++++++++------- docs/reference/SFO.solution.html | 67 ++++++++----- docs/reference/SFORB.solution.html | 67 ++++++++----- docs/reference/add_err-4.png | Bin 0 -> 26860 bytes docs/reference/add_err-6.png | Bin 0 -> 15779 bytes docs/reference/add_err-8.png | Bin 0 -> 14754 bytes docs/reference/add_err.html | 88 ++++++++++------- docs/reference/endpoints.html | 64 +++++++----- docs/reference/geometric_mean.html | 57 +++++++---- docs/reference/ilr.html | 78 +++++++++------ docs/reference/index.html | 78 +++++++++------ docs/reference/mccall81_245T.html | 77 +++++++++------ docs/reference/mkin_long_to_wide.html | 58 +++++++---- docs/reference/mkin_wide_to_long.html | 58 +++++++---- docs/reference/mkinds.html | 78 +++++++++------ docs/reference/mkinerrmin.html | 88 ++++++++++------- docs/reference/mkinfit.html | 130 ++++++++++++++----------- docs/reference/mkinmod.html | 86 +++++++++------- docs/reference/mkinparplot-4.png | Bin 0 -> 5373 bytes docs/reference/mkinparplot.html | 68 ++++++++----- docs/reference/mkinplot.html | 60 +++++++----- docs/reference/mkinpredict.html | 74 +++++++++----- docs/reference/mkinresplot-4.png | Bin 0 -> 5255 bytes docs/reference/mkinresplot.html | 76 +++++++++------ docs/reference/mkinsub.html | 68 ++++++++----- docs/reference/mmkin.html | 76 +++++++++------ docs/reference/plot.mkinfit-10.png | Bin 0 -> 18197 bytes docs/reference/plot.mkinfit-4.png | Bin 0 -> 13748 bytes docs/reference/plot.mkinfit-6.png | Bin 0 -> 16810 bytes docs/reference/plot.mkinfit-8.png | Bin 0 -> 13728 bytes docs/reference/plot.mkinfit.html | 72 +++++++++----- docs/reference/plot.mmkin-2.png | Bin 0 -> 10552 bytes docs/reference/plot.mmkin-4.png | Bin 0 -> 10559 bytes docs/reference/plot.mmkin-6.png | Bin 0 -> 7945 bytes docs/reference/plot.mmkin.html | 70 ++++++++----- docs/reference/print.mkinds.html | 48 ++++++--- docs/reference/print.mkinmod.html | 48 ++++++--- docs/reference/schaefer07_complex_case.html | 71 +++++++++----- docs/reference/summary.mkinfit.html | 80 +++++++++------ docs/reference/synthetic_data_for_UBA.html | 69 ++++++++----- docs/reference/transform_odeparms.html | 78 +++++++++------ 54 files changed, 1739 insertions(+), 1014 deletions(-) create mode 100644 docs/reference/DFOP.solution-2.png create mode 100644 docs/reference/FOMC.solution-2.png create mode 100644 docs/reference/HS.solution-2.png create mode 100644 docs/reference/IORE.solution-2.png create mode 100644 docs/reference/add_err-4.png create mode 100644 docs/reference/add_err-6.png create mode 100644 docs/reference/add_err-8.png create mode 100644 docs/reference/mkinparplot-4.png create mode 100644 docs/reference/mkinresplot-4.png create mode 100644 docs/reference/plot.mkinfit-10.png create mode 100644 docs/reference/plot.mkinfit-4.png create mode 100644 docs/reference/plot.mkinfit-6.png create mode 100644 docs/reference/plot.mkinfit-8.png create mode 100644 docs/reference/plot.mmkin-2.png create mode 100644 docs/reference/plot.mmkin-4.png create mode 100644 docs/reference/plot.mmkin-6.png (limited to 'docs/reference') diff --git a/docs/reference/DFOP.solution-2.png b/docs/reference/DFOP.solution-2.png new file mode 100644 index 00000000..91efcebb Binary files /dev/null and b/docs/reference/DFOP.solution-2.png differ diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 3422c206..5c90809c 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -6,14 +6,14 @@ -DFOP.solution. mkin + + — DFOP.solution • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

Function describing decline from a defined starting value using the sum of two exponential decline functions.

@@ -84,7 +86,7 @@ 
DFOP.solution(t, parent.0, k1, k2, g)
-

Arguments

+

Arguments

t
Time.
@@ -100,31 +102,49 @@
-
-

Value

- -

The value of the response variable at time t.

-
+

Value

-
-

References

+

The value of the response variable at time t.

+ +

References

-

FOCUS (2006) “Guidance Document on Estimating Persistence and +

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://focus.jrc.ec.europa.eu/dk

-
-

Examples

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

+ + Examples +

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

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index b513fac1..ee86854a 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -6,14 +6,13 @@ -[.mmkin. mkin +Subsetting method for mmkin objects — [.mmkin • mkin - - + @@ -22,6 +21,7 @@ + @@ -34,10 +34,9 @@ -
+
- -
-
-

Subsetting method for mmkin objects

-
+
+
+
+

Subsetting method for mmkin objects

+
-
-

Subsetting method for mmkin objects.

@@ -83,10 +84,10 @@ 
# S3 method for mmkin
 [(x, i, j, ..., drop = FALSE)
-

Arguments

+

Arguments

x
-
An mmkin object
+
An mmkin object
i
Row index selecting the fits for specific models
j
@@ -98,15 +99,17 @@ a list of mkinfit objects or a single mkinfit object.
-
-

Value

+

Value

-

An object of class mmkin.

-
+

An object of class mmkin.

-

Examples

+ +

+ + Examples + 

  # Only use one core, to pass R CMD check --as-cran
-  fits <- mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C),
+  fits <- mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C),
                 cores = 1, quiet = TRUE)
   fits["FOMC", ]
#>       dataset
 #> model  B       C      
@@ -192,7 +195,7 @@
 #> 
 #> $time
 #>    user  system elapsed 
-#>   0.252   0.000   0.253 
+#>   0.268   0.000   0.264 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -378,7 +381,7 @@
 #>     }
 #>     return(mC)
 #> }
-#> <environment: 0x3e9c368>
+#> <environment: 0x49c37f0>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -400,7 +403,7 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <environment: 0x3e9c368>
+#> <environment: 0x49c37f0>
 #> 
 #> $hessian_notrans
 #>            parent_0     alpha       beta
@@ -466,7 +469,7 @@
 #> 99.66619 
 #> 
 #> $date
-#> [1] "Thu Oct  6 10:47:28 2016"
+#> [1] "Wed Oct 26 23:16:41 2016"
 #> 
 #> attr(,"class")
 #> [1] "mkinfit" "modFit" 
@@ -547,7 +550,7 @@
 #> 
 #> $time
 #>    user  system elapsed 
-#>   0.064   0.000   0.067 
+#>   0.072   0.004   0.074 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -734,7 +737,7 @@
 #>     }
 #>     return(mC)
 #> }
-#> <environment: 0x3c1a660>
+#> <environment: 0x4ae0880>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -756,7 +759,7 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <environment: 0x3c1a660>
+#> <environment: 0x4ae0880>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -819,7 +822,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Thu Oct  6 10:47:28 2016"
+#> [1] "Wed Oct 26 23:16:41 2016"
 #> 
 #> attr(,"class")
 #> [1] "mkinfit" "modFit" 
@@ -896,7 +899,7 @@
 #> 
 #> $time
 #>    user  system elapsed 
-#>   0.064   0.000   0.067 
+#>   0.072   0.004   0.074 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -1083,7 +1086,7 @@
 #>     }
 #>     return(mC)
 #> }
-#> <environment: 0x3c1a660>
+#> <environment: 0x4ae0880>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -1105,7 +1108,7 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <environment: 0x3c1a660>
+#> <environment: 0x4ae0880>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -1168,14 +1171,23 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Thu Oct  6 10:47:28 2016"
+#> [1] "Wed Oct 26 23:16:41 2016"
 #> 
 #> attr(,"class")
 #> [1] "mkinfit" "modFit" 
 #> 
 #>
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
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 5c0faa43..61871ba9 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -6,14 +6,14 @@ -FOCUS_2006_DFOP_ref_A_to_B. mkin + + — FOCUS_2006_DFOP_ref_A_to_B • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -87,10 +89,9 @@ in this fit.

data(FOCUS_2006_DFOP_ref_A_to_B)
-
-

Format

+

Format

-

A data frame containing the following variables. +

A data frame containing the following variables.

package
a factor giving the name of the software package
M0
The fitted initial concentration of the parent compound
@@ -101,27 +102,45 @@ in this fit.

