From 8b7edd4eaf0d196e674a085f744d1a69260a6c91 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Nov 2023 06:02:05 +0100 Subject: Update pkgdown docs to bootstrap 5 with search --- docs/reference/AIC.mmkin.html | 195 ++-- docs/reference/CAKE_export.html | 191 ++-- docs/reference/D24_2014.html | 194 ++-- docs/reference/DFOP.solution-1.png | Bin 31230 -> 31964 bytes docs/reference/DFOP.solution.html | 199 ++-- docs/reference/Extract.mmkin.html | 194 ++-- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 190 ++-- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 190 ++-- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 190 ++-- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 190 ++-- docs/reference/FOCUS_2006_datasets.html | 186 ++-- docs/reference/FOMC.solution-1.png | Bin 29016 -> 29520 bytes docs/reference/FOMC.solution.html | 207 ++-- docs/reference/HS.solution-1.png | Bin 29376 -> 29572 bytes docs/reference/HS.solution.html | 199 ++-- docs/reference/IORE.solution-1.png | Bin 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docs/reference/summary_listing.html | 183 ++-- docs/reference/synthetic_data_for_UBA_2014-1.png | Bin 67454 -> 67638 bytes docs/reference/synthetic_data_for_UBA_2014.html | 209 ++-- docs/reference/test_data_from_UBA_2014-1.png | Bin 57306 -> 56257 bytes docs/reference/test_data_from_UBA_2014-2.png | Bin 72597 -> 73864 bytes docs/reference/test_data_from_UBA_2014.html | 187 ++-- docs/reference/transform_odeparms.html | 201 ++-- docs/reference/update.mkinfit-1.png | Bin 42522 -> 44071 bytes docs/reference/update.mkinfit-2.png | Bin 43527 -> 43998 bytes docs/reference/update.mkinfit.html | 189 ++-- 161 files changed, 7500 insertions(+), 10354 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index 78296f28..ede8eb3d 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -1,120 +1,87 @@ -Calculate the AIC for a column of an mmkin object — AIC.mmkin • mkinCalculate the AIC for a column of an mmkin object — AIC.mmkin • mkin + + Skip to contents -
-
-
-
-

Calculate the AIC for a column of an mmkin object

- Source: R/AIC.mmkin.R - +
+ + +
+
+
+
+

Calculate the AIC for a column of an mmkin object

+ Source: R/AIC.mmkin.R +
AIC.mmkin.Rd
-
+

Provides a convenient way to compare different kinetic models fitted to the same dataset.

-
+
+

Usage

# S3 method for mmkin
 AIC(object, ..., k = 2)
 
@@ -122,8 +89,8 @@ same dataset.

 BIC(object, ...)
-
-

Arguments

+
+

Arguments

object

An object of class mmkin, containing only one column.

@@ -137,20 +104,20 @@ column.

As in the generic method

-
-

Value

+
+

Value

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

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


    # skip, as it takes > 10 s on winbuilder
   f <- mmkin(c("SFO", "FOMC", "DFOP"),
@@ -199,26 +166,22 @@ dataframe if there are several fits in the column).
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index 92cb2755..a9aac1ef 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -1,120 +1,87 @@ -Export a list of datasets format to a CAKE study file — CAKE_export • mkinExport a list of datasets format to a CAKE study file — CAKE_export • mkin + + Skip to contents -
-
-
-
-

Export a list of datasets format to a CAKE study file

- Source: R/CAKE_export.R - +
+ + +
+
+
+
+

Export a list of datasets format to a CAKE study file

+ Source: R/CAKE_export.R +
CAKE_export.Rd
-
+

In addition to the datasets, the pathways in the degradation model can be specified as well.

-
+
+

Usage

CAKE_export(
   ds,
   map = c(parent = "Parent"),
@@ -132,8 +99,8 @@ specified as well.

 )
-
-

Arguments

+
+

Arguments

ds

A named list of datasets in long format as compatible with mkinfit.

@@ -191,37 +158,33 @@ compatible with CAKE.

Can be OLS or IRLS.

-
-

Value

+
+

Value

The function is called for its side effect.

-
-

Author

+
+

Author

Johannes Ranke

-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/D24_2014.html b/docs/reference/D24_2014.html index 1e35e864..075321c0 100644 --- a/docs/reference/D24_2014.html +++ b/docs/reference/D24_2014.html @@ -1,5 +1,10 @@ -Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014 • mkinAerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014 • mkin + + Skip to contents -
-
-
-
-

Aerobic soil degradation data on 2,4-D from the EU assessment in 2014

- Source: R/D24_2014.R - + +
+
+
+
+

Aerobic soil degradation data on 2,4-D from the EU assessment in 2014

+ Source: R/D24_2014.R +
D24_2014.Rd
-
+

The five datasets were extracted from the active substance evaluation dossier published by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate and advance kinetic modelling. The fact that these data and @@ -119,23 +92,24 @@ context of pesticide registrations, as the use of the data may be constrained by data protection regulations.

-
+
+

Usage

D24_2014
-
-

Format

+
+

Format

An mkindsg object grouping five datasets

-
-

Source

+
+

Source

Hellenic Ministry of Rural Development and Agriculture (2014) Final addendum to the Renewal Assessment Report - public version - 2,4-D Volume 3 Annex B.8 Fate and behaviour in the environment https://open.efsa.europa.eu/study-inventory/EFSA-Q-2013-00811

-
-

Details

+
+

Details

Data for the first dataset are from p. 685. Data for the other four datasets were used in the preprocessed versions given in the kinetics section (p. 761ff.), with the exception of residues smaller than 1 for DCP @@ -145,8 +119,8 @@ in the 'dataset_generation' directory. In the code, page numbers are given for specific pieces of information in the comments.

-
-

Examples

+
+

Examples

print(D24_2014)
 #> <mkindsg> holding 5 mkinds objects
 #> Title $title:  Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 
@@ -235,26 +209,22 @@ specific pieces of information in the comments.

 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/DFOP.solution-1.png b/docs/reference/DFOP.solution-1.png index 5ebba336..6b78836f 100644 Binary files a/docs/reference/DFOP.solution-1.png and b/docs/reference/DFOP.solution-1.png differ diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index b526ac9e..62b78f3e 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -1,125 +1,92 @@ -Double First-Order in Parallel kinetics — DFOP.solution • mkinDouble First-Order in Parallel kinetics — DFOP.solution • mkin + + Skip to contents -
-
-
-
-

Double First-Order in Parallel kinetics

- Source: R/parent_solutions.R - +
+ + +
+
+
+
+

Double First-Order in Parallel kinetics

+ Source: R/parent_solutions.R +
DFOP.solution.Rd
-
+

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

-
+
+

Usage

DFOP.solution(t, parent_0, k1, k2, g)
-
-

Arguments

+
+

Arguments

t

Time.

@@ -141,14 +108,14 @@ two exponential decline functions.

kinetic constant.

-
-

Value

+
+

Value

The value of the response variable at time t.

-
-

References

+
+

References

FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -160,8 +127,8 @@ EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

-
-

See also

+
+

See also

Other parent solutions: FOMC.solution(), HS.solution(), @@ -171,34 +138,30 @@ Version 1.1, 18 December 2014 logistic.solution()

-
-

Examples

+
+

Examples


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

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 76a2cda8..35825b88 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -1,124 +1,90 @@ -Subsetting method for mmkin objects — [.mmkin • mkinSubsetting method for mmkin objects — [.mmkin • mkin + + Skip to contents -
-
-
-
-

Subsetting method for mmkin objects

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

Subsetting method for mmkin objects

+ Source: R/mmkin.R +
Extract.mmkin.Rd
-
+

Subsetting method for mmkin objects

-
+
+

Usage

# S3 method for mmkin
 [(x, i, j, ..., drop = FALSE)
-
-

Arguments

+
+

Arguments

x

An mmkin object

@@ -140,19 +106,19 @@ either a list of mkinfit objects or a single mkinfit object.

-
-

Value

+
+

Value

An object of class mmkin.

-
-

Author

+
+

Author

Johannes Ranke

-
-

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),
@@ -212,26 +178,22 @@ either a list of mkinfit objects or a single mkinfit object.

 #>
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- 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 2483a632..62059414 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -1,118 +1,87 @@ -Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkinResults of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin + + Skip to contents -
-
-
-
-

Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)

- +
+
+
+
+

Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)

+ +
FOCUS_2006_DFOP_ref_A_to_B.Rd
-
+

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 @@ -120,12 +89,13 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.

-
+
+

Usage

FOCUS_2006_DFOP_ref_A_to_B
-
-

Format

+
+

Format

A data frame containing the following variables.

package

a factor giving the name of the software package

@@ -152,8 +122,8 @@ in this fit.

-
-

Source

+
+

Source

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, @@ -161,31 +131,27 @@ in this fit.

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

-
-

Examples

+
+

Examples

data(FOCUS_2006_DFOP_ref_A_to_B)
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- 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 d3ee5aba..3aca90d2 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -1,118 +1,87 @@ -Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkinResults of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin + + Skip to contents -
-
-
-
-

Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)

- +
+
+
+
+

Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)

+ +
FOCUS_2006_FOMC_ref_A_to_F.Rd
-
+

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 @@ -120,12 +89,13 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.

-
+
+

Usage

FOCUS_2006_FOMC_ref_A_to_F
-
-

Format

+
+

Format

A data frame containing the following variables.

package

a factor giving the name of the software package

@@ -149,8 +119,8 @@ in this fit.

-
-

Source

+
+

Source

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, @@ -158,31 +128,27 @@ in this fit.

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

-
-

Examples

+
+

Examples

data(FOCUS_2006_FOMC_ref_A_to_F)
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- 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 cb563cdf..d7e0d269 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -1,118 +1,87 @@ -Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F • mkinResults of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F • mkin + + Skip to contents -
-
-
-
-

Results of fitting the HS model to Datasets A to F of FOCUS (2006)

- +
+
+
+
+

Results of fitting the HS model to Datasets A to F of FOCUS (2006)

+ +
FOCUS_2006_HS_ref_A_to_F.Rd
-
+

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 @@ -120,12 +89,13 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.

-
+
+

Usage

FOCUS_2006_HS_ref_A_to_F
-
-

Format

+
+

Format

A data frame containing the following variables.

package

a factor giving the name of the software package

@@ -152,8 +122,8 @@ in this fit.

-
-

Source

+
+

Source

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, @@ -161,31 +131,27 @@ in this fit.

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

-
-

Examples

+
+

Examples

data(FOCUS_2006_HS_ref_A_to_F)
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- 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 93fc9030..b92d94d4 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -1,118 +1,87 @@ -Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F • mkinResults of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F • mkin + + Skip to contents -
-
-
-
-

Results of fitting the SFO model to Datasets A to F of FOCUS (2006)

- +
+
+
+
+

Results of fitting the SFO model to Datasets A to F of FOCUS (2006)

+ +
FOCUS_2006_SFO_ref_A_to_F.Rd
-
+

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 @@ -120,12 +89,13 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.

-
+
+

Usage

FOCUS_2006_SFO_ref_A_to_F
-
-

Format

+
+

Format

A data frame containing the following variables.

package

a factor giving the name of the software package

@@ -146,8 +116,8 @@ in this fit.

-
-

Source

+
+

Source

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, @@ -155,31 +125,27 @@ in this fit.

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

-
-

Examples

+
+

Examples

data(FOCUS_2006_SFO_ref_A_to_F)
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index f1343c5c..72d9c7db 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -1,118 +1,84 @@ -Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets • mkinDatasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets • mkin + + Skip to contents -
-
-
-
-

Datasets A to F from the FOCUS Kinetics report from 2006

- +
+
+
+
+

Datasets A to F from the FOCUS Kinetics report from 2006

+ +
FOCUS_2006_datasets.Rd
-
+

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

-
+
+

Usage

FOCUS_2006_A
   FOCUS_2006_B
   FOCUS_2006_C
@@ -121,8 +87,8 @@
   FOCUS_2006_F
-
-

Format

+
+

Format

6 datasets with observations on the following variables.

name

a factor containing the name of the observed variable

@@ -134,8 +100,8 @@
-
-

Source

+
+

Source

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, @@ -143,8 +109,8 @@ http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

-
-

Examples

+
+

Examples

FOCUS_2006_C
 #>     name time value
 #> 1 parent    0  85.1
@@ -158,26 +124,22 @@
 #> 9 parent  119   0.6
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/FOMC.solution-1.png b/docs/reference/FOMC.solution-1.png index 9d222d42..18a4b586 100644 Binary files a/docs/reference/FOMC.solution-1.png and b/docs/reference/FOMC.solution-1.png differ diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index e5087117..2f668032 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -1,125 +1,92 @@ -First-Order Multi-Compartment kinetics — FOMC.solution • mkinFirst-Order Multi-Compartment kinetics — FOMC.solution • mkin + + Skip to contents -
-
-
-
-

First-Order Multi-Compartment kinetics

- Source: R/parent_solutions.R - +
+ + +
+
+
+
+

First-Order Multi-Compartment kinetics

+ Source: R/parent_solutions.R +
FOMC.solution.Rd
-
+

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

-
+
+

Usage

FOMC.solution(t, parent_0, alpha, beta)
-
-

Arguments

+
+

Arguments

t

Time.

@@ -137,26 +104,26 @@ constant values.

Location parameter.

-
-

Value

+
+

Value

The value of the response variable at time t.

-
-

Details

+
+

Details

The form given here differs slightly from the original reference by Gustafson and Holden (1990). The parameter beta corresponds to 1/beta in the original equation.

-
-

Note

+
+

Note

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

-
-

References

+
+

References

FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -171,8 +138,8 @@ Version 1.1, 18 December 2014 A new model based on spatial variability. Environmental Science and Technology 24, 1032-1038

-
-

See also

+
+

See also

Other parent solutions: DFOP.solution(), HS.solution(), @@ -182,34 +149,30 @@ Technology 24, 1032-1038

logistic.solution()

-
-

Examples

+
+

Examples


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

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/HS.solution-1.png b/docs/reference/HS.solution-1.png index dd7a76c8..61d89dbc 100644 Binary files a/docs/reference/HS.solution-1.png and b/docs/reference/HS.solution-1.png differ diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index d24015a0..d7f339b7 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -1,125 +1,92 @@ -Hockey-Stick kinetics — HS.solution • mkinHockey-Stick kinetics — HS.solution • mkin + + Skip to contents -
-
-
-
-

Hockey-Stick kinetics

- Source: R/parent_solutions.R - +
+ + +
+
+
+
+

Hockey-Stick kinetics

+ Source: R/parent_solutions.R +
HS.solution.Rd
-
+

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

-
+
+

Usage

HS.solution(t, parent_0, k1, k2, tb)
-
-

Arguments

+
+

Arguments

t

Time.

@@ -142,14 +109,14 @@ between them.

according to k2.

-
-

Value

+
+

Value

The value of the response variable at time t.

-
-

References

+
+

References

FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -161,8 +128,8 @@ EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

-
-

See also

+
+

See also

Other parent solutions: DFOP.solution(), FOMC.solution(), @@ -172,34 +139,30 @@ Version 1.1, 18 December 2014 logistic.solution()

-
-

Examples

+
+

Examples


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

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/IORE.solution-1.png b/docs/reference/IORE.solution-1.png index 9b6ab58f..54c9dcae 100644 Binary files a/docs/reference/IORE.solution-1.png and b/docs/reference/IORE.solution-1.png differ diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 0ab484cd..24bf2e20 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -1,125 +1,92 @@ -Indeterminate order rate equation kinetics — IORE.solution • mkinIndeterminate order rate equation kinetics — IORE.solution • mkin + + Skip to contents -
-
-
-
-

Indeterminate order rate equation kinetics

- Source: R/parent_solutions.R - +
+ + +
+
+
+
+

Indeterminate order rate equation kinetics

+ Source: R/parent_solutions.R +
IORE.solution.Rd
-
+

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

-
+
+

Usage

IORE.solution(t, parent_0, k__iore, N)
-
-

Arguments

+
+

Arguments

t

Time.

@@ -137,26 +104,26 @@ units used.

Exponent describing the nonlinearity of the rate equation

-
-

Value

+
+

Value

The value of the response variable at time t.

-
-

Note

+
+

Note

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

-
-

References

+
+

References

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

-
-

See also

+
+

See also

Other parent solutions: DFOP.solution(), FOMC.solution(), @@ -166,8 +133,8 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media

logistic.solution()

-
-

Examples

+
+

Examples


   plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2, ylim = c(0, 100))
 
@@ -195,26 +162,22 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/NAFTA_SOP_2015-1.png b/docs/reference/NAFTA_SOP_2015-1.png index 5d2d434b..98d4246c 100644 Binary files a/docs/reference/NAFTA_SOP_2015-1.png and b/docs/reference/NAFTA_SOP_2015-1.png differ diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 9a4f668e..a1888fdf 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -1,124 +1,90 @@ -Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015 • mkinExample datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015 • mkin + + Skip to contents -
-
-
-
-

Example datasets from the NAFTA SOP published 2015

- +
+
+
+
+

Example datasets from the NAFTA SOP published 2015

+ +
NAFTA_SOP_2015.Rd
-
+

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

-
+
+

Usage

NAFTA_SOP_Appendix_B
   NAFTA_SOP_Appendix_D
-
-

Format

+
+

Format

2 datasets with observations on the following variables.

name

a factor containing the name of the observed variable

@@ -130,8 +96,8 @@
-
-

Source

+
+

Source

NAFTA (2011) Guidance for evaluating and calculating degradation kinetics in environmental media. NAFTA Technical Working Group on Pesticides https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation @@ -142,8 +108,8 @@ https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance

-
-

Examples

+
+

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
@@ -192,26 +158,22 @@
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/NAFTA_SOP_Attachment-1.png b/docs/reference/NAFTA_SOP_Attachment-1.png index d8951fc3..a6066441 100644 Binary files a/docs/reference/NAFTA_SOP_Attachment-1.png and b/docs/reference/NAFTA_SOP_Attachment-1.png differ diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index 02b33e7d..caca03f5 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -1,128 +1,94 @@ -Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment • mkinExample datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment • mkin + + Skip to contents -
-
-
-
-

Example datasets from Attachment 1 to the NAFTA SOP published 2015

- +
+
+
+
+

Example datasets from Attachment 1 to the NAFTA SOP published 2015

+ +
NAFTA_SOP_Attachment.Rd
-
+

Data taken from from Attachment 1 of the SOP.

