From de040ca33f6b13ef89be89718510f30631b67903 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 31 Jan 2019 15:35:31 +0100 Subject: Static documentation rebuilt by pkgdown --- docs/reference/AIC.mmkin.html | 49 +- docs/reference/CAKE_export.html | 241 +++++++ docs/reference/DFOP.solution.html | 25 +- docs/reference/Extract.mmkin.html | 435 +---------- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 25 +- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 25 +- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 25 +- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 25 +- docs/reference/FOCUS_2006_datasets.html | 23 +- docs/reference/FOMC.solution.html | 25 +- docs/reference/HS.solution.html | 25 +- docs/reference/IORE.solution.html | 42 +- docs/reference/SFO.solution.html | 25 +- docs/reference/SFORB.solution.html | 25 +- docs/reference/add_err.html | 59 +- docs/reference/endpoints.html | 39 +- docs/reference/geometric_mean.html | 25 +- docs/reference/ilr.html | 44 +- docs/reference/index.html | 29 +- docs/reference/logLik.mkinfit.html | 51 +- docs/reference/max_twa_parent.html | 31 +- docs/reference/mccall81_245T.html | 214 +----- docs/reference/mkin_long_to_wide.html | 51 +- docs/reference/mkin_wide_to_long.html | 37 +- docs/reference/mkinds.html | 23 +- docs/reference/mkinerrmin.html | 35 +- docs/reference/mkinfit.html | 957 ++----------------------- docs/reference/mkinmod.html | 66 +- docs/reference/mkinparplot.html | 34 +- docs/reference/mkinplot.html | 27 +- docs/reference/mkinpredict.html | 214 ++---- docs/reference/mkinresplot.html | 38 +- docs/reference/mkinsub.html | 35 +- docs/reference/mmkin.html | 69 +- docs/reference/plot.mkinfit.html | 46 +- docs/reference/plot.mmkin.html | 42 +- docs/reference/print.mkinds.html | 25 +- docs/reference/print.mkinmod.html | 47 +- docs/reference/schaefer07_complex_case.html | 53 +- docs/reference/sigma_twocomp.html | 23 +- docs/reference/summary.mkinfit.html | 102 +-- docs/reference/synthetic_data_for_UBA.html | 23 +- docs/reference/test_data_from_UBA_2014.html | 73 +- docs/reference/transform_odeparms.html | 353 +-------- 44 files changed, 993 insertions(+), 2887 deletions(-) create mode 100644 docs/reference/CAKE_export.html (limited to 'docs/reference') diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index a2ce9885..a90e81bb 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -1,6 +1,6 @@ - + @@ -9,17 +9,17 @@ Calculated the AIC for a column of an mmkin object — AIC.mmkin • mkin - + - - + + - + - + @@ -39,7 +39,8 @@ - + + + + + + + + + +Export a list of datasets in wide format to a CAKE study file — CAKE_export • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + +
+ +
+
+
+

Export a list of datasets in wide format to a CAKE study file

+ + +
+ +
+ +

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

+ +
+ + 
CAKE_export(ds, map = c(parent = "Parent"),
+  links = NA,
+  filename = "CAKE_export.csf", path = ".", overwrite = FALSE,
+  study = "Codlemone aerobic soil degradation",
+  description = "",
+  time_unit = "days",
+  res_unit = "% AR",
+  comment = "Created using mkin::CAKE_export",
+  date = Sys.Date(),
+  optimiser = "IRLS")
+ +

Arguments

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ds

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

map

A character vector with CAKE compartment names (Parent, A1, ...), + named with the names used in the list of datasets.

links

An optional character vector of target compartments, named with + the names of the source compartments. In order to make this + easier, the names are used as in the datasets supplied.

filename

Where to write the result. Should end in .csf in order to be compatible + with CAKE.

path

An optional path to the output file.

overwrite

If TRUE, existing files are overwritten.

study

The name of the study.

description

An optional description.

time_unit

The time unit for the residue data.

res_unit

The unit used for the residues.

comment

An optional comment.

date

The date of file creation.

optimiser

Can be OLS or IRLS.

+ +

Value

+ +

The function is called for its side effect.

+ + +
+ +
+ +
+
+

Developed by Johannes Ranke.

+
+ +
+

Site built with pkgdown 1.3.0.

