diff --git a/R/tm_g_forest_rsp.R b/R/tm_g_forest_rsp.R index 27fadd25e..37c042fa0 100644 --- a/R/tm_g_forest_rsp.R +++ b/R/tm_g_forest_rsp.R @@ -14,7 +14,7 @@ #' * `pval`: p-value of the effect. #' Note, the statistics `n_tot`, `or`, and `ci` are required. #' @param riskdiff (`list`)\cr if a risk (proportion) difference column should be added, a list of settings to apply -#' within the column. See [control_riskdiff()] for details. If `NULL`, no risk difference column will be added. +#' within the column. See [tern::control_riskdiff()] for details. If `NULL`, no risk difference column will be added. #' @param obj_var_name (`character`)\cr additional text to append to the table title. #' @param responders (`character`)\cr values of `aval_var` that are considered to be responders. #' @param col_symbol_size (`integer` or `NULL`)\cr column index to be used to determine relative size for diff --git a/R/tm_t_coxreg.R b/R/tm_t_coxreg.R index 4df6ea848..44af30ae1 100644 --- a/R/tm_t_coxreg.R +++ b/R/tm_t_coxreg.R @@ -3,7 +3,7 @@ #' Creates a valid expression to generate a univariable Cox regression analysis. #' #' @inheritParams template_arguments -#' @param control (`list`)\cr list of settings for the analysis (see [control_coxreg()]). +#' @param control (`list`)\cr list of settings for the analysis (see [tern::control_coxreg()]). #' @param at (`list` of `numeric`)\cr when the candidate covariate is a `numeric` type variable, use `at` #' to specify the value of the covariate at which the effect should be estimated. #' @param append (`logical`)\cr whether the result should be appended to the previous one. diff --git a/R/tm_t_tte.R b/R/tm_t_tte.R index 612788b1e..8043aad6a 100644 --- a/R/tm_t_tte.R +++ b/R/tm_t_tte.R @@ -385,12 +385,12 @@ template_tte <- function(dataname = "ANL", #' pre-selected option for confidence level, each within range of (0, 1). #' @param conf_level_survfit ([teal.transform::choices_selected()])\cr object with all available choices and #' pre-selected option for confidence level, each within range of (0, 1). -#' @param event_desc_var (`character` or [data_extract_spec()])\cr variable name with the event description -#' information, optional. +#' @param event_desc_var (`character` or [teal.transform::data_extract_spec()])\cr variable name with the +#' event description information, optional. #' #' @details -#' * The core functionality of this module is based on [coxph_pairwise()], [surv_timepoint()], and [surv_time()] from -#' the `tern` package. +#' * The core functionality of this module is based on [tern::coxph_pairwise()], [tern::surv_timepoint()], +#' and [tern::surv_time()] from the `tern` package. #' * The arm and stratification variables are taken from the `parentname` data. #' * The following variables are used in the module: #' diff --git a/R/utils.R b/R/utils.R index eba21ecfd..3e0c1b9b8 100644 --- a/R/utils.R +++ b/R/utils.R @@ -434,7 +434,7 @@ split_col_expr <- function(compare, combine, ref, arm_var) { #' #' @note uses the regex `\\*|:` to perform the split. #' -#' @return a [choices_selected()] object. +#' @return a [teal.transform::choices_selected()] object. #' #' @examples #' split_choices(choices_selected(choices = c("x:y", "a*b"), selected = all_choices())) diff --git a/man/split_choices.Rd b/man/split_choices.Rd index bea53ac31..13c4389bd 100644 --- a/man/split_choices.Rd +++ b/man/split_choices.Rd @@ -12,7 +12,7 @@ split_choices(x) object with interaction terms} } \value{ -a \code{\link[=choices_selected]{choices_selected()}} object. +a \code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}} object. } \description{ Split \code{choices_selected} objects with interactions into diff --git a/man/template_coxreg_m.Rd b/man/template_coxreg_m.Rd index d259da420..52e8cc999 100644 --- a/man/template_coxreg_m.Rd +++ b/man/template_coxreg_m.Rd @@ -45,7 +45,7 @@ to specify the value of the covariate at which the effect should be estimated.} \item{combine_comp_arms}{(\code{logical})\cr triggers the combination of comparison arms.} -\item{control}{(\code{list})\cr list of settings for the analysis (see \code{\link[=control_coxreg]{control_coxreg()}}).} +\item{control}{(\code{list})\cr list of settings for the analysis (see \code{\link[tern:control_coxreg]{tern::control_coxreg()}}).} \item{na_level}{(\code{string})\cr used to replace all \code{NA} or empty values in character or factor variables in the data. Defaults to \code{""}. To set a diff --git a/man/template_coxreg_u.Rd b/man/template_coxreg_u.Rd index b336dc303..8205d16d7 100644 --- a/man/template_coxreg_u.Rd +++ b/man/template_coxreg_u.Rd @@ -46,7 +46,7 @@ to specify the value of the covariate at which the effect should be estimated.} \item{combine_comp_arms}{(\code{logical})\cr triggers the combination of comparison arms.} -\item{control}{(\code{list})\cr list of settings for the analysis (see \code{\link[=control_coxreg]{control_coxreg()}}).} +\item{control}{(\code{list})\cr list of settings for the analysis (see \code{\link[tern:control_coxreg]{tern::control_coxreg()}}).