-
+
+

Usage

NAFTA_SOP_Attachment
-
-

Format

+
+

Format

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

-
-

Source

+
+

Source

NAFTA (2011) Guidance for evaluating and calculating degradation kinetics in environmental media. NAFTA Technical Working Group on Pesticides https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation @@ -133,8 +99,8 @@ https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance

-
-

Examples

+
+

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
@@ -181,26 +147,22 @@
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png index ca982688..5de2bdc7 100644 Binary files a/docs/reference/Rplot001.png and b/docs/reference/Rplot001.png differ diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png index de2d61aa..556ca0a7 100644 Binary files a/docs/reference/Rplot002.png and b/docs/reference/Rplot002.png differ diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png index 8fd02b8e..b50287c2 100644 Binary files a/docs/reference/Rplot003.png and b/docs/reference/Rplot003.png differ diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png index 2c12ceb1..d5fef0f0 100644 Binary files a/docs/reference/Rplot004.png and b/docs/reference/Rplot004.png differ diff --git a/docs/reference/Rplot005.png b/docs/reference/Rplot005.png index 1d28b587..7274c79d 100644 Binary files a/docs/reference/Rplot005.png and b/docs/reference/Rplot005.png differ diff --git a/docs/reference/Rplot006.png b/docs/reference/Rplot006.png index 48f5bbd8..f646fa66 100644 Binary files a/docs/reference/Rplot006.png and b/docs/reference/Rplot006.png differ diff --git a/docs/reference/Rplot007.png b/docs/reference/Rplot007.png index 21a6ea76..d3b6ddd4 100644 Binary files a/docs/reference/Rplot007.png and b/docs/reference/Rplot007.png differ diff --git a/docs/reference/SFO.solution-1.png b/docs/reference/SFO.solution-1.png index a00499cb..34fdd460 100644 Binary files a/docs/reference/SFO.solution-1.png and b/docs/reference/SFO.solution-1.png differ diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 67c7abc7..7bf78114 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -1,123 +1,89 @@ -Single First-Order kinetics — SFO.solution • mkinSingle First-Order kinetics — SFO.solution • mkin + + Skip to contents -
-
-
-
-

Single First-Order kinetics

- Source: R/parent_solutions.R - +
+ + +
+
+
+
+

Single First-Order kinetics

+ Source: R/parent_solutions.R +
SFO.solution.Rd
-
+

Function describing exponential decline from a defined starting value.

-
+
+

Usage

SFO.solution(t, parent_0, k)
-
-

Arguments

+
+

Arguments

t

Time.

@@ -130,14 +96,14 @@

Kinetic rate constant.

-
-

Value

+
+

Value

The value of the response variable at time t.

-
-

References

+
+

References

FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -149,8 +115,8 @@ EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

-
-

See also

+
+

See also

Other parent solutions: DFOP.solution(), FOMC.solution(), @@ -160,34 +126,30 @@ Version 1.1, 18 December 2014 logistic.solution()

-
-

Examples

+
+

Examples


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

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/SFORB.solution-1.png b/docs/reference/SFORB.solution-1.png index 7bea3b78..08d25616 100644 Binary files a/docs/reference/SFORB.solution-1.png and b/docs/reference/SFORB.solution-1.png differ diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index a99deac7..70ea8779 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -1,118 +1,87 @@ -Single First-Order Reversible Binding kinetics — SFORB.solution • mkinSingle First-Order Reversible Binding kinetics — SFORB.solution • mkin + + Skip to contents -
-
-
-
-

Single First-Order Reversible Binding kinetics

- Source: R/parent_solutions.R - +
+ + +
+
+
+
+

Single First-Order Reversible Binding kinetics

+ Source: R/parent_solutions.R +
SFORB.solution.Rd
-
+

Function describing the solution of the differential equations describing the kinetic model with first-order terms for a two-way transfer from a free to a bound fraction, and a first-order degradation term for the free @@ -120,12 +89,13 @@ fraction. The initial condition is a defined amount in the free fraction and no substance in the bound fraction.

-
+
+

Usage

SFORB.solution(t, parent_0, k_12, k_21, k_1output)
-
-

Arguments

+
+

Arguments

t

Time.

@@ -147,15 +117,15 @@ and no substance in the bound fraction.

fraction.

-
-

Value

+
+

Value

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 Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -167,8 +137,8 @@ EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

-
-

See also

+
+

See also

Other parent solutions: DFOP.solution(), FOMC.solution(), @@ -178,34 +148,30 @@ Version 1.1, 18 December 2014 logistic.solution()

-
-

Examples

+
+

Examples


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

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png index 4a3b4062..68cfb344 100644 Binary files a/docs/reference/add_err-1.png and b/docs/reference/add_err-1.png differ diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png index 5aec1744..d2f0cf08 100644 Binary files a/docs/reference/add_err-2.png and b/docs/reference/add_err-2.png differ diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png index 2e71f02f..17b5416a 100644 Binary files a/docs/reference/add_err-3.png and b/docs/reference/add_err-3.png differ diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 4db51d10..ea29115c 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -1,122 +1,90 @@ -Add normally distributed errors to simulated kinetic degradation data — add_err • mkinAdd normally distributed errors to simulated kinetic degradation data — add_err • mkin + + Skip to contents -
-
-
-
-

Add normally distributed errors to simulated kinetic degradation data

- Source: R/add_err.R - +
+ + +
+
+
+
+

Add normally distributed errors to simulated kinetic degradation data

+ Source: R/add_err.R +
add_err.Rd
-
+

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

-
+
+

Usage

add_err(
   prediction,
   sdfunc,
@@ -129,8 +97,8 @@ may depend on the predicted value and is specified as a standard deviation.

 )
-
-

Arguments

+
+

Arguments

prediction

A prediction from a kinetic model as produced by mkinpredict.

@@ -169,27 +137,27 @@ adding the random error will be set to NA.

seed is not set.

-
-

Value

+
+

Value

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

-
-

References

+
+

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 https://jrwb.de/posters/piacenza_2015.pdf

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


 # The kinetic model
 m_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
@@ -239,26 +207,22 @@ https://jrwb.de/posters/piacenza_2015.pdf
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/anova.saem.mmkin.html b/docs/reference/anova.saem.mmkin.html index 03ca588d..a514800a 100644 --- a/docs/reference/anova.saem.mmkin.html +++ b/docs/reference/anova.saem.mmkin.html @@ -1,124 +1,93 @@ -Anova method for saem.mmkin objects — anova.saem.mmkin • mkinAnova method for saem.mmkin objects — anova.saem.mmkin • mkin + + Skip to contents -
-
-
-
-

Anova method for saem.mmkin objects

- Source: R/anova.saem.mmkin.R - +
+ + +
+
+
+
+

Anova method for saem.mmkin objects

+ Source: R/anova.saem.mmkin.R +
anova.saem.mmkin.Rd
-
+

Generate an anova object. The method to calculate the BIC is that from the saemix package. As in other prominent anova methods, models are sorted by number of parameters, and the tests (if requested) are always relative to the model on the previous line.

-
+
+

Usage

# S3 method for saem.mmkin
 anova(
   object,
@@ -129,8 +98,8 @@ the model on the previous line.

 )
-
-

Arguments

+
+

Arguments

object

An saem.mmkin object

@@ -155,33 +124,29 @@ only be done for nested models.

Optional character vector of model names

-
-

Value

+
+

Value

an "anova" data frame; the traditional (S3) result of anova()

-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/aw.html b/docs/reference/aw.html index 5740d67d..953d9e22 100644 --- a/docs/reference/aw.html +++ b/docs/reference/aw.html @@ -1,122 +1,90 @@ -Calculate Akaike weights for model averaging — aw • mkinCalculate Akaike weights for model averaging — aw • mkin + + Skip to contents -
-
-
-
-

Calculate Akaike weights for model averaging

- Source: R/aw.R - +
+ + +
+
+
+
+

Calculate Akaike weights for model averaging

+ Source: R/aw.R +
aw.Rd
-
+

Akaike weights are calculated based on the relative expected Kullback-Leibler information as specified by Burnham and Anderson (2004).

-
+
+

Usage

aw(object, ...)
 
 # S3 method for mkinfit
@@ -132,8 +100,8 @@ by Burnham and Anderson (2004).

 aw(object, ...)
-
-

Arguments

+
+

Arguments

object

An mmkin column object, containing two or more mkinfit models that have been fitted to the same data, @@ -147,15 +115,15 @@ as dots arguments.

further mkinfit objects in the method for mkinfit objects.

-
-

References

+
+

References

Burnham KP and Anderson DR (2004) Multimodel Inference: Understanding AIC and BIC in Model Selection. Sociological Methods & Research 33(2) 261-304

-
-

Examples

+
+

Examples

# \dontrun{
 f_sfo <- mkinfit("SFO", FOCUS_2006_D, quiet = TRUE)
 f_dfop <- mkinfit("DFOP", FOCUS_2006_D, quiet = TRUE)
@@ -174,26 +142,22 @@ Inference: Understanding AIC and BIC in Model Selection.
 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 48240abc..4d4fa012 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -1,5 +1,12 @@ -Confidence intervals for parameters of mkinfit objects — confint.mkinfit • mkinConfidence intervals for parameters of mkinfit objects — confint.mkinfit • mkin + + Skip to contents -
-
-
-
-

Confidence intervals for parameters of mkinfit objects

- Source: R/confint.mkinfit.R - +
+ + +
+
+
+
+

Confidence intervals for parameters of mkinfit objects

+ Source: R/confint.mkinfit.R +
confint.mkinfit.Rd
-
+

The default method 'quadratic' is based on the quadratic approximation of the curvature of the likelihood function at the maximum likelihood parameter estimates. @@ -126,7 +98,8 @@ platforms. The speed of the method could likely be improved by using the method of Venzon and Moolgavkar (1988).

-
+
+

Usage

# S3 method for mkinfit
 confint(
   object,
@@ -144,8 +117,8 @@ method of Venzon and Moolgavkar (1988).

 )
-
-

Arguments

+
+

Arguments

object

An mkinfit object

@@ -207,15 +180,15 @@ the quadratic method?

Not used

-
-

Value

+
+

Value

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

-
-

References

+
+

References

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

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

@@ -224,8 +197,8 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, 87–94.

-
-

Examples

+
+

Examples

f <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE)
 confint(f, method = "quadratic")
 #>                2.5%      97.5%
@@ -257,7 +230,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
 f_d_1 <- mkinfit(SFO_SFO, subset(FOCUS_2006_D, value != 0), quiet = TRUE)
 system.time(ci_profile <- confint(f_d_1, method = "profile", cores = 1, quiet = TRUE))
 #>    user  system elapsed 
-#>   2.578   0.005   2.599 
+#>   1.203   0.000   1.203 
 # Using more cores does not save much time here, as parent_0 takes up most of the time
 # If we additionally exclude parent_0 (the confidence of which is often of
 # minor interest), we get a nice performance improvement if we use at least 4 cores
@@ -265,7 +238,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
   c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores))
 #> Profiling the likelihood
 #>    user  system elapsed 
-#>   0.963   0.255   0.636 
+#>   0.438   0.097   0.301 
 ci_profile
 #>                       2.5%        97.5%
 #> parent_0      96.456003640 1.027703e+02
@@ -400,26 +373,22 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,
 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html index bf02afe3..c2b609f7 100644 --- a/docs/reference/create_deg_func.html +++ b/docs/reference/create_deg_func.html @@ -1,123 +1,89 @@ -Create degradation functions for known analytical solutions — create_deg_func • mkinCreate degradation functions for known analytical solutions — create_deg_func • mkin + + Skip to contents -
-
-
-
-

Create degradation functions for known analytical solutions

- Source: R/create_deg_func.R - +
+ + +
+
+
+
+

Create degradation functions for known analytical solutions

+ Source: R/create_deg_func.R +
create_deg_func.Rd
-
+

Create degradation functions for known analytical solutions

-
+
+

Usage

create_deg_func(spec, use_of_ff = c("min", "max"))
-
-

Arguments

+
+

Arguments

spec

List of model specifications as contained in mkinmod objects

@@ -126,15 +92,15 @@

Minimum or maximum use of formation fractions

-
-

Value

+
+

Value

Degradation function to be attached to mkinmod objects

-
-

Examples

+
+

Examples


 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
@@ -151,8 +117,8 @@
     replications = 2)
 #> Loading required package: rbenchmark
 #>         test replications elapsed relative user.self sys.self user.child
-#> 1 analytical            2   0.421    1.000     0.412    0.000          0
-#> 2    deSolve            2   0.601    1.428     0.566    0.024          0
+#> 1 analytical            2   0.233    1.000     0.232    0.001          0
+#> 2    deSolve            2   0.293    1.258     0.293    0.000          0
 #>   sys.child
 #> 1         0
 #> 2         0
@@ -165,34 +131,30 @@
     deSolve = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE),
     replications = 2)
 #>         test replications elapsed relative user.self sys.self user.child
-#> 1 analytical            2   0.762    1.000     0.758    0.004          0
-#> 2    deSolve            2   1.194    1.567     1.140    0.052          0
+#> 1 analytical            2   0.375    1.000     0.375        0          0
+#> 2    deSolve            2   0.508    1.355     0.508        0          0
 #>   sys.child
 #> 1         0
 #> 2         0
 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index 961b28d2..71f1f5d1 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -1,5 +1,10 @@ -Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 — dimethenamid_2018 • mkinAerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 — dimethenamid_2018 • mkin + + Skip to contents -
-
-
-
-

Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018

- Source: R/dimethenamid_2018.R - + +
+
+
+
+

Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018

+ Source: R/dimethenamid_2018.R +
dimethenamid_2018.Rd
-
+

The datasets were extracted from the active substance evaluation dossier published by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate and advance kinetic modelling. The fact that these data and @@ -119,30 +92,31 @@ context of pesticide registrations, as the use of the data may be constrained by data protection regulations.

-
+
+

Usage

dimethenamid_2018
-
-

Format

+
+

Format

An mkindsg object grouping seven datasets with some meta information

-
-

Source

+
+

Source

Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria (2018) Renewal Assessment Report Dimethenamid-P Volume 3 - B.8 Environmental fate and behaviour Rev. 2 - November 2017 https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716

-
-

Details

+
+

Details

The R code used to create this data object is installed with this package in the 'dataset_generation' directory. In the code, page numbers are given for specific pieces of information in the comments.

-
-

Examples

+
+

Examples

print(dimethenamid_2018)
 #> <mkindsg> holding 7 mkinds objects
 #> Title $title:  Aerobic soil degradation data on dimethenamid-P from the EU assessment in 2018 
@@ -222,10 +196,10 @@ specific pieces of information in the comments.

 #saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")
 summary(f_dmta_saem_tc)
 #> saemix version used for fitting:      3.2 
-#> mkin version used for pre-fitting:  1.2.5 
-#> R version used for fitting:         4.3.1 
-#> Date of fit:     Wed Aug  9 17:55:36 2023 
-#> Date of summary: Wed Aug  9 17:55:36 2023 
+#> mkin version used for pre-fitting:  1.2.6 
+#> R version used for fitting:         4.3.2 
+#> Date of fit:     Thu Nov 16 04:14:53 2023 
+#> Date of summary: Thu Nov 16 04:14:53 2023 
 #> 
 #> Equations:
 #> d_DMTA/dt = - k_DMTA * DMTA
@@ -238,7 +212,7 @@ specific pieces of information in the comments.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted in 796.123 s
+#> Fitted in 302.335 s
 #> Using 300, 100 iterations and 9 chains
 #> 
 #> Variance model: Two-component variance function 
@@ -364,26 +338,22 @@ specific pieces of information in the comments.

 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/ds_mixed-1.png b/docs/reference/ds_mixed-1.png index 053a7253..7b73613a 100644 Binary files a/docs/reference/ds_mixed-1.png and b/docs/reference/ds_mixed-1.png differ diff --git a/docs/reference/ds_mixed.html b/docs/reference/ds_mixed.html index fdf72593..10f58c11 100644 --- a/docs/reference/ds_mixed.html +++ b/docs/reference/ds_mixed.html @@ -1,123 +1,89 @@ -Synthetic data for hierarchical kinetic degradation models — ds_mixed • mkinSynthetic data for hierarchical kinetic degradation models — ds_mixed • mkin + + Skip to contents -
-
-
-
-

Synthetic data for hierarchical kinetic degradation models

- Source: R/ds_mixed.R - + +
+
+
+
+

Synthetic data for hierarchical kinetic degradation models

+ Source: R/ds_mixed.R +
ds_mixed.Rd
-
+

The R code used to create this data object is installed with this package in the 'dataset_generation' directory.

-
-

Examples

+
+

Examples

# \dontrun{
   sfo_mmkin <- mmkin("SFO", ds_sfo, quiet = TRUE, error_model = "tc", cores = 15)
   sfo_saem <- saem(sfo_mmkin, no_random_effect = "parent_0")
@@ -234,26 +200,21 @@ the 'dataset_generation' directory.

 #> #save(ds_sfo, ds_fomc, ds_dfop, ds_hs, ds_dfop_sfo, file = "data/ds_mixed.rda", version = 2)
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 4ce6a8ca..c6e216d9 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -1,6 +1,10 @@ -Function to calculate endpoints for further use from kinetic models fitted -with mkinfit — endpoints • mkinFunction to calculate endpoints for further use from kinetic models fitted +with mkinfit — endpoints • mkin + + Skip to contents -
-
-
-
-

Function to calculate endpoints for further use from kinetic models fitted + +

+
+
+
+

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

- Source: R/endpoints.R - + Source: R/endpoints.R +
endpoints.Rd
-
+

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, the Eigenvalues are returned. These @@ -123,12 +92,13 @@ are equivalent to the rate constants of the DFOP model, but with the advantage that the SFORB model can also be used for metabolites.

