Merge pull request #198 from pharmaverse/197_exprs@1627_exprs@208_exp…

…rs@devel

Closes #197 197_exprs: replace vars() with exprs()

NAMESPACE

@@ -50,9 +50,9 @@ importFrom(admiraldev,assert_vars)
 importFrom(admiraldev,assert_varval_list)
 importFrom(admiraldev,enumerate)
 importFrom(admiraldev,expect_dfs_equal)
+importFrom(admiraldev,expr_c)
 importFrom(admiraldev,extract_vars)
 importFrom(admiraldev,filter_if)
-importFrom(admiraldev,quo_c)
 importFrom(admiraldev,squote)
 importFrom(admiraldev,suppress_warning)
 importFrom(admiraldev,vars2chr)
@@ -69,16 +69,14 @@ importFrom(dplyr,right_join)
 importFrom(dplyr,select)
 importFrom(dplyr,slice)
 importFrom(dplyr,ungroup)
-importFrom(dplyr,vars)
 importFrom(lifecycle,deprecate_stop)
 importFrom(lifecycle,deprecate_warn)
 importFrom(lifecycle,deprecated)
 importFrom(lubridate,days)
 importFrom(magrittr,`%>%`)
 importFrom(rlang,abort)
-importFrom(rlang,enquo)
+importFrom(rlang,enexpr)
+importFrom(rlang,exprs)
 importFrom(rlang,inform)
-importFrom(rlang,quo_get_expr)
-importFrom(rlang,quo_is_null)
 importFrom(rlang,warn)
 importFrom(tidyselect,all_of)

NEWS.md

@@ -1,3 +1,12 @@
+# admiralonco 0.3.0
+
+## Breaking Changes
+
+- All function arguments which expected a list of quosures created by `vars()`
+are now expecting a list of expressions created by `exprs()`. For example,
+instead of `by_vars = vars(STUDYID, USUBJID)` `by_vars = exprs(STUDYID,
+USUBJID)` must be used now.
+
 # admiralonco 0.2.0
 
 ## Updates of Existing Functions

R/admiralonco-package.R

@@ -9,12 +9,12 @@
 #'   assert_integer_scalar assert_list_of assert_logical_scalar
 #'   assert_order_vars assert_param_does_not_exist assert_s3_class assert_symbol
 #'   assert_vars assert_varval_list enumerate expect_dfs_equal extract_vars
-#'   filter_if quo_c squote suppress_warning vars2chr
+#'   filter_if expr_c squote suppress_warning vars2chr
 #' @importFrom dplyr arrange bind_rows case_when filter group_by if_else
-#'   left_join mutate rename right_join select slice vars ungroup
+#'   left_join mutate rename right_join select slice ungroup
 #' @importFrom lifecycle deprecate_warn deprecated deprecate_stop
 #' @importFrom lubridate days
 #' @importFrom magrittr `%>%`
-#' @importFrom rlang abort enquo inform quo_get_expr quo_is_null warn
+#' @importFrom rlang abort enexpr exprs inform warn
 #' @importFrom tidyselect all_of
 "_PACKAGE"

R/check_crpr.R

@@ -2,14 +2,14 @@
 #'
 #' @param dataset A data frame
 #'
-#' @param order A list of variables created using `vars()` determining the order
+#' @param order A list of variables created using `exprs()` determining the order
 #'   or the records
 #'
 #' @param msg The condition message
 #'
 #' @param subject_keys Variables to uniquely identify a subject
 #'
-#'   A list of symbols created using `vars()` is expected.
+#'   A list of symbols created using `exprs()` is expected.
 #'
 #' @param check_type Type of message to issue when detecting PR after CR.
 #'
@@ -32,6 +32,7 @@
 #' library(dplyr)
 #' library(lubridate)
 #' library(admiralonco)
+#' library(rlang)
 #'
 #' adrs <- tribble(
 #'   ~USUBJID, ~ADTC,        ~AVALC,
@@ -48,7 +49,7 @@
 #'     STUDYID = "XX1234"
 #'   )
 #'
-#' signal_crpr(adrs, order = vars(ADT))
+#' signal_crpr(adrs, order = exprs(ADT))
 signal_crpr <- function(dataset,
                         order,
                         msg = "Dataset contains CR records followed by PR.",
@@ -62,7 +63,7 @@ signal_crpr <- function(dataset,
     dataset,
     by_vars = subject_keys,
     order = order,
-    join_vars = vars(AVALC),
+    join_vars = exprs(AVALC),
     join_type = "after",
     filter = AVALC == "CR" & AVALC.join == "PR"
   )
@@ -72,7 +73,7 @@ signal_crpr <- function(dataset,
       dataset,
       by_vars = subject_keys,
       order = order,
-      join_vars = vars(AVALC),
+      join_vars = exprs(AVALC),
       join_type = "before",
       filter = AVALC == "PR" & AVALC.join == "CR"
     )
@@ -120,6 +121,7 @@ signal_crpr <- function(dataset,
 #' library(dplyr)
 #' library(lubridate)
 #' library(admiralonco)
+#' library(rlang)
 #'
 #' adrs <- tribble(
 #'   ~USUBJID, ~ADTC,        ~AVALC,
@@ -136,7 +138,7 @@ signal_crpr <- function(dataset,
 #'     STUDYID = "XX1234"
 #'   )
 #'
-#' signal_crpr(adrs, order = vars(ADT))
+#' signal_crpr(adrs, order = exprs(ADT))
 #'
 #' get_crpr_dataset()
 get_crpr_dataset <- function() {

