updated documentation

.Rbuildignore

@@ -63,3 +63,10 @@
 ^data-raw/dataverse/fn_type_lup_tb/fn_type_lup_tb\.csv$
 ^data-raw/dataverse/fn_type_lup_tb/fn_type_lup_tb\.RDS$
 ^data-raw/MAKE_HOUSESTYLE_DSS\.R$
+^data-raw/dataverse/abbreviations_lup/abbreviations_lup\.csv$
+^data-raw/dataverse/abbreviations_lup/abbreviations_lup\.RDS$
+^data-raw/dataverse/object_type_lup/object_type_lup\.csv$
+^data-raw/dataverse/object_type_lup/object_type_lup\.RDS$
+^data-raw/dataverse/seed_obj_lup_tb/seed_obj_lup_tb\.csv$
+^data-raw/dataverse/seed_obj_lup_tb/seed_obj_lup_tb\.RDS$
+^data-raw/name_changes\.txt$

NAMESPACE

@@ -4,8 +4,8 @@ export("%>%")
 export(add_aqol6d_predn_to_ds)
 export(add_change_in_ds_var)
 export(add_costs_by_tmpt)
-export(add_costs_from_gamma_dist)
-export(add_dates_from_dist)
+export(add_costs_from_gamma_dstr)
+export(add_dates_from_dstr)
 export(add_diffs_by_group_and_tmpt)
 export(add_qalys)
 export(add_qalys_to_ds)
@@ -14,11 +14,11 @@ export(get_mdl_from_dv)
 export(get_mdls_using_predrs)
 export(get_tfmn_from_lup)
 export(make_balanced_fake_ds)
-export(make_ce_smry)
-export(make_costs_vec_from_gamma_dist)
+export(make_costs_vec_from_gamma_dstr)
+export(make_cst_efns_smry)
 export(make_fake_trial_ds)
 export(make_formula)
-export(make_he_smry)
+export(make_hlth_ec_smry)
 export(make_matched_ds)
 export(make_matched_ds_spine)
 export(make_sngl_grp_ds)