-
+
+

Usage

endpoints(fit, covariates = NULL, covariate_quantile = 0.5)
-
-

Arguments

+
+

Arguments

fit

An object of class mkinfit, nlme.mmkin or saem.mmkin, or another object that has list components mkinmod containing an mkinmod @@ -147,8 +117,8 @@ object has covariate models. If so, the default is to show endpoints for the median of the covariate values (50th percentile).

-
-

Value

+
+

Value

A list with a matrix of dissipation times named distimes, and, if @@ -156,23 +126,23 @@ applicable, a vector of formation fractions named ff and, if the SFORB model was in use, a vector of eigenvalues of these SFORB models, equivalent to DFOP rate constants

-
-

Details

+
+

Details

Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models

-
-

Note

+
+

Note

The function is used internally by summary.mkinfit, summary.nlme.mmkin and summary.saem.mmkin.

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


   fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
   endpoints(fit)
@@ -205,26 +175,22 @@ HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png index 4de80e3a..f0dfab85 100644 Binary files a/docs/reference/experimental_data_for_UBA-1.png and b/docs/reference/experimental_data_for_UBA-1.png differ diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index 6a02f430..8940bbc2 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -1,5 +1,33 @@ -Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019 • mkinExperimental datasets used for development and testing of error models — experimental_data_for_UBA_2019 • mkin + + Skip to contents -
-
-
-
-

Experimental datasets used for development and testing of error models

- +
+
+
+
+

Experimental datasets used for development and testing of error models

+ +
experimental_data_for_UBA.Rd
-
+

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 @@ -168,12 +161,13 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl (United Kingdom, 2014, p. 81).

-
+
+

Usage

experimental_data_for_UBA_2019
-
-

Format

+
+

Format

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

title

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

@@ -183,8 +177,8 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
-
-

Source

+
+

Source

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

@@ -206,8 +200,8 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl 1141/2010 for renewal of an active substance

-
-

Examples

+
+

Examples

# \dontrun{
 
 # Model definitions
@@ -252,26 +246,22 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/f_time_norm_focus.html b/docs/reference/f_time_norm_focus.html index ace7c028..8d177fe2 100644 --- a/docs/reference/f_time_norm_focus.html +++ b/docs/reference/f_time_norm_focus.html @@ -1,120 +1,87 @@ -Normalisation factors for aerobic soil degradation according to FOCUS guidance — f_time_norm_focus • mkinNormalisation factors for aerobic soil degradation according to FOCUS guidance — f_time_norm_focus • mkin + + Skip to contents -
-
-
-
-

Normalisation factors for aerobic soil degradation according to FOCUS guidance

- Source: R/f_time_norm_focus.R - +
+ + +
+
+
+
+

Normalisation factors for aerobic soil degradation according to FOCUS guidance

+ Source: R/f_time_norm_focus.R +
f_time_norm_focus.Rd
-
+

Time step normalisation factors for aerobic soil degradation as described in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369).

-
+
+

Usage

f_time_norm_focus(object, ...)
 
 # S3 method for numeric
@@ -140,8 +107,8 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369).

 )
-
-

Arguments

+
+

Arguments

object

An object containing information used for the calculations

@@ -183,8 +150,8 @@ to a reference moisture given in the meta information, otherwise the focus soil moisture for the soil class is used

-
-

References

+
+

References

FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -196,13 +163,13 @@ EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

-
-

See also

+
+

See also

focus_soil_moisture

-
-

Examples

+
+

Examples

f_time_norm_focus(25, 20, 25) # 1.37, compare FOCUS 2014 p. 184
 #> [1] 1.373956
 
@@ -225,26 +192,22 @@ Version 1.1, 18 December 2014
 #> $f_time_norm was (re)set to normalised values
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/focus_soil_moisture.html b/docs/reference/focus_soil_moisture.html index 4cb95b77..08721143 100644 --- a/docs/reference/focus_soil_moisture.html +++ b/docs/reference/focus_soil_moisture.html @@ -1,136 +1,103 @@ -FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar — focus_soil_moisture • mkinFOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar — focus_soil_moisture • mkin + + Skip to contents -
-
-
-
-

FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar

- Source: R/focus_soil_moisture.R - +
+ + +
+
+
+
+

FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar

+ Source: R/focus_soil_moisture.R +
focus_soil_moisture.Rd
-
+

The value were transcribed from p. 36. The table assumes field capacity corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5.

-
+
+

Usage

focus_soil_moisture
-
-

Format

+
+

Format

A matrix with upper case USDA soil classes as row names, and water tension ('pF1', 'pF2', 'pF 2.5') as column names

-
-

Source

+
+

Source

Anonymous (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessment Version 2.2, May 2014 https://esdac.jrc.ec.europa.eu/projects/ground-water

-
-

Examples

+
+

Examples

focus_soil_moisture
 #>                 pF1 pF2 pF2.5
 #> Sand             24  12     7
@@ -147,26 +114,22 @@ Version 2.2, May 2014 #> Clay             53  48    43
-
- -
+
-
- diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index 79c88c54..7f7e0e71 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -1,149 +1,111 @@ -Retrieve a degradation function from the mmkin namespace — get_deg_func • mkinRetrieve a degradation function from the mmkin namespace — get_deg_func • mkin + + Skip to contents -
-
-
-
-

Retrieve a degradation function from the mmkin namespace

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

Retrieve a degradation function from the mmkin namespace

+ Source: R/nlme.mmkin.R +
get_deg_func.Rd
-
+

Retrieve a degradation function from the mmkin namespace

-
+
+

Usage

get_deg_func()
-
-

Value

+
+

Value

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

-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/hierarchical_kinetics.html b/docs/reference/hierarchical_kinetics.html index ab0b3d04..5cc24e79 100644 --- a/docs/reference/hierarchical_kinetics.html +++ b/docs/reference/hierarchical_kinetics.html @@ -1,5 +1,12 @@ -Hierarchical kinetics template — hierarchical_kinetics • mkinHierarchical kinetics template — hierarchical_kinetics • mkin + + Skip to contents -
-
-
-
-

Hierarchical kinetics template

- Source: R/hierarchical_kinetics.R - +
+ + +
+
+
+
+

Hierarchical kinetics template

+ Source: R/hierarchical_kinetics.R +
hierarchical_kinetics.Rd
-
+

R markdown format for setting up hierarchical kinetics based on a template provided with the mkin package. This format is based on rmarkdown::pdf_document. Chunk options are adapted. Echoing R code from code chunks and caching are @@ -126,12 +98,13 @@ figures will not move around in the document, but stay where the user includes them.

-
+
+

Usage

hierarchical_kinetics(..., keep_tex = FALSE)
-
-

Arguments

+
+

Arguments

...

Arguments to rmarkdown::pdf_document

@@ -140,8 +113,8 @@ includes them.

Keep the intermediate tex file used in the conversion to PDF

-
-

Value

+
+

Value

R Markdown output format to pass to @@ -149,8 +122,8 @@ includes them.

-
-

Details

+
+

Details

The latter feature (positioning the figures with "H") depends on the LaTeX package 'float'. In addition, the LaTeX package 'listing' is used in the template for showing model fit summaries in the Appendix. This means that @@ -162,8 +135,8 @@ is present before) is to install the 'tinytex' R package, to run and then to run 'tinytex::tlmgr_install(c("float", "listing"))'.

-
-

Examples

+
+

Examples


 # \dontrun{
 library(rmarkdown)
@@ -174,26 +147,22 @@ and then to run 'tinytex::tlmgr_install(c("float", "listing"))'.
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/illparms.html b/docs/reference/illparms.html index bd90c0ed..75c540cc 100644 --- a/docs/reference/illparms.html +++ b/docs/reference/illparms.html @@ -1,118 +1,87 @@ -Method to get the names of ill-defined parameters — illparms • mkinMethod to get the names of ill-defined parameters — illparms • mkin + + Skip to contents -
-
-
-
-

Method to get the names of ill-defined parameters

- Source: R/illparms.R - +
+ + +
+
+
+
+

Method to get the names of ill-defined parameters

+ Source: R/illparms.R +
illparms.Rd
-
+

The method for generalised nonlinear regression fits as obtained with mkinfit and mmkin checks if the degradation parameters pass the Wald test (in degradation kinetics often simply called t-test) for @@ -120,7 +89,8 @@ significant difference from zero. For this test, the parameterisation without parameter transformations is used.

-
+
+

Usage

illparms(object, ...)
 
 # S3 method for mkinfit
@@ -155,8 +125,8 @@ without parameter transformations is used.

 print(x, ...)
-
-

Arguments

+
+

Arguments

object

The object to investigate

@@ -188,16 +158,16 @@ should slope parameters in the covariate model(starting with 'beta_') be tested?

-
-

Value

+
+

Value

For mkinfit or saem objects, a character vector of parameter names. For mmkin or mhmkin objects, a matrix like object of class 'illparms.mmkin' or 'illparms.mhmkin'.

-
-

Details

+
+

Details

The method for hierarchical model fits, also known as nonlinear mixed-effects model fits as obtained with saem and mhmkin checks if any of the confidence intervals for the random @@ -205,14 +175,14 @@ effects expressed as standard deviations include zero, and if the confidence intervals for the error model parameters include zero.

-
-

Note

+
+

Note

All return objects have printing methods. For the single fits, printing does not output anything in the case no ill-defined parameters are found.

-
-

Examples

+
+

Examples

fit <- mkinfit("FOMC", FOCUS_2006_A, quiet = TRUE)
 #> Warning: Optimisation did not converge:
 #> false convergence (8)
@@ -232,26 +202,22 @@ does not output anything in the case no ill-defined parameters are found.

 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 7937d770..04a8ab76 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -1,157 +1,124 @@ -Function to perform isometric log-ratio transformation — ilr • mkinFunction to perform isometric log-ratio transformation — ilr • mkin + + Skip to contents -
-
-
-
-

Function to perform isometric log-ratio transformation

- Source: R/ilr.R - +
+ + +
+
+
+
+

Function to perform isometric log-ratio transformation

+ Source: R/ilr.R +
ilr.Rd
-
+

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

-
+
+

Usage

ilr(x)
 
 invilr(x)
-
-

Arguments

+
+

Arguments

x

A numeric vector. Naturally, the forward transformation is only sensible for vectors with all elements being greater than zero.

-
-

Value

+
+

Value

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

-
-

References

+
+

References

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

-
-

See also

+
+

See also

Another implementation can be found in R package robCompositions.

-
-

Author

+
+

Author

René Lehmann and Johannes Ranke

-
-

Examples

+
+

Examples


 # Order matters
 ilr(c(0.1, 1, 10))
@@ -187,26 +154,22 @@ Compositional Data Using Robust Methods. Math Geosci 40 233-248
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/index.html b/docs/reference/index.html index a7f02199..d4a1b253 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,530 +1,661 @@ -Function reference • mkinFunction reference • mkin + + Skip to contents -
-
+
+
+
+

Function reference

+
+
+

Main functions

+

Essential functionality

-
-
-
-

Reference

-
+ +
+ + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-

Main functions

-

Essential functionality

-
-

mkinmod() print(<mkinmod>) mkinsub()

-

Function to set up a kinetic model with one or more state variables

-

mkinfit()

-

Fit a kinetic model to data with one or more state variables

-

mmkin() print(<mmkin>)

-

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

-

mhmkin() `[`(<mhmkin>) print(<mhmkin>)

-

Fit nonlinear mixed-effects models built from one or more kinetic -degradation models and one or more error models

-

Generics

-

Generic functions introduced by the package

-
-

parms()

-

Extract model parameters

-

status() print(<status.mmkin>) print(<status.mhmkin>)

-

Method to get status information for fit array objects

-

illparms() print(<illparms.mkinfit>) print(<illparms.mmkin>) print(<illparms.saem.mmkin>) print(<illparms.mhmkin>)

-

Method to get the names of ill-defined parameters

-

endpoints()

-

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

-

aw()

-

Calculate Akaike weights for model averaging

-

Show results

-

Functions working with mkinfit objects

-
-

plot(<mkinfit>) plot_sep() plot_res() plot_err()

-

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

-

summary(<mkinfit>) print(<summary.mkinfit>)

-

Summary method for class "mkinfit"

-

confint(<mkinfit>)

-

Confidence intervals for parameters of mkinfit objects

-

update(<mkinfit>)

-

Update an mkinfit model with different arguments

-

lrtest(<mkinfit>) lrtest(<mmkin>)

-

Likelihood ratio test for mkinfit models

-

loftest()

-

Lack-of-fit test for models fitted to data with replicates

-

mkinerrmin()

-

Calculate the minimum error to assume in order to pass the variance test

-

CAKE_export()

-

Export a list of datasets format to a CAKE study file

-

Work with mmkin objects

-

Functions working with aggregated results

-
-

`[`(<mmkin>)

-

Subsetting method for mmkin objects

-

plot(<mmkin>)

-

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

-

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

-

Calculate the AIC for a column of an mmkin object

-

summary(<mmkin>) print(<summary.mmkin>)

-

Summary method for class "mmkin"

-

Mixed models

-

Create and work with nonlinear hierarchical models

-
-

hierarchical_kinetics()

-

Hierarchical kinetics template

-

read_spreadsheet()

-

Read datasets and relevant meta information from a spreadsheet file

-

nlme(<mmkin>) print(<nlme.mmkin>) update(<nlme.mmkin>)

-

Create an nlme model for an mmkin row object

-

saem() print(<saem.mmkin>) saemix_model() saemix_data()

-

Fit nonlinear mixed models with SAEM

-

mhmkin() `[`(<mhmkin>) print(<mhmkin>)

-

Fit nonlinear mixed-effects models built from one or more kinetic -degradation models and one or more error models

-

plot(<mixed.mmkin>)

-

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

-

summary(<nlme.mmkin>) print(<summary.nlme.mmkin>)

-

Summary method for class "nlme.mmkin"

-

summary(<saem.mmkin>) print(<summary.saem.mmkin>)

-

Summary method for class "saem.mmkin"

-

anova(<saem.mmkin>)

-

Anova method for saem.mmkin objects

-

logLik(<saem.mmkin>)

-

logLik method for saem.mmkin objects

-

nlme_function() nlme_data()

-

Helper functions to create nlme models from mmkin row objects

-

get_deg_func()

-

Retrieve a degradation function from the mmkin namespace

-

mixed() print(<mixed.mmkin>)

-

Create a mixed effects model from an mmkin row object

-

reexports intervals lrtest nlme

-

Objects exported from other packages

-

intervals(<saem.mmkin>)

-

Confidence intervals for parameters in saem.mmkin objects

-

multistart() print(<multistart>) best() which.best()

-

Perform a hierarchical model fit with multiple starting values

-

llhist()

-

Plot the distribution of log likelihoods from multistart objects

-

parplot()

-

Plot parameter variability of multistart objects

-

Datasets and known results

-

-
-

ds_mixed ds_sfo ds_fomc ds_dfop ds_hs ds_dfop_sfo

-

Synthetic data for hierarchical kinetic degradation models

-

D24_2014

-

Aerobic soil degradation data on 2,4-D from the EU assessment in 2014

-

dimethenamid_2018

-

Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018

-

FOCUS_2006_A FOCUS_2006_B FOCUS_2006_C FOCUS_2006_D FOCUS_2006_E FOCUS_2006_F

-

Datasets A to F from the FOCUS Kinetics report from 2006

-

FOCUS_2006_SFO_ref_A_to_F

-

Results of fitting the SFO model to Datasets A to F of FOCUS (2006)

-

FOCUS_2006_FOMC_ref_A_to_F

-

Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)

-

FOCUS_2006_HS_ref_A_to_F

-

Results of fitting the HS model to Datasets A to F of FOCUS (2006)

-

FOCUS_2006_DFOP_ref_A_to_B

-

Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)

-

NAFTA_SOP_Appendix_B NAFTA_SOP_Appendix_D

-

Example datasets from the NAFTA SOP published 2015

-

NAFTA_SOP_Attachment

-

Example datasets from Attachment 1 to the NAFTA SOP published 2015

-

mccall81_245T

-

Datasets on aerobic soil metabolism of 2,4,5-T in six soils

-

schaefer07_complex_case

-

Metabolism data set used for checking the software quality of KinGUI

-

synthetic_data_for_UBA_2014

-

Synthetic datasets for one parent compound with two metabolites

-

experimental_data_for_UBA_2019

-

Experimental datasets used for development and testing of error models

-

test_data_from_UBA_2014

-

Three experimental datasets from two water sediment systems and one soil

-

focus_soil_moisture

-

FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar

-

print(<mkinds>)

-

A dataset class for mkin

-

print(<mkindsg>)

-

A class for dataset groups for mkin

-

NAFTA guidance

-

-
-

nafta() print(<nafta>)

-

Evaluate parent kinetics using the NAFTA guidance

-

plot(<nafta>)

-

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

-

Utility functions

-

-
-

summary_listing() tex_listing() html_listing()

-

Display the output of a summary function according to the output format

-

f_time_norm_focus()

-

Normalisation factors for aerobic soil degradation according to FOCUS guidance

-

set_nd_nq() set_nd_nq_focus()

-

Set non-detects and unquantified values in residue series without replicates

-

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

-

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

-

mkin_wide_to_long()

-

Convert a dataframe with observations over time into long format

-

mkin_long_to_wide()

-

Convert a dataframe from long to wide format

-

Helper functions mainly used internally

-

-
-

mkinpredict()

-

Produce predictions from a kinetic model using specific parameters

-

transform_odeparms() backtransform_odeparms()

-

Functions to transform and backtransform kinetic parameters for fitting

-

ilr() invilr()

-

Function to perform isometric log-ratio transformation

-

logLik(<mkinfit>)

-

Calculated the log-likelihood of a fitted mkinfit object

-

residuals(<mkinfit>)

-

Extract residuals from an mkinfit model

-

nobs(<mkinfit>)

-

Number of observations on which an mkinfit object was fitted

-

mkinresplot()

-

Function to plot residuals stored in an mkin object

-

mkinparplot()

-

Function to plot the confidence intervals obtained using mkinfit

-

mkinerrplot()

-

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

-

mean_degparms()

-

Calculate mean degradation parameters for an mmkin row object

-

create_deg_func()

-

Create degradation functions for known analytical solutions

-

Analytical solutions

-

Parent only model solutions

-
-

SFO.solution()

-

Single First-Order kinetics

-

FOMC.solution()

-

First-Order Multi-Compartment kinetics

-

DFOP.solution()

-

Double First-Order in Parallel kinetics

-

SFORB.solution()

-

Single First-Order Reversible Binding kinetics

-

HS.solution()

-

Hockey-Stick kinetics

-

IORE.solution()

-

Indeterminate order rate equation kinetics

-

logistic.solution()

-

Logistic kinetics

-

Generate synthetic datasets

-

-
-

add_err()

-

Add normally distributed errors to simulated kinetic degradation data

-

sigma_twocomp()

-

Two-component error model

-

Deprecated functions

-

Functions that have been superseded

-
-

mkinplot()

-

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

- - -
+
+ + mkinmod() print(<mkinmod>) mkinsub() +
+
Function to set up a kinetic model with one or more state variables
+
+ + mkinfit() +
+
Fit a kinetic model to data with one or more state variables
+
+ + mmkin() print(<mmkin>) +
+
Fit one or more kinetic models with one or more state variables to one or +more datasets
+
+ + mhmkin() `[`(<mhmkin>) print(<mhmkin>) +
+
Fit nonlinear mixed-effects models built from one or more kinetic +degradation models and one or more error models
+
+

Generics

+ +

Generic functions introduced by the package

+ +
+ + + -
+ + +

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/intervals.saem.mmkin.html b/docs/reference/intervals.saem.mmkin.html index d52d8501..36341eba 100644 --- a/docs/reference/intervals.saem.mmkin.html +++ b/docs/reference/intervals.saem.mmkin.html @@ -1,124 +1,90 @@ -Confidence intervals for parameters in saem.mmkin objects — intervals.saem.mmkin • mkinConfidence intervals for parameters in saem.mmkin objects — intervals.saem.mmkin • mkin + + Skip to contents -
-
-
-
-

Confidence intervals for parameters in saem.mmkin objects

- Source: R/intervals.R - +
+ + +
+
+
+
+

Confidence intervals for parameters in saem.mmkin objects

+ Source: R/intervals.R +
intervals.saem.mmkin.Rd
-
+

Confidence intervals for parameters in saem.mmkin objects

-
+
+

Usage

# S3 method for saem.mmkin
 intervals(object, level = 0.95, backtransform = TRUE, ...)
-
-

Arguments

+
+

Arguments

object

The fitted saem.mmkin object

@@ -138,34 +104,30 @@ between transformed and backtransformed parameters exists?

