Improve docs

2 files changed, 15 insertions, 23 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,
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
index a8efb7e6..710b0875 100644
--- a/man/transform_odeparms.Rd
+++ b/man/transform_odeparms.Rd
@@ -47,8 +47,7 @@ transformations is the \code{\link{ilr}} transformation.}
 fitting procedure.}
 }
 \value{
-A vector of transformed or backtransformed parameters with the same
-names as the original parameters.
+A vector of transformed or backtransformed parameters
 }
 \description{
 The transformations are intended to map parameters that should only take on
@@ -63,11 +62,6 @@ 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}}.
 }
-\section{Functions}{
-\itemize{
-\item \code{backtransform_odeparms}: Backtransform the set of transformed parameters
-}}
-
 \examples{
 
 SFO_SFO <- mkinmod(