From f59b8a93a9956ac46eac24d294f7a26642b995dc Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 14 Sep 2017 12:15:58 +0200 Subject: Convert FOCUS Z vignette to rmarkdown/html - Static documentation rebuilt by pkgdown::build_articles() - DESCRIPTION: Version bump and current date --- docs/articles/mkin.R | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 docs/articles/mkin.R (limited to 'docs/articles/mkin.R') diff --git a/docs/articles/mkin.R b/docs/articles/mkin.R new file mode 100644 index 00000000..67dc3623 --- /dev/null +++ b/docs/articles/mkin.R @@ -0,0 +1,34 @@ +## ---- include = FALSE---------------------------------------------------- +require(knitr) +opts_chunk$set(engine='R', tidy=FALSE) + +## ---- echo = TRUE, cache = TRUE, fig = TRUE, fig.width = 8, fig.height = 7---- +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) + + +# 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, + f_M1_to_M2 = 0.9, k_M2 = log(2)/50), + c(parent = 100, M1 = 0, M2 = 0), + sampling_times) + +# 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")) + -- cgit v1.2.1