} \item{na_level}{(\code{string})\cr used to replace all \code{NA} or empty values in character or factor variables in the data. Defaults to \code{""}. To set a diff --git a/man/template_forest_rsp.Rd b/man/template_forest_rsp.Rd index c0b824327..a367aef88 100644 --- a/man/template_forest_rsp.Rd +++ b/man/template_forest_rsp.Rd @@ -58,7 +58,7 @@ Note, the statistics \code{n_tot}, \code{or}, and \code{ci} are required. }} \item{riskdiff}{(\code{list})\cr if a risk (proportion) difference column should be added, a list of settings to apply -within the column. See \code{\link[=control_riskdiff]{control_riskdiff()}} for details. If \code{NULL}, no risk difference column will be added.} +within the column. See \code{\link[tern:control_riskdiff]{tern::control_riskdiff()}} for details. If \code{NULL}, no risk difference column will be added.} \item{conf_level}{(\code{numeric})\cr value for the confidence level within the range of (0, 1).} diff --git a/man/template_forest_tte.Rd b/man/template_forest_tte.Rd index 084845064..332f2f07c 100644 --- a/man/template_forest_tte.Rd +++ b/man/template_forest_tte.Rd @@ -61,7 +61,7 @@ are required. }} \item{riskdiff}{(\code{list})\cr if a risk (proportion) difference column should be added, a list of settings to apply -within the column. See \code{\link[=control_riskdiff]{control_riskdiff()}} for details. If \code{NULL}, no risk difference column will be added.} +within the column. See \code{\link[tern:control_riskdiff]{tern::control_riskdiff()}} for details. If \code{NULL}, no risk difference column will be added.} \item{conf_level}{(\code{numeric})\cr value for the confidence level within the range of (0, 1).} diff --git a/man/tm_g_forest_rsp.Rd b/man/tm_g_forest_rsp.Rd index c627cc585..f20db1db1 100644 --- a/man/tm_g_forest_rsp.Rd +++ b/man/tm_g_forest_rsp.Rd @@ -74,7 +74,7 @@ Note, the statistics \code{n_tot}, \code{or}, and \code{ci} are required. }} \item{riskdiff}{(\code{list})\cr if a risk (proportion) difference column should be added, a list of settings to apply -within the column. See \code{\link[=control_riskdiff]{control_riskdiff()}} for details. If \code{NULL}, no risk difference column will be added.} +within the column. See \code{\link[tern:control_riskdiff]{tern::control_riskdiff()}} for details. If \code{NULL}, no risk difference column will be added.} \item{fixed_symbol_size}{(\code{logical})\cr When (\code{TRUE}), the same symbol size is used for plotting each estimate. Otherwise, the symbol size will be proportional to the sample size in each each subgroup.} diff --git a/man/tm_g_forest_tte.Rd b/man/tm_g_forest_tte.Rd index fd262399b..a8ddd026f 100644 --- a/man/tm_g_forest_tte.Rd +++ b/man/tm_g_forest_tte.Rd @@ -82,7 +82,7 @@ are required. }} \item{riskdiff}{(\code{list})\cr if a risk (proportion) difference column should be added, a list of settings to apply -within the column. See \code{\link[=control_riskdiff]{control_riskdiff()}} for details. If \code{NULL}, no risk difference column will be added.} +within the column. See \code{\link[tern:control_riskdiff]{tern::control_riskdiff()}} for details. If \code{NULL}, no risk difference column will be added.} \item{conf_level}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}})\cr object with all available choices and pre-selected option for the confidence level, each within range of (0, 1).} diff --git a/man/tm_t_tte.Rd b/man/tm_t_tte.Rd index c8d8d6f5f..17ada77bc 100644 --- a/man/tm_t_tte.Rd +++ b/man/tm_t_tte.Rd @@ -75,8 +75,8 @@ for time points that can be used in \code{\link[tern:survival_timepoint]{tern::s \item{time_unit_var}{(\code{\link[teal.transform:choices_selected]{teal.transform::choices_selected()}})\cr object with all available choices and pre-selected option for the time unit variable.} -\item{event_desc_var}{(\code{character} or \code{\link[=data_extract_spec]{data_extract_spec()}})\cr variable name with the event description -information, optional.} +\item{event_desc_var}{(\code{character} or \code{\link[teal.transform:data_extract_spec]{teal.transform::data_extract_spec()}})\cr variable name with the +event description information, optional.} \item{add_total}{(\code{logical})\cr whether to include column with total number of patients.} @@ -108,8 +108,8 @@ template for \code{TTET01} available \href{https://insightsengineering.github.io } \details{ \itemize{ -\item The core functionality of this module is based on \code{\link[=coxph_pairwise]{coxph_pairwise()}}, \code{\link[=surv_timepoint]{surv_timepoint()}}, and \code{\link[=surv_time]{surv_time()}} from -the \code{tern} package. +\item The core functionality of this module is based on \code{\link[tern:survival_coxph_pairwise]{tern::coxph_pairwise()}}, \code{\link[tern:survival_timepoint]{tern::surv_timepoint()}}, +and \code{\link[tern:survival_time]{tern::surv_time()}} from the \code{tern} package. \item The arm and stratification variables are taken from the \code{parentname} data. \item The following variables are used in the module: \itemize{