For compatibility with the generic method

-
-

Value

+
+

Value

An object with 'intervals.saem.mmkin' and 'intervals.lme' in the class attribute

-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/llhist.html b/docs/reference/llhist.html index d53d6319..690536b8 100644 --- a/docs/reference/llhist.html +++ b/docs/reference/llhist.html @@ -1,125 +1,92 @@ -Plot the distribution of log likelihoods from multistart objects — llhist • mkinPlot the distribution of log likelihoods from multistart objects — llhist • mkin + + Skip to contents -
-
-
-
-

Plot the distribution of log likelihoods from multistart objects

- Source: R/llhist.R - +
+ + +
+
+
+
+

Plot the distribution of log likelihoods from multistart objects

+ Source: R/llhist.R +
llhist.Rd
-
+

Produces a histogram of log-likelihoods. In addition, the likelihood of the original fit is shown as a red vertical line.

-
+
+

Usage

llhist(object, breaks = "Sturges", lpos = "topleft", main = "", ...)
-
-

Arguments

+
+

Arguments

object

The multistart object

@@ -140,31 +107,27 @@ original fit is shown as a red vertical line.

Passed to hist

-
-

See also

+
+

See also

multistart

-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/loftest-1.png b/docs/reference/loftest-1.png index f1dc5fa7..750a2acf 100644 Binary files a/docs/reference/loftest-1.png and b/docs/reference/loftest-1.png differ diff --git a/docs/reference/loftest-2.png b/docs/reference/loftest-2.png index 3f1015a9..d12c26e7 100644 Binary files a/docs/reference/loftest-2.png and b/docs/reference/loftest-2.png differ diff --git a/docs/reference/loftest-3.png b/docs/reference/loftest-3.png index e876cbab..1b2fd838 100644 Binary files a/docs/reference/loftest-3.png and b/docs/reference/loftest-3.png differ diff --git a/docs/reference/loftest-4.png b/docs/reference/loftest-4.png index ac44c162..3beb9d1a 100644 Binary files a/docs/reference/loftest-4.png and b/docs/reference/loftest-4.png differ diff --git a/docs/reference/loftest-5.png b/docs/reference/loftest-5.png index 14537feb..f60f5ff7 100644 Binary files a/docs/reference/loftest-5.png and b/docs/reference/loftest-5.png differ diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html index b474ad20..ed4141a8 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -1,132 +1,101 @@ -Lack-of-fit test for models fitted to data with replicates — loftest • mkinLack-of-fit test for models fitted to data with replicates — loftest • mkin + + Skip to contents -
-
-
-
-

Lack-of-fit test for models fitted to data with replicates

- Source: R/loftest.R - + +
+
+
+
+

Lack-of-fit test for models fitted to data with replicates

+ Source: R/loftest.R +
loftest.Rd
-
+

This is a generic function with a method currently only defined for mkinfit objects. It fits an anova model to the data contained in the object and compares the likelihoods using the likelihood ratio test lrtest.default from the lmtest package.

-
+
+

Usage

loftest(object, ...)
 
 # S3 method for mkinfit
 loftest(object, ...)
-
-

Arguments

+
+

Arguments

object

A model object with a defined loftest method

@@ -135,20 +104,20 @@ compares the likelihoods using the likelihood ratio test

Not used

-
-

Details

+
+

Details

The anova model is interpreted as the simplest form of an mkinfit model, assuming only a constant variance about the means, but not enforcing any structure of the means, so we have one model parameter for every mean of replicate samples.

-
-

See also

+
+

See also

lrtest

-
-

Examples

+
+

Examples

# \dontrun{
 test_data <- subset(synthetic_data_for_UBA_2014[[12]]$data, name == "parent")
 sfo_fit <- mkinfit("SFO", test_data, quiet = TRUE)
@@ -319,26 +288,22 @@ of replicate samples.

 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 07884f26..7b7b15b6 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -1,118 +1,87 @@ -Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit • mkinCalculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit • mkin + + Skip to contents -
-
-
-
-

Calculated the log-likelihood of a fitted mkinfit object

- Source: R/logLik.mkinfit.R - +
+ + +
+
+
+
+

Calculated the log-likelihood of a fitted mkinfit object

+ Source: R/logLik.mkinfit.R +
logLik.mkinfit.Rd
-
+

This function returns the product of the likelihood densities of each observed value, as calculated as part of the fitting procedure using dnorm, i.e. assuming normal distribution, and with the means @@ -120,13 +89,14 @@ predicted by the degradation model, and the standard deviations predicted by the error model.

-
+
+

Usage

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

Arguments

+
+

Arguments

object

An object of class mkinfit.

@@ -135,32 +105,32 @@ the error model.

For compatibility with the generic method

-
-

Value

+
+

Value

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

-
-

Details

+
+

Details

The total number of estimated parameters returned with the value of the likelihood is calculated as the sum of fitted degradation model parameters and the fitted error model parameters.

-
-

See also

+
+

See also

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

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


   # \dontrun{
   sfo_sfo <- mkinmod(
@@ -181,26 +151,22 @@ and the fitted error model parameters.
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/logLik.saem.mmkin.html b/docs/reference/logLik.saem.mmkin.html index 92d14aed..912abece 100644 --- a/docs/reference/logLik.saem.mmkin.html +++ b/docs/reference/logLik.saem.mmkin.html @@ -1,124 +1,90 @@ -logLik method for saem.mmkin objects — logLik.saem.mmkin • mkinlogLik method for saem.mmkin objects — logLik.saem.mmkin • mkin + + Skip to contents -
-
-
-
-

logLik method for saem.mmkin objects

- Source: R/saem.R - +
+ + +
+
+
+
+

logLik method for saem.mmkin objects

+ Source: R/saem.R +
logLik.saem.mmkin.Rd
-
+

logLik method for saem.mmkin objects

-
+
+

Usage

# S3 method for saem.mmkin
 logLik(object, ..., method = c("is", "lin", "gq"))
-
-

Arguments

+
+

Arguments

object

The fitted saem.mmkin object

@@ -132,26 +98,22 @@
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/logistic.solution-1.png b/docs/reference/logistic.solution-1.png index 73dad0a4..23c031de 100644 Binary files a/docs/reference/logistic.solution-1.png and b/docs/reference/logistic.solution-1.png differ diff --git a/docs/reference/logistic.solution-2.png b/docs/reference/logistic.solution-2.png index 8d2514a3..b56db0cb 100644 Binary files a/docs/reference/logistic.solution-2.png and b/docs/reference/logistic.solution-2.png differ diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index 412a981c..ff97c83a 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -1,125 +1,92 @@ -Logistic kinetics — logistic.solution • mkinLogistic kinetics — logistic.solution • mkin + + Skip to contents -
-
-
-
-

Logistic kinetics

- Source: R/parent_solutions.R - + +
+
+
+
+

Logistic kinetics

+ Source: R/parent_solutions.R +
logistic.solution.Rd
-
+

Function describing exponential decline from a defined starting value, with an increasing rate constant, supposedly caused by microbial growth

-
+
+

Usage

logistic.solution(t, parent_0, kmax, k0, r)
-
-

Arguments

+
+

Arguments

t

Time.

@@ -140,19 +107,19 @@ an increasing rate constant, supposedly caused by microbial growth

Growth rate of the increase in the rate constant.

-
-

Value

+
+

Value

The value of the response variable at time t.

-
-

Note

+
+

Note

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

-
-

References

+
+

References

FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -164,8 +131,8 @@ EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

-
-

See also

+
+

See also

Other parent solutions: DFOP.solution(), FOMC.solution(), @@ -175,8 +142,8 @@ Version 1.1, 18 December 2014 SFORB.solution()

-
-

Examples

+
+

Examples


   # Reproduce the plot on page 57 of FOCUS (2014)
   plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.2),
@@ -230,26 +197,22 @@ Version 1.1, 18 December 2014
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/lrtest.mkinfit.html b/docs/reference/lrtest.mkinfit.html index 45466262..9e784c43 100644 --- a/docs/reference/lrtest.mkinfit.html +++ b/docs/reference/lrtest.mkinfit.html @@ -1,118 +1,87 @@ -Likelihood ratio test for mkinfit models — lrtest.mkinfit • mkinLikelihood ratio test for mkinfit models — lrtest.mkinfit • mkin + + Skip to contents -
-
-
-
-

Likelihood ratio test for mkinfit models

- Source: R/lrtest.mkinfit.R - +
+ + +
+
+
+
+

Likelihood ratio test for mkinfit models

+ Source: R/lrtest.mkinfit.R +
lrtest.mkinfit.Rd
-
+

Compare two mkinfit models based on their likelihood. If two fitted mkinfit objects are given as arguments, it is checked if they have been fitted to the same data. It is the responsibility of the user to make sure @@ -120,7 +89,8 @@ that the models are nested, i.e. one of them has less degrees of freedom and can be expressed by fixing the parameters of the other.

-
+
+

Usage

# S3 method for mkinfit
 lrtest(object, object_2 = NULL, ...)
 
@@ -128,8 +98,8 @@ and can be expressed by fixing the parameters of the other.

 lrtest(object, ...)
-
-

Arguments

+
+

Arguments

object

An mkinfit object, or an mmkin column object containing two fits to the same data.

@@ -144,8 +114,8 @@ object containing two fits to the same data.

update.mkinfit for creating the alternative fitted object.

-
-

Details

+
+

Details

Alternatively, an argument to mkinfit can be given which is then passed to update.mkinfit to obtain the alternative model.

The comparison is then made by the lrtest.default @@ -154,8 +124,8 @@ parameters (alternative hypothesis) is listed first, then the model with the lower number of fitted parameters (null hypothesis).

-
-

Examples

+
+

Examples

# \dontrun{
 test_data <- subset(synthetic_data_for_UBA_2014[[12]]$data, name == "parent")
 sfo_fit <- mkinfit("SFO", test_data, quiet = TRUE)
@@ -210,26 +180,22 @@ lower number of fitted parameters (null hypothesis).

 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 892aa4e1..c560a763 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -1,6 +1,10 @@ -Function to calculate maximum time weighted average concentrations from -kinetic models fitted with mkinfit — max_twa_parent • mkinFunction to calculate maximum time weighted average concentrations from +kinetic models fitted with mkinfit — max_twa_parent • mkin + + Skip to contents -
-
-
-
-

Function to calculate maximum time weighted average concentrations from + +

+
+
+
+

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

- Source: R/max_twa_parent.R - + Source: R/max_twa_parent.R +
max_twa_parent.Rd
-
+

This function calculates maximum moving window time weighted average concentrations (TWAs) for kinetic models fitted with mkinfit. Currently, only calculations for the parent are implemented for the SFO, @@ -123,7 +92,8 @@ FOMC, DFOP and HS models, using the analytical formulas given in the PEC soil section of the FOCUS guidance.

-
+
+

Usage

max_twa_parent(fit, windows)
 
 max_twa_sfo(M0 = 1, k, t)
@@ -135,8 +105,8 @@ soil section of the FOCUS guidance.

 max_twa_hs(M0 = 1, k1, k2, tb, t)
-
-

Arguments

+
+

Arguments

fit

An object of class mkinfit.

@@ -185,29 +155,29 @@ factor (f_twa) is calculated.

Parameter of the HS model.

-
-

Value

+
+

Value

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

-
-

References

+
+

References

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

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


   fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
   max_twa_parent(fit, c(7, 21))
@@ -216,26 +186,22 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mccall81_245T-1.png b/docs/reference/mccall81_245T-1.png index 79c45fe6..5e4ea6ef 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 6b057c9d..6de846be 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -1,127 +1,95 @@ -Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkinDatasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin + + Skip to contents -
-
-
-
-

Datasets on aerobic soil metabolism of 2,4,5-T in six soils

- +
+
+
+
+

Datasets on aerobic soil metabolism of 2,4,5-T in six soils

+ +
mccall81_245T.Rd
-
+

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.

-
+
+

Usage

mccall81_245T
-
-

Format

+
+

Format

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 @@ -140,14 +108,14 @@

-
-

Source

+
+

Source

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

-
-

Examples

+
+

Examples

  SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"),
     phenol = list(type = "SFO", to = "anisole"),
     anisole = list(type = "SFO"))
@@ -224,26 +192,22 @@
   # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mean_degparms.html b/docs/reference/mean_degparms.html index 6e17045a..e6d11323 100644 --- a/docs/reference/mean_degparms.html +++ b/docs/reference/mean_degparms.html @@ -1,118 +1,84 @@ -Calculate mean degradation parameters for an mmkin row object — mean_degparms • mkinCalculate mean degradation parameters for an mmkin row object — mean_degparms • mkin + + Skip to contents -
-
-
-
-

Calculate mean degradation parameters for an mmkin row object

- Source: R/mean_degparms.R - +
+ + +
+
+
+
+

Calculate mean degradation parameters for an mmkin row object

+ Source: R/mean_degparms.R +
mean_degparms.Rd
-
+

Calculate mean degradation parameters for an mmkin row object

-
+
+

Usage

mean_degparms(
   object,
   random = FALSE,
@@ -122,8 +88,8 @@
 )
-
-

Arguments

+
+

Arguments

object

An mmkin row object containing several fits of the same model to different datasets

@@ -149,8 +115,8 @@ as a default value for the tested log parameters that failed the t-test.

-
-

Value

+
+

Value

If random is FALSE (default), a named vector containing mean values @@ -159,26 +125,22 @@ fixed and random effects, in the format required by the start argument of nlme for the case of a single grouping variable ds.

-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mhmkin-1.png b/docs/reference/mhmkin-1.png index 2ecb6759..1c99aead 100644 Binary files a/docs/reference/mhmkin-1.png and b/docs/reference/mhmkin-1.png differ diff --git a/docs/reference/mhmkin-2.png b/docs/reference/mhmkin-2.png index 70cd7723..3051bddc 100644 Binary files a/docs/reference/mhmkin-2.png and b/docs/reference/mhmkin-2.png differ diff --git a/docs/reference/mhmkin.html b/docs/reference/mhmkin.html index 7fcb98fb..36003f7c 100644 --- a/docs/reference/mhmkin.html +++ b/docs/reference/mhmkin.html @@ -1,127 +1,96 @@ -Fit nonlinear mixed-effects models built from one or more kinetic -degradation models and one or more error models — mhmkin • mkinFit nonlinear mixed-effects models built from one or more kinetic +degradation models and one or more error models — mhmkin • mkin + + Skip to contents -
-
-
-
-

Fit nonlinear mixed-effects models built from one or more kinetic + +

+
+
+
+

Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models

- Source: R/mhmkin.R - + Source: R/mhmkin.R +
mhmkin.Rd
-
+

The name of the methods expresses that (multiple) hierarchichal (also known as multilevel) multicompartment kinetic models are fitted. Our kinetic models are nonlinear, so we can use various nonlinear mixed-effects model fitting functions.

-
+
+

Usage

mhmkin(objects, ...)
 
 # S3 method for mmkin
@@ -145,8 +114,8 @@ mhmkin(
 print(x, ...)
-
-

Arguments

+
+

Arguments

objects

A list of mmkin objects containing fits of the same degradation models to the same data, but using different error models. @@ -210,8 +179,8 @@ parallel execution.

either a list of fit objects or a single fit object.

-
-

Value

+
+

Value

A two-dimensional array of fit objects and/or try-errors that can @@ -222,17 +191,17 @@ attribute 'mhmkin'.

An object inheriting from mhmkin.

-
-

See also

+
+

See also

[.mhmkin for subsetting mhmkin objects

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples

# \dontrun{
 # We start with separate evaluations of all the first six datasets with two
 # degradation models and two error models
@@ -313,26 +282,22 @@ attribute 'mhmkin'.