R/derive_param_bor.R

@@ -121,16 +121,14 @@
 #'
 #' @param set_values_to New columns to set
 #'
-#'   A named list returned by `vars()` defining the columns to be set for the
-#'   new parameter, e.g. `vars(PARAMCD = "BOR", PARAM = "Best Overall
+#'   A named list returned by `exprs()` defining the columns to be set for the
+#'   new parameter, e.g. `exprs(PARAMCD = "BOR", PARAM = "Best Overall
 #'   Response")` is expected. The values must be symbols, character strings,
 #'   numeric values, or `NA`.
 #'
 #' @param subject_keys Columns to uniquely identify a subject
 #'
-#'   A list of symbols created using `vars()`.
-#'
-#'   *Permitted Values:* an `vars` object
+#'   *Permitted Values:* A list of symbols created using `exprs()`.
 #'
 #' @examples
 #'
@@ -209,8 +207,8 @@
 #'   select(-ADTC) %>%
 #'   derive_vars_merged(
 #'     dataset_add = adsl,
-#'     by_vars     = vars(STUDYID, USUBJID),
-#'     new_vars    = vars(TRTSDT)
+#'     by_vars     = exprs(STUDYID, USUBJID),
+#'     new_vars    = exprs(TRTSDT)
 #'   )
 #'
 #' pd_date <- date_source(
@@ -242,7 +240,7 @@
 #'   aval_fun = aval_fun_pass,
 #'   reference_date = TRTSDT,
 #'   ref_start_window = 28,
-#'   set_values_to = vars(
+#'   set_values_to = exprs(
 #'     PARAMCD = "BOR",
 #'     PARAM = "Best Overall Response"
 #'   )
@@ -274,25 +272,25 @@ derive_param_bor <- function(dataset,
   # Assert statements (checked in order of signature) ----
   #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
-  reference_date <- assert_symbol(arg = enquo(reference_date))
+  reference_date <- assert_symbol(arg = enexpr(reference_date))
 
   assert_vars(arg = subject_keys)
 
   assert_data_frame(
     arg = dataset,
-    required_vars = quo_c(
+    required_vars = expr_c(
       subject_keys,
       reference_date,
-      vars(PARAMCD, ADT, AVALC)
+      exprs(PARAMCD, ADT, AVALC)
     )
   )
 
   assert_data_frame(
     arg           = dataset_adsl,
-    required_vars = quo_c(subject_keys)
+    required_vars = expr_c(subject_keys)
   )
 
-  filter_source <- assert_filter_cond(arg = enquo(filter_source))
+  filter_source <- assert_filter_cond(arg = enexpr(filter_source))
 
   assert_integer_scalar(
     arg      = ref_start_window,
@@ -308,7 +306,7 @@ derive_param_bor <- function(dataset,
 
   assert_param_does_not_exist(
     dataset = dataset,
-    param   = quo_get_expr(set_values_to$PARAMCD)
+    param   = set_values_to$PARAMCD
   )
 
   #++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
@@ -341,7 +339,7 @@ derive_param_bor <- function(dataset,
     err_msg <- sprintf(
       "dataframe passed into %s argument with the filter %s has 0 records",
       "dataset",
-      deparse(quo_get_expr(filter_source))
+      deparse(filter_source)
     )
 
     abort(err_msg)
@@ -410,7 +408,7 @@ derive_param_bor <- function(dataset,
   ) %>%
     filter_extreme(
       by_vars = subject_keys,
-      order = vars(tmp_order, ADT),
+      order = exprs(tmp_order, ADT),
       mode = "first"
     ) %>%
     select(-tmp_order)
@@ -433,7 +431,7 @@ derive_param_bor <- function(dataset,
             " ",
             names(set_values_to),
             "=",
-            lapply(set_values_to, quo_get_expr),
+            set_values_to,
             collapse = "\n"
           ),
           "\n)\nError message:\n  ",