DT90
The resulting DT90 of the parent compound
dataset
The FOCUS dataset that was used

-
- -
-

Source

+ +

Source

-

FOCUS (2006) “Guidance Document on Estimating Persistence and +

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://focus.jrc.ec.europa.eu/dk

-
-

Examples

+ +

+ + Examples + 

data(FOCUS_2006_DFOP_ref_A_to_B)
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index 89faecbf..4fdb5f45 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -6,14 +6,14 @@ -FOCUS_2006_FOMC_ref_A_to_F. mkin + + — FOCUS_2006_FOMC_ref_A_to_F • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -87,10 +89,9 @@ in this fit.

data(FOCUS_2006_FOMC_ref_A_to_F)
-
-

Format

+

Format

-

A data frame containing the following variables. +

A data frame containing the following variables.

package
a factor giving the name of the software package
M0
The fitted initial concentration of the parent compound
@@ -100,27 +101,45 @@ in this fit.

DT90
The resulting DT90 of the parent compound
dataset
The FOCUS dataset that was used

-
- -
-

Source

+ +

Source

-

FOCUS (2006) “Guidance Document on Estimating Persistence and +

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://focus.jrc.ec.europa.eu/dk

-
-

Examples

+ +

+ + Examples + 

data(FOCUS_2006_FOMC_ref_A_to_F)
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index 2dfafec6..d9e43f4a 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -6,14 +6,14 @@ -FOCUS_2006_HS_ref_A_to_F. mkin + + — FOCUS_2006_HS_ref_A_to_F • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -87,10 +89,9 @@ in this fit.

data(FOCUS_2006_HS_ref_A_to_F)
-
-

Format

+

Format

-

A data frame containing the following variables. +

A data frame containing the following variables.

package
a factor giving the name of the software package
M0
The fitted initial concentration of the parent compound
@@ -101,27 +102,45 @@ in this fit.

DT90
The resulting DT90 of the parent compound
dataset
The FOCUS dataset that was used

-
- -
-

Source

+ +

Source

-

FOCUS (2006) “Guidance Document on Estimating Persistence and +

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://focus.jrc.ec.europa.eu/dk

-
-

Examples

+ +

+ + Examples + 

data(FOCUS_2006_HS_ref_A_to_F)
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index ed3a4aff..68475b64 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -6,14 +6,14 @@ -FOCUS_2006_SFO_ref_A_to_F. mkin + + — FOCUS_2006_SFO_ref_A_to_F • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). @@ -87,10 +89,9 @@ in this fit.

data(FOCUS_2006_SFO_ref_A_to_F)
-
-

Format

+

Format

-

A data frame containing the following variables. +

A data frame containing the following variables.

package
a factor giving the name of the software package
M0
The fitted initial concentration of the parent compound
@@ -99,27 +100,45 @@ in this fit.

DT90
The resulting DT90 of the parent compound
dataset
The FOCUS dataset that was used

-
- -
-

Source

+ +

Source

-

FOCUS (2006) “Guidance Document on Estimating Persistence and +

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://focus.jrc.ec.europa.eu/dk

-
-

Examples

+ +

+ + Examples + 

data(FOCUS_2006_SFO_ref_A_to_F)
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index c1eacbd8..6221f53f 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -6,14 +6,14 @@ -FOCUS_2006_datasets. mkin + + — FOCUS_2006_datasets • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

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

FOCUS_2006_datasets
-
-

Format

+

Format

-

6 datasets with observations on the following variables. +

6 datasets with observations on the following variables.

name
a factor containing the name of the observed variable
time
a numeric vector containing time points
value
a numeric vector containing concentrations in percent of applied radioactivity

-
- -
-

Source

+ +

Source

-

FOCUS (2006) “Guidance Document on Estimating Persistence and +

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://focus.jrc.ec.europa.eu/dk

-
-

Examples

+ +

+ + Examples + 

FOCUS_2006_C
#>     name time value
 #> 1 parent    0  85.1
 #> 2 parent    1  57.9
@@ -117,12 +119,29 @@
 #> 9 parent  119   0.6
 #>
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/FOMC.solution-2.png b/docs/reference/FOMC.solution-2.png new file mode 100644 index 00000000..0efe8f07 Binary files /dev/null and b/docs/reference/FOMC.solution-2.png differ diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 912cf414..99d95fcb 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -6,14 +6,13 @@ -FOMC.solution. mkin + First-Order Multi-Compartment kinetics — FOMC.solution • mkin - - + @@ -22,6 +21,7 @@ + @@ -34,10 +34,9 @@ -
+
- -
-
-

First-Order Multi-Compartment kinetics

-
+
+
+
+

First-Order Multi-Compartment kinetics

+
-
-

Function describing exponential decline from a defined starting value, with a decreasing rate constant.

@@ -87,7 +88,7 @@ 
FOMC.solution(t, parent.0, alpha, beta)
-

Arguments

+

Arguments

t
Time.
@@ -103,43 +104,61 @@
-
-

Note

+

Note

-

The solution of the FOMC kinetic model reduces to the - SFO.solution for large values of alpha and +

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

-
- -
-

Value

- -

The value of the response variable at time t.

-
+ +

Value

-
-

References

+

The value of the response variable at time t.

+ +

References

-

FOCUS (2006) “Guidance Document on Estimating Persistence and +

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://focus.jrc.ec.europa.eu/dk

-

Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A +

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

-
-

Examples

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

+ + Examples +

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

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/HS.solution-2.png b/docs/reference/HS.solution-2.png new file mode 100644 index 00000000..0bdb37a9 Binary files /dev/null and b/docs/reference/HS.solution-2.png differ diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 994f8373..06c6e3c1 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -6,14 +6,13 @@ -HS.solution. mkin + Hockey-Stick kinetics — HS.solution • mkin - - + @@ -22,6 +21,7 @@ + @@ -34,10 +34,9 @@ -
+
- -
-
-

Hockey-Stick kinetics

-
+
+
+
+

Hockey-Stick kinetics

+
-
-

Function describing two exponential decline functions with a break point between them.

@@ -83,7 +84,7 @@ 
HS.solution(t, parent.0, k1, k2, tb)
-

Arguments

+

Arguments

t
Time.
@@ -99,31 +100,49 @@ according to k2.
-
-

Value

- -

The value of the response variable at time t.

-
+

Value

-
-

References

+

The value of the response variable at time t.

