update with failing vignettes

.Rbuildignore

@@ -39,7 +39,7 @@
 ^data-raw/aqol6d_adult_vldn_pop_with_STATA_scores_tb\.csv$
 ^data-raw/aqol6d_dim_sclg_con_lup_tb\.csv$
 ^data-raw/aqol6d_domain_qs_lup_tb\.csv$
-^data-raw/aqol6d_from_8d_coeffs_lup_tb\.csv$
+^data-raw/aqol6d_from_8d_coefs_lup_tb\.csv$
 ^data-raw/predictors_lup\.csv$
 ^data-raw/fn_type_lup_tb\.csv$
 ^data-raw/fns_dmt_tb\.csv$
@@ -60,3 +60,6 @@
 ^doc$
 ^Meta$
 ^data-raw/vignettes/_Clippings\.Rmd$
+^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$

R/db_abbreviations_lup.R

@@ -9,4 +9,5 @@
 #' \item{long_name_chr}{Long name (a character vector)}
 #' \item{plural_lgl}{Plural (a logical vector)}
 #' }
+#' @source \url{https://doi.org/10.7910/DVN/2Y9VF9}
 "abbreviations_lup"

R/db_fn_type_lup_tb.R

@@ -12,4 +12,5 @@
 #' \item{is_generic_lgl}{Is generic (a logical vector)}
 #' \item{is_method_lgl}{Is method (a logical vector)}
 #' }
+#' @source \url{https://doi.org/10.7910/DVN/2Y9VF9}
 "fn_type_lup_tb"

R/db_mdls_lup.R

@@ -6,7 +6,7 @@
 #' 
 #' \describe{
 #' \item{mdl_nms_chr}{Model names (a character vector)}
-#' \item{predrs_ls}{Predrs (a list)}
+#' \item{predrs_ls}{Predictors (a list)}
 #' \item{mdl_type_chr}{Model type (a character vector)}
 #' \item{tfmn_chr}{Transformation (a character vector)}
 #' }

