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author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-29 16:05:11 +0200 |
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committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-29 16:05:11 +0200 |
commit | e6f9e9ca89e35e610d9895b979f1351a47451db0 (patch) | |
tree | dd9d389c05e35db7a86abd578751199cd2c6a1be /man | |
parent | 510436646b1bdd5b8cfab70be29334bd3cc9c828 (diff) |
Improve handling of warnings, reorganize tests
Diffstat (limited to 'man')
-rw-r--r-- | man/mkinfit.Rd | 65 |
1 files changed, 65 insertions, 0 deletions
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index 748dcb50..7f5092c5 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -214,6 +214,71 @@ When using the "IORE" submodel for metabolites, fitting with numerical ODE solver. In this situation it may help to switch off the internal rate transformation. } +\examples{ + +# Use shorthand notation for parent only degradation +fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) +summary(fit) + +# One parent compound, one metabolite, both single first order. +# We remove zero values from FOCUS dataset D in order to avoid warnings +FOCUS_D <- subset(FOCUS_2006_D, value != 0) +# Use mkinsub for convenience in model formulation. Pathway to sink included per default. +SFO_SFO <- mkinmod( + parent = mkinsub("SFO", "m1"), + m1 = mkinsub("SFO")) + +# Fit the model quietly to the FOCUS example dataset D using defaults +fit <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE) +# Since mkin 0.9.50.3, we get a warning about non-normality of residuals, +# so we try an alternative error model +fit.tc <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc") +# This avoids the warning, and the likelihood ratio test confirms it is preferable +lrtest(fit.tc, fit) +# We can also allow for different variances of parent and metabolite as error model +fit.obs <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "obs") +# This also avoids the warning about non-normality, but the two-component error model +# has significantly higher likelihood +lrtest(fit.obs, fit.tc) +parms(fit.tc) +endpoints(fit.tc) + +# We can show a quick (only one replication) benchmark for this case, as we +# have several alternative solution methods for the model. We skip +# uncompiled deSolve, as it is so slow. More benchmarks are found in the +# benchmark vignette +\dontrun{ +if(require(rbenchmark)) { + benchmark(replications = 1, order = "relative", columns = c("test", "relative", "elapsed"), + deSolve_compiled = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc", + solution_type = "deSolve", use_compiled = TRUE), + eigen = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc", + solution_type = "eigen"), + analytical = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc", + solution_type = "analytical")) +} +} + +# Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO +\dontrun{ +FOMC_SFO <- mkinmod( + parent = mkinsub("FOMC", "m1"), + m1 = mkinsub("SFO")) +fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE) +# Again, we get a warning and try a more sophisticated error model +fit.FOMC_SFO.tc <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE, error_model = "tc") +# This model has a higher likelihood, but not significantly so +lrtest(fit.tc, fit.FOMC_SFO.tc) +# Also, the missing standard error for log_beta and the t-tests for alpha +# and beta indicate overparameterisation +summary(fit.FOMC_SFO.tc, data = FALSE) + +# We can easily use starting parameters from the parent only fit (only for illustration) +fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, quiet = TRUE, error_model = "tc") +fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE, + parms.ini = fit.FOMC$bparms.ode, error_model = "tc") +} +} \references{ Rocke DM and Lorenzato S (1995) A two-component model for measurement error in analytical chemistry. \emph{Technometrics} 37(2), 176-184. |