From 5345a2ce262d9bcd4da1e0b77aa98065dd838d79 Mon Sep 17 00:00:00 2001 From: dincerti Date: Sun, 28 Jan 2024 15:57:45 -0800 Subject: [PATCH 1/5] docs: remove unnecessary braces with itemize --- R/params.R | 12 ++++++------ man/create_params.Rd | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/R/params.R b/R/params.R index 7e6cee17..46aa21ff 100644 --- a/R/params.R +++ b/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 diff --git a/man/create_params.Rd b/man/create_params.Rd index fc7bc459..3fec39ba 100644 --- a/man/create_params.Rd +++ b/man/create_params.Rd @@ -55,12 +55,12 @@ the \code{silent} argument of \code{\link[=try]{try()}}.} An object prefixed by \code{params_}. Mapping between \code{create_params} and the classes of the returned objects are: \itemize{ -\item{\code{create_params.lm} ->}{ \code{\link{params_lm}}} -\item{\code{create_params.multinom} ->}{ \code{\link{params_mlogit}}} -\item{\code{create_params.multinom_list} ->}{ \code{\link{params_mlogit_list}}} -\item{\code{create_params.flexsurvreg} ->}{ \code{\link{params_surv}}} -\item{\code{create_params.flexsurvreg_list} ->}{ \code{\link{params_surv_list}}} -\item{\code{create_params.partsurvfit} ->}{ \code{\link{params_surv_list}}} +\item \code{create_params.lm} -> \code{\link{params_lm}} +\item \code{create_params.multinom} -> \code{\link{params_mlogit}} +\item \code{create_params.multinom_list} -> \code{\link{params_mlogit_list}} +\item \code{create_params.flexsurvreg} -> \code{\link{params_surv}} +\item \code{create_params.flexsurvreg_list} -> \code{\link{params_surv_list}} +\item \code{create_params.partsurvfit} -> \code{\link{params_surv_list}} } } \description{ From 5a3b6065110f4a19bb4130fab3de992780d9998b Mon Sep 17 00:00:00 2001 From: dincerti Date: Sun, 28 Jan 2024 22:19:14 -0800 Subject: [PATCH 2/5] docs: replace itemize with describe --- R/params_surv.R | 4 ++-- man/params_surv.Rd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/params_surv.R b/R/params_surv.R index 8ea2a153..bca2cb60 100644 --- a/R/params_surv.R +++ b/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 diff --git a/man/params_surv.Rd b/man/params_surv.Rd index 10f70592..693a5a05 100644 --- a/man/params_surv.Rd +++ b/man/params_surv.Rd @@ -45,10 +45,10 @@ inverse transformation function \eqn{g^{-1}()}, and the identity function if the parameter space is unrestricted. The types of distributions that can be specified are: -\itemize{ +\describe{ \item{\code{exponential} or \code{exp}}{ Exponential distribution. \code{coef} must contain the \code{rate} parameter on the log scale and the same parameterization as in -\code{\link[stats:Exponential]{stats::Exponential}}}. +\code{\link[stats:Exponential]{stats::Exponential}}.} \item{\code{weibull} or \code{weibull.quiet}}{ Weibull distribution. The first element of \code{coef} is the \code{shape} parameter (on the log scale) and the second From 14357685df6ad99d4334ebd301e011cae4e43157 Mon Sep 17 00:00:00 2001 From: dincerti Date: Sun, 28 Jan 2024 22:24:23 -0800 Subject: [PATCH 3/5] docs: once again use describe instead of itemize --- R/data.R | 4 ++-- man/psm4_exdata.Rd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/data.R b/R/data.R index e0c0eb34..b84e9131 100644 --- a/R/data.R +++ b/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.} #' } diff --git a/man/psm4_exdata.Rd b/man/psm4_exdata.Rd index ac8c157f..43d7a4a2 100644 --- a/man/psm4_exdata.Rd +++ b/man/psm4_exdata.Rd @@ -6,8 +6,8 @@ \title{Example data for a 4-state partitioned survival model} \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.