+ +

References

-

FOCUS (2006) “Guidance Document on Estimating Persistence and +

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://focus.jrc.ec.europa.eu/dk

-
-

Examples

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

+ + Examples +

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

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/IORE.solution-2.png b/docs/reference/IORE.solution-2.png new file mode 100644 index 00000000..df268b64 Binary files /dev/null and b/docs/reference/IORE.solution-2.png differ diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 06f5c1ad..58546489 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -6,14 +6,13 @@ -IORE.solution. mkin + Indeterminate order rate equation kinetics — IORE.solution • mkin - - + @@ -22,6 +21,7 @@ + @@ -34,10 +34,9 @@ -
+
- -
-
-

Indeterminate order rate equation kinetics

-
+
+
+
+

Indeterminate order rate equation kinetics

+
-
-

Function describing exponential decline from a defined starting value, with a concentration dependent rate constant.

@@ -83,7 +84,7 @@ 
IORE.solution(t, parent.0, k__iore, N)
-

Arguments

+

Arguments

t
Time.
@@ -95,53 +96,71 @@
Exponent describing the nonlinearity of the rate equation
-
-

Note

+

Note

-

The solution of the IORE kinetic model reduces to the - SFO.solution if N = 1. +

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.

-
- -
-

Value

- -

The value of the response variable at time t.

-
+ +

Value

-
-

References

+

The value of the response variable at time t.

+ +

References

-

NAFTA Technical Working Group on Pesticides (not dated) Guidance for +

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

-
-

Examples

+ +

+ + Examples + 

  plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2,
-                                       ylim = c(0, 100))
  fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-  fit.iore <- mkinfit("IORE", FOCUS_2006_C, quiet = TRUE)
-  fit.iore.deS <- mkinfit("IORE", FOCUS_2006_C, solution_type = "deSolve", quiet = TRUE)
+                                       ylim = c(0, 100))
  fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
+  fit.iore <- mkinfit("IORE", FOCUS_2006_C, quiet = TRUE)
+  fit.iore.deS <- mkinfit("IORE", FOCUS_2006_C, solution_type = "deSolve", quiet = TRUE)
 
   print(data.frame(coef(fit.fomc), coef(fit.iore), coef(fit.iore.deS),
                    row.names = paste("model par", 1:3)))
#>             coef.fit.fomc. coef.fit.iore. coef.fit.iore.deS.
 #> model par 1    85.87489063      85.874891          85.874890
 #> model par 2     0.05192238      -4.826631          -4.826631
 #> model par 3     0.65096665       1.949403           1.949403
-#> 
  print(rbind(fomc = endpoints(fit.fomc)$distimes, iore = endpoints(fit.iore)$distimes,
-              iore.deS = endpoints(fit.iore)$distimes))
#>              DT50    DT90 DT50back
+#> 
  print(rbind(fomc = endpoints(fit.fomc)$distimes, iore = endpoints(fit.iore)$distimes,
+              iore.deS = endpoints(fit.iore)$distimes))
#>              DT50    DT90 DT50back
 #> fomc     1.785233 15.1479 4.559973
 #> iore     1.785233 15.1479 4.559973
 #> iore.deS 1.785233 15.1479 4.559973
 #>
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 9cf069d7..b2d5526e 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -6,14 +6,13 @@ -SFO.solution. mkin + Single First-Order kinetics — SFO.solution • mkin - - + @@ -22,6 +21,7 @@ + @@ -34,10 +34,9 @@ -
+
- -
-
-

Single First-Order kinetics

-
+
+
+
+

Single First-Order kinetics

+
-
-

Function describing exponential decline from a defined starting value.

SFO.solution(t, parent.0, k)
-

Arguments

+

Arguments

t
Time.
@@ -92,31 +93,49 @@
Kinetic constant.
-
-

Value

- -

The value of the response variable at time t.

-
+

Value

-
-

References

+

The value of the response variable at time t.

+ +

References

-

FOCUS (2006) “Guidance Document on Estimating Persistence and +

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://focus.jrc.ec.europa.eu/dk

-
-

Examples

+ +

+ + Examples + 

  ## Not run: plot(function(x) SFO.solution(x, 100, 3), 0, 2)
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 57959f26..135edb51 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -6,14 +6,13 @@ -SFORB.solution. mkin + Single First-Order Reversible Binding kinetics — SFORB.solution • mkin - - + @@ -22,6 +21,7 @@ + @@ -34,10 +34,9 @@ -
+
- -
-
-

Single First-Order Reversible Binding kinetics

-
+
+
+
+

Single First-Order Reversible Binding kinetics

+
-
-

Function describing the solution of the differential equations describing the kinetic model with first-order terms for a two-way transfer from a free @@ -86,7 +87,7 @@ 

SFORB.solution(t, parent.0, k_12, k_21, k_1output)
-

Arguments

+

Arguments

t
Time.
@@ -100,32 +101,50 @@
Kinetic constant describing degradation of the free fraction.
-
-

Value

+

Value

-

The value of the response variable, which is the sum of free and bound +

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

-
- -
-

References

+ +

References

-

FOCUS (2006) “Guidance Document on Estimating Persistence and +

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://focus.jrc.ec.europa.eu/dk

-
-

Examples

+ +

+ + Examples + 

  ## Not run: plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/add_err-4.png b/docs/reference/add_err-4.png new file mode 100644 index 00000000..f3d04134 Binary files /dev/null and b/docs/reference/add_err-4.png differ diff --git a/docs/reference/add_err-6.png b/docs/reference/add_err-6.png new file mode 100644 index 00000000..05b27247 Binary files /dev/null and b/docs/reference/add_err-6.png differ diff --git a/docs/reference/add_err-8.png b/docs/reference/add_err-8.png new file mode 100644 index 00000000..b0182d2a Binary files /dev/null and b/docs/reference/add_err-8.png differ diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index cbc925ca..9020a486 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -6,14 +6,14 @@ -add_err. mkin + + — add_err • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

Normally distributed errors are added to data predicted for a specific - degradation model using mkinpredict. The variance of the error + degradation model using mkinpredict. The variance of the error may depend on the predicted value and is specified as a standard deviation.

@@ -87,11 +89,11 @@ n = 1000, LOD = 0.1, reps = 2, digits = 1, seed = NA) -

Arguments

+

Arguments

prediction
- A prediction from a kinetic model as produced by mkinpredict. + A prediction from a kinetic model as produced by mkinpredict.
sdfunc
@@ -123,31 +125,31 @@
-
-

Value

+

Value

-

A list of datasets compatible with mmkin, i.e. +

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

-
- -
-

References

+ mkinfit.

+ +

References

-

Ranke J and Lehmann R (2015) To t-test or not to t-test, that is the question. XV Symposium on Pesticide Chemistry 2-4 September 2015, Piacenza, Italy +

Ranke J and Lehmann R (2015) To t-test or not to t-test, that is the question. XV Symposium on Pesticide Chemistry 2-4 September 2015, Piacenza, Italy http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf

-
-

Examples

+ +

+ + Examples + 

# The kinetic model
-m_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
-                     M1 = mkinsub("SFO"), use_of_ff = "max")
Successfully compiled differential equation model from auto-generated C code.

+m_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
+                     M1 = mkinsub("SFO"), use_of_ff = "max")
Successfully compiled differential equation model from auto-generated C code.