+
+
+
+ + + + + + diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index ad0ff22a..c82eb161 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -1,6 +1,6 @@ - + @@ -9,17 +9,17 @@ Double First-Order in Parallel kinetics — DFOP.solution • mkin - + - - + + - + - + @@ -39,7 +39,8 @@ - + + - + @@ -9,17 +9,17 @@ Subsetting method for mmkin objects — [.mmkin • mkin - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin - + - - + + - + - + @@ -42,7 +42,8 @@ in this fit." /> - + + - + @@ -9,17 +9,17 @@ Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin - + - - + + - + - + @@ -42,7 +42,8 @@ in this fit." /> - + + - + @@ -9,17 +9,17 @@ Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F • mkin - + - - + + - + - + @@ -42,7 +42,8 @@ in this fit." /> - + + - + @@ -9,17 +9,17 @@ Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F • mkin - + - - + + - + - + @@ -42,7 +42,8 @@ in this fit." /> - + + - + @@ -9,17 +9,17 @@ Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets • mkin - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ First-Order Multi-Compartment kinetics — FOMC.solution • mkin - + - - + + - + - + @@ -42,7 +42,8 @@ The form given here differs slightly from the original reference by Gustafson - + + - + @@ -9,17 +9,17 @@ Hockey-Stick kinetics — HS.solution • mkin - + - - + + - + - + @@ -39,7 +39,8 @@ - + + - + @@ -9,17 +9,17 @@ Indeterminate order rate equation kinetics — IORE.solution • mkin - + - - + + - + - + @@ -39,7 +39,8 @@ - + + - + @@ -9,17 +9,17 @@ Single First-Order kinetics — SFO.solution • mkin - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Single First-Order Reversible Binding kinetics — SFORB.solution • mkin - + - - + + - + - + @@ -42,7 +42,8 @@ - + + - + @@ -9,17 +9,17 @@ Add normally distributed errors to simulated kinetic degradation data — add_err • mkin - + - - + + - + - + @@ -40,7 +40,8 @@ - + + - + @@ -9,17 +9,17 @@ Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints • mkin - + - - + + - + - + @@ -41,7 +41,8 @@ with the advantage that the SFORB model can also be used for metabolites." /> - + + - + @@ -9,17 +9,17 @@ Calculate the geometric mean — geometric_mean • mkin - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Function to perform isometric log-ratio transformation — ilr • mkin - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Function reference • mkin - + - - + + - + - + @@ -35,7 +35,8 @@ - + + - + @@ -9,17 +9,17 @@ Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit • mkin - + - - + + - + - + @@ -55,7 +55,8 @@ In the case of iterative reweighting, the variances obtained by this - + + - + @@ -9,17 +9,17 @@ Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit — max_twa_parent • mkin - + - - + + - + - + @@ -42,7 +42,8 @@ guidance." /> - + + - + @@ -9,17 +9,17 @@ Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin - + - - + + - + - + @@ -40,7 +40,8 @@ - + + - + @@ -9,17 +9,17 @@ Convert a dataframe from long to wide format — mkin_long_to_wide • mkin - + - - + + - + - + @@ -40,7 +40,8 @@ - + + - + @@ -9,17 +9,17 @@ Convert a dataframe with observations over time into long format — mkin_wide_to_long • mkin - + - - + + - + - + @@ -39,7 +39,8 @@ - + + - + @@ -9,17 +9,17 @@ A dataset class for mkin — mkinds • mkin - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Calculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkin - + - - + + - + - + @@ -39,7 +39,8 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." /> - + + - + @@ -9,17 +9,17 @@ Fit a kinetic model to data with one or more state variables — mkinfit • mkin - + - - + + - + - + @@ -48,7 +48,8 @@ - + + - + @@ -9,17 +9,17 @@ Function to set up a kinetic model with one or more state variables — mkinmod • mkin - + - - + + - + - + @@ -43,7 +43,8 @@ For the definition of model types and their parameters, the equations given - + + - + @@ -9,17 +9,17 @@ Function to plot the confidence intervals obtained using mkinfit — mkinparplot • mkin - + - - + + - + - + @@ -39,7 +39,8 @@ - + + - + @@ -9,17 +9,17 @@ Plot the observed data and the fitted model of an mkinfit object — mkinplot • mkin - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin - + - - + + - + - + @@ -40,7 +40,8 @@ - + + - + @@ -9,17 +9,17 @@ Function to plot residuals stored in an mkin object — mkinresplot • mkin - + - - + + - + - + @@ -41,7 +41,8 @@ - + + - + @@ -9,17 +9,17 @@ Function to set up a kinetic submodel for one state variable — mkinsub • mkin - + - - + + - + - + @@ -39,7 +39,8 @@ - + + - + @@ -9,17 +9,17 @@ Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin • mkin - + - - + + - + - + @@ -39,7 +39,8 @@ - + + - + @@ -9,17 +9,17 @@ Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin - + - - + + - + - + @@ -43,7 +43,8 @@ If the current plot device is a tikz device, - + + - + @@ -9,17 +9,17 @@ Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin • mkin - + - - + + - + - + @@ -42,7 +42,8 @@ If the current plot device is a tikz device, - + + - + @@ -9,17 +9,17 @@ Print mkinds objects — print.mkinds • mkin - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Print mkinmod objects — print.mkinmod • mkin - + - - + + - + - + @@ -38,7 +38,8 @@ - + + - + @@ -9,17 +9,17 @@ Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • mkin - + - - + + - + - + @@ -40,7 +40,8 @@ - + + - + @@ -9,17 +9,17 @@ Two component error model — sigma_twocomp • mkin - + - - + + - + - + @@ -43,7 +43,8 @@ This is the error model used for example by Werner et al. (1978). The model - + + - + @@ -9,17 +9,17 @@ Summary method for class "mkinfit" — summary.mkinfit • mkin - + - - + + - + - + @@ -41,7 +41,8 @@ - + + - + @@ -9,17 +9,17 @@ Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin - + - - + + - + - + @@ -53,7 +53,8 @@ Compare also the code in the example section to see the degradation models." /> - + + - + @@ -9,17 +9,17 @@ Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014 • mkin - + - - + + - + - + @@ -39,7 +39,8 @@ - + + - + @@ -9,17 +9,17 @@ Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin - + - - + + - + - + @@ -46,7 +46,8 @@ The transformation of sets of formation fractions is fragile, as it supposes - + +