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author | Johannes Ranke <jranke@uni-bremen.de> | 2017-09-14 12:15:58 +0200 |
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committer | Johannes Ranke <jranke@uni-bremen.de> | 2017-09-14 12:22:12 +0200 |
commit | f59b8a93a9956ac46eac24d294f7a26642b995dc (patch) | |
tree | 4124ed6d8763062d4e1aa097230688728bf159ff /docs/articles/mkin.R | |
parent | 14f8f9f9071fcfa5a51ed42ad3408e495b253207 (diff) |
Convert FOCUS Z vignette to rmarkdown/html
- Static documentation rebuilt by pkgdown::build_articles()
- DESCRIPTION: Version bump and current date
Diffstat (limited to 'docs/articles/mkin.R')
-rw-r--r-- | docs/articles/mkin.R | 34 |
1 files changed, 34 insertions, 0 deletions
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")) + |