remove merge conflict nonsense

pharmaverse · Oct 6, 2023 · e34b55b · e34b55b
1 parent 5ce0b17
commit e34b55b
Show file tree

Hide file tree

Showing 21 changed files with 0 additions and 304 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,11 +1,7 @@
 Package: admiral
 Type: Package
 Title: ADaM in R Asset Library
-<<<<<<< HEAD
-Version: 0.12.1
-=======
 Version: 0.12.2.9000
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
 Authors@R: c(
     person("Ben", "Straub", email = "ben.x.straub@gsk.com", role = c("aut", "cre")),
     person("Stefan", "Bundfuss", role = "aut"),

diff --git a/NAMESPACE b/NAMESPACE
@@ -84,10 +84,6 @@ export(derive_var_atoxgr)
 export(derive_var_atoxgr_dir)
 export(derive_var_base)
 export(derive_var_chg)
-<<<<<<< HEAD
-export(derive_var_confirmation_flag)
-=======
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
 export(derive_var_dthcaus)
 export(derive_var_extreme_dt)
 export(derive_var_extreme_dtm)

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,3 @@
-<<<<<<< HEAD
-=======
 # admiral (development version)
 
 ## New Features
@@ -38,7 +36,6 @@
 
 - A unit test for `derive_param_computed()` was modified in anticipation of major user-facing changes to R version 4.4 (#2147)
 
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
 # admiral 0.12.1
 
 - `derive_extreme_records()` no longer fails if `dataset_add` is specified and a

diff --git a/R/compute_kidney.R b/R/compute_kidney.R
@@ -137,13 +137,7 @@
 compute_egfr <- function(creat, creatu = "SI", age, weight, sex, race = NULL, method, wt) {
   ### BEGIN DEPRECATION
   if (!missing(wt)) {
-<<<<<<< HEAD
-    deprecate_warn("0.12.0", "compute_egfr(old_param = 'wt')", "compute_egfr(new_param = 'weight')")
-    # old_param is given using exprs()
-    weight <- wt
-=======
     deprecate_stop("0.12.0", "compute_egfr(old_param = 'wt')", "compute_egfr(new_param = 'weight')")
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
   }
   ### END DEPRECATION
 

diff --git a/R/derive_expected_records.R b/R/derive_expected_records.R
@@ -6,16 +6,8 @@
 #' @param dataset
 #' `r roxygen_param_dataset(expected_vars = c("dataset_ref", "by_vars"))`
 #'
-<<<<<<< HEAD
 #' @param dataset_expected_obs *Deprecated*, please use `dataset_ref` instead.
 #'
-=======
-#'   A data frame, the columns from `dataset_ref` and specified by the
-#'   `by_vars` parameter are expected.
-#'
-#' @param dataset_expected_obs *Deprecated*, please use `dataset_ref` instead.
-#'
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
 #' @param dataset_ref Expected observations dataset
 #'
 #'   Data frame with the expected observations, e.g., all the expected
@@ -97,11 +89,7 @@ derive_expected_records <- function(dataset,
                                     by_vars = NULL,
                                     set_values_to = NULL) {
   if (!missing(dataset_expected_obs)) {
-<<<<<<< HEAD
-    deprecate_warn(
-=======
     deprecate_stop(
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
       "0.12.0",
       "derive_expected_records(dataset_expected_obs = )",
       "derive_expected_records(dataset_ref = )"

diff --git a/R/derive_extreme_records.R b/R/derive_extreme_records.R
@@ -265,21 +265,7 @@ derive_extreme_records <- function(dataset = NULL,
                                    true_value = "Y",
                                    false_value = "N",
                                    keep_source_vars = exprs(everything()),
-<<<<<<< HEAD
-                                   set_values_to,
-                                   filter) {
-  if (!missing(filter)) {
-    deprecate_stop(
-      "0.11.0",
-      "derive_extreme_records(filter = )",
-      "derive_extreme_records(filter_add = )"
-    )
-    filter_add <- enexpr(filter)
-  }
-
-=======
                                    set_values_to) {
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
   # Check input arguments
   assert_vars(by_vars, optional = is.null(dataset_ref))
   assert_expr_list(order, optional = TRUE)

diff --git a/R/derive_locf_records.R b/R/derive_locf_records.R
@@ -8,11 +8,6 @@
 #'
 #' @param dataset_expected_obs *Deprecated*, please use `dataset_ref` instead.
 #'
-<<<<<<< HEAD
-=======
-#' @param dataset_expected_obs *Deprecated*, please use `dataset_ref` instead.
-#'
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
 #' @param dataset_ref Expected observations dataset
 #'
 #'   Data frame with all the combinations of `PARAMCD`, `PARAM`, `AVISIT`,
@@ -122,11 +117,7 @@ derive_locf_records <- function(dataset,
                                 order,
                                 keep_vars = NULL) {
   if (!missing(dataset_expected_obs)) {
-<<<<<<< HEAD
-    deprecate_warn(
-=======
     deprecate_stop(
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
       "0.12.0",
       "derive_locf_records(dataset_expected_obs = )",
       "derive_locf_records(dataset_ref = )"

diff --git a/R/derive_merged.R b/R/derive_merged.R
@@ -396,81 +396,6 @@ derive_vars_merged <- function(dataset,
   dataset
 }
 