 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png index 3992b681..846ca6a1 100644 Binary files a/docs/reference/mixed-1.png and b/docs/reference/mixed-1.png differ diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html index b0cce30b..1da5e4e0 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -1,118 +1,84 @@ -Create a mixed effects model from an mmkin row object — mixed • mkinCreate a mixed effects model from an mmkin row object — mixed • mkin + + Skip to contents -
-
-
-
-

Create a mixed effects model from an mmkin row object

- Source: R/mixed.mmkin.R - +
+ + +
+
+
+
+

Create a mixed effects model from an mmkin row object

+ Source: R/mixed.mmkin.R +
mixed.Rd
-
+

Create a mixed effects model from an mmkin row object

-
+
+

Usage

mixed(object, ...)
 
 # S3 method for mmkin
@@ -122,8 +88,8 @@
 print(x, digits = max(3, getOption("digits") - 3), ...)
-
-

Arguments

+
+

Arguments

object

An mmkin row object

@@ -144,16 +110,16 @@

Number of digits to use for printing.

-
-

Value

+
+

Value

An object of class 'mixed.mmkin' which has the observed data in a single dataframe which is convenient for plotting

-
-

Examples

+
+

Examples

sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
 n_biphasic <- 8
 err_1 = list(const = 1, prop = 0.07)
@@ -224,26 +190,22 @@ single dataframe which is convenient for plotting

 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 9e1487bd..5c1f9c09 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -1,127 +1,95 @@ -Convert a dataframe from long to wide format — mkin_long_to_wide • mkinConvert a dataframe from long to wide format — mkin_long_to_wide • mkin + + Skip to contents -
-
-
-
-

Convert a dataframe from long to wide format

- Source: R/mkin_long_to_wide.R - +
+ + +
+
+
+
+

Convert a dataframe from long to wide format

+ Source: R/mkin_long_to_wide.R +
mkin_long_to_wide.Rd
-
+

This function takes a dataframe in the long form, i.e. with a row for each observed value, and converts it into a dataframe with one independent variable and several dependent variables as columns.

-
+
+

Usage

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

Arguments

+
+

Arguments

long_data

The dataframe must contain one variable called "time" with the time values specified by the time argument, one column called @@ -137,19 +105,19 @@ observed values called "value".

The name of the time variable in the wide output data.

-
-

Value

+
+

Value

Dataframe in wide format.

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


 mkin_long_to_wide(FOCUS_2006_D)
 #>    time parent    m1
@@ -178,26 +146,22 @@ observed values called "value".
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 8bf04bdf..3d8a2950 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -1,127 +1,95 @@ -Convert a dataframe with observations over time into long format — mkin_wide_to_long • mkinConvert a dataframe with observations over time into long format — mkin_wide_to_long • mkin + + Skip to contents -
-
-
-
-

Convert a dataframe with observations over time into long format

- Source: R/mkin_wide_to_long.R - +
+ + +
+
+
+
+

Convert a dataframe with observations over time into long format

+ Source: R/mkin_wide_to_long.R +
mkin_wide_to_long.Rd
-
+

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

-
+
+

Usage

mkin_wide_to_long(wide_data, time = "t")
-
-

Arguments

+
+

Arguments

wide_data

The dataframe must contain one variable with the time values specified by the time argument and usually more than one @@ -132,19 +100,19 @@ column of observed values.

The name of the time variable.

-
-

Value

+
+

Value

Dataframe in long format as needed for mkinfit.

-
-

Author

+
+

Author

Johannes Ranke

-
-

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)
@@ -158,26 +126,22 @@ column of observed values.
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index dda44620..4d4ac772 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -1,130 +1,99 @@ -A dataset class for mkin — mkinds • mkinA dataset class for mkin — mkinds • mkin + + Skip to contents -
-
-
-
-

A dataset class for mkin

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

A dataset class for mkin

+ Source: R/mkinds.R +
mkinds.Rd
-
+

At the moment this dataset class is hardly used in mkin. For example, mkinfit does not take mkinds datasets as argument, but works with dataframes such as the on contained in the data field of mkinds objects. Some datasets provided by this package come as mkinds objects nevertheless.

-
+
+

Usage

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

Arguments

+
+

Arguments

x

An mkinds object.

@@ -137,8 +106,8 @@ provided by this package come as mkinds objects nevertheless.

Not used.

-
-

Public fields

+
+

Public fields

title

A full title for the dataset

@@ -170,8 +139,8 @@ and value in order to be compatible with mkinfit

-
-

Methods

+
+

Methods

Public methods

@@ -186,7 +155,7 @@ and value in order to be compatible with mkinfit

-

Arguments

+

Arguments

title

The dataset title

@@ -214,7 +183,7 @@ and value in order to be compatible with mkinfit

-

Arguments

+

Arguments

deep

Whether to make a deep clone.

@@ -226,8 +195,8 @@ and value in order to be compatible with mkinfit

-
-

Examples

+
+

Examples


 mds <- mkinds$new("FOCUS A", FOCUS_2006_A)
 print(mds)
@@ -239,26 +208,22 @@ and value in order to be compatible with mkinfit
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index ac6a2471..c8d73c1a 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -1,130 +1,99 @@ -A class for dataset groups for mkin — mkindsg • mkinA class for dataset groups for mkin — mkindsg • mkin + + Skip to contents -
-
-
-
-

A class for dataset groups for mkin

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

A class for dataset groups for mkin

+ Source: R/mkinds.R +
mkindsg.Rd
-
+

A container for working with datasets that share at least one compound, so that combined evaluations are desirable.

Time normalisation factors are initialised with a value of 1 for each dataset if no data are supplied.

-
+
+

Usage

# S3 method for mkindsg
 print(x, data = FALSE, verbose = data, ...)
-
-

Arguments

+
+

Arguments

x

An mkindsg object.

@@ -141,8 +110,8 @@ dataset if no data are supplied.

Not used.

-
-

Public fields

+
+

Public fields

title

A title for the dataset group

@@ -169,8 +138,8 @@ or covariates like soil pH).

-
-

Methods

+
+

Methods

Public methods

@@ -185,7 +154,7 @@ or covariates like soil pH).

-

Arguments

+

Arguments

title

The title

@@ -213,7 +182,7 @@ or covariates like soil pH).

-

Arguments

+

Arguments

deep

Whether to make a deep clone.

@@ -225,8 +194,8 @@ or covariates like soil pH).

-
-

Examples

+
+

Examples


 mdsg <- mkindsg$new("Experimental X", experimental_data_for_UBA_2019[6:10])
 print(mdsg)
@@ -427,26 +396,22 @@ or covariates like soil pH).
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 11837e63..3c984039 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -1,125 +1,92 @@ -Calculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkinCalculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkin + + Skip to contents -
-
-
-
-

Calculate the minimum error to assume in order to pass the variance test

- Source: R/mkinerrmin.R - +
+ + +
+
+
+
+

Calculate the minimum error to assume in order to pass the variance test

+ Source: R/mkinerrmin.R +
mkinerrmin.Rd
-
+

This function finds the smallest relative error still resulting in passing the chi-squared test as defined in the FOCUS kinetics report from 2006.

-
+
+

Usage

mkinerrmin(fit, alpha = 0.05)
-
-

Arguments

+
+

Arguments

fit

an object of class mkinfit.

@@ -128,8 +95,8 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006.

The confidence level chosen for the chi-squared test.

-
-

Value

+
+

Value

A dataframe with the following components:

@@ -148,12 +115,12 @@ point with observed values in the series only counts one time.

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

-
-

Details

+
+

Details

This function is used internally by summary.mkinfit.

-
-

References

+
+

References

FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC @@ -161,8 +128,8 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

-
-

Examples

+
+

Examples


 SFO_SFO = mkinmod(parent = mkinsub("SFO", to = "m1"),
                   m1 = mkinsub("SFO"),
@@ -187,26 +154,22 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mkinerrplot-1.png b/docs/reference/mkinerrplot-1.png index 49bb1c0e..078614fc 100644 Binary files a/docs/reference/mkinerrplot-1.png and b/docs/reference/mkinerrplot-1.png differ diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 6996eb86..cd1d93f1 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -1,118 +1,87 @@ -Function to plot squared residuals and the error model for an mkin object — mkinerrplot • mkinFunction to plot squared residuals and the error model for an mkin object — mkinerrplot • mkin + + Skip to contents -
-
-
-
-

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

- Source: R/mkinerrplot.R - +
+ + +
+
+
+
+

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

+ Source: R/mkinerrplot.R +
mkinerrplot.Rd
-
+

This function plots the squared residuals for the specified subset of the observed variables from an mkinfit object. In addition, one or more dashed line(s) show the fitted error model. A combined plot of the fitted model @@ -120,7 +89,8 @@ and this error model plot can be obtained with show_errplot = TRUE.

-
+
+

Usage

mkinerrplot(
   object,
   obs_vars = names(object$mkinmod$map),
@@ -137,8 +107,8 @@ using the argument show_errplot = TRUE.

 )
-
-

Arguments

+
+

Arguments

object

A fit represented in an mkinfit object.

@@ -191,25 +161,25 @@ be passed on to plot.

-
-

Value

+
+

Value

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

-
-

See also

+
+

See also

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

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


 # \dontrun{
 model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
@@ -222,26 +192,22 @@ lines of the mkinfit object.
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mkinfit-1.png b/docs/reference/mkinfit-1.png index 7c51deb6..578f64a5 100644 Binary files a/docs/reference/mkinfit-1.png and b/docs/reference/mkinfit-1.png differ diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 865bdc28..7cd4eaa3 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -1,5 +1,13 @@ -Fit a kinetic model to data with one or more state variables — mkinfit • mkinFit a kinetic model to data with one or more state variables — mkinfit • mkin + + Skip to contents -
-
-
-
-

Fit a kinetic model to data with one or more state variables

- Source: R/mkinfit.R - +
+ + +
+
+
+
+

Fit a kinetic model to data with one or more state variables

+ Source: R/mkinfit.R +
mkinfit.Rd
-
+

This function maximises the likelihood of the observed data using the Port algorithm stats::nlminb(), and the specified initial or fixed parameters and starting values. In each step of the optimisation, the @@ -128,7 +101,8 @@ degradation model parameters, as both of them are arguments of the likelihood function.

-
+
+

Usage

mkinfit(
   mkinmod,
   observed,
@@ -158,8 +132,8 @@ likelihood function.

 )
-
-

Arguments

+
+

Arguments

mkinmod

A list of class mkinmod, containing the kinetic model to be fitted to the data, or one of the shorthand names ("SFO", @@ -357,27 +331,27 @@ the error model parameters in IRLS fits.

deSolve::ode().

-
-

Value

+
+

Value

A list with "mkinfit" in the class attribute.

-
-

Details

+
+

Details

Per default, parameters in the kinetic models are internally transformed in order to better satisfy the assumption of a normal distribution of their estimators.

-
-

Note

+
+

Note

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

-
-

References

+
+

References

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

Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical @@ -385,36 +359,36 @@ Degradation Data. Environments 6(12) 124 doi:10.3390/environments6120124 .

-
-

See also

+
+

See also

summary.mkinfit, plot.mkinfit, parms and lrtest.

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

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

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


 # Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
 #> mkin version used for fitting:    1.2.6 
-#> R version used for fitting:       4.3.1 
-#> Date of fit:     Mon Oct 30 09:30:09 2023 
-#> Date of summary: Mon Oct 30 09:30:09 2023 
+#> R version used for fitting:       4.3.2 
+#> Date of fit:     Thu Nov 16 04:15:31 2023 
+#> Date of summary: Thu Nov 16 04:15:31 2023 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.031 s
+#> Fitted using 222 model solutions performed in 0.014 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -555,9 +529,9 @@ Degradation Data. Environments 6(12) 124
       solution_type = "analytical"))
 }
 #>               test relative elapsed
-#> 3       analytical    1.000   0.465
-#> 2            eigen    2.260   1.051
-#> 1 deSolve_compiled    2.282   1.061
+#> 3       analytical    1.000   0.223
+#> 2            eigen    1.973   0.440
+#> 1 deSolve_compiled    2.072   0.462
 # }
 
 # Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO
@@ -585,9 +559,9 @@ Degradation Data. Environments 6(12) 124
 #> Warning: NaNs produced
 #> Warning: diag(.) had 0 or NA entries; non-finite result is doubtful
 #> mkin version used for fitting:    1.2.6 
-#> R version used for fitting:       4.3.1 
-#> Date of fit:     Mon Oct 30 09:30:19 2023 
-#> Date of summary: Mon Oct 30 09:30:19 2023 
+#> R version used for fitting:       4.3.2 
+#> Date of fit:     Thu Nov 16 04:15:35 2023 
+#> Date of summary: Thu Nov 16 04:15:35 2023 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -596,7 +570,7 @@ Degradation Data. Environments 6(12) 124
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 4062 model solutions performed in 1.981 s
+#> Fitted using 4062 model solutions performed in 0.768 s
 #> 
 #> Error model: Two-component variance function 
 #> 
@@ -696,26 +670,22 @@ Degradation Data. Environments 6(12) 124
 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 11a87acc..9d73ea9f 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -1,118 +1,87 @@ -Function to set up a kinetic model with one or more state variables — mkinmod • mkinFunction to set up a kinetic model with one or more state variables — mkinmod • mkin + + Skip to contents -
-
-
-
-

Function to set up a kinetic model with one or more state variables

- Source: R/mkinmod.R, R/mkinsub.R - +
+ + +
+
+
+
+

Function to set up a kinetic model with one or more state variables

+ Source: R/mkinmod.R, R/mkinsub.R +
mkinmod.Rd
-
+

This function is usually called using a call to mkinsub() for each observed variable, specifying the corresponding submodel as well as outgoing pathways (see examples).

@@ -120,7 +89,8 @@ variable, specifying the corresponding submodel as well as outgoing pathways components.

-
+
+

Usage

mkinmod(
   ...,
   use_of_ff = "max",
@@ -139,8 +109,8 @@ components.

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

Arguments

+
+

Arguments

...

For each observed variable, a list as obtained by mkinsub() has to be specified as an argument (see examples). Currently, single @@ -230,8 +200,8 @@ your R code will not be portable, i.e. may produce unintended plot results on other operating systems or system configurations.

-
-

Value

+
+

Value

A list of class mkinmod for use with mkinfit(), @@ -262,8 +232,8 @@ returned by cfunction.

A list for use with mkinmod.

-
-

Details

+
+

Details

For the definition of model types and their parameters, the equations given in the FOCUS and NAFTA guidance documents are used.

For kinetic models with more than one observed variable, a symbolic solution @@ -274,14 +244,14 @@ is more than one observed variable in the specification, C code is generated for evaluating the differential equations, compiled using inline::cfunction() and added to the resulting mkinmod object.

-
-

Note

+
+

Note

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

-
-

References

+
+

References

FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -290,13 +260,13 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,

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

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


 # Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)
 SFO <- mkinmod(parent = mkinsub("SFO"))
@@ -333,7 +303,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

    m1 = mkinsub("SFO", full_name = "Metabolite M1"),
    name = "SFO_SFO", dll_dir = DLL_dir, unload = TRUE, overwrite = TRUE)
 #> Temporary DLL for differentials generated and loaded
-#> Copied DLL from /tmp/RtmpkUSV6I/file244bcd2ba24b1a.so to /home/agsad.admin.ch/f80868656/.local/share/mkin/SFO_SFO.so
+#> Copied DLL from /tmp/Rtmpjn19MY/filee5f2f55ca8372.so to /home/jranke/.local/share/mkin/SFO_SFO.so
 # Now we can save the model and restore it in a new session
 saveRDS(SFO_SFO.2, file = "~/SFO_SFO.rds")
 # Terminate the R session here if you would like to check, and then do
@@ -386,7 +356,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media

 #>     })
 #>     return(predicted)
 #> }
-#> <environment: 0x560630960080>
+#> <environment: 0x555555f44b28>
 
 # If we have several parallel metabolites
 # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
@@ -403,26 +373,22 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png index 5d6fde87..8d34b451 100644 Binary files a/docs/reference/mkinparplot-1.png and b/docs/reference/mkinparplot-1.png differ diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 71957650..fd123d92 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -1,143 +1,110 @@ -Function to plot the confidence intervals obtained using mkinfit — mkinparplot • mkinFunction to plot the confidence intervals obtained using mkinfit — mkinparplot • mkin + + Skip to contents -
-
-
-
-

Function to plot the confidence intervals obtained using mkinfit

- Source: R/mkinparplot.R - +
+ + +
+
+
+
+

Function to plot the confidence intervals obtained using mkinfit

+ Source: R/mkinparplot.R +
mkinparplot.Rd
-
+

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

-
+
+

Usage

mkinparplot(object)
-
-

Arguments

+
+

Arguments

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.

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


 # \dontrun{
 model <- mkinmod(
@@ -152,26 +119,22 @@ effect, namely to produce a plot.

 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index da047bf7..01e08e16 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -1,125 +1,92 @@ -Plot the observed data and the fitted model of an mkinfit object — mkinplot • mkinPlot the observed data and the fitted model of an mkinfit object — mkinplot • mkin + + Skip to contents -
-
-
-
-

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

- Source: R/plot.mkinfit.R - +
+ + +
+
+
+
+

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

+ Source: R/plot.mkinfit.R +
mkinplot.Rd
-
+

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

-
+
+

Usage

mkinplot(fit, ...)
-
-

Arguments

+
+

Arguments

fit

an object of class mkinfit.

@@ -128,37 +95,33 @@ plot.mkinfit.">Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin + + Skip to contents -
-
-
-
-

Produce predictions from a kinetic model using specific parameters

- Source: R/mkinpredict.R - +
+ + +
+
+
+
+

Produce predictions from a kinetic model using specific parameters

+ Source: R/mkinpredict.R +
mkinpredict.Rd
-
+

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 parameters and initial values for the state variables.

-
+
+

Usage

mkinpredict(x, odeparms, odeini, outtimes, ...)
 
