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authorJohannes Ranke <jranke@uni-bremen.de>2020-05-15 11:06:06 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-05-15 11:06:06 +0200
commitda33f5c04ab9d98cad0b3ef5ab9f173f612f14ef (patch)
tree1abb1cf3d0213182300b40bacdec378f45e78679 /R
parented68dee95554c43b150836106ff4036660989b47 (diff)
Improve docs
Diffstat (limited to 'R')
-rw-r--r--R/transform_odeparms.R30
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,

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