 # Generate a prediction for a specific set of parameters
 sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
 
 # This is the prediction used for the "Type 2 datasets" on the Piacenza poster
 # from 2015
-d_SFO_SFO <- mkinpredict(m_SFO_SFO,
+d_SFO_SFO <- mkinpredict(m_SFO_SFO,
                          c(k_parent = 0.1, f_parent_to_M1 = 0.5,
                            k_M1 = log(2)/1000),
                          c(parent = 100, M1 = 0),
@@ -165,21 +167,32 @@
 # Be quiet and use the faster Levenberg-Marquardt algorithm, as the datasets
 # are easy and examples are run often. Use only one core not to offend CRAN
 # checks
-f_SFO_SFO <- mmkin(list("SFO-SFO" = m_SFO_SFO),
+f_SFO_SFO <- mmkin(list("SFO-SFO" = m_SFO_SFO),
                    d_SFO_SFO_err, cores = 1,
                    quiet = TRUE, method.modFit = "Marq")
 
-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])
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 8ceb39d9..89e9cf52 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -6,14 +6,14 @@ -endpoints. mkin + + — endpoints • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

This function calculates DT50 and DT90 values as well as formation fractions from kinetic models fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, @@ -86,27 +88,34 @@ with the advantage that the SFORB model can also be used for metabolites.

endpoints(fit)
-

Arguments

+

Arguments

fit
- An object of class mkinfit. + An object of class mkinfit.
-
-

Note

+

Note

-

The function is used internally by summary.mkinfit.

-
+

The function is used internally by summary.mkinfit.

+ +

Value

+ +

A list with the components mentioned above.

+ -
-

Value

+
+ -
-

Author

Johannes Ranke @@ -115,7 +124,14 @@ with the advantage that the SFORB model can also be used for metabolites.

-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 1d9a9e66..793d893c 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -6,14 +6,13 @@ -geometric_mean. mkin + Calculate the geometric mean — geometric_mean • mkin - - + @@ -22,6 +21,7 @@ + @@ -34,10 +34,9 @@ -
+
- -
-
-

Calculate the geometric mean

-
+
+
+
+

Calculate the geometric mean

+
-
-

Function calculating the geometric mean of numeric vectors

geometric_mean(x, na.rm = FALSE)
-

Arguments

+

Arguments

x
A numeric vector
@@ -90,24 +91,42 @@
Should NA values be ignored
-
-

Value

+

Value

-

The geometric mean.

-
+

The geometric mean.

-

Examples

+ +

+ + Examples + 

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

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 355cbb78..d249101d 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -6,14 +6,14 @@ -ilr. mkin + + — ilr • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

This implementation is a special case of the class of isometric log-ratio transformations.

@@ -84,7 +86,7 @@ 
ilr(x)
   invilr(x)
-

Arguments

+

Arguments

x
@@ -93,26 +95,24 @@
-
-

Value

+

Value

-

The result of the forward or backward transformation. The returned components always +

The result of the forward or backward transformation. The returned 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

-
+ +

References

-
-

See also

+

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

+ +

See also

-

Another implementation can be found in R package robCompositions.

-
+

Another implementation can be found in R package robCompositions.

-

Examples

+ +

+ + Examples + 

# Order matters
 ilr(c(0.1, 1, 10))
#> [1] -1.628174 -2.820079
 #> 
ilr(c(10, 1, 0.1))
#> [1] 1.628174 2.820079
@@ -135,7 +135,20 @@
 #> 
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
 #>
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/index.html b/docs/reference/index.html index 869f61dd..60d11171 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -6,14 +6,13 @@ -Function reference. mkin +Function reference • mkin - - + @@ -22,6 +21,7 @@ + @@ -34,10 +34,9 @@ -
+
- -
-
-

Function reference version 0.9.44.9000

-
- -
+
-
-

Main functions

+
+

Function reference

+

version 0.9.44.9000

+
+ +
+

Main functions

Essential functionality

-
-
mkinfit
-
-
-
mkinmod
-
-
-
mmkin
-
-
-
-
-
-

Show results

+

+

+ +

+

+ +

+

+ +

Show results

-
-
+
+ +
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 63635f9a..7a96be3b 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -6,14 +6,14 @@ -mccall81_245T. mkin + + — mccall81_245T • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether @@ -85,31 +87,31 @@ 

mccall81_245T
-
-

Format

+

Format

-

A dataframe containing the following variables. +

A dataframe containing the following variables.

name
the name of the compound observed. Note that T245 is used as an acronym for 2,4,5-T. T245 is a legitimate object name in R, which is necessary for specifying models using - mkinmod.
+ mkinmod.
time
a numeric vector containing sampling times in days after treatment
value
a numeric vector containing concentrations in percent of applied radioactivity
soil
a factor containing the name of the soil

-
- -
-

Source

+ +

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 +

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"),
+
+    

+      
+      Examples
+    

+    
  SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"),
                          phenol = list(type = "SFO", to = "anisole"),
                          anisole = list(type = "SFO"))
Successfully compiled differential equation model from auto-generated C code.
  ## Not run: ------------------------------------
 #     fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))
@@ -117,13 +119,13 @@
 #   
 ## ---------------------------------------------
   # No covariance matrix and k_phenol_sink is really small, therefore fix it to zero
-  fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),
+  fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),
                  parms.ini = c(k_phenol_sink = 0),
                  fixed_parms = "k_phenol_sink", quiet = TRUE)
   summary(fit.2, data = FALSE)
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.1 
-#> Date of fit:     Thu Oct  6 10:47:34 2016 
-#> Date of summary: Thu Oct  6 10:47:34 2016 
+#> Date of fit:     Wed Oct 26 23:16:47 2016 
+#> Date of summary: Wed Oct 26 23:16:47 2016 
 #> 
 #> Equations:
 #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -133,7 +135,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.492 s
+#> Fitted with method Port using 246 model solutions performed in 1.487 s
 #> 
 #> Weighting: none
 #> 
@@ -216,12 +218,29 @@
 #> anisole 103.784 344.763
 #> 

   

-  

+  
 

 
       

-      
Built by pkgdown. Styled with Bootstrap 3.

+      

+  
Developed by Johannes Ranke, Eurofins Regulatory AG.

+

+
+

+  
Site built with pkgdown.

+

+
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 5b1a8353..d8b616c2 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -6,14 +6,14 @@ -mkin_long_to_wide. mkin + + — mkin_long_to_wide • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

This function takes a dataframe in the long form as required by modCost and converts it into a dataframe with one independent variable and several @@ -85,7 +87,7 @@ 

mkin_long_to_wide(long_data, time = "time", outtime = "time")
-

Arguments

+

Arguments

long_data
@@ -103,13 +105,15 @@
-
-

Value

+

Value

-

Dataframe in wide format.

-
+

Dataframe in wide format.

-

Examples

+ +

+ + Examples + 

mkin_long_to_wide(FOCUS_2006_D)
#>    time parent    m1
 #> 1     0  99.46  0.00
 #> 2     0 102.04  0.00
@@ -135,7 +139,16 @@
 #> 22  120     NA 33.31
 #>
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 2a70ebbe..31207861 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -6,14 +6,14 @@ -mkin_wide_to_long. mkin + + — mkin_wide_to_long • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

This function simply takes a dataframe with one independent variable and several dependent variable and converts it into the long form as required by modCost.

@@ -84,7 +86,7 @@ 
mkin_wide_to_long(wide_data, time = "t")
-

Arguments

+

Arguments

wide_data
@@ -97,13 +99,15 @@
-
-

Value

+

Value

-

Dataframe in long format as needed for modCost.

-
+

Dataframe in long format as needed for modCost.

-

Examples

+ +

+ + Examples + 

wide <- data.frame(t = c(1,2,3), x = c(1,4,7), y = c(3,4,5))
 mkin_wide_to_long(wide)
#>   name time value
 #> 1    x    1     1
@@ -114,7 +118,16 @@
 #> 6    y    3     5
 #>
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index 0b4341aa..45cc315f 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -6,14 +6,13 @@ -mkinds. mkin +A dataset class for mkin — mkinds • mkin - - + @@ -22,6 +21,7 @@ + @@ -34,10 +34,9 @@ -
+
- -
-
-

A dataset class for mkin

-
+
+
+
+

A dataset class for mkin

+
-
-

A dataset class for mkin

mkinds
-
-

Format

- -

An R6Class generator object.