 # S3 method for mkinmod
@@ -153,8 +121,8 @@ kinetic parameters and initial values for the state variables.

 )
-
-

Arguments

+
+

Arguments

x

A kinetic model as produced by mkinmod, or a kinetic fit as fitted by mkinfit. In the latter case, the fitted parameters are used for @@ -231,19 +199,19 @@ as these always return mapped output.

Should it be an error if ode returns NaN values

-
-

Value

+
+

Value

A matrix with the numeric solution in wide format

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


 SFO <- mkinmod(degradinol = mkinsub("SFO"))
 # Compare solution types
@@ -398,10 +366,10 @@ as these always return mapped output.

       solution_type = "analytical", use_compiled = FALSE)[201,])
 }
 #>               test relative elapsed
-#> 2 deSolve_compiled      1.0   0.005
-#> 4       analytical      1.0   0.005
-#> 1            eigen      3.2   0.016
-#> 3          deSolve     24.4   0.122
+#> 4       analytical        1   0.001
+#> 2 deSolve_compiled        2   0.002
+#> 1            eigen        8   0.008
+#> 3          deSolve       64   0.064
 
 # \dontrun{
   # Predict from a fitted model
@@ -413,26 +381,22 @@ as these always return mapped output.
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png index 97ccd762..7c64d0f0 100644 Binary files a/docs/reference/mkinresplot-1.png and b/docs/reference/mkinresplot-1.png differ diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 4bfd033e..420c3190 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -1,124 +1,93 @@ -Function to plot residuals stored in an mkin object — mkinresplot • mkinFunction to plot residuals stored in an mkin object — mkinresplot • mkin + + Skip to contents -
-
-
-
-

Function to plot residuals stored in an mkin object

- Source: R/mkinresplot.R - +
+ + +
+
+
+
+

Function to plot residuals stored in an mkin object

+ Source: R/mkinresplot.R +
mkinresplot.Rd
-
+

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 using the argument show_residuals = TRUE.

-
+
+

Usage

mkinresplot(
   object,
   obs_vars = names(object$mkinmod$map),
@@ -136,8 +105,8 @@ argument show_residuals = TRUE.

 )
-
-

Arguments

+
+

Arguments

object

A fit represented in an mkinfit object.

@@ -195,26 +164,26 @@ be passed on to plot.

-
-

Value

+
+

Value

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

-
-

See also

+
+

See also

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

-
-

Author

+
+

Author

Johannes Ranke and Katrin Lindenberger

-
-

Examples

+
+

Examples


 model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
 #> Temporary DLL for differentials generated and loaded
@@ -225,26 +194,22 @@ combining the plot of the fit and the residual plot.
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png index 2361d3dc..9642db70 100644 Binary files a/docs/reference/mmkin-1.png and b/docs/reference/mmkin-1.png differ diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png index 6ce2010f..d9aa755d 100644 Binary files a/docs/reference/mmkin-2.png and b/docs/reference/mmkin-2.png differ diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png index 5d56da86..ed8e87e6 100644 Binary files a/docs/reference/mmkin-3.png and b/docs/reference/mmkin-3.png differ diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png index 132380a8..11eae1f9 100644 Binary files a/docs/reference/mmkin-4.png and b/docs/reference/mmkin-4.png differ diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png index 4bfcc55e..e88bd59f 100644 Binary files a/docs/reference/mmkin-5.png and b/docs/reference/mmkin-5.png differ diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 57039604..1035c681 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -1,123 +1,90 @@ -Fit one or more kinetic models with one or more state variables to one or -more datasets — mmkin • mkinFit one or more kinetic models with one or more state variables to one or +more datasets — mmkin • mkin + + Skip to contents -
-
-
-
-

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

+
+
+
+

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

- Source: R/mmkin.R - + Source: R/mmkin.R +
mmkin.Rd
-
+

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

-
+
+

Usage

mmkin(
   models = c("SFO", "FOMC", "DFOP"),
   datasets,
@@ -130,8 +97,8 @@ datasets specified in its first two arguments.

 print(x, ...)
-
-

Arguments

+
+

Arguments

models

Either a character vector of shorthand names like c("SFO", "FOMC", "DFOP", "HS", "SFORB"), or an optionally named @@ -165,8 +132,8 @@ for parallel execution.

An mmkin object.

-
-

Value

+
+

Value

A two-dimensional array of mkinfit

@@ -176,18 +143,18 @@ for parallel execution.

first index (row index) and the dataset names for the second index (column index).

-
-

See also

+
+

See also

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

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


 # \dontrun{
 m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
@@ -209,10 +176,10 @@ plotting.
time_default #> user system elapsed -#> 3.540 1.287 1.429 +#> 1.653 0.553 0.654 time_1 #> user system elapsed -#> 4.074 0.037 4.142 +#> 2.013 0.008 2.021 endpoints(fits.0[["SFO_lin", 2]]) #> $ff @@ -268,26 +235,22 @@ plotting.

-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/multistart-1.png b/docs/reference/multistart-1.png index cf3cdca3..8133170b 100644 Binary files a/docs/reference/multistart-1.png and b/docs/reference/multistart-1.png differ diff --git a/docs/reference/multistart-2.png b/docs/reference/multistart-2.png index 05a160d0..5cfdbd63 100644 Binary files a/docs/reference/multistart-2.png and b/docs/reference/multistart-2.png differ diff --git a/docs/reference/multistart.html b/docs/reference/multistart.html index 840f0e01..fadb500f 100644 --- a/docs/reference/multistart.html +++ b/docs/reference/multistart.html @@ -1,5 +1,10 @@ -Perform a hierarchical model fit with multiple starting values — multistart • mkinPerform a hierarchical model fit with multiple starting values — multistart • mkin + + Skip to contents -
-
-
-
-

Perform a hierarchical model fit with multiple starting values

- Source: R/multistart.R - +
+ + +
+
+
+
+

Perform a hierarchical model fit with multiple starting values

+ Source: R/multistart.R +
multistart.Rd
-
+

The purpose of this method is to check if a certain algorithm for fitting nonlinear hierarchical models (also known as nonlinear mixed-effects models) will reliably yield results that are sufficiently similar to each other, if @@ -122,7 +92,8 @@ inspired by the article on practical identifiabiliy in the frame of nonlinear mixed-effects models by Duchesne et al (2021).

-
+
+

Usage

multistart(
   object,
   n = 50,
@@ -148,8 +119,8 @@ mixed-effects models by Duchesne et al (2021).

 which.best(object, ...)
-
-

Arguments

+
+

Arguments

object

The fit object to work with

@@ -176,8 +147,8 @@ for parallel execution.

The multistart object to print

-
-

Value

+
+

Value

A list of saem.mmkin objects, with class attributes @@ -189,20 +160,20 @@ for parallel execution.

The index of the object with the highest likelihood

-
-

References

+
+

References

Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical identifiability in the frame of nonlinear mixed effects models: the example of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478. doi: 10.1186/s12859-021-04373-4.

-
-

See also

+
+

See also

parplot, llhist

-
-

Examples

+
+

Examples

# \dontrun{
 library(mkin)
 dmta_ds <- lapply(1:7, function(i) {
@@ -236,26 +207,22 @@ doi: 10.1186/s12859-021-04373-4.

 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/nafta-1.png b/docs/reference/nafta-1.png index 5d2d434b..98d4246c 100644 Binary files a/docs/reference/nafta-1.png and b/docs/reference/nafta-1.png differ diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 011b766a..af4d778a 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -1,118 +1,87 @@ -Evaluate parent kinetics using the NAFTA guidance — nafta • mkinEvaluate parent kinetics using the NAFTA guidance — nafta • mkin + + Skip to contents -
-
-
-
-

Evaluate parent kinetics using the NAFTA guidance

- Source: R/nafta.R - + +
+
+
+
+

Evaluate parent kinetics using the NAFTA guidance

+ Source: R/nafta.R +
nafta.Rd
-
+

The function fits the SFO, IORE and DFOP models using mmkin and returns an object of class nafta that has methods for printing and plotting.

@@ -120,15 +89,16 @@ and plotting.

order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP.

-
+
+

Usage

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

Source

+
+

Source

NAFTA (2011) Guidance for evaluating and calculating degradation kinetics in environmental media. NAFTA Technical Working Group on Pesticides @@ -139,8 +109,8 @@ 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

-
-

Arguments

+
+

Arguments

ds

A dataframe that must contain one variable called "time" with the time values specified by the time argument, one column called @@ -170,8 +140,8 @@ printing method).

dissipation times.

-
-

Value

+
+

Value

An list of class nafta. The list element named "mmkin" is the @@ -179,13 +149,13 @@ dissipation times.

list element named "title" contains the title of the dataset used. The list element "data" contains the dataset used in the fits.

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

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
@@ -236,26 +206,22 @@ list element "data" contains the dataset used in the fits.
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png index 0134107f..9583da2a 100644 Binary files a/docs/reference/nlme-1.png and b/docs/reference/nlme-1.png differ diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png index 95739890..02aa0573 100644 Binary files a/docs/reference/nlme-2.png and b/docs/reference/nlme-2.png differ diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index 26c56e54..d94e4bbe 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -1,137 +1,106 @@ -Helper functions to create nlme models from mmkin row objects — nlme_function • mkinHelper functions to create nlme models from mmkin row objects — nlme_function • mkin + + Skip to contents -
-
-
-
-

Helper functions to create nlme models from mmkin row objects

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

Helper functions to create nlme models from mmkin row objects

+ Source: R/nlme.R +
nlme.Rd
-
+

These functions facilitate setting up a nonlinear mixed effects model for an mmkin row object. An mmkin row object is essentially a list of mkinfit objects that have been obtained by fitting the same model to a list of datasets. They are used internally by the nlme.mmkin() method.

-
+
+

Usage

nlme_function(object)
 
 nlme_data(object)
-
-

Arguments

+
+

Arguments

object

An mmkin row object containing several fits of the same model to different datasets

-
-

Value

+
+

Value

A function that can be used with nlme

@@ -139,13 +108,13 @@ datasets. They are used internally by the nlme.m

A groupedData object

-
-

See also

+
+

See also

nlme.mmkin

-
-

Examples

+
+

Examples

sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
 m_SFO <- mkinmod(parent = mkinsub("SFO"))
 d_SFO_1 <- mkinpredict(m_SFO,
@@ -221,26 +190,22 @@ datasets. They are used internally by the nlme.m
-
- -
+
-
- diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png index 7cabb086..762d5412 100644 Binary files a/docs/reference/nlme.mmkin-1.png and b/docs/reference/nlme.mmkin-1.png differ diff --git a/docs/reference/nlme.mmkin-2.png b/docs/reference/nlme.mmkin-2.png index b9a68e92..779adbdb 100644 Binary files a/docs/reference/nlme.mmkin-2.png and b/docs/reference/nlme.mmkin-2.png differ diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png index ce7999bd..046d0238 100644 Binary files a/docs/reference/nlme.mmkin-3.png and b/docs/reference/nlme.mmkin-3.png differ diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 05fbac5c..0e0412c6 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -1,122 +1,90 @@ -Create an nlme model for an mmkin row object — nlme.mmkin • mkinCreate an nlme model for an mmkin row object — nlme.mmkin • mkin + + Skip to contents -
-
-
-
-

Create an nlme model for an mmkin row object

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

Create an nlme model for an mmkin row object

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

This functions sets up a nonlinear mixed effects model for an mmkin row object. An mmkin row object is essentially a list of mkinfit objects that have been obtained by fitting the same model to a list of datasets.

-
+
+

Usage

# S3 method for mmkin
 nlme(
   model,
@@ -143,8 +111,8 @@ have been obtained by fitting the same model to a list of datasets.

 update(object, ...)
-
-

Arguments

+
+

Arguments

model

An mmkin row object.

@@ -221,33 +189,33 @@ parameters taken from the mmkin object are used

An nlme.mmkin object to update

-
-

Value

+
+

Value

Upon success, a fitted 'nlme.mmkin' object, which is an nlme object with additional elements. It also inherits from 'mixed.mmkin'.

-
-

Details

+
+

Details

Note that the convergence of the nlme algorithms depends on the quality of the data. In degradation kinetics, we often only have few datasets (e.g. data for few soils) and complicated degradation models, which may make it impossible to obtain convergence with nlme.

-
-

Note

+
+

Note

As the object inherits from nlme::nlme, there is a wealth of methods that will automatically work on 'nlme.mmkin' objects, such as nlme::intervals(), nlme::anova.lme() and nlme::coef.lme().

-
-

See also

+
+

See also

nlme_function(), plot.mixed.mmkin, summary.nlme.mmkin

-
-

Examples

+
+

Examples

ds <- lapply(experimental_data_for_UBA_2019[6:10],
  function(x) subset(x$data[c("name", "time", "value")], name == "parent"))
 
@@ -438,26 +406,22 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/nobs.mkinfit.html b/docs/reference/nobs.mkinfit.html index c3e24a08..d4f6fe40 100644 --- a/docs/reference/nobs.mkinfit.html +++ b/docs/reference/nobs.mkinfit.html @@ -1,124 +1,90 @@ -Number of observations on which an mkinfit object was fitted — nobs.mkinfit • mkinNumber of observations on which an mkinfit object was fitted — nobs.mkinfit • mkin + + Skip to contents -
-
-
-
-

Number of observations on which an mkinfit object was fitted

- Source: R/nobs.mkinfit.R - +
+ + +
+
+
+
+

Number of observations on which an mkinfit object was fitted

+ Source: R/nobs.mkinfit.R +
nobs.mkinfit.Rd
-
+

Number of observations on which an mkinfit object was fitted

-
+
+

Usage

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

Arguments

+
+

Arguments

object

An mkinfit object

@@ -127,33 +93,29 @@

For compatibility with the generic method

-
-

Value

+
+

Value

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

-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/parms.html b/docs/reference/parms.html index 89831adb..f5833ffa 100644 --- a/docs/reference/parms.html +++ b/docs/reference/parms.html @@ -1,122 +1,90 @@ -Extract model parameters — parms • mkinExtract model parameters — parms • mkin + + Skip to contents -
-
-
-
-

Extract model parameters

- Source: R/parms.R, R/saem.R - +
+ + +
+
+
+
+

Extract model parameters

+ Source: R/parms.R, R/saem.R +
parms.Rd
-
+

This function returns degradation model parameters as well as error model parameters per default, in order to avoid working with a fitted model without considering the error structure that was assumed for the fit.

-
+
+

Usage

parms(object, ...)
 
 # S3 method for mkinfit
@@ -132,8 +100,8 @@ without considering the error structure that was assumed for the fit.

 parms(object, ci = FALSE, covariates = NULL, ...)
-
-

Arguments

+
+

Arguments

object

A fitted model object.

@@ -169,21 +137,21 @@ each column corresponding to a row of the data frame holding the covariates

< return parameter values. Only has an effect if 'ci' is FALSE.

-
-

Value

+
+

Value

Depending on the object, a numeric vector of fitted model parameters, a matrix (e.g. for mmkin row objects), or a list of matrices (e.g. for mmkin objects with more than one row).

-
-

See also

+
+

See also

saem, multistart

-
-

Examples

+
+

Examples

# mkinfit objects
 fit <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE)
 parms(fit)
@@ -273,26 +241,22 @@ mmkin objects with more than one row).

 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/parplot.html b/docs/reference/parplot.html index 2ae8d39f..5a4bada1 100644 --- a/docs/reference/parplot.html +++ b/docs/reference/parplot.html @@ -1,122 +1,90 @@ -Plot parameter variability of multistart objects — parplot • mkinPlot parameter variability of multistart objects — parplot • mkin + + Skip to contents -
-
-
-
-

Plot parameter variability of multistart objects

- Source: R/parplot.R - +
+ + +
+
+
+
+

Plot parameter variability of multistart objects

+ Source: R/parplot.R +
parplot.Rd
-
+

Produces a boxplot with all parameters from the multiple runs, scaled either by the parameters of the run with the highest likelihood, or by their medians as proposed in the paper by Duchesne et al. (2021).

-
+
+

Usage

parplot(object, ...)
 
 # S3 method for multistart.saem.mmkin
@@ -131,8 +99,8 @@ or by their medians as proposed in the paper by Duchesne et al. (2021).

 )
-
-

Arguments

+
+

Arguments

object

The multistart object

@@ -164,44 +132,40 @@ If 'median', parameters are scaled using the median parameters from all fits.

Title of the plot

-
-

Details

+
+

Details

Starting values of degradation model parameters and error model parameters are shown as green circles. The results obtained in the original run are shown as red circles.

-
-

References

+
+

References

Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical identifiability in the frame of nonlinear mixed effects models: the example of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478. doi: 10.1186/s12859-021-04373-4.

-
-

See also

+
+

See also

multistart

-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/plot.mixed.mmkin-1.png b/docs/reference/plot.mixed.mmkin-1.png index 8a09a167..2e145bb7 100644 Binary files a/docs/reference/plot.mixed.mmkin-1.png and b/docs/reference/plot.mixed.mmkin-1.png differ diff --git a/docs/reference/plot.mixed.mmkin-2.png b/docs/reference/plot.mixed.mmkin-2.png index 68a76b47..65f5593b 100644 Binary files a/docs/reference/plot.mixed.mmkin-2.png and b/docs/reference/plot.mixed.mmkin-2.png differ diff --git a/docs/reference/plot.mixed.mmkin-3.png b/docs/reference/plot.mixed.mmkin-3.png index e18a0da1..ef4fa3a7 100644 Binary files a/docs/reference/plot.mixed.mmkin-3.png and b/docs/reference/plot.mixed.mmkin-3.png differ diff --git a/docs/reference/plot.mixed.mmkin-4.png b/docs/reference/plot.mixed.mmkin-4.png index f574fdd9..d7030dea 100644 Binary files a/docs/reference/plot.mixed.mmkin-4.png and b/docs/reference/plot.mixed.mmkin-4.png differ diff --git a/docs/reference/plot.mixed.mmkin.html b/docs/reference/plot.mixed.mmkin.html index b0e0f159..9ec5d65a 100644 --- a/docs/reference/plot.mixed.mmkin.html +++ b/docs/reference/plot.mixed.mmkin.html @@ -1,118 +1,84 @@ -Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot.mixed.mmkin • mkinPlot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot.mixed.mmkin • mkin + + Skip to contents -
-
-
-
-

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

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

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

+ Source: R/plot.mixed.mmkin.R +
plot.mixed.mmkin.Rd
-
+

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

-
+
+

Usage

# S3 method for mixed.mmkin
 plot(
   x,
@@ -143,8 +109,8 @@
 )
-
-

Arguments

+
+

Arguments

x

An object of class mixed.mmkin, saem.mmkin or nlme.mmkin

@@ -265,23 +231,23 @@ corresponding model prediction lines for the different datasets.