R/fn_add.R

@@ -1,14 +1,14 @@
 #' Add Assessment of Quality of Life Six Dimension prediction to dataset
 #' @description add_aqol6d_predn_to_ds() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add assessment of quality of life six dimension prediction to dataset. Function argument data_tb specifies the object to be updated. The function returns Updated (a tibble).
 #' @param data_tb Data (a tibble)
-#' @param model_mdl PARAM_DESCRIPTION
+#' @param model_mdl Model (a model)
 #' @param tfmn_1L_chr Transformation (a character vector of length one)
-#' @param predr_vars_nms_chr Predr vars names (a character vector), Default: NULL
-#' @param utl_var_nm_1L_chr Utl var name (a character vector of length one), Default: NULL
-#' @param id_var_nm_1L_chr Id var name (a character vector of length one), Default: 'fkClientID'
-#' @param round_var_nm_1L_chr Round var name (a character vector of length one), Default: 'round'
-#' @param round_bl_val_1L_chr Round bl value (a character vector of length one), Default: 'Baseline'
-#' @param utl_cls_fn Utl class (a function), Default: youthvars::youthvars_aqol6d_adol
+#' @param predr_vars_nms_chr Predictor variables names (a character vector), Default: NULL
+#' @param utl_var_nm_1L_chr Utility variable name (a character vector of length one), Default: NULL
+#' @param id_var_nm_1L_chr Identity variable name (a character vector of length one), Default: 'fkClientID'
+#' @param round_var_nm_1L_chr Round variable name (a character vector of length one), Default: 'round'
+#' @param round_bl_val_1L_chr Round baseline value (a character vector of length one), Default: 'Baseline'
+#' @param utl_cls_fn Utility class (a function), Default: youthvars::youthvars_aqol6d_adol
 #' @param predictors_lup Predictors (a lookup table), Default: NULL
 #' @return Updated (a tibble)
 #' @rdname add_aqol6d_predn_to_ds
@@ -46,12 +46,12 @@ add_aqol6d_predn_to_ds <- function (data_tb, model_mdl, tfmn_1L_chr, predr_vars_
  c(mdl_predr_terms_chr, ifelse(!is.null(utl_var_nm_1L_chr), 
  utl_var_nm_1L_chr, mdl_dep_var_1L_chr))]
  updated_tb <- data_tb %>% transform_ds_to_predn_ds(predr_vars_nms_chr = mdl_predr_terms_chr, 
- tfmn_1L_chr = tfmn_1L_chr, dep_var_nm_1L_chr = mdl_dep_var_1L_chr, 
+ tfmn_1L_chr = tfmn_1L_chr, depnt_var_nm_1L_chr = mdl_dep_var_1L_chr, 
  id_var_nm_1L_chr = id_var_nm_1L_chr, round_var_nm_1L_chr = round_var_nm_1L_chr, 
  round_bl_val_1L_chr = round_bl_val_1L_chr, predictors_lup = predictors_lup) %>% 
  TTU::add_utility_predn_to_ds(model_mdl = model_mdl, tfmn_1L_chr = tfmn_1L_chr, 
- dep_var_nm_1L_chr = mdl_dep_var_1L_chr, predr_vars_nms_chr = mdl_predr_terms_chr, 
- utl_cls_fn = utl_cls_fn, rmv_tfmd_dep_var_1L_lgl = T)
+ depnt_var_nm_1L_chr = mdl_dep_var_1L_chr, predr_vars_nms_chr = mdl_predr_terms_chr, 
+ utl_cls_fn = utl_cls_fn, rmv_tfd_depnt_var_1L_lgl = T)
  if (!is.null(utl_var_nm_1L_chr)) {
  updated_tb <- updated_tb %>% dplyr::rename(`:=`(!!rlang::sym(utl_var_nm_1L_chr), 
  tidyselect::all_of(mdl_dep_var_1L_chr)))
@@ -70,15 +70,15 @@ add_aqol6d_predn_to_ds <- function (data_tb, model_mdl, tfmn_1L_chr, predr_vars_
  names(updated_tb)]))
  return(updated_tb)
 }
-#' Add change in dataset var
-#' @description add_change_in_ds_var() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add change in dataset var. Function argument ds_tb specifies the object to be updated. The function returns Updated dataset (a tibble).
+#' Add change in dataset variable
+#' @description add_change_in_ds_var() is an Add function that updates an object by adding data to that object. Specifically, this function implements an algorithm to add change in dataset variable. Function argument ds_tb specifies the object to be updated. The function returns Updated dataset (a tibble).
 #' @param ds_tb Dataset (a tibble)
-#' @param id_var_nm_1L_chr Id var name (a character vector of length one), Default: 'fkClientID'
-#' @param round_var_nm_1L_chr Round var name (a character vector of length one), Default: 'round'
-#' @param round_bl_val_1L_chr Round bl value (a character vector of length one), Default: 'Baseline'
-#' @param change_var_nm_1L_chr Change var name (a character vector of length one)
-#' @param var_nm_1L_chr Var name (a character vector of length one)
-#' @param arrange_by_id_lgl Arrange by id (a logical vector), Default: T
+#' @param id_var_nm_1L_chr Identity variable name (a character vector of length one), Default: 'fkClientID'
+#' @param round_var_nm_1L_chr Round variable name (a character vector of length one), Default: 'round'
+#' @param round_bl_val_1L_chr Round baseline value (a character vector of length one), Default: 'Baseline'
+#' @param change_var_nm_1L_chr Change variable name (a character vector of length one)
+#' @param var_nm_1L_chr Variable name (a character vector of length one)
+#' @param arrange_by_id_lgl Arrange by identity (a logical vector), Default: T
 #' @return Updated dataset (a tibble)
 #' @rdname add_change_in_ds_var
 #' @export 
@@ -102,7 +102,7 @@ add_change_in_ds_var <- function (ds_tb, id_var_nm_1L_chr = "fkClientID", round_
 #' 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).
 #' @param ds_tb Dataset (a tibble)
-#' @param round_var_nm_1L_chr Round var name (a character vector of length one)
+#' @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 costs_mean_dbl Costs mean (a double vector)
 #' @param costs_sd_dbl Costs sd (a double vector)
@@ -134,7 +134,7 @@ add_costs_by_tmpt <- function (ds_tb, round_var_nm_1L_chr, round_lvls_chr = c("B
 #' @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_var_nm_1L_chr Costs var name (a character vector of length one), Default: 'costs_dbl'
+#' @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
 #' @export 
@@ -151,14 +151,14 @@ add_costs_from_gamma_dist <- function (ds_tb, costs_mean_dbl, costs_sd_dbl, cost
 #' 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).
 #' @param ds_tb Dataset (a tibble)
-#' @param bl_start_date_dtm PARAM_DESCRIPTION
-#' @param bl_end_date_dtm PARAM_DESCRIPTION
+#' @param bl_start_date_dtm Baseline start date (a date vector)
+#' @param bl_end_date_dtm Baseline end date (a date vector)
 #' @param duration_args_ls Duration arguments (a list)
 #' @param duration_fn Duration (a function), Default: stats::rnorm
-#' @param date_var_nm_1L_chr Date var name (a character vector of length one), Default: 'date_psx'
-#' @param id_var_nm_1L_chr Id var name (a character vector of length one), Default: 'fkClientID'
-#' @param round_var_nm_1L_chr Round var name (a character vector of length one), Default: 'round'
-#' @param round_bl_val_1L_chr Round bl value (a character vector of length one), Default: 'Baseline'
+#' @param date_var_nm_1L_chr Date variable name (a character vector of length one), Default: 'date_psx'
+#' @param id_var_nm_1L_chr Identity variable name (a character vector of length one), Default: 'fkClientID'
+#' @param round_var_nm_1L_chr Round variable name (a character vector of length one), Default: 'round'
+#' @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
@@ -194,18 +194,18 @@ add_dates_from_dist <- function (ds_tb, bl_start_date_dtm, bl_end_date_dtm, dura
 #' 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).
 #' @param ds_tb Dataset (a tibble), Default: trial_ds_tb
-#' @param cmprsn_var_nm_1L_chr Cmprsn var name (a character vector of length one), Default: 'study_arm_chr'
-#' @param cmprsn_group_match_val_chr Cmprsn group match value (a character vector), Default: c("Intervention")
-#' @param round_var_nm_1L_chr Round var name (a character vector of length one), Default: 'round'
+#' @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")
+#' @param round_var_nm_1L_chr Round variable name (a character vector of length one), Default: 'round'
 #' @param timepoint_match_val_1L_chr Timepoint match value (a character vector of length one), Default: 'Follow-up'
-#' @param match_idx_var_nm_1L_chr Match index var name (a character vector of length one), Default: 'match_idx_int'
-#' @param var_nms_chr Var names (a character vector)
+#' @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 multiplier_dbl Multiplier (a double vector)
-#' @param min_dbl Min (a double vector)
-#' @param max_dbl Max (a double vector)
+#' @param min_dbl Minimum (a double vector)
+#' @param max_dbl Maximum (a double vector)
 #' @param integer_lgl Integer (a logical vector)
 #' @return Updated dataset (a tibble)
 #' @rdname add_diffs_by_group_and_tmpt
@@ -235,14 +235,14 @@ add_diffs_by_group_and_tmpt <- function (ds_tb = trial_ds_tb, cmprsn_var_nm_1L_c
 #' 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).
 #' @param ds_tb Dataset (a tibble)
-#' @param cmprsn_var_nm_1L_chr Cmprsn var name (a character vector of length one), Default: 'study_arm_chr'
-#' @param duration_var_nm_1L_chr Duration var name (a character vector of length one), Default: 'duration_prd'
-#' @param id_var_nm_1L_chr Id var name (a character vector of length one), Default: 'fkClientID'
-#' @param match_idx_var_nm_1L_chr Match index var name (a character vector of length one), Default: 'match_idx_int'
-#' @param qalys_var_nm_1L_chr Qalys var name (a character vector of length one), Default: 'qalys_dbl'
-#' @param round_var_nm_1L_chr Round var name (a character vector of length one), Default: 'round'
-#' @param utl_change_var_nm_1L_chr Utl change var name (a character vector of length one), Default: 'utl_change_dbl'
-#' @param utl_var_nm_1L_chr Utl var name (a character vector of length one), Default: 'utility_dbl'
+#' @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 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'
 #' @param reshape_1L_lgl Reshape (a logical vector of length one), Default: T
 #' @return Updated dataset (a tibble)
 #' @rdname add_qalys

