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authorJohannes Ranke <jranke@uni-bremen.de>2016-11-17 22:58:28 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2016-11-17 22:58:28 +0100
commit98d684becd9495d370e1bcc8f9c7ca758caa4dd8 (patch)
tree94c5e18f755d1c3328fad3fe517fe28b45c2df2f /docs/articles/mkin.R
parent3f6ce570824616f5be0d6289ed65910d455dd266 (diff)
Static documentation rebuilt by pkgdown::build_site()
Diffstat (limited to 'docs/articles/mkin.R')
-rw-r--r--docs/articles/mkin.R24
1 files changed, 18 insertions, 6 deletions
diff --git a/docs/articles/mkin.R b/docs/articles/mkin.R
index 175bd33b..67dc3623 100644
--- a/docs/articles/mkin.R
+++ b/docs/articles/mkin.R
@@ -1,22 +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----
-require(mkin)
+library(mkin)
+# Define the kinetic model
m_SFO_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
M1 = mkinsub("SFO", "M2"),
- M2 = mkinsub("SFO"),
+ 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,
+ 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)
-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"))

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