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Diffstat (limited to 'vignettes/mkin.Rmd')
| -rw-r--r-- | vignettes/mkin.Rmd | 16 |
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 |