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| author | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-04 11:24:22 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2021-02-04 11:41:06 +0100 |
| commit | ac183c732317cf6ede26a2ee127604a407f0a6b3 (patch) | |
| tree | 2283709a2e01206af576a9cf324f54fbfab972d0 /man/transform_odeparms.Rd | |
| parent | 83798cce97e73ec3bfd11b8cb4e2929e5089aaeb (diff) | |
Documentation improvements, mainly fixing example code
The errors in the example code were in the \dontrun sections, so they
were not caught by CRAN checks. In addition, the static help files
generated with pkgdown were cached, so I noticed the errors only
after completely regenerating the documentation for version 1.0.0.
Diffstat (limited to 'man/transform_odeparms.Rd')
| -rw-r--r-- | man/transform_odeparms.Rd | 18 |
1 files changed, 11 insertions, 7 deletions
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd index f38bb051..3a97ff8d 100644 --- a/man/transform_odeparms.Rd +++ b/man/transform_odeparms.Rd @@ -69,17 +69,21 @@ This is no problem for the internal use in \link{mkinfit}. SFO_SFO <- mkinmod( parent = list(type = "SFO", to = "m1", sink = TRUE), - m1 = list(type = "SFO")) + m1 = list(type = "SFO"), use_of_ff = "min") + # Fit the model to the FOCUS example dataset D using defaults -fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) +FOCUS_D <- subset(FOCUS_2006_D, value != 0) # remove zero values to avoid warning +fit <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE) fit.s <- summary(fit) # Transformed and backtransformed parameters print(fit.s$par, 3) print(fit.s$bpar, 3) \dontrun{ -# Compare to the version without transforming rate parameters -fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE) +# Compare to the version without transforming rate parameters (does not work +# with analytical solution, we get NA values for m1 in predictions) +fit.2 <- mkinfit(SFO_SFO, FOCUS_D, transform_rates = FALSE, + solution_type = "deSolve", quiet = TRUE) fit.2.s <- summary(fit.2) print(fit.2.s$par, 3) print(fit.2.s$bpar, 3) @@ -93,13 +97,13 @@ transform_odeparms(initials, SFO_SFO) backtransform_odeparms(transformed, SFO_SFO) \dontrun{ -# The case of formation fractions +# The case of formation fractions (this is now the default) SFO_SFO.ff <- mkinmod( parent = list(type = "SFO", to = "m1", sink = TRUE), m1 = list(type = "SFO"), use_of_ff = "max") -fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) +fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_D, quiet = TRUE) fit.ff.s <- summary(fit.ff) print(fit.ff.s$par, 3) print(fit.ff.s$bpar, 3) @@ -114,7 +118,7 @@ SFO_SFO.ff.2 <- mkinmod( use_of_ff = "max") -fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE) +fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_D, quiet = TRUE) fit.ff.2.s <- summary(fit.ff.2) print(fit.ff.2.s$par, 3) print(fit.ff.2.s$bpar, 3) |