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-rw-r--r--vignettes/mkin.Rmd16
1 files changed, 12 insertions, 4 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

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