diff options
Diffstat (limited to 'R/transform_odeparms.R')
| -rw-r--r-- | R/transform_odeparms.R | 30 |
1 files changed, 14 insertions, 16 deletions
diff --git a/R/transform_odeparms.R b/R/transform_odeparms.R index 8f6eb57f..0a25ee8c 100644 --- a/R/transform_odeparms.R +++ b/R/transform_odeparms.R @@ -1,17 +1,16 @@ #' Functions to transform and backtransform kinetic parameters for fitting -#' +#' #' The transformations are intended to map parameters that should only take on #' restricted values to the full scale of real numbers. For kinetic rate #' constants and other parameters that can only take on positive values, a #' simple log transformation is used. For compositional parameters, such as the #' formations fractions that should always sum up to 1 and can not be negative, #' the \code{\link{ilr}} transformation is used. -#' +#' #' The transformation of sets of formation fractions is fragile, as it supposes #' the same ordering of the components in forward and backward transformation. #' This is no problem for the internal use in \code{\link{mkinfit}}. -#' -#' @aliases transform_odeparms backtransform_odeparms +#' #' @param parms Parameters of kinetic models as used in the differential #' equations. #' @param transparms Transformed parameters of kinetic models as used in the @@ -33,11 +32,10 @@ #' parameter of the DFOP and HS models are also transformed, as they can also #' be seen as compositional data. The transformation used for these #' transformations is the \code{\link{ilr}} transformation. -#' @return A vector of transformed or backtransformed parameters with the same -#' names as the original parameters. +#' @return A vector of transformed or backtransformed parameters #' @author Johannes Ranke #' @examples -#' +#' #' SFO_SFO <- mkinmod( #' parent = list(type = "SFO", to = "m1", sink = TRUE), #' m1 = list(type = "SFO")) @@ -47,7 +45,7 @@ #' # 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) @@ -55,21 +53,21 @@ #' print(fit.2.s$par, 3) #' print(fit.2.s$bpar, 3) #' } -#' +#' #' initials <- fit$start$value #' names(initials) <- rownames(fit$start) #' transformed <- fit$start_transformed$value #' names(transformed) <- rownames(fit$start_transformed) #' transform_odeparms(initials, SFO_SFO) #' backtransform_odeparms(transformed, SFO_SFO) -#' +#' #' \dontrun{ #' # The case of formation fractions #' 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.s <- summary(fit.ff) #' print(fit.ff.s$par, 3) @@ -77,20 +75,20 @@ #' initials <- c("f_parent_to_m1" = 0.5) #' transformed <- transform_odeparms(initials, SFO_SFO.ff) #' backtransform_odeparms(transformed, SFO_SFO.ff) -#' +#' #' # And without sink #' SFO_SFO.ff.2 <- mkinmod( #' parent = list(type = "SFO", to = "m1", sink = FALSE), #' m1 = list(type = "SFO"), #' use_of_ff = "max") -#' -#' +#' +#' #' fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE) #' fit.ff.2.s <- summary(fit.ff.2) #' print(fit.ff.2.s$par, 3) #' print(fit.ff.2.s$bpar, 3) #' } -#' +#' #' @export transform_odeparms transform_odeparms <- function(parms, mkinmod, transform_rates = TRUE, @@ -172,7 +170,7 @@ transform_odeparms <- function(parms, mkinmod, return(transparms) } -#' @describeIn transform_odeparms Backtransform the set of transformed parameters +#' @rdname transform_odeparms #' @export backtransform_odeparms backtransform_odeparms <- function(transparms, mkinmod, transform_rates = TRUE, |