Further arguments passed to plot.

-
-

Value

+
+

Value

The function is called for its side effect.

-
-

Note

+
+

Note

Covariate models are currently only supported for saem.mmkin objects.

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples

ds <- lapply(experimental_data_for_UBA_2019[6:10],
  function(x) x$data[c("name", "time", "value")])
 names(ds) <- paste0("ds ", 6:10)
@@ -319,26 +285,22 @@ corresponding model prediction lines for the different datasets.

 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/plot.mkinfit-1.png b/docs/reference/plot.mkinfit-1.png index ea1032fb..a48ea72b 100644 Binary files a/docs/reference/plot.mkinfit-1.png and b/docs/reference/plot.mkinfit-1.png differ diff --git a/docs/reference/plot.mkinfit-2.png b/docs/reference/plot.mkinfit-2.png index 4a3ddf29..43184bcb 100644 Binary files a/docs/reference/plot.mkinfit-2.png and b/docs/reference/plot.mkinfit-2.png differ diff --git a/docs/reference/plot.mkinfit-3.png b/docs/reference/plot.mkinfit-3.png index 8a9dbd13..8de1babc 100644 Binary files a/docs/reference/plot.mkinfit-3.png and b/docs/reference/plot.mkinfit-3.png differ diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png index a7164caa..4b7a5f27 100644 Binary files a/docs/reference/plot.mkinfit-4.png and b/docs/reference/plot.mkinfit-4.png differ diff --git a/docs/reference/plot.mkinfit-5.png b/docs/reference/plot.mkinfit-5.png index 3545b8d8..50c13686 100644 Binary files a/docs/reference/plot.mkinfit-5.png and b/docs/reference/plot.mkinfit-5.png differ diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png index 3d0fb25e..878e3dd6 100644 Binary files a/docs/reference/plot.mkinfit-6.png and b/docs/reference/plot.mkinfit-6.png differ diff --git a/docs/reference/plot.mkinfit-7.png b/docs/reference/plot.mkinfit-7.png index 85045bc3..e81d2737 100644 Binary files a/docs/reference/plot.mkinfit-7.png and b/docs/reference/plot.mkinfit-7.png differ diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index bc4c743f..96cf564c 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -1,122 +1,90 @@ -Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkinPlot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin + + Skip to contents -
-
-
-
-

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

- Source: R/plot.mkinfit.R - +
+ + +
+
+
+
+

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

+ Source: R/plot.mkinfit.R +
plot.mkinfit.Rd
-
+

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

-
+
+

Usage

# S3 method for mkinfit
 plot(
   x,
@@ -163,8 +131,8 @@ observed data together with the solution of the fitted model.

 plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)
-
-

Arguments

+
+

Arguments

x

Alias for fit introduced for compatibility with the generic S3 method.

@@ -288,25 +256,25 @@ chi2 error percentage.

standardized in the residual plot?

-
-

Value

+
+

Value

The function is called for its side effect.

-
-

Details

+
+

Details

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

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


 # One parent compound, one metabolite, both single first order, path from
 # parent to sink included
@@ -344,26 +312,22 @@ latex is being used for the formatting of the chi2 error level, if
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/plot.mmkin-1.png b/docs/reference/plot.mmkin-1.png index 235e33a7..c4fcb9ac 100644 Binary files a/docs/reference/plot.mmkin-1.png and b/docs/reference/plot.mmkin-1.png differ diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png index 7af84edf..8cc727c3 100644 Binary files a/docs/reference/plot.mmkin-2.png and b/docs/reference/plot.mmkin-2.png differ diff --git a/docs/reference/plot.mmkin-3.png b/docs/reference/plot.mmkin-3.png index 56bfac50..066958c9 100644 Binary files a/docs/reference/plot.mmkin-3.png and b/docs/reference/plot.mmkin-3.png differ diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png index 29439156..09caa509 100644 Binary files a/docs/reference/plot.mmkin-4.png and b/docs/reference/plot.mmkin-4.png differ diff --git a/docs/reference/plot.mmkin-5.png b/docs/reference/plot.mmkin-5.png index 77aa611d..c35f7c80 100644 Binary files a/docs/reference/plot.mmkin-5.png and b/docs/reference/plot.mmkin-5.png differ diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index f3d56cd2..14e63a73 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -1,125 +1,93 @@ -Plot model fits (observed and fitted) and the residuals for a row or column -of an mmkin object — plot.mmkin • mkinPlot model fits (observed and fitted) and the residuals for a row or column +of an mmkin object — plot.mmkin • mkin + + Skip to contents -
-
-
-
-

Plot model fits (observed and fitted) and the residuals for a row or column + +

+
+
+
+

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

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

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.

-
+
+

Usage

# S3 method for mmkin
 plot(
   x,
@@ -138,8 +106,8 @@ the fit of at least one model to the same dataset is shown.

 )
-
-

Arguments

+
+

Arguments

x

An object of class mmkin, with either one row or one column.

@@ -202,24 +170,24 @@ than two rows of plots are shown.

mkinresplot.

-
-

Value

+
+

Value

The function is called for its side effect.

-
-

Details

+
+

Details

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

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


   # \dontrun{
   # Only use one core not to offend CRAN checks
@@ -248,26 +216,22 @@ latex is being used for the formatting of the chi2 error level.
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/plot.nafta.html b/docs/reference/plot.nafta.html index 81cfd7b2..2c45a94b 100644 --- a/docs/reference/plot.nafta.html +++ b/docs/reference/plot.nafta.html @@ -1,126 +1,93 @@ -Plot the results of the three models used in the NAFTA scheme. — plot.nafta • mkinPlot the results of the three models used in the NAFTA scheme. — plot.nafta • mkin + + Skip to contents -
-
-
-
-

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

- Source: R/nafta.R - +
+ + +
+
+
+
+

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

+ Source: R/nafta.R +
plot.nafta.Rd
-
+

The plots are ordered with increasing complexity of the model in this function (SFO, then IORE, then DFOP).

-
+
+

Usage

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

Arguments

+
+

Arguments

x

An object of class nafta.

@@ -137,41 +104,37 @@ function (SFO, then IORE, then DFOP).

Further arguments passed to plot.mmkin.

-
-

Value

+
+

Value

The function is called for its side effect.

-
-

Details

+
+

Details

Calls plot.mmkin.

-
-

Author

+
+

Author

Johannes Ranke

-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/read_spreadsheet.html b/docs/reference/read_spreadsheet.html index 7603cee2..be291403 100644 --- a/docs/reference/read_spreadsheet.html +++ b/docs/reference/read_spreadsheet.html @@ -1,5 +1,10 @@ -Read datasets and relevant meta information from a spreadsheet file — read_spreadsheet • mkinRead datasets and relevant meta information from a spreadsheet file — read_spreadsheet • mkin + + Skip to contents -
-
-
-
-

Read datasets and relevant meta information from a spreadsheet file

- Source: R/read_spreadsheet.R - +
+ + +
+
+
+
+

Read datasets and relevant meta information from a spreadsheet file

+ Source: R/read_spreadsheet.R +
read_spreadsheet.Rd
-
+

This function imports one dataset from each sheet of a spreadsheet file. These sheets are selected based on the contents of a sheet 'Datasets', with a column called 'Dataset Number', containing numbers identifying the dataset @@ -119,7 +92,8 @@ variable, which will often be named 'Soil'. Optionally, time normalization factors can be given in columns named 'Temperature' and 'Moisture'.

-
+
+

Usage

read_spreadsheet(
   path,
   valid_datasets = "all",
@@ -128,8 +102,8 @@ factors can be given in columns named 'Temperature' and 'Moisture'.

 )
-
-

Arguments

+
+

Arguments

path

Absolute or relative path to the spreadsheet file

@@ -148,8 +122,8 @@ to use all datasets

and moisture normalisation factors in the sheet 'Datasets'?

-
-

Details

+
+

Details

There must be a sheet 'Compounds', with columns 'Name' and 'Acronym'. The first row read after the header read in from this sheet is assumed to contain name and acronym of the parent compound.

@@ -170,26 +144,22 @@ so they can be easily used for specifying covariate models.

is probably more complicated to use.

-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 847be2cb..e713acfe 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -1,5 +1,16 @@ -Objects exported from other packages — reexports • mkinObjects exported from other packages — reexports • mkin + + Skip to contents -
-
-
-
-

Objects exported from other packages

- Source: R/intervals.R, R/lrtest.mkinfit.R, R/nlme.mmkin.R - +
+ + +
+
+
+
+

Objects exported from other packages

+ Source: R/intervals.R, R/lrtest.mkinfit.R, R/nlme.mmkin.R +
reexports.Rd
-
+

These objects are imported from other packages. Follow the links below to see their documentation.

lmtest
@@ -134,26 +110,21 @@ below to see their documentation.

-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html index 0115cc3f..332f2bfd 100644 --- a/docs/reference/residuals.mkinfit.html +++ b/docs/reference/residuals.mkinfit.html @@ -1,124 +1,90 @@ -Extract residuals from an mkinfit model — residuals.mkinfit • mkinExtract residuals from an mkinfit model — residuals.mkinfit • mkin + + Skip to contents -
-
-
-
-

Extract residuals from an mkinfit model

- Source: R/residuals.mkinfit.R - +
+ + +
+
+
+
+

Extract residuals from an mkinfit model

+ Source: R/residuals.mkinfit.R +
residuals.mkinfit.Rd
-
+

Extract residuals from an mkinfit model

-
+
+

Usage

# S3 method for mkinfit
 residuals(object, standardized = FALSE, ...)
-
-

Arguments

+
+

Arguments

object

A mkinfit object

@@ -133,8 +99,8 @@ standard deviation obtained from the fitted error model?

-
-

Examples

+
+

Examples

f <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE)
 residuals(f)
 #> [1]  0.09726374 -0.13912142 -0.15351210  0.73388322 -0.08657004 -0.93204702
@@ -144,26 +110,22 @@ standard deviation obtained from the fitted error model?

 #> [7] -0.04695355  2.08761977 -1.27002287
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/saem-1.png b/docs/reference/saem-1.png index 9e310252..1fa206c4 100644 Binary files a/docs/reference/saem-1.png and b/docs/reference/saem-1.png differ diff --git a/docs/reference/saem-2.png b/docs/reference/saem-2.png index de1bcf57..e5c62c35 100644 Binary files a/docs/reference/saem-2.png and b/docs/reference/saem-2.png differ diff --git a/docs/reference/saem-3.png b/docs/reference/saem-3.png index 8667ef06..09eb2d40 100644 Binary files a/docs/reference/saem-3.png and b/docs/reference/saem-3.png differ diff --git a/docs/reference/saem-4.png b/docs/reference/saem-4.png index cd464533..36deeada 100644 Binary files a/docs/reference/saem-4.png and b/docs/reference/saem-4.png differ diff --git a/docs/reference/saem.html b/docs/reference/saem.html index 527718ef..b295ab64 100644 --- a/docs/reference/saem.html +++ b/docs/reference/saem.html @@ -1,122 +1,90 @@ -Fit nonlinear mixed models with SAEM — saem • mkinFit nonlinear mixed models with SAEM — saem • mkin + + Skip to contents -
-
-
-
-

Fit nonlinear mixed models with SAEM

- Source: R/saem.R - +
+ + +
+
+
+
+

Fit nonlinear mixed models with SAEM

+ Source: R/saem.R +
saem.Rd
-
+

This function uses saemix::saemix() as a backend for fitting nonlinear mixed effects models created from mmkin row objects using the Stochastic Approximation Expectation Maximisation algorithm (SAEM).

-
+
+

Usage

saem(object, ...)
 
 # S3 method for mmkin
@@ -166,8 +134,8 @@ Expectation Maximisation algorithm (SAEM).

 saemix_data(object, covariates = NULL, verbose = FALSE, ...)
-
-

Arguments

+
+

Arguments

object

An mmkin row object containing several fits of the same mkinmod model to different datasets

@@ -275,8 +243,8 @@ and the end of the optimisation process?

Number of digits to use for printing

-
-

Value

+
+

Value

An S3 object of class 'saem.mmkin', containing the fitted @@ -289,21 +257,21 @@ object also inherits from 'mixed.mmkin'.

An saemix::SaemixData object.

-
-

Details

+
+

Details

An mmkin row object is essentially a list of mkinfit objects that have been obtained by fitting the same model to a list of datasets using mkinfit.

Starting values for the fixed effects (population mean parameters, argument psi0 of saemix::saemixModel() are the mean values of the parameters found using mmkin.

-
-

See also

+
+

See also

summary.saem.mmkin plot.mixed.mmkin

-
-

Examples

+
+

Examples

# \dontrun{
 ds <- lapply(experimental_data_for_UBA_2019[6:10],
  function(x) subset(x$data[c("name", "time", "value")]))
@@ -445,9 +413,9 @@ using mmkin.

 summary(f_saem_dfop_sfo, data = TRUE)
 #> saemix version used for fitting:      3.2 
 #> mkin version used for pre-fitting:  1.2.6 
-#> R version used for fitting:         4.3.1 
-#> Date of fit:     Mon Oct 30 09:34:35 2023 
-#> Date of summary: Mon Oct 30 09:34:35 2023 
+#> R version used for fitting:         4.3.2 
+#> Date of fit:     Thu Nov 16 04:17:34 2023 
+#> Date of summary: Thu Nov 16 04:17:34 2023 
 #> 
 #> Equations:
 #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -462,7 +430,7 @@ using mmkin.

 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted in 8.745 s
+#> Fitted in 3.385 s
 #> Using 300, 100 iterations and 10 chains
 #> 
 #> Variance model: Constant variance 
@@ -758,26 +726,22 @@ using mmkin.

 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/schaefer07_complex_case-1.png b/docs/reference/schaefer07_complex_case-1.png index a1d7d2f2..41665b13 100644 Binary files a/docs/reference/schaefer07_complex_case-1.png and b/docs/reference/schaefer07_complex_case-1.png differ diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index abef385d..211c4559 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -1,127 +1,95 @@ -Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • mkinMetabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • mkin + + Skip to contents -
-
-
-
-

Metabolism data set used for checking the software quality of KinGUI

- +
+
+
+
+

Metabolism data set used for checking the software quality of KinGUI

+ +
schaefer07_complex_case.Rd
-
+

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.

-
+
+

Usage

schaefer07_complex_case
-
-

Format

+
+

Format

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

time

a numeric vector

@@ -143,16 +111,16 @@

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

-
-

References

+
+

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

+
+

Examples

data <- mkin_wide_to_long(schaefer07_complex_case, time = "time")
 model <- mkinmod(
   parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE),
@@ -198,26 +166,22 @@
 #> 14 metabolite A2               DT50 28.2400    28.4500       0.7
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/set_nd_nq.html b/docs/reference/set_nd_nq.html index 249a7600..a2063d05 100644 --- a/docs/reference/set_nd_nq.html +++ b/docs/reference/set_nd_nq.html @@ -1,118 +1,87 @@ -Set non-detects and unquantified values in residue series without replicates — set_nd_nq • mkinSet non-detects and unquantified values in residue series without replicates — set_nd_nq • mkin + + Skip to contents -
-
-
-
-

Set non-detects and unquantified values in residue series without replicates

- Source: R/set_nd_nq.R - +
+ + +
+
+
+
+

Set non-detects and unquantified values in residue series without replicates

+ Source: R/set_nd_nq.R +
set_nd_nq.Rd
-
+

This function automates replacing unquantified values in residue time and depth series. For time series, the function performs part of the residue processing proposed in the FOCUS kinetics guidance for parent compounds @@ -120,7 +89,8 @@ and metabolites. For two-dimensional residue series over time and depth, it automates the proposal of Boesten et al (2015).

-
+
+

Usage

set_nd_nq(res_raw, lod, loq = NA, time_zero_presence = FALSE)
 
 set_nd_nq_focus(
@@ -133,8 +103,8 @@ it automates the proposal of Boesten et al (2015).

 )
-
-

Arguments

+
+

Arguments

res_raw

Character vector of a residue time series, or matrix of residue values with rows representing depth profiles for a specific sampling @@ -174,19 +144,19 @@ in case it is a non-detection?

non-detection that occurs after the quantified values?

-
-

Value

+
+

Value

A numeric vector, if a vector was supplied, or a numeric matrix otherwise

-
-

Functions

+
+

Functions

  • set_nd_nq_focus(): Set non-detects in residue time series according to FOCUS rules

-
-

References

+
+

References

Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H. J. and Pol, J. W. (2015). Leaching of plant protection products and their transformation products; Proposals for improving the assessment of leaching @@ -197,8 +167,8 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi 18 December 2014, p. 251

-
-

Examples

+
+

Examples

# FOCUS (2014) p. 75/76 and 131/132
 parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
 set_nd_nq(parent_1, 0.02)
@@ -255,26 +225,22 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi
 #> [7,]    NA    NA    NA   NA   NA   NA
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/sigma_twocomp-1.png b/docs/reference/sigma_twocomp-1.png index 0353b72c..3671c658 100644 Binary files a/docs/reference/sigma_twocomp-1.png and b/docs/reference/sigma_twocomp-1.png differ diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 06bae61f..93641862 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -1,125 +1,92 @@ -Two-component error model — sigma_twocomp • mkinTwo-component error model — sigma_twocomp • mkin + + Skip to contents -
-
-
-
-

Two-component error model

- Source: R/sigma_twocomp.R - +
+ + +
+
+
+
+

Two-component error model

+ Source: R/sigma_twocomp.R +
sigma_twocomp.Rd
-
+

Function describing the standard deviation of the measurement error in dependence of the measured value \(y\):

-
+
+

Usage

sigma_twocomp(y, sigma_low, rsd_high)
-
-

Arguments

+
+

Arguments

y

The magnitude of the observed value

@@ -134,14 +101,14 @@ observed values

deviation with the magnitude of the observed value

-
-

Value

+
+

Value

The standard deviation of the response variable.

