From ac183c732317cf6ede26a2ee127604a407f0a6b3 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 4 Feb 2021 11:24:22 +0100 Subject: 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. --- R/transform_odeparms.R | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) (limited to 'R/transform_odeparms.R') diff --git a/R/transform_odeparms.R b/R/transform_odeparms.R index f21d31fc..4fe4e5c2 100644 --- a/R/transform_odeparms.R +++ b/R/transform_odeparms.R @@ -42,17 +42,21 @@ #' #' 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) @@ -66,13 +70,13 @@ #' 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) @@ -87,7 +91,7 @@ #' 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) -- cgit v1.2.1