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/mkinmod.html | 214 +++++++++++++++++++------------------------- 1 file changed, 90 insertions(+), 124 deletions(-) (limited to 'docs/reference/mkinmod.html') 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 -
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Function to set up a kinetic model with one or more state variables

- Source: R/mkinmod.R, R/mkinsub.R - +
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Function to set up a kinetic model with one or more state variables

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

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Usage

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

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

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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.

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Value

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Value

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

A list for use with mkinmod.

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Details

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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.

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Note

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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.

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References

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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

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Author

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Author

Johannes Ranke

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Examples

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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
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Developed by Johannes Ranke.

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Site built with pkgdown 2.0.7.

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- -- cgit v1.2.1 From 6476f5f49b373cd4cf05f2e73389df83e437d597 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 13 Feb 2025 16:30:31 +0100 Subject: Axis legend formatting, update vignettes --- docs/reference/mkinmod.html | 147 ++++++++++++++++++++------------------------ 1 file changed, 67 insertions(+), 80 deletions(-) (limited to 'docs/reference/mkinmod.html') diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 9d73ea9f..9ddbdc59 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -1,82 +1,69 @@ -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 +components."> Skip to contents - -
- - + + -- cgit v1.2.1