R/fn_add.R

@@ -99,15 +99,15 @@ add_change_in_ds_var <- function (ds_tb, id_var_nm_1L_chr = "fkClientID", round_
  updated_ds_tb <- updated_ds_tb %>% dplyr::arrange(!!rlang::sym(id_var_nm_1L_chr))
  return(updated_ds_tb)
 }
-#' Add costs by tmpt
-#' @description add_costs_by_tmpt() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add costs by tmpt. Function argument ds_tb specifies the object to be updated. The function returns Updated dataset (a tibble).
+#' Add costs by time point
+#' @description add_costs_by_tmpt() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add costs by time point. Function argument ds_tb specifies the object to be updated. The function returns Updated dataset (a tibble).
 #' @param ds_tb Dataset (a tibble)
 #' @param round_var_nm_1L_chr Round variable name (a character vector of length one)
-#' @param round_lvls_chr Round lvls (a character vector), Default: c("Baseline", "Follow-up")
+#' @param round_lvls_chr Round levels (a character vector), Default: c("Baseline", "Follow-up")
 #' @param costs_mean_dbl Costs mean (a double vector)
-#' @param costs_sd_dbl Costs sd (a double vector)
+#' @param costs_sd_dbl Costs standard deviation (a double vector)
 #' @param extra_cost_args_ls Extra cost arguments (a list), Default: list(costs_var_nm_1L_chr = "costs_dbl")
-#' @param fn Function (a function), Default: add_costs_from_gamma_dist
+#' @param fn Function (a function), Default: add_costs_from_gamma_dstr
 #' @return Updated dataset (a tibble)
 #' @rdname add_costs_by_tmpt
 #' @export 
@@ -117,7 +117,7 @@ add_change_in_ds_var <- function (ds_tb, id_var_nm_1L_chr = "fkClientID", round_
 #' @keywords internal
 add_costs_by_tmpt <- function (ds_tb, round_var_nm_1L_chr, round_lvls_chr = c("Baseline", 
  "Follow-up"), costs_mean_dbl, costs_sd_dbl, extra_cost_args_ls = list(costs_var_nm_1L_chr = "costs_dbl"), 
- fn = add_costs_from_gamma_dist) 
+ fn = add_costs_from_gamma_dstr) 
 {
  updated_ds_tb <- purrr::pmap_dfr(list(round_lvls_chr, costs_mean_dbl, 
  costs_sd_dbl), ~{
@@ -129,27 +129,27 @@ add_costs_by_tmpt <- function (ds_tb, round_var_nm_1L_chr, round_lvls_chr = c("B
  })
  return(updated_ds_tb)
 }
-#' Add costs from gamma dist
-#' @description add_costs_from_gamma_dist() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add costs from gamma dist. Function argument ds_tb specifies the object to be updated. The function returns Updated dataset (a tibble).
+#' Add costs from gamma distribution
+#' @description add_costs_from_gamma_dstr() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add costs from gamma distribution. Function argument ds_tb specifies the object to be updated. The function returns Updated dataset (a tibble).
 #' @param ds_tb Dataset (a tibble)
 #' @param costs_mean_dbl Costs mean (a double vector)
-#' @param costs_sd_dbl Costs sd (a double vector)
+#' @param costs_sd_dbl Costs standard deviation (a double vector)
 #' @param costs_var_nm_1L_chr Costs variable name (a character vector of length one), Default: 'costs_dbl'
 #' @return Updated dataset (a tibble)
-#' @rdname add_costs_from_gamma_dist
+#' @rdname add_costs_from_gamma_dstr
 #' @export 
 #' @importFrom dplyr mutate
 #' @importFrom rlang sym
 #' @keywords internal
-add_costs_from_gamma_dist <- function (ds_tb, costs_mean_dbl, costs_sd_dbl, costs_var_nm_1L_chr = "costs_dbl") 
+add_costs_from_gamma_dstr <- function (ds_tb, costs_mean_dbl, costs_sd_dbl, costs_var_nm_1L_chr = "costs_dbl") 
 {
  updated_ds_tb <- dplyr::mutate(ds_tb, `:=`(!!rlang::sym(costs_var_nm_1L_chr), 
- make_costs_vec_from_gamma_dist(n_int = nrow(ds_tb), costs_mean_dbl = costs_mean_dbl, 
+ make_costs_vec_from_gamma_dstr(n_int = nrow(ds_tb), costs_mean_dbl = costs_mean_dbl, 
  costs_sd_dbl = costs_sd_dbl)))
  return(updated_ds_tb)
 }
-#' Add dates from dist
-#' @description add_dates_from_dist() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add dates from dist. Function argument ds_tb specifies the object to be updated. The function returns Updated dataset (a tibble).
+#' Add dates from distribution
+#' @description add_dates_from_dstr() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add dates from distribution. Function argument ds_tb specifies the object to be updated. The function returns Updated dataset (a tibble).
 #' @param ds_tb Dataset (a tibble)
 #' @param bl_start_date_dtm Baseline start date (a date vector)
 #' @param bl_end_date_dtm Baseline end date (a date vector)
@@ -161,14 +161,14 @@ add_costs_from_gamma_dist <- function (ds_tb, costs_mean_dbl, costs_sd_dbl, cost
 #' @param round_bl_val_1L_chr Round baseline value (a character vector of length one), Default: 'Baseline'
 #' @param origin_1L_chr Origin (a character vector of length one), Default: '1970-01-01'
 #' @return Updated dataset (a tibble)
-#' @rdname add_dates_from_dist
+#' @rdname add_dates_from_dstr
 #' @export 
 #' @importFrom stats rnorm
 #' @importFrom rlang exec sym
 #' @importFrom dplyr mutate case_when n group_by lag ungroup select everything
 #' @importFrom lubridate days
 #' @keywords internal
-add_dates_from_dist <- function (ds_tb, bl_start_date_dtm, bl_end_date_dtm, duration_args_ls, 
+add_dates_from_dstr <- function (ds_tb, bl_start_date_dtm, bl_end_date_dtm, duration_args_ls, 
  duration_fn = stats::rnorm, date_var_nm_1L_chr = "date_psx", 
  id_var_nm_1L_chr = "fkClientID", round_var_nm_1L_chr = "round", 
  round_bl_val_1L_chr = "Baseline", origin_1L_chr = "1970-01-01") 