-
+

Format

-
-

Fields

+

An R6Class generator object.

+ +

Fields

-

-

+

+

title
A full title for the dataset

-

sampling
times The sampling times

-

time_unit
The time unit

-

observed
Names of the observed compounds

-

unit
The unit of the observations

-

replicates
The number of replicates

-

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

sampling
times The sampling times

+

time_unit
The time unit

+

observed
Names of the observed compounds

+

unit
The unit of the observations

+

replicates
The number of replicates

+

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

-
-

Examples

+ +

+ + Examples + 

mds <- mkinds$new("FOCUS A", FOCUS_2006_A)
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index cd9faf1a..2e1833da 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -6,14 +6,14 @@ -mkinerrmin. mkin + + — mkinerrmin • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

This function uses optimize in order to iteratively find the smallest relative error still resulting in passing the chi-squared test @@ -85,11 +87,11 @@ as defined in the FOCUS kinetics report from 2006.

mkinerrmin(fit, alpha = 0.05)
-

Arguments

+

Arguments

fit
- an object of class mkinfit. + an object of class mkinfit.
alpha
@@ -97,52 +99,70 @@ as defined in the FOCUS kinetics report from 2006.

-
-

Value

+

Value

-

A dataframe with the following components:

-

The dataframe has one row for the total dataset and one further row for +

A dataframe with the following components:

+

The dataframe has one row for the total dataset and one further row for each observed state variable in the model.

-
- -
-

Details

- -

This function is used internally by summary.mkinfit.

-
+ +

Details

-
-

References

+

This function is used internally by summary.mkinfit.

+ +

References

-

FOCUS (2006) “Guidance Document on Estimating Persistence and +

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://focus.jrc.ec.europa.eu/dk

-
-

Examples

- 
SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),
+
+    

+      
+      Examples
+    

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

-fit_FOCUS_D = mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+fit_FOCUS_D = mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 round(mkinerrmin(fit_FOCUS_D), 4)
#>          err.min n.optim df
 #> All data  0.0640       4 15
 #> parent    0.0646       2  7
 #> m1        0.0469       2  8
-#> 
fit_FOCUS_E = mkinfit(SFO_SFO, FOCUS_2006_E, quiet = TRUE)
+#> 
fit_FOCUS_E = mkinfit(SFO_SFO, FOCUS_2006_E, quiet = TRUE)
 round(mkinerrmin(fit_FOCUS_E), 4)
#>          err.min n.optim df
 #> All data  0.1544       4 13
 #> parent    0.1659       2  7
 #> m1        0.1095       2  6
 #> 

   

-  

+  
 

 
       

-      
Built by pkgdown. Styled with Bootstrap 3.

+      

+  
Developed by Johannes Ranke, Eurofins Regulatory AG.

+

+
+

+  
Site built with pkgdown.

+

+
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 7acbbe5a..3c9bd05c 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -6,14 +6,14 @@ -mkinfit. mkin + + — mkinfit • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

This function uses the Flexible Modelling Environment package FME to create a function calculating the model cost, i.e. the @@ -86,7 +88,7 @@ Per default, parameters in the kinetic models are internally transformed in order to better satisfy the assumption of a normal distribution of their estimators. In each step of the optimsation, the kinetic model is solved using the - function mkinpredict. The variance of the residuals for each + function mkinpredict. The variance of the residuals for each observed variable can optionally be iteratively reweighted until convergence using the argument reweight.method = "obs".

@@ -111,11 +113,11 @@ reweight.tol = 1e-8, reweight.max.iter = 10, trace_parms = FALSE, ...) -

Arguments

+

Arguments

mkinmod
- A list of class mkinmod, containing the kinetic model to be + A list of class mkinmod, containing the kinetic model to be fitted to the data, or one of the shorthand names ("SFO", "FOMC", "DFOP", "HS", "SFORB"). If a shorthand name is given, a parent only degradation model is generated for the variable with the highest value in @@ -151,7 +153,7 @@ A named vector of initial values for the state variables of the model. In case the observed variables are represented by more than one model variable, the names will differ from the names of the observed variables - (see map component of mkinmod). The default is to set + (see map component of mkinmod). The default is to set the initial value of the first model variable to the mean of the time zero values for the variable with the maximum observed value, and all others to 0. If this variable has no time zero observations, its initial value is set to 100. @@ -187,18 +189,18 @@ otherwise "eigen" if the model can be expressed using eigenvalues and eigenvectors, and finally "deSolve" for the remaining models (time dependence of degradation rates and metabolites). This argument is passed - on to the helper function mkinpredict. + on to the helper function mkinpredict.
method.ode
- The solution method passed via mkinpredict to + The solution method passed via mkinpredict to ode in case the solution type is "deSolve". The default "lsoda" is performant, but sometimes fails to converge.
use_compiled
- If set to FALSE, no compiled version of the mkinmod - model is used, in the calls to mkinpredict even if + If set to FALSE, no compiled version of the mkinmod + model is used, in the calls to mkinpredict even if a compiled verion is present.
method.modFit
@@ -251,7 +253,7 @@ to do transformations. If TRUE, the g parameter of the DFOP and HS models are also transformed, as they can also be seen as compositional data. The transformation used for these transformations is the - ilr transformation. + ilr transformation.
plot
@@ -290,7 +292,7 @@
n.outtimes
The length of the dataseries that is produced by the model prediction - function mkinpredict. This impacts the accuracy of + function mkinpredict. This impacts the accuracy of the numerical solver if that is used (see solution_type argument. The default value is 100.
@@ -324,54 +326,50 @@
-
-

Value

- -

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

-
- -
-

See also

+

Value

-

Plotting methods plot.mkinfit and - mkinparplot.

-

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

-
+

A list with "mkinfit" and "modFit" in the class attribute. + A summary can be obtained by summary.mkinfit.

+ +

See also

-
-

Note

+

Plotting methods plot.mkinfit and + mkinparplot.

+

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

+ +

Note

-

The implementation of iteratively reweighted least squares is inspired by the +

The implementation of iteratively reweighted least squares is inspired by the work of the KinGUII team at Bayer Crop Science (Walter Schmitt and Zhenglei Gao). A similar implemention can also be found in CAKE 2.0, which is the other GUI derivative of mkin, sponsored by Syngenta.

-
- -
-

Note

+ +

Note

-

When using the "IORE" submodel for metabolites, fitting with +

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.

-
-

Examples

+ +

+ + Examples + 

# Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.1 
-#> Date of fit:     Thu Oct  6 10:47:36 2016 
-#> Date of summary: Thu Oct  6 10:47:36 2016 
+#> Date of fit:     Wed Oct 26 23:16:49 2016 
+#> Date of summary: Wed Oct 26 23:16:49 2016 
 #> 
 #> Equations:
 #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 64 model solutions performed in 0.152 s
+#> Fitted with method Port using 64 model solutions performed in 0.148 s
 #> 
 #> Weighting: none
 #> 
@@ -436,15 +434,15 @@
 #> 

 # One parent compound, one metabolite, both single first order.
 # Use mkinsub for convenience in model formulation. Pathway to sink included per default.
-SFO_SFO <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
+SFO_SFO <- mkinmod(
+  parent = mkinsub("SFO", "m1"),
+  m1 = mkinsub("SFO"))
Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#>    user  system elapsed 
-#>   1.240   1.280   0.973 
+#>   1.224   1.196   0.913 
 #> 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
-#> 
endpoints(fit)
#> $ff
+#> 
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -514,7 +512,22 @@
 # summary(f.w.man.irls)
 ## ---------------------------------------------
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 9dd8fca0..53c87e92 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -6,14 +6,14 @@ -mkinmod. mkin + + — mkinmod • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

The function usually takes several expressions, each assigning a compound name to a list, specifying the kinetic model type and reaction or transfer to other @@ -89,7 +91,7 @@ 

mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verbose = FALSE)
-

Arguments

+

Arguments

...
@@ -131,41 +133,39 @@
-
-

Value

+

Value

-

A list of class mkinmod for use with mkinfit, containing

-
- -
-

Note

+

A list of class mkinmod for use with mkinfit, containing

+ +

Note

-

The IORE submodel is not well tested (yet). When using this model for metabolites, +

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

-
- -
-

References

+ mkinfit.