R/derive_param_clinbenefit.R

@@ -103,11 +103,11 @@
 #' @param clinben_vals A vector of response values to be considered when determining
 #' clinical benefit.
 #'
-#' @param set_values_to A named list returned by `vars()` containing new variables
+#' @param set_values_to A named list returned by `exprs()` containing new variables
 #' and their static value to be populated for the clinical benefit rate parameter
-#' records, e.g. `vars(PARAMCD = "CBR", PARAM = "Clinical Benefit Rate")`.
+#' records, e.g. `exprs(PARAMCD = "CBR", PARAM = "Clinical Benefit Rate")`.
 #'
-#' @param subject_keys A named list returned by `vars()` containing variables
+#' @param subject_keys A named list returned by `exprs()` containing variables
 #' used to uniquely identify subjects.
 #'
 #' @return The input dataset with a new parameter for clinical benefit
@@ -157,8 +157,8 @@
 #'   mutate(STUDYID = "AB42", ANL01FL = "Y") %>%
 #'   derive_vars_merged(
 #'     dataset_add = adsl,
-#'     by_vars = vars(STUDYID, USUBJID),
-#'     new_vars = vars(TRTSDT)
+#'     by_vars = exprs(STUDYID, USUBJID),
+#'     new_vars = exprs(TRTSDT)
 #'   )
 #'
 #' pd <- date_source(
@@ -182,7 +182,7 @@
 #'   source_datasets = list(adrs = adrs),
 #'   reference_date = TRTSDT,
 #'   ref_start_window = 28,
-#'   set_values_to = vars(
+#'   set_values_to = exprs(
 #'     PARAMCD = "CBR"
 #'   )
 #' ) %>%
@@ -200,26 +200,26 @@ derive_param_clinbenefit <- function(dataset,
                                      set_values_to,
                                      subject_keys = get_admiral_option("subject_keys")) {
   # Assertions and quotes
-  reference_date <- assert_symbol(enquo(reference_date))
+  reference_date <- assert_symbol(enexpr(reference_date))
   assert_vars(subject_keys)
   assert_data_frame(
     dataset_adsl,
     required_vars = subject_keys
   )
   assert_data_frame(
     dataset,
-    required_vars = quo_c(subject_keys, reference_date, vars(PARAMCD, AVALC, ADT))
+    required_vars = expr_c(subject_keys, reference_date, exprs(PARAMCD, AVALC, ADT))
   )
 
   filter_source <- assert_filter_cond(
-    enquo(filter_source),
+    enexpr(filter_source),
     optional = FALSE
   )
 
   assert_function(aval_fun)
-  assert_s3_class(source_resp, "date_source", optional = FALSE)
-  assert_s3_class(source_pd, "date_source")
-  assert_list_of(source_datasets, "data.frame", optional = FALSE)
+  assert_s3_class(source_resp, "date_source")
+  assert_s3_class(source_pd, "date_source", optional = TRUE)
+  assert_list_of(source_datasets, "data.frame")
   assert_character_vector(clinben_vals)
 
   source_names <- names(source_datasets)
@@ -250,7 +250,7 @@ derive_param_clinbenefit <- function(dataset,
 
   ref_start_window <- assert_integer_scalar(ref_start_window, subset = "non-negative")
   assert_varval_list(set_values_to, optional = TRUE)
-  assert_param_does_not_exist(dataset, quo_get_expr(set_values_to$PARAMCD))
+  assert_param_does_not_exist(dataset, set_values_to$PARAMCD)
 
   # ADSL variables
   adsl_vars <- intersect(colnames(dataset_adsl), colnames(dataset))
@@ -295,7 +295,7 @@ derive_param_clinbenefit <- function(dataset,
         ADT >= !!reference_date + days(ref_start_window)
     ) %>%
     filter_extreme(
-      order = vars(ADT),
+      order = exprs(ADT),
       by_vars = subject_keys,
       mode = "first",
       check_type = "none"
@@ -305,7 +305,7 @@ derive_param_clinbenefit <- function(dataset,
   # without records in ovr_data and rsp_data
   new_param <- bind_rows(ovr_data, rsp_data, adsl) %>%
     filter_extreme(
-      order = vars(ADT),
+      order = exprs(ADT),
       by_vars = subject_keys,
       mode = "first",
       check_type = "none"