-
-

Details

+
+

Details

$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$ sigma = sqrt(sigma_low^2 + y^2 * rsd_high^2)

This is the error model used for example by Werner et al. (1978). The model @@ -149,8 +116,8 @@ proposed by Rocke and Lorenzato (1995) can be written in this form as well, but assumes approximate lognormal distribution of errors for high values of y.

-
-

References

+
+

References

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

@@ -162,8 +129,8 @@ Degradation Data. Environments 6(12) 124 .

-
-

Examples

+
+

Examples

times <- c(0, 1, 3, 7, 14, 28, 60, 90, 120)
 d_pred <- data.frame(time = times, parent = 100 * exp(- 0.03 * times))
 set.seed(123456)
@@ -193,26 +160,22 @@ Degradation Data. Environments 6(12) 124
 #> f_mkin_tc     4 101.6446
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/status.html b/docs/reference/status.html index 2ff35423..80745bf3 100644 --- a/docs/reference/status.html +++ b/docs/reference/status.html @@ -1,118 +1,84 @@ -Method to get status information for fit array objects — status • mkinMethod to get status information for fit array objects — status • mkin + + Skip to contents -
-
-
-
-

Method to get status information for fit array objects

- Source: R/status.R - +
+ + +
+
+
+
+

Method to get status information for fit array objects

+ Source: R/status.R +
status.Rd
-
+

Method to get status information for fit array objects

-
+
+

Usage

status(object, ...)
 
 # S3 method for mmkin
@@ -128,8 +94,8 @@
 print(x, ...)
-
-

Arguments

+
+

Arguments

object

The object to investigate

@@ -142,16 +108,16 @@

The object to be printed

-
-

Value

+
+

Value

An object with the same dimensions as the fit array suitable printing method.

-
-

Examples

+
+

Examples

# \dontrun{
 fits <- mmkin(
   c("SFO", "FOMC"),
@@ -170,26 +136,22 @@ suitable printing method.

 # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index fe24f3a4..3b732076 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -1,118 +1,87 @@ -Summary method for class "mkinfit" — summary.mkinfit • mkinSummary method for class "mkinfit" — summary.mkinfit • mkin + + Skip to contents -
-
-
-
-

Summary method for class "mkinfit"

- Source: R/summary.mkinfit.R - +
+ + +
+
+
+
+

Summary method for class "mkinfit"

+ Source: R/summary.mkinfit.R +
summary.mkinfit.Rd
-
+

Lists model equations, initial parameter values, optimised parameters with some uncertainty statistics, the chi2 error levels calculated according to FOCUS guidance (2006) as defined therein, formation fractions, DT50 values @@ -120,7 +89,8 @@ and optionally the data, consisting of observed, predicted and residual values.

-
+
+

Usage

# S3 method for mkinfit
 summary(object, data = TRUE, distimes = TRUE, alpha = 0.05, ...)
 
@@ -128,8 +98,8 @@ values.

 print(x, digits = max(3, getOption("digits") - 3), ...)
-
-

Arguments

+
+

Arguments

object

an object of class mkinfit.

@@ -161,8 +131,8 @@ distribution

Number of digits to use for printing

-
-

Value

+
+

Value

The summary function returns a list with components, among others

@@ -217,34 +187,34 @@ g of SFORB systems in the model.

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

-
-

References

+
+

References

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

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


   summary(mkinfit("SFO", FOCUS_2006_A, quiet = TRUE))
 #> mkin version used for fitting:    1.2.6 
-#> R version used for fitting:       4.3.1 
-#> Date of fit:     Mon Oct 30 09:39:49 2023 
-#> Date of summary: Mon Oct 30 09:39:49 2023 
+#> R version used for fitting:       4.3.2 
+#> Date of fit:     Thu Nov 16 04:19:39 2023 
+#> Date of summary: Thu Nov 16 04:19:39 2023 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 131 model solutions performed in 0.02 s
+#> Fitted using 131 model solutions performed in 0.009 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -311,26 +281,22 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/summary.mmkin.html b/docs/reference/summary.mmkin.html index 9b10a415..6f79cfe9 100644 --- a/docs/reference/summary.mmkin.html +++ b/docs/reference/summary.mmkin.html @@ -1,120 +1,87 @@ -Summary method for class "mmkin" — summary.mmkin • mkinSummary method for class "mmkin" — summary.mmkin • mkin + + Skip to contents -
-
-
-
-

Summary method for class "mmkin"

- Source: R/summary.mmkin.R - +
+ + +
+
+
+
+

Summary method for class "mmkin"

+ Source: R/summary.mmkin.R +
summary.mmkin.Rd
-
+

Shows status information on the mkinfit objects contained in the object and gives an overview of ill-defined parameters calculated by illparms.

-
+
+

Usage

# S3 method for mmkin
 summary(object, conf.level = 0.95, ...)
 
@@ -122,8 +89,8 @@ and gives an overview of ill-defined parameters calculated by print(x, digits = max(3, getOption("digits") - 3), ...)
-
-

Arguments

+
+

Arguments

object

an object of class mmkin

@@ -145,8 +112,8 @@ and gives an overview of ill-defined parameters calculated by -

Examples

+
+

Examples


 fits <- mmkin(
   c("SFO", "FOMC"),
@@ -157,7 +124,7 @@ and gives an overview of ill-defined parameters calculated by #> false convergence (8)
   summary(fits)
 #> Error model: Constant variance 
-#> Fitted in 0.705 s
+#> Fitted in 0.454 s
 #> 
 #> Status:
 #>       dataset
@@ -177,26 +144,22 @@ and gives an overview of ill-defined parameters calculated by
-
- -
+
-
- diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index 58eb3e21..e16b550a 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -1,118 +1,87 @@ -Summary method for class "nlme.mmkin" — summary.nlme.mmkin • mkinSummary method for class "nlme.mmkin" — summary.nlme.mmkin • mkin + + Skip to contents -
-
-
-
-

Summary method for class "nlme.mmkin"

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

Summary method for class "nlme.mmkin"

+ Source: R/summary.nlme.mmkin.R +
summary.nlme.mmkin.Rd
-
+

Lists model equations, initial parameter values, optimised parameters for fixed effects (population), random effects (deviations from the population mean) and residual error model, as well as the resulting @@ -120,7 +89,8 @@ endpoints such as formation fractions and DT50 values. Optionally (default is FALSE), the data are listed in full.

-
+
+

Usage

# S3 method for nlme.mmkin
 summary(
   object,
@@ -135,8 +105,8 @@ endpoints such as formation fractions and DT50 values. Optionally
 print(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...)
-
-

Arguments

+
+

Arguments

object

an object of class nlme.mmkin

@@ -172,8 +142,8 @@ distribution

Number of digits to use for printing

-
-

Value

+
+

Value

The summary function returns a list based on the nlme object @@ -212,14 +182,14 @@ model.

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

-
-

Author

+
+

Author

Johannes Ranke for the mkin specific parts José Pinheiro and Douglas Bates for the components inherited from nlme

-
-

Examples

+
+

Examples


 # Generate five datasets following SFO kinetics
 sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
@@ -256,9 +226,9 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

 summary(f_nlme, data = TRUE)
 #> nlme version used for fitting:      3.1.163 
 #> mkin version used for pre-fitting:  1.2.6 
-#> R version used for fitting:         4.3.1 
-#> Date of fit:     Mon Oct 30 09:39:53 2023 
-#> Date of summary: Mon Oct 30 09:39:53 2023 
+#> R version used for fitting:         4.3.2 
+#> Date of fit:     Thu Nov 16 04:19:41 2023 
+#> Date of summary: Thu Nov 16 04:19:41 2023 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -268,7 +238,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted in 0.451 s using 4 iterations
+#> Fitted in 0.182 s using 4 iterations
 #> 
 #> Variance model: Two-component variance function 
 #> 
@@ -412,26 +382,22 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/summary.saem.mmkin.html b/docs/reference/summary.saem.mmkin.html index 54e5260b..bf42a4d9 100644 --- a/docs/reference/summary.saem.mmkin.html +++ b/docs/reference/summary.saem.mmkin.html @@ -1,118 +1,87 @@ -Summary method for class "saem.mmkin" — summary.saem.mmkin • mkinSummary method for class "saem.mmkin" — summary.saem.mmkin • mkin + + Skip to contents -
-
-
-
-

Summary method for class "saem.mmkin"

- Source: R/summary.saem.mmkin.R - +
+ + +
+
+
+
+

Summary method for class "saem.mmkin"

+ Source: R/summary.saem.mmkin.R +
summary.saem.mmkin.Rd
-
+

Lists model equations, initial parameter values, optimised parameters for fixed effects (population), random effects (deviations from the population mean) and residual error model, as well as the resulting @@ -120,7 +89,8 @@ endpoints such as formation fractions and DT50 values. Optionally (default is FALSE), the data are listed in full.

-
+
+

Usage

# S3 method for saem.mmkin
 summary(
   object,
@@ -136,8 +106,8 @@ endpoints such as formation fractions and DT50 values. Optionally
 print(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...)
-
-

Arguments

+
+

Arguments

object

an object of class saem.mmkin

@@ -179,8 +149,8 @@ included.

Number of digits to use for printing

-
-

Value

+
+

Value

The summary function returns a list based on the saemix::SaemixObject

@@ -224,14 +194,14 @@ model.

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

-
-

Author

+
+

Author

Johannes Ranke for the mkin specific parts saemix authors for the parts inherited from saemix.

-
-

Examples

+
+

Examples

# Generate five datasets following DFOP-SFO kinetics
 sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
 dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "m1"),
@@ -334,9 +304,9 @@ saemix authors for the parts inherited from saemix.

 summary(f_saem_dfop_sfo_2, data = TRUE)
 #> saemix version used for fitting:      3.2 
 #> mkin version used for pre-fitting:  1.2.6 
-#> R version used for fitting:         4.3.1 
-#> Date of fit:     Mon Oct 30 09:40:27 2023 
-#> Date of summary: Mon Oct 30 09:40:27 2023 
+#> R version used for fitting:         4.3.2 
+#> Date of fit:     Thu Nov 16 04:19:57 2023 
+#> Date of summary: Thu Nov 16 04:19:57 2023 
 #> 
 #> Equations:
 #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -351,7 +321,7 @@ saemix authors for the parts inherited from saemix.

 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted in 19.763 s
+#> Fitted in 9.193 s
 #> Using 300, 100 iterations and 10 chains
 #> 
 #> Variance model: Two-component variance function 
@@ -654,26 +624,22 @@ saemix authors for the parts inherited from saemix.
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/summary_listing.html b/docs/reference/summary_listing.html index 315f7192..92c3be1e 100644 --- a/docs/reference/summary_listing.html +++ b/docs/reference/summary_listing.html @@ -1,120 +1,87 @@ -Display the output of a summary function according to the output format — summary_listing • mkinDisplay the output of a summary function according to the output format — summary_listing • mkin + + Skip to contents -
-
-
-
-

Display the output of a summary function according to the output format

- Source: R/summary_listing.R - +
+ + +
+
+
+
+

Display the output of a summary function according to the output format

+ Source: R/summary_listing.R +
summary_listing.Rd
-
+

This function is intended for use in a R markdown code chunk with the chunk option results = "asis".

-
+
+

Usage

summary_listing(object, caption = NULL, label = NULL, clearpage = TRUE)
 
 tex_listing(object, caption = NULL, label = NULL, clearpage = TRUE)
@@ -122,8 +89,8 @@ option results = "asis".

 html_listing(object, caption = NULL)
-
-

Arguments

+
+

Arguments

object

The object for which the summary is to be listed

@@ -141,26 +108,22 @@ option results = "asis".

-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/synthetic_data_for_UBA_2014-1.png b/docs/reference/synthetic_data_for_UBA_2014-1.png index 132380a8..11eae1f9 100644 Binary files a/docs/reference/synthetic_data_for_UBA_2014-1.png and b/docs/reference/synthetic_data_for_UBA_2014-1.png differ diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html index ee71a4dd..7fd2de80 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -1,5 +1,20 @@ -Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkinSynthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin + + Skip to contents -
-
-
-
-

Synthetic datasets for one parent compound with two metabolites

- +
+
+
+
+

Synthetic datasets for one parent compound with two metabolites

+ +
synthetic_data_for_UBA_2014.Rd
-
+

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 two sequential or two parallel metabolites.

@@ -142,12 +122,13 @@ Compare also the code in the example section to see the degradation models.">Compare also the code in the example section to see the degradation models.

-
+
+

Usage

synthetic_data_for_UBA_2014
-
-

Format

+
+

Format

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

title

The name of the dataset, e.g. SFO_lin_a

@@ -157,16 +138,16 @@ Compare also the code in the example section to see the degradation models.">
-
-

Source

+
+

Source

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

-
-

Examples

+
+

Examples

# \dontrun{
 # The data have been generated using the following kinetic models
 m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
@@ -273,9 +254,9 @@ Compare also the code in the example section to see the degradation models.">
   summary(fit)
 #> mkin version used for fitting:    1.2.6 
-#> R version used for fitting:       4.3.1 
-#> Date of fit:     Mon Oct 30 09:40:49 2023 
-#> Date of summary: Mon Oct 30 09:40:49 2023 
+#> R version used for fitting:       4.3.2 
+#> Date of fit:     Thu Nov 16 04:20:07 2023 
+#> Date of summary: Thu Nov 16 04:20:07 2023 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -284,7 +265,7 @@ Compare also the code in the example section to see the degradation models.">#> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 848 model solutions performed in 0.408 s
+#> Fitted using 848 model solutions performed in 0.166 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -423,26 +404,22 @@ Compare also the code in the example section to see the degradation models."># }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png index e4fc2a4c..a007a102 100644 Binary files a/docs/reference/test_data_from_UBA_2014-1.png and b/docs/reference/test_data_from_UBA_2014-1.png differ diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png index 4ce36561..f460ac83 100644 Binary files a/docs/reference/test_data_from_UBA_2014-2.png and b/docs/reference/test_data_from_UBA_2014-2.png differ diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index 67acdb54..c124bd9a 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -1,125 +1,92 @@ -Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014 • mkinThree experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014 • mkin + + Skip to contents -
-
-
-
-

Three experimental datasets from two water sediment systems and one soil

- +
+
+
+
+

Three experimental datasets from two water sediment systems and one soil

+ +
test_data_from_UBA_2014.Rd
-
+

The datasets were used for the comparative validation of several kinetic evaluation software packages (Ranke, 2014).

-
+
+

Usage

test_data_from_UBA_2014
-
-

Format

+
+

Format

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

title

The name of the dataset, e.g. UBA_2014_WS_river

@@ -129,14 +96,14 @@
-
-

Source

+
+

Source

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

-
-

Examples

+
+

Examples

  # \dontrun{
   # This is a level P-II evaluation of the dataset according to the FOCUS kinetics
   # guidance. Due to the strong correlation of the parameter estimates, the
@@ -213,26 +180,22 @@
   # }
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index aade8415..1e28ddc2 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -1,5 +1,10 @@ -Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkinFunctions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin + + Skip to contents -
-
-
-
-

Functions to transform and backtransform kinetic parameters for fitting

- Source: R/transform_odeparms.R - + +
+
+
+
+

Functions to transform and backtransform kinetic parameters for fitting

+ Source: R/transform_odeparms.R +
transform_odeparms.Rd
-
+

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 parameters that can only take on positive values, a @@ -122,7 +92,8 @@ formations fractions that should always sum up to 1 and can not be negative, the ilr transformation is used.

-
+
+

Usage

transform_odeparms(
   parms,
   mkinmod,
@@ -138,8 +109,8 @@ the ilr transformation is used.

 )
-
-

Arguments

+
+

Arguments

parms

Parameters of kinetic models as used in the differential equations.

@@ -179,25 +150,25 @@ exceed one, the ilr transformation is used.

fitting procedure.

-
-

Value

+
+

Value

A vector of transformed or backtransformed parameters

-
-

Details

+
+

Details

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.

-
-

Author

+
+

Author

Johannes Ranke

-
-

Examples

+
+

Examples


 SFO_SFO <- mkinmod(
   parent = list(type = "SFO", to = "m1", sink = TRUE),
@@ -313,26 +284,22 @@ This is no problem for the internal use in mkinfit.
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- diff --git a/docs/reference/update.mkinfit-1.png b/docs/reference/update.mkinfit-1.png index 12fe1f5b..9278aefd 100644 Binary files a/docs/reference/update.mkinfit-1.png and b/docs/reference/update.mkinfit-1.png differ diff --git a/docs/reference/update.mkinfit-2.png b/docs/reference/update.mkinfit-2.png index 21817f94..f73a6180 100644 Binary files a/docs/reference/update.mkinfit-2.png and b/docs/reference/update.mkinfit-2.png differ diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index 10f9e8a2..5d4812bf 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -1,130 +1,99 @@ -Update an mkinfit model with different arguments — update.mkinfit • mkinUpdate an mkinfit model with different arguments — update.mkinfit • mkin + + Skip to contents -
-
-
-
-

Update an mkinfit model with different arguments

- Source: R/update.mkinfit.R - +
+ + +
+
+
+
+

Update an mkinfit model with different arguments

+ Source: R/update.mkinfit.R +
update.mkinfit.Rd
-
+

This function will return an updated mkinfit object. The fitted degradation model parameters from the old fit are used as starting values for the updated fit. Values specified as 'parms.ini' and/or 'state.ini' will override these starting values.

-
+
+

Usage

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

Arguments

+
+

Arguments

object

An mkinfit object to be updated

@@ -140,8 +109,8 @@ remove arguments given in the original call

-
-

Examples

+
+

Examples

# \dontrun{
 fit <- mkinfit("SFO", subset(FOCUS_2006_D, value != 0), quiet = TRUE)
 parms(fit)
@@ -158,26 +127,22 @@ remove arguments given in the original call

 # }
-
- -
+
-
- -- cgit v1.2.1