+ +

References

-

FOCUS (2006) “Guidance Document on Estimating Persistence and +

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://focus.jrc.ec.europa.eu/dk

-

NAFTA Technical Working Group on Pesticides (not dated) Guidance for +

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

-
-

Examples

+ +

+ + Examples + 

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

+  parent = mkinsub("SFO", "m1"),
+  m1 = mkinsub("SFO"))
Successfully compiled differential equation model from auto-generated C code.

 ## Not run: ------------------------------------
 # # The above model used to be specified like this, before the advent of mkinsub()
 # SFO_SFO <- mkinmod(
@@ -189,7 +189,20 @@
 #                           quiet = TRUE)
 ## ---------------------------------------------
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/mkinparplot-4.png b/docs/reference/mkinparplot-4.png new file mode 100644 index 00000000..77eafd95 Binary files /dev/null and b/docs/reference/mkinparplot-4.png differ diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index f2fae22d..6d4f2cfd 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -6,14 +6,14 @@ -mkinparplot. mkin + + — mkinparplot • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

This function plots the confidence intervals for the parameters - fitted using mkinfit.

+ fitted using mkinfit.

mkinparplot(object)
-

Arguments

+

Arguments

object
- A fit represented in an mkinfit object. + A fit represented in an mkinfit object.
-
-

Value

+

Value

-

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

-
+

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

-

Examples

- 
model <- mkinmod(
+
+    

+      
+      Examples
+    

+    
model <- mkinmod(
   T245 = list(type = "SFO", to = c("phenol"), sink = FALSE),
   phenol = list(type = "SFO", to = c("anisole")),
-  anisole = list(type = "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)
-mkinparplot(fit)

+  anisole = list(type = "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)
+mkinparplot(fit)
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 51ca3992..925a6683 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -6,14 +6,14 @@ -mkinplot. mkin + + — mkinplot • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-
-

Deprecated function. It now only calls the plot method plot.mkinfit.

+

Deprecated function. It now only calls the plot method plot.mkinfit.

mkinplot(fit, ...)
-

Arguments

+

Arguments

fit
- an object of class mkinfit. + an object of class mkinfit.
&#8230;
- further arguments passed to plot.mkinfit. + further arguments passed to plot.mkinfit.
-
-

Value

+

Value

+ +

The function is called for its side effect.

+ + +
+ -
-

Author

Johannes Ranke @@ -110,7 +119,14 @@
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 5b7cdb32..cf04c6b6 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -6,14 +6,14 @@ -mkinpredict. mkin + + — mkinpredict • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

This function produces a time series for all the observed variables in a - kinetic model as specified by mkinmod, using a specific set of + kinetic model as specified by mkinmod, using a specific set of kinetic parameters and initial values for the state variables.

@@ -87,11 +89,11 @@ use_compiled = "auto", method.ode = "lsoda", atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...) -

Arguments

+

Arguments

mkinmod
- A kinetic model as produced by mkinmod. + A kinetic model as produced by mkinmod.
odeparms
@@ -125,7 +127,7 @@
use_compiled
- If set to FALSE, no compiled version of the mkinmod + If set to FALSE, no compiled version of the mkinmod model is used, even if is present.
atol
@@ -149,14 +151,16 @@
-
-

Value

+

Value

-

A matrix in the same format as the output of ode.

-
+

A matrix in the same format as the output of ode.

-

Examples

- 
  SFO <- mkinmod(degradinol = list(type = "SFO"))
+
+    

+      
+      Examples
+    

+    
  SFO <- mkinmod(degradinol = list(type = "SFO"))
   # Compare solution types
   mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
               solution_type = "analytical")
#>    time  degradinol
@@ -277,31 +281,40 @@
 #> 2001   20  0.2478752
 #> 

   # Check compiled model versions - they are faster than the eigenvalue based solutions!
-  SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),
+  SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),
                     m1 = list(type = "SFO"))
Successfully compiled differential equation model from auto-generated C code.
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "eigen")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
 #> 
#>    user  system elapsed 
-#>   0.008   0.020   0.004 
+#>   0.008   0.024   0.004 
 #> 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
 #> 
#>    user  system elapsed 
-#>   0.016   0.004   0.003 
+#>   0.000   0.020   0.002 
 #> 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve", use_compiled = FALSE)[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
 #> 
#>    user  system elapsed 
-#>   0.032   0.000   0.034 
+#>   0.036   0.000   0.035 
 #> 

   

-  

+  
 
       

-      
Built by pkgdown. Styled with Bootstrap 3.

+      

+  
Developed by Johannes Ranke, Eurofins Regulatory AG.

+

+
+

+  
Site built with pkgdown.

+

+
       

    

 
diff --git a/docs/reference/mkinresplot-4.png b/docs/reference/mkinresplot-4.png
new file mode 100644
index 00000000..7dbd7522
Binary files /dev/null and b/docs/reference/mkinresplot-4.png differ
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index fb9ab40d..f16dee5d 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -6,14 +6,14 @@
 
 
 
-mkinresplot. mkin
+
+ — mkinresplot • mkin
 
 
 
-
 
-
 
+
 
 
 
@@ -22,6 +22,7 @@
 
 
 
+
 
 
 
@@ -34,10 +35,9 @@
   
 
   
-    

+    

       

-      
-

 
-      

-  

+      

+  

+    

+    

 

-

+    

 
-

-  

     
     
This function plots the residuals for the specified subset of the 
   observed variables from an mkinfit object. A combined plot of the fitted
-  model and the residuals can be obtained using plot.mkinfit
+  model and the residuals can be obtained using plot.mkinfit
   using the argument show_residuals = TRUE.

     
 
@@ -90,11 +92,11 @@
     xlab = "Time", ylab = "Residual",
     maxabs = "auto", legend = TRUE, lpos = "topright", ...)
-

Arguments

+

Arguments

object
- A fit represented in an mkinfit object. + A fit represented in an mkinfit object.
obs_vars
@@ -132,24 +134,35 @@
-
-

Value

- -

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

-
+

Value

-
-

See also

+

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

+ +

See also

-

mkinplot, for a way to plot the data and the fitted lines of the +

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

-
-

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)
-mkinresplot(fit, "m1")
+ +

+ + 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)
+mkinresplot(fit, "m1")
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 6b079c40..2432e981 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -6,14 +6,14 @@ -mkinsub. mkin + + — mkinsub • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

This is a convenience function to set up the lists used as arguments for - mkinmod.

+ mkinmod.

mkinsub(submodel, to = NULL, sink = TRUE, full_name = NA)
-

Arguments

+

Arguments

submodel
Character vector of length one to specify the submodel type. See - mkinmod for the list of allowed submodel names. + mkinmod for the list of allowed submodel names.
to
@@ -110,27 +112,38 @@
-
-

Value

+

Value

-

A list for use with mkinmod.

