Merge pull request #118 from hesim-dev/116-fix-problems-with-rd-files

doc: fix problems with rd files

R/data.R

@@ -7,8 +7,8 @@
 #' 
 #' @format 
 #' A list containing the following elements:
-#' \itemize{
-#' \item{Survival}{ A data frame containing patient information and time to 3 separate survival endpoints.}
+#' \describe{
+#' \item{Survival}{A data frame containing patient information and time to 3 separate survival endpoints.}
 #' \item{Costs}{A list of data frames. The first data frame contains medical cost data and the
 #' second data frame contains drug cost data.}
 #' }
@@ -52,12 +52,12 @@
 #' are also included to facilitate cost-effectiveness analysis. 
 #' @format 
 #' A list containing the following elements:
-#' \itemize{
-#' \item{transitions}{ A data frame containing the times at which patient transitions between health states based
+#' \describe{
+#' \item{transitions}{A data frame containing the times at which patient transitions between health states based
 #' on the [prothr][mstate::prothr] dataset from the [mstate][mstate::mstate] package.}
-#' \item{costs}{ A list of data frames. The first data frame contains summary medical cost estimates and the
+#' \item{costs}{A list of data frames. The first data frame contains summary medical cost estimates and the
 #' second data frame contains drug cost data.}
-#' \item{utility}{ A data frame of summary utility estimates.}
+#' \item{utility}{A data frame of summary utility estimates.}
 #' }
 #' 
 #' @section Transitions data:
@@ -111,7 +111,7 @@
 #'
 #' @format 
 #' A list containing the following elements:
-#' \itemize{
+#' \describe{
 #' \item{transitions}{ A data frame containing patient transitions between health
 #' states at discrete time intervals (i.e., on a yearly basis).}
 #' \item{costs}{ A list of data frames. The first data frame contains 

R/params.R

@@ -112,12 +112,12 @@ summary_params_list <- function(object, prob = 0.95, idcol = "model", ...) {
 #' @return An object prefixed by `params_`. Mapping between `create_params` 
 #' and the classes of the returned objects are: 
 #' \itemize{
-#' \item{`create_params.lm` ->}{ [`params_lm`]}
-#' \item{`create_params.multinom` ->}{ [`params_mlogit`]}
-#' \item{`create_params.multinom_list` ->}{ [`params_mlogit_list`]}
-#' \item{`create_params.flexsurvreg` ->}{ [`params_surv`]}
-#' \item{`create_params.flexsurvreg_list` ->}{ [`params_surv_list`]}
-#' \item{`create_params.partsurvfit` ->}{ [`params_surv_list`]}
+#' \item `create_params.lm` -> [`params_lm`]
+#' \item `create_params.multinom` -> [`params_mlogit`]
+#' \item `create_params.multinom_list` ->  [`params_mlogit_list`]
+#' \item `create_params.flexsurvreg` -> [`params_surv`]
+#' \item `create_params.flexsurvreg_list` -> [`params_surv_list`]
+#' \item `create_params.partsurvfit` ->  [`params_surv_list`]
 #' }
 #' @name create_params
 #' @examples 

R/params_surv.R

@@ -33,10 +33,10 @@
 #' and the identity function if the parameter space is unrestricted.
 #' 
 #' The types of distributions that can be specified are: 
-#' \itemize{
+#' \describe{
 #' \item{`exponential` or `exp`}{ Exponential distribution. `coef`
 #' must contain the `rate` parameter on the log scale and the same parameterization as in 
-#' [`stats::Exponential`]}.
+#' [`stats::Exponential`].}
 #' 
 #' \item{`weibull` or `weibull.quiet`}{ Weibull distribution. The first 
 #' element of `coef` is the `shape` parameter (on the log scale) and the second

R/sim-general.R

@@ -663,9 +663,9 @@ sim_costs <- function(object, models, dr = .03,
 #' 
 #' @format 
 #' A list containing two elements:
-#' \itemize{
-#' \item{`costs`}{ Total (discounted) costs by category.}
-#' \item{`qalys`}{ (Discounted) quality-adjusted life-years.}
+#' \describe{
+#' \item{`costs`}{Total (discounted) costs by category.}
+#' \item{`qalys`}{(Discounted) quality-adjusted life-years.}
 #' }
 #' 
 #' @section Costs:
@@ -692,4 +692,4 @@ sim_costs <- function(object, models, dr = .03,
 #' }
 #' 
 #' @name ce
-NULL
+NULL

R/utils.R

@@ -3,8 +3,6 @@
 #' 
 #' \code{check} is a generic function for validating the inputs of class objects.
 #' @param object object to check.
-#' @param inner_class When checking a list of objects, the class of elements within
-#' the inner most list.
 #' @param ... Further arguments passed to or from other methods.
 #' 
 #' @return If validation is successful, returns the object in question; otherwise,