R/fn_get.R

@@ -1,5 +1,5 @@
 #' Get model from dataverse
-#' @description get_mdl_from_dv() is a Get function that retrieves a pre-existing data object from memory, local file system or online repository. Specifically, this function implements an algorithm to get model from dataverse. Function argument mdl_nm_1L_chr specifies the where to look for the required object. The function is called for its side effects and does not return a value.
+#' @description get_mdl_from_dv() is a Get function that retrieves a pre-existing data object from memory, local file system or online repository. Specifically, this function implements an algorithm to get model from dataverse. Function argument mdl_nm_1L_chr specifies the where to look for the required object. The function returns Model (a model).
 #' @param mdl_nm_1L_chr Model name (a character vector of length one)
 #' @param dv_ds_nm_1L_chr Dataverse dataset name (a character vector of length one), Default: 'https://doi.org/10.7910/DVN/JC6PTV'
 #' @param server_1L_chr Server (a character vector of length one), Default: 'dataverse.harvard.edu'
@@ -21,9 +21,9 @@ get_mdl_from_dv <- function (mdl_nm_1L_chr, dv_ds_nm_1L_chr = "https://doi.org/1
  ds_ls[[idx_1L_int]]$dataFile$id)))
  return(model_mdl)
 }
-#' Get models using predrs
-#' @description get_mdls_using_predrs() is a Get function that retrieves a pre-existing data object from memory, local file system or online repository. Specifically, this function implements an algorithm to get models using predrs. Function argument mdl_predrs_in_ds_chr specifies the where to look for the required object. The function returns Filtered models (a lookup table).
-#' @param mdl_predrs_in_ds_chr Model predrs in dataset (a character vector)
+#' Get models using predictors
+#' @description get_mdls_using_predrs() is a Get function that retrieves a pre-existing data object from memory, local file system or online repository. Specifically, this function implements an algorithm to get models using predictors. Function argument mdl_predrs_in_ds_chr specifies the where to look for the required object. The function returns Filtered models (a lookup table).
+#' @param mdl_predrs_in_ds_chr Model predictors in dataset (a character vector)
 #' @param mdls_lup Models (a lookup table), Default: NULL
 #' @return Filtered models (a lookup table)
 #' @rdname get_mdls_using_predrs