-
+

A list for use with mkinmod.

-

Examples

+ +

+ + Examples + 

# One parent compound, one metabolite, both single first order.
-SFO_SFO <- mkinmod(
+SFO_SFO <- mkinmod(
   parent = list(type = "SFO", to = "m1"),
   m1 = list(type = "SFO"))
Successfully compiled differential equation model from auto-generated C code.

 # The same model using mkinsub
-SFO_SFO.2 <- mkinmod(
+SFO_SFO.2 <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))
Successfully compiled differential equation model from auto-generated C code.

 # Now supplying full names
-SFO_SFO.2 <- mkinmod(
+SFO_SFO.2 <- mkinmod(
   parent = mkinsub("SFO", "m1", full_name = "Test compound"),
   m1 = mkinsub("SFO", full_name = "Metabolite M1"))
Successfully compiled differential equation model from auto-generated C code.
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 5b624893..0ad3321c 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -6,14 +6,14 @@ -mmkin. mkin + + — mmkin • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-
-

This function calls mkinfit on all combinations of models and datasets +

This function calls mkinfit on all combinations of models and datasets specified in its first two arguments.

mmkin(models, datasets,
       cores = round(detectCores()/2), cluster = NULL, ...)
-

Arguments

+

Arguments

models
Either a character vector of shorthand names ("SFO", "FOMC", "DFOP", - "HS", "SFORB"), or an optionally named list of mkinmod + "HS", "SFORB"), or an optionally named list of mkinmod objects.
datasets
An optionally named list of datasets suitable as observed data for - mkinfit. + mkinfit.
cores
@@ -110,24 +112,24 @@
&#8230;
- Further arguments that will be passed to mkinfit. + Further arguments that will be passed to mkinfit.
-
-

Value

+

Value

-

A matrix of mkinfit objects that can be indexed using the model +

A matrix of mkinfit objects that can be indexed using the model and dataset names as row and column indices.

-
- -
-

See also

+ +

See also

-

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

-
+

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

-

Examples

+ +

+ + Examples + 

## Not run: ------------------------------------
 # m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
 #                            M1 = mkinsub("SFO", "M2"),
@@ -161,7 +163,18 @@
 # plot(fits.0[1, 1])
 ## ---------------------------------------------
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/plot.mkinfit-10.png b/docs/reference/plot.mkinfit-10.png new file mode 100644 index 00000000..09bb687c Binary files /dev/null and b/docs/reference/plot.mkinfit-10.png differ diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png new file mode 100644 index 00000000..1e90d789 Binary files /dev/null and b/docs/reference/plot.mkinfit-4.png differ diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png new file mode 100644 index 00000000..1dfbbe4c Binary files /dev/null and b/docs/reference/plot.mkinfit-6.png differ diff --git a/docs/reference/plot.mkinfit-8.png b/docs/reference/plot.mkinfit-8.png new file mode 100644 index 00000000..e4ab674a Binary files /dev/null and b/docs/reference/plot.mkinfit-8.png differ diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 94aebf63..631ea429 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -6,14 +6,14 @@ -plot.mkinfit. mkin + + — plot.mkinfit • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

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

@@ -98,7 +100,7 @@ plot(x, fit = x, show_errmin = FALSE, errmin_digits = 3, …) plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …) -

Arguments

+

Arguments

x
@@ -106,7 +108,7 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …
fit
- An object of class mkinfit. + An object of class mkinfit.
obs_vars
@@ -194,27 +196,38 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …
-
-

Value

+

Value

-

The function is called for its side effect.

-
+

The function is called for its side effect.

-

Examples

+ +

+ + Examples + 

# One parent compound, one metabolite, both single first order, path from
 # parent to sink included, use Levenberg-Marquardt for speed
-SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),
-                   m1 = mkinsub("SFO", full = "Metabolite M1" ))
Successfully compiled differential equation model from auto-generated C code.
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = "Marq")
-plot(fit)
plot(fit, show_residuals = TRUE)

+SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),
+                   m1 = mkinsub("SFO", full = "Metabolite M1" ))
Successfully compiled differential equation model from auto-generated C code.
fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = "Marq")
+plot(fit)
plot(fit, show_residuals = TRUE)

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

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

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

+     show_errmin = TRUE)

 # The same can be obtained with less typing, using the convenience function plot_sep
 plot_sep(fit, lpos = c("topright", "bottomright"))
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png new file mode 100644 index 00000000..a26e413f Binary files /dev/null and b/docs/reference/plot.mmkin-2.png differ diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png new file mode 100644 index 00000000..f23ed172 Binary files /dev/null and b/docs/reference/plot.mmkin-4.png differ diff --git a/docs/reference/plot.mmkin-6.png b/docs/reference/plot.mmkin-6.png new file mode 100644 index 00000000..dc24d92f Binary files /dev/null and b/docs/reference/plot.mmkin-6.png differ diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 358da679..44ae760f 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -6,14 +6,14 @@ -plot.mmkin. mkin + + — plot.mmkin • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-
-

When x is a row selected from an mmkin object ([.mmkin), the same model +

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

@@ -87,11 +89,11 @@ plot(x, main = "auto", legends = 1, errmin_var = "All data", errmin_digits = 3, cex = 0.7, rel.height.middle = 0.9, ...) -

Arguments

+

Arguments

x
- An object of class mmkin, with either one row or one column. + An object of class mmkin, with either one row or one column.
main
@@ -119,27 +121,38 @@
&#8230;
- Further arguments passed to plot.mkinfit and mkinresplot. + Further arguments passed to plot.mkinfit and mkinresplot.
-
-

Value

+

Value

-

The function is called for its side effect.

-
+

The function is called for its side effect.

-

Examples

+ +

+ + Examples + 

  # Only use one core not to offend CRAN checks, use Levenberg-Marquardt for speed
-  fits <- mmkin(c("FOMC", "HS"), list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C),
+  fits <- mmkin(c("FOMC", "HS"), list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C),
                 cores = 1, quiet = TRUE, method.modFit = "Marq")
-  plot(fits[, "FOCUS C"])
  plot(fits["FOMC", ])

+  plot(fits[, "FOCUS C"])
  plot(fits["FOMC", ])

   # We can also plot a single fit, if we like the way mmkin works, but then the plot 
   # height should be smaller than the plot width (this is not possible for the html pages
   # generated by staticdocs, 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])
-
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index dea5f75c..c4bc08d5 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -6,14 +6,14 @@ -print.mkinds. mkin + + — print.mkinds • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

Print mkinds objects.

@@ -84,24 +86,38 @@ 
# S3 method for mkinds
 print(x, ...)
-

Arguments

+

Arguments

x
- An mkinds object. + An mkinds object.
&#8230;
Not used.
-
-
+ + +
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 38663f8f..edc9cde7 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -6,14 +6,14 @@ -print.mkinmod. mkin + + — print.mkinmod • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

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

@@ -84,24 +86,38 @@ 
# S3 method for mkinmod
 print(x, ...)
-

Arguments

+

Arguments

x
- An mkinmod object. + An mkinmod object.
&#8230;
Not used.
-
-
+ + +
+
-

Built by pkgdown. Styled with Bootstrap 3.

+
+

Developed by Johannes Ranke, Eurofins Regulatory AG.

+
+ +
+

Site built with pkgdown.