@@ -191,8 +191,8 @@ add_dates_from_dist <- function (ds_tb, bl_start_date_dtm, bl_end_date_dtm, dura
  duration_prd, dplyr::everything())
  return(updated_ds_tb)
 }
-#' Add diffs by group and tmpt
-#' @description add_diffs_by_group_and_tmpt() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add diffs by group and tmpt. Function argument ds_tb specifies the object to be updated. The function returns Updated dataset (a tibble).
+#' Add differences by group and time point
+#' @description add_diffs_by_group_and_tmpt() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add differences by group and time point. Function argument ds_tb specifies the object to be updated. The function returns Updated dataset (a tibble).
 #' @param ds_tb Dataset (a tibble), Default: trial_ds_tb
 #' @param cmprsn_var_nm_1L_chr Comparison variable name (a character vector of length one), Default: 'study_arm_chr'
 #' @param cmprsn_group_match_val_chr Comparison group match value (a character vector), Default: c("Intervention")
@@ -201,8 +201,8 @@ add_dates_from_dist <- function (ds_tb, bl_start_date_dtm, bl_end_date_dtm, dura
 #' @param match_idx_var_nm_1L_chr Match index variable name (a character vector of length one), Default: 'match_idx_int'
 #' @param var_nms_chr Variable names (a character vector)
 #' @param fns_ls Functions (a list)
-#' @param abs_mean_diff_dbl Abs mean diff (a double vector)
-#' @param diff_sd_dbl Diff sd (a double vector)
+#' @param abs_mean_diff_dbl Absolute mean difference (a double vector)
+#' @param diff_sd_dbl Difference standard deviation (a double vector)
 #' @param multiplier_dbl Multiplier (a double vector)
 #' @param min_dbl Minimum (a double vector)
 #' @param max_dbl Maximum (a double vector)
@@ -232,14 +232,14 @@ add_diffs_by_group_and_tmpt <- function (ds_tb = trial_ds_tb, cmprsn_var_nm_1L_c
  dplyr::arrange(!!rlang::sym(match_idx_var_nm_1L_chr))
  return(updated_ds_tb)
 }
-#' Add qalys
-#' @description add_qalys() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add qalys. Function argument ds_tb specifies the object to be updated. The function returns Updated dataset (a tibble).
+#' Add Quality Adjusted Life Years
+#' @description add_qalys() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add quality adjusted life years. Function argument ds_tb specifies the object to be updated. The function returns Updated dataset (a tibble).
 #' @param ds_tb Dataset (a tibble)
 #' @param cmprsn_var_nm_1L_chr Comparison variable name (a character vector of length one), Default: 'study_arm_chr'
 #' @param duration_var_nm_1L_chr Duration variable name (a character vector of length one), Default: 'duration_prd'
 #' @param id_var_nm_1L_chr Identity variable name (a character vector of length one), Default: 'fkClientID'
 #' @param match_idx_var_nm_1L_chr Match index variable name (a character vector of length one), Default: 'match_idx_int'
-#' @param qalys_var_nm_1L_chr Qalys variable name (a character vector of length one), Default: 'qalys_dbl'
+#' @param qalys_var_nm_1L_chr Quality Adjusted Life Years variable name (a character vector of length one), Default: 'qalys_dbl'
 #' @param round_var_nm_1L_chr Round variable name (a character vector of length one), Default: 'round'
 #' @param utl_change_var_nm_1L_chr Utility change variable name (a character vector of length one), Default: 'utl_change_dbl'
 #' @param utl_var_nm_1L_chr Utility variable name (a character vector of length one), Default: 'utility_dbl'
@@ -271,8 +271,8 @@ add_qalys <- function (ds_tb, cmprsn_var_nm_1L_chr = "study_arm_chr", duration_v
  }
  return(updated_ds_tb)
 }
-#' Add qalys to dataset
-#' @description add_qalys_to_ds() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add qalys to dataset. Function argument ds_tb specifies the object to be updated. The function returns Dataset (a tibble).
+#' Add Quality Adjusted Life Years to dataset
+#' @description add_qalys_to_ds() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add quality adjusted life years to dataset. Function argument ds_tb specifies the object to be updated. The function returns Dataset (a tibble).
 #' @param ds_tb Dataset (a tibble)
 #' @param ds_smry_ls Dataset summary (a list)
 #' @return Dataset (a tibble)

R/fn_extract.R

@@ -1,15 +1,15 @@
 #' Extract guide box legend
-#' @description extract_guide_box_lgd() is an Extract function that extracts data from an object. Specifically, this function implements an algorithm to extract guide box legend. The function is called for its side effects and does not return a value.
-#' @param a.gplot PARAM_DESCRIPTION
-#' @return NA ()
+#' @description extract_guide_box_lgd() is an Extract function that extracts data from an object. Specifically, this function implements an algorithm to extract guide box legend. The function returns Legend (a character vector of length one).
+#' @param plot_plt Plot (a plot)
+#' @return Legend (a character vector of length one)
 #' @rdname extract_guide_box_lgd
 #' @export 
 #' @importFrom ggplot2 ggplot_gtable ggplot_build
 #' @keywords internal
-extract_guide_box_lgd <- function (a.gplot) 
+extract_guide_box_lgd <- function (plot_plt) 
 {
- tmp <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(a.gplot))
+ tmp <- ggplot2::ggplot_gtable(ggplot2::ggplot_build(plot_plt))
  leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
- legend <- tmp$grobs[[leg]]
- return(legend)
+ legend_1L_chr <- tmp$grobs[[leg]]
+ return(legend_1L_chr)
 }