-<<<<<<< HEAD
-#' Merge a Categorization Variable
-#'
-#' @description
-#' `r lifecycle::badge("deprecated")`
-#'
-#' This function is *deprecated*, please use `derive_vars_merged()` instead.
-#'
-#' Merge a categorization variable from a dataset to the input dataset. The
-#' observations to merge can be selected by a condition and/or selecting the
-#' first or last observation for each by group.
-#'
-#' @param dataset_add Additional dataset
-#'
-#'   The variables specified by the `by_vars`, the `source_var`, and the `order`
-#'   argument are expected.
-#'
-#' @param new_var New variable
-#'
-#'   The specified variable is added to the additional dataset and set to the
-#'   categorized values, i.e., `cat_fun(<source variable>)`.
-#'
-#' @param source_var Source variable
-#'
-#' @param cat_fun Categorization function
-#'
-#'   A function must be specified for this argument which expects the values of
-#'   the source variable as input and returns the categorized values.
-#'
-#' @param missing_value Values used for missing information
-#'
-#'   The new variable is set to the specified value for all by groups without
-#'   observations in the additional dataset.
-#'
-#'   *Default*: `NA_character_`
-#'
-#' @inheritParams derive_vars_merged
-#'
-#' @return The output dataset contains all observations and variables of the
-#'   input dataset and additionally the variable specified for `new_var` derived
-#'   from the additional dataset (`dataset_add`).
-#'
-#' @details
-#'
-#'   1. The additional dataset is restricted to the observations matching the
-#'   `filter_add` condition.
-#'
-#'   1. The categorization variable is added to the additional dataset.
-#'
-#'   1. If `order` is specified, for each by group the first or last observation
-#'   (depending on `mode`) is selected.
-#'
-#'   1. The categorization variable is merged to the input dataset.
-#'
-#'
-#' @family deprecated
-#' @keywords deprecated
-#'
-#' @export
-#'
-derive_var_merged_cat <- function(dataset,
-                                  dataset_add,
-                                  by_vars,
-                                  order = NULL,
-                                  new_var,
-                                  source_var,
-                                  cat_fun,
-                                  filter_add = NULL,
-                                  mode = NULL,
-                                  missing_value = NA_character_) {
-  deprecate_stop("0.11.0", "derive_var_merged_cat()", "derive_vars_merged()")
-}
-
-=======
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
 #' Merge an Existence Flag
 #'
 #' @description Adds a flag variable to the input dataset which indicates if
@@ -635,86 +560,6 @@ derive_var_merged_exist_flag <- function(dataset,
     mutate(!!new_var := if_else(!!new_var == 1, true_value, false_value, missing_value))
 }
 
-<<<<<<< HEAD
-#' Merge a Character Variable
-#'
-#' @description
-#' `r lifecycle::badge("deprecated")`
-#'
-#' This function is *deprecated*, please use `derive_vars_merged()` instead.
-#'
-#' Merge a character variable from a dataset to the input dataset. The
-#' observations to merge can be selected by a condition and/or selecting the
-#' first or last observation for each by group.
-#'
-#' @param dataset_add Additional dataset
-#'
-#'   The variables specified by the `by_vars`, the `source_var`, and the `order`
-#'   argument are expected.
-#'
-#' @param new_var New variable
-#'
-#'   The specified variable is added to the additional dataset and set to the
-#'   transformed value with respect to the `case` argument.
-#'
-#' @param source_var Source variable
-#'
-#' @param case Change case
-#'
-#'   Changes the case of the values of the new variable.
-#'
-#'   *Default*: `NULL`
-#'
-#'   *Permitted Values*: `NULL`, `"lower"`, `"upper"`, `"title"`
-#'
-#' @param missing_value Values used for missing information
-#'
-#'   The new variable is set to the specified value for all by groups without
-#'   observations in the additional dataset.
-#'
-#'   *Default*: `NA_character_`
-#'
-#'   *Permitted Value*: A character scalar
-#'
-#' @inheritParams derive_vars_merged
-#'
-#' @return The output dataset contains all observations and variables of the
-#'   input dataset and additionally the variable specified for `new_var` derived
-#'   from the additional dataset (`dataset_add`).
-#'
-#' @details
-#'
-#'   1. The additional dataset is restricted to the observations matching the
-#'   `filter_add` condition.
-#'
-#'   1. The (transformed) character variable is added to the additional dataset.
-#'
-#'   1. If `order` is specified, for each by group the first or last observation
-#'   (depending on `mode`) is selected.
-#'
-#'   1. The character variable is merged to the input dataset.
-#'
-#'
-#' @family deprecated
-#' @keywords deprecated
-#'
-#' @export
-derive_var_merged_character <- function(dataset,
-                                        dataset_add,
-                                        by_vars,
-                                        order = NULL,
-                                        new_var,
-                                        source_var,
-                                        case = NULL,
-                                        filter_add = NULL,
-                                        mode = NULL,
-                                        missing_value = NA_character_) {
-  deprecate_stop("0.11.0", "derive_var_merged_character()", "derive_vars_merged()")
-}
-
-
-=======
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
 #' Merge Lookup Table with Source Dataset
 #'
 #' Merge user-defined lookup table with the input dataset. Optionally print a