+
+
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 12776c74..1cd71697 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -6,14 +6,14 @@ -schaefer07_complex_case. mkin + + — schaefer07_complex_case • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

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). @@ -85,10 +87,9 @@ 

data(schaefer07_complex_case)
-
-

Format

+

Format

-

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

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

time
a numeric vector
parent
a numeric vector
@@ -97,33 +98,51 @@
C1
a numeric vector
A2
a numeric vector

-

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

-
- -
-

References

+

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 +

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")
-model <- mkinmod(
+
+    

+      
+      Examples
+    

+    
data <- mkin_wide_to_long(schaefer07_complex_case, time = "time")
+model <- mkinmod(
   parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),
   A1 = list(type = "SFO", to = "A2"),
   B1 = list(type = "SFO"),
   C1 = list(type = "SFO"),
   A2 = list(type = "SFO"), use_of_ff = "max")
Successfully compiled differential equation model from auto-generated C code.
## Not run: mkinfit(model, data, plot=TRUE)

   

-  

+  
 

 
       

-      
Built by pkgdown. Styled with Bootstrap 3.

+      

+  
Developed by Johannes Ranke, Eurofins Regulatory AG.

+

+
+

+  
Site built with pkgdown.

+

+
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index acbf36dc..1e1a0e2f 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -6,14 +6,14 @@ -summary.mkinfit. mkin + + — summary.mkinfit • mkin - - + @@ -22,6 +22,7 @@ + @@ -34,10 +35,9 @@ -
+
- -
-
-

+
+
+
+

-
+
-
-

Lists model equations, the summary as returned by summary.modFit, the chi2 error levels calculated according to FOCUS guidance (2006) as far @@ -89,11 +91,11 @@ # S3 method for summary.mkinfit print(x, digits = max(3, getOption("digits") - 3), ...) -

Arguments

+

Arguments

object
- an object of class mkinfit. + an object of class mkinfit.
x
@@ -121,36 +123,36 @@
-
-

Value

+

Value

-

The summary function returns a list derived from +

The summary function returns a list derived from summary.modFit, with components, among others

-

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

-
- -
-

References

+

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

+ +

References

-

FOCUS (2006) “Guidance Document on Estimating Persistence and +

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://focus.jrc.ec.europa.eu/dk

-
-

Examples

- 
  summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version:    0.9.44.9000 
+
+    

+      
+      Examples
+    

+    
  summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.1 
-#> Date of fit:     Thu Oct  6 10:47:44 2016 
-#> Date of summary: Thu Oct  6 10:47:44 2016 
+#> Date of fit:     Wed Oct 26 23:16:57 2016 
+#> Date of summary: Wed Oct 26 23:16:57 2016 
 #> 
 #> Equations:
 #> d_parent = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.079 s
+#> Fitted with method Port using 35 model solutions performed in 0.089 s
 #> 
 #> Weighting: none
 #> 
@@ -212,7 +214,18 @@
 #>   118   parent     0.39     1.351  -0.9613
 #> 

   

-  

+  
 
       

-      
Built by pkgdown. Styled with Bootstrap 3.

+      

+  
Developed by Johannes Ranke, Eurofins Regulatory AG.

+

+
+

+  
Site built with pkgdown.

+

+
       

    

 
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 04550199..b45c07fc 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -6,14 +6,14 @@
 
 
 
-synthetic_data_for_UBA_2014. mkin
+
+ — synthetic_data_for_UBA_2014 • mkin
 
 
 
-
 
-
 
+
 
 
 
@@ -22,6 +22,7 @@
 
 
 
+
 
 
 
@@ -34,10 +35,9 @@
   
 
   
-    

+    

       

-      
-

 
-      

-  

+      

+  

+    

+    

 

-

+    

 
-

-  

     
     
The 12 datasets were generated using four different models and three different
  variance components. The four models are either the SFO or the DFOP model with either
@@ -99,28 +101,28 @@
 
     
synthetic_data_for_UBA_2014

         
-    

-      
Format

+    
Format

 
-      
A list containing datasets in the form internally used by the 'gmkin' package.
+    
A list containing datasets in the form internally used by the 'gmkin' package.
   The list has twelfe components. Each of the components is one dataset that has,
   among others, the following components
   

     
title
The name of the dataset, e.g. SFO_lin_a

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

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

   

-    

-
-    

-      
Source

+    
+    
Source

 
-      
Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative
+    
Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative
   zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452

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

-    

     
-    
Examples

+
+    

+      
+      Examples
+    

     
## Not run: ------------------------------------
 # m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
 #                            M1 = list(type = "SFO", to = "M2"),
@@ -144,12 +146,29 @@
 # mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data)
 ## ---------------------------------------------

   

-  

+  
 

 
       

-      
Built by pkgdown. Styled with Bootstrap 3.

+      

+  
Developed by Johannes Ranke, Eurofins Regulatory AG.

+

+
+

+  
Site built with pkgdown.

+

+
       

    

 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 66253bba..a07be0a0 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -6,14 +6,14 @@
 
 
 
-transform_odeparms. mkin
+
+ — transform_odeparms • mkin
 
 
 
-
 
-
 
+
 
 
 
@@ -22,6 +22,7 @@
 
 
 
+
 
 
 
@@ -34,10 +35,9 @@
   
 
   
-    

+    

       

-      
-

 
-      

-  

+      

+  

+    

+    

 

-

+    

 
-

-  

     
     
The transformations are intended to map parameters that should only take 
   on restricted values to the full scale of real numbers. For kinetic rate
   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.

+  negative, the ilr transformation is used.

 
     
The transformation of sets of formation fractions is fragile, as it supposes
   the same ordering of the components in forward and backward transformation.
-  This is no problem for the internal use in mkinfit.

+  This is no problem for the internal use in mkinfit.

     
 
     
transform_odeparms(parms, mkinmod,
@@ -95,7 +97,7 @@
 backtransform_odeparms(transparms, mkinmod,
                        transform_rates = TRUE, transform_fractions = TRUE)

     
-    
Arguments

+    
 Arguments

     

       
parms

       

@@ -107,9 +109,9 @@
   

       
mkinmod

       

-    The kinetic model of class mkinmod, containing the names of
+    The kinetic model of class mkinmod, containing the names of
     the model variables that are needed for grouping the formation fractions
-    before ilr transformation, the parameter names and 
+    before ilr transformation, the parameter names and 
     the information if the pathway to sink is included in the model. 
   

       
transform_rates

@@ -128,27 +130,29 @@
     assumption of normal distribution of the estimator. The default (TRUE) is 
     to do transformations. The g parameter of the DFOP and HS models are also 
     transformed, as they can also be seen as compositional data. The
-    transformation used for these transformations is the ilr
+    transformation used for these transformations is the ilr
     transformation.
   
     

     
-    

-      
Value

+    
Value

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

-    

     
-    
Examples

-    
SFO_SFO <- mkinmod(
+
+    

+      
+      Examples
+    

+    
SFO_SFO <- mkinmod(
   parent = list(type = "SFO", to = "m1", sink = TRUE),
   m1 = list(type = "SFO"))
Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
-fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.1 
-#> Date of fit:     Thu Oct  6 10:47:45 2016 
-#> Date of summary: Thu Oct  6 10:47:45 2016 
+#> Date of fit:     Wed Oct 26 23:16:59 2016 
+#> Date of summary: Wed Oct 26 23:16:59 2016 
 #> 
 #> Equations:
 #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -156,7 +160,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.638 s
+#> Fitted with method Port using 153 model solutions performed in 0.721 s
 #> 
 #> Weighting: none
 #> 
@@ -259,7 +263,16 @@
 # summary(fit.ff.2, data = FALSE)
 ## ---------------------------------------------

   

-  

+  
 
       
    

 
-- 
cgit v1.2.1