From b2779693fad072b6bdf5046ca2f1e9e9655eb5a2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Nov 2016 16:59:50 +0100 Subject: Add comments to R code in mkin vignette --- vignettes/mkin.Rmd | 16 ++++++++++++---- vignettes/mkin.html | 36 +++++++++++++++++++++++------------- 2 files changed, 35 insertions(+), 17 deletions(-) diff --git a/vignettes/mkin.Rmd b/vignettes/mkin.Rmd index 906b3b01..a3982df9 100644 --- a/vignettes/mkin.Rmd +++ b/vignettes/mkin.Rmd @@ -34,14 +34,16 @@ measures for data series within one or more compartments, for parent and metabolites. ```{r, echo = TRUE, cache = TRUE, fig = TRUE, fig.width = 8, fig.height = 7} -require(mkin) +library(mkin) +# Define the kinetic model m_SFO_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"), M1 = mkinsub("SFO", "M2"), M2 = mkinsub("SFO"), use_of_ff = "max", quiet = TRUE) -sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) +# Produce model predictions using some arbitrary parameters +sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) d_SFO_SFO_SFO <- mkinpredict(m_SFO_SFO_SFO, c(k_parent = 0.03, f_parent_to_M1 = 0.5, k_M1 = log(2)/100, @@ -49,17 +51,23 @@ d_SFO_SFO_SFO <- mkinpredict(m_SFO_SFO_SFO, c(parent = 100, M1 = 0, M2 = 0), sampling_times) -d_SFO_SFO_SFO_err <- add_err(d_SFO_SFO_SFO, function(x) 3, n = 1, seed = 123456789 ) +# Generate a dataset by adding normally distributed errors with +# standard deviation 3, for two replicates at each sampling time +d_SFO_SFO_SFO_err <- add_err(d_SFO_SFO_SFO, reps = 2, + sdfunc = function(x) 3, + n = 1, seed = 123456789 ) +# Fit the model to the dataset f_SFO_SFO_SFO <- mkinfit(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[1]], quiet = TRUE) +# Plot the results separately for parent and metabolites plot_sep(f_SFO_SFO_SFO, lpos = c("topright", "bottomright", "bottomright")) ``` # Background Many approaches are possible regarding the evaluation of chemical degradation -data. +data. The now deprecated `kinfit` package [@pkg:kinfit] in `R` [@rcore2016] implements the approach recommended in the kinetics report provided by the diff --git a/vignettes/mkin.html b/vignettes/mkin.html index a32c1375..172712f5 100644 --- a/vignettes/mkin.html +++ b/vignettes/mkin.html @@ -11,7 +11,7 @@ - + mkin - Kinetic evaluation of chemical degradation data @@ -24,10 +24,12 @@ + + + + - - -