} } From 634a9f1c62fb7836cb8f6187aaaa5dc468305d45 Mon Sep 17 00:00:00 2001 From: dincerti Date: Sun, 28 Jan 2024 22:29:40 -0800 Subject: [PATCH 4/5] docs: yet again, replace itemize with describe --- R/data.R | 10 +++++----- R/sim-general.R | 6 +++--- man/ce.Rd | 2 +- man/mstate3_exdata.Rd | 8 ++++---- man/multinom3_exdata.Rd | 2 +- 5 files changed, 14 insertions(+), 14 deletions(-) diff --git a/R/data.R b/R/data.R index b84e9131..591b6681 100644 --- a/R/data.R +++ b/R/data.R @@ -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 diff --git a/R/sim-general.R b/R/sim-general.R index d570fbc7..a8555129 100644 --- a/R/sim-general.R +++ b/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: diff --git a/man/ce.Rd b/man/ce.Rd index 47a4bdc0..1772cad1 100644 --- a/man/ce.Rd +++ b/man/ce.Rd @@ -5,7 +5,7 @@ \title{A cost-effectiveness object} \format{ A list containing two elements: -\itemize{ +\describe{ \item{\code{costs}}{ Total (discounted) costs by category.} \item{\code{qalys}}{ (Discounted) quality-adjusted life-years.} } diff --git a/man/mstate3_exdata.Rd b/man/mstate3_exdata.Rd index 8938e826..ed2a1316 100644 --- a/man/mstate3_exdata.Rd +++ b/man/mstate3_exdata.Rd @@ -6,12 +6,12 @@ \title{Example data for a reversible 3-state multi-state model} \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 \link[mstate:Liver-cirrhosis-data]{prothr} dataset from the \link[mstate:mstate-package]{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.} } } \usage{ diff --git a/man/multinom3_exdata.Rd b/man/multinom3_exdata.Rd index 4ab0f92e..51638cce 100644 --- a/man/multinom3_exdata.Rd +++ b/man/multinom3_exdata.Rd @@ -6,7 +6,7 @@ \title{Example data for a 3-state multinomial model} \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 From e6786c8a01f0b687be8dd2bdb8b3d6924df48636 Mon Sep 17 00:00:00 2001 From: dincerti Date: Wed, 7 Feb 2024 11:41:50 -0800 Subject: [PATCH 5/5] docs: remove documentation for a function argument that was not being used --- R/sim-general.R | 2 +- R/utils.R | 2 -- man/ce.Rd | 4 ++-- man/check.Rd | 3 --- 4 files changed, 3 insertions(+), 8 deletions(-) diff --git a/R/sim-general.R b/R/sim-general.R index a8555129..a6ba9e5a 100644 --- a/R/sim-general.R +++ b/R/sim-general.R @@ -692,4 +692,4 @@ sim_costs <- function(object, models, dr = .03, #' } #' #' @name ce -NULL \ No newline at end of file +NULL diff --git a/R/utils.R b/R/utils.R index 901a002a..a0c7842c 100644 --- a/R/utils.R +++ b/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, diff --git a/man/ce.Rd b/man/ce.Rd index 1772cad1..cc22c60c 100644 --- a/man/ce.Rd +++ b/man/ce.Rd @@ -6,8 +6,8 @@ \format{ A list containing two elements: \describe{ -\item{\code{costs}}{ Total (discounted) costs by category.} -\item{\code{qalys}}{ (Discounted) quality-adjusted life-years.} +\item{\code{costs}}{Total (discounted) costs by category.} +\item{\code{qalys}}{(Discounted) quality-adjusted life-years.} } } \description{ diff --git a/man/check.Rd b/man/check.Rd index f20b0b18..2a7e89a0 100644 --- a/man/check.Rd +++ b/man/check.Rd @@ -36,9 +36,6 @@ check(object, ...) \item{object}{object to check.} \item{...}{Further arguments passed to or from other methods.} - -\item{inner_class}{When checking a list of objects, the class of elements within -the inner most list.} } \value{ If validation is successful, returns the object in question; otherwise,