From 39b2c2c762b03922a2648b1b226d0f308600cc87 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 6 Jun 2018 01:24:15 +0200 Subject: Static documentation rebuilt by pkgdown 1.1.0 --- docs/reference/index.html | 655 +++++++++++++++++++++++----------------------- 1 file changed, 332 insertions(+), 323 deletions(-) (limited to 'docs/reference/index.html') diff --git a/docs/reference/index.html b/docs/reference/index.html index 6c05941d..5785b5aa 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -21,13 +21,19 @@ + + + - - - + + + + + + @@ -50,8 +56,12 @@ - mkin + + mkin + 0.9.47.1 + + @@ -99,330 +110,326 @@ -
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- Reference - version 0.9.47.1 -

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Reference

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Main functions

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Essential functionality

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mkinmod

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

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mkinfit

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

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mmkin

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

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Show results

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Functions working with mkinfit objects

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plot.mkinfit

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

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summary print

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Summary method for class "mkinfit"

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mkinresplot

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Function to plot residuals stored in an mkin object

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mkinparplot

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Function to plot the confidence intervals obtained using mkinfit

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endpoints

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

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mkinerrmin

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

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Work with mmkin objects

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Functions working with aggregated results

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[.mmkin

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Subsetting method for mmkin objects

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plot

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

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Datasets and known results

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FOCUS_2006_datasets

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Datasets A to F from the FOCUS Kinetics report from 2006

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FOCUS_2006_SFO_ref_A_to_F

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

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FOCUS_2006_FOMC_ref_A_to_F

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

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FOCUS_2006_HS_ref_A_to_F

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

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FOCUS_2006_DFOP_ref_A_to_B

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

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mccall81_245T

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

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schaefer07_complex_case

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Metabolism data set used for checking the software quality of KinGUI

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synthetic_data_for_UBA_2014

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Synthetic datasets for one parent compound with two metabolites

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test_data_from_UBA_2014

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Three experimental datasets from two water sediment systems and one soil

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mkinds

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A dataset class for mkin

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print

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Print mkinds objects

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Helper functions

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geometric_mean

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Calculate the geometric mean

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mkinsub

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Function to set up a kinetic submodel for one state variable

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max_twa_parent

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

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mkinpredict

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Produce predictions from a kinetic model using specific parameters

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mkin_wide_to_long

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Convert a dataframe with observations over time into long format

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mkin_long_to_wide

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Convert a dataframe from long to wide format

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print

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Print mkinmod objects

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transform_odeparms backtransform_odeparms

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Functions to transform and backtransform kinetic parameters for fitting

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ilr invilr

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Function to perform isometric log-ratio transformation

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sigma_rl

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Two component error model of Rocke and Lorenzato

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Analytical solutions

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Parent only model solutions

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SFO.solution

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Single First-Order kinetics

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FOMC.solution

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First-Order Multi-Compartment kinetics

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DFOP.solution

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Double First-Order in Parallel kinetics

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SFORB.solution

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Single First-Order Reversible Binding kinetics

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HS.solution

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Hockey-Stick kinetics

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IORE.solution

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Indeterminate order rate equation kinetics

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Generate synthetic datasets

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add_err

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Add normally distributed errors to simulated kinetic degradation data

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Deprecated functions

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Functions that have been superseeded

-
-

mkinplot

-

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

-
+ + + +

Main functions

+

Essential functionality

+ + + + + +

mkinmod()

+ +

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()

+ +

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

+ + + + +

Show results

+

Functions working with mkinfit objects

+ + + + + +

plot(<mkinfit>) plot_sep()

+ +

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

+ + + +

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

+ +

Summary method for class "mkinfit"

+ + + +

mkinresplot()

+ +

Function to plot residuals stored in an mkin object

+ + + +

mkinparplot()

+ +

Function to plot the confidence intervals obtained using mkinfit

+ + + +

endpoints()

+ +

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

+ + + +

mkinerrmin()

+ +

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

+ + + + +

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

+ + + + +

Datasets and known results

+

+ + + + + +

FOCUS_2006_datasets

+ +

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)

+ + + +

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

+ + + +

test_data_from_UBA_2014

+ +

Three experimental datasets from two water sediment systems and one soil

+ + + +

mkinds

+ +

A dataset class for mkin

+ + + +

print(<mkinds>)

+ +

Print mkinds objects

+ + + + +

Helper functions

+

+ + + + + +

geometric_mean()

+ +

Calculate the geometric mean

+ + + +

mkinsub()

+ +

Function to set up a kinetic submodel for one state variable

+ + + +

max_twa_parent()

+ +

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

+ + + +

mkinpredict()

+ +

Produce predictions from a kinetic model using specific parameters

+ + + +

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

+ + + +

print(<mkinmod>)

+ +

Print mkinmod objects

+ + + +

transform_odeparms() backtransform_odeparms()

+ +

Functions to transform and backtransform kinetic parameters for fitting

+ + + +

ilr() invilr()

+ +

Function to perform isometric log-ratio transformation

+ + + +

sigma_rl()

+ +

Two component error model of Rocke and Lorenzato

+ + + + +

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

+ + + + +

Generate synthetic datasets

+

+ + + + + +

add_err()

+ +

Add normally distributed errors to simulated kinetic degradation data

+ + + + +

Deprecated functions

+

Functions that have been superseeded

+ + + + + +

mkinplot()

+ +

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

+ + +
+ + -- cgit v1.2.1