diff --git a/R/derive_param_computed.R b/R/derive_param_computed.R
@@ -304,11 +304,7 @@ derive_param_computed <- function(dataset = NULL,
   assert_logical_scalar(keep_nas)
   ### BEGIN DEPRECATION
   if (!missing(analysis_var)) {
-<<<<<<< HEAD
-    deprecate_warn(
-=======
     deprecate_stop(
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
       "0.12.0",
       "derive_param_computed(analysis_var = )",
       "derive_param_computed(set_values_to = )"
@@ -317,11 +313,7 @@ derive_param_computed <- function(dataset = NULL,
   analysis_var <- assert_symbol(enexpr(analysis_var))
 
   if (!missing(analysis_value)) {
-<<<<<<< HEAD
-    deprecate_warn(
-=======
     deprecate_stop(
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
       "0.12.0",
       "derive_param_computed(analysis_value = )",
       "derive_param_computed(set_values_to = )"

diff --git a/R/derive_param_exist_flag.R b/R/derive_param_exist_flag.R
@@ -168,29 +168,7 @@ derive_param_exist_flag <- function(dataset = NULL,
                                     missing_value = NA_character_,
                                     filter_add = NULL,
                                     by_vars = get_admiral_option("subject_keys"),
-<<<<<<< HEAD
-                                    set_values_to,
-                                    dataset_adsl,
-                                    subject_keys) {
-  ### BEGIN DEPRECATION
-  if (!missing(dataset_adsl)) {
-    deprecate_stop(
-      "0.11.0", "derive_param_exist_flag(dataset_adsl = )",
-      "derive_param_exit_flag(dataset_ref = )"
-    )
-  }
-
-  if (!missing(subject_keys)) {
-    deprecate_stop(
-      "0.11.0", "derive_param_exist_flag(subject_keys = )",
-      "derive_param_exit_flag(by_vars = )"
-    )
-  }
-  ### END DEPRECATION
-
-=======
                                     set_values_to) {
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
   # Check input parameters
   condition <- assert_filter_cond(enexpr(condition))
   assert_character_scalar(true_value)
@@ -210,18 +188,6 @@ derive_param_exist_flag <- function(dataset = NULL,
     assert_param_does_not_exist(dataset, set_values_to$PARAMCD)
   }
 
-<<<<<<< HEAD
-  if (!missing(aval_fun)) {
-    assert_function(aval_fun)
-    deprecate_stop(
-      "0.11.0",
-      "derive_param_exist_flag(aval_fun = )",
-      "derive_param_exist_flag(set_values_to = )"
-    )
-  }
-
-=======
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
   # Create new observations
   new_obs <- derive_var_merged_exist_flag(
     dataset_ref,

diff --git a/R/derive_var_dthcaus.R b/R/derive_var_dthcaus.R
@@ -316,11 +316,7 @@ dthcaus_source <- function(dataset_name,
                            set_values_to = NULL,
                            traceability_vars = NULL) {
   if (!is.null(traceability_vars)) {
-<<<<<<< HEAD
-    deprecate_warn(
-=======
     deprecate_stop(
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
       "0.12.0",
       "dthcaus_source(traceability_vars = )",
       "dthcaus_source(set_values_to = )"

diff --git a/R/derive_var_extreme_date.R b/R/derive_var_extreme_date.R
@@ -620,11 +620,7 @@ date_source <- function(dataset_name,
                         traceability_vars = NULL,
                         set_values_to = NULL) {
   if (!is.null(traceability_vars)) {
-<<<<<<< HEAD
-    deprecate_warn(
-=======
     deprecate_stop(
->>>>>>> b800ab103ddbf55701d4f6b2ed0080d3c3525f27
       "0.12.0",
       "date_source(traceability_vars = )",
       "date_source(set_values_to = )"