Closes #1968 compute multiple variables in derive_param_computed() (#…

…2036) * #1968 compute_multiple_vars: update arguments of derive_param_computed() * #1968 compute_multiple_vars: update documentation * #1968 compute_multiple_vars: update documentation * #1968 compute_multiple_vars: style files * #1968 compute_multiple_vars: fix R-CMD checks * #1968 compute_multiple_vars: update error message of get_hori_data() * #1968 compute_multiple_vars: improve documentation * #1968 compute_multiple_vars: use deprecation badge * #1968 compute_multiple_vars: use deprecation badge * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * #1968 compute_multiple_vars: use @Keywords internal * #1968 compute_multiple_vars: fix typo in NEWS.md --------- Co-authored-by: Daniel Sjoberg <[email protected]> Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]>
pharmaverse · Aug 21, 2023 · 1d44b96 · 1d44b96
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diff --git a/NEWS.md b/NEWS.md
@@ -9,6 +9,13 @@
 
 - The function `derive_var_extreme_flag()` has a new function argument, `flag_all` that additionally flags all records if the first or last record is not unique. (#1979)
 
+- The function `derive_param_computed()` was enhanced: (#1968)
+
+  - The `analysis_value` and `analysis_var` arguments were deprecated in favor of
+  `set_values_to`. This enables users to compute more than one variable.
+  - The `keep_nas` argument was added. If it is set to `TRUE`, observations are
+  created even if values contributing to the computed values are `NA`.
+
 - The function `derive_vars_dy()` is updated to avoid potential error when the input `dataset` with columns ending with `temp`. (#2012)
 
 
@@ -40,6 +47,9 @@
 - The `filter` argument in `derive_extreme_records()` was deprecated in favor of
 the `filter_add` using the next phase of the deprecation process. (#1950)
 
+- The `analysis_value` and `analysis_var` arguments in `derive_param_computed()`
+were deprecated in favor of `set_values_to` (#1968).
+
 - The `na_val` argument in `derive_var_shift()` has been deprecated in favor of 
 `missing_value` using the first phase of the deprecation process. (#2014)
 

diff --git a/R/derive_adeg_params.R b/R/derive_adeg_params.R
@@ -47,6 +47,8 @@
 #'
 #'   Permitted Values: A variable of the input dataset or a function call
 #'
+#' @inheritParams derive_param_map
+#'
 #' @inheritParams derive_param_computed
 #'
 #' @seealso [compute_qtc()]
@@ -152,12 +154,14 @@ derive_param_qtc <- function(dataset,
     filter = !!filter,
     parameters = c(qt_code, rr_code),
     by_vars = by_vars,
-    analysis_value = compute_qtc(
-      qt = !!sym(paste0("AVAL.", qt_code)),
-      rr = !!sym(paste0("AVAL.", rr_code)),
-      method = !!method
-    ),
-    set_values_to = set_values_to
+    set_values_to = exprs(
+      AVAL = compute_qtc(
+        qt = !!sym(paste0("AVAL.", qt_code)),
+        rr = !!sym(paste0("AVAL.", rr_code)),
+        method = !!method
+      ),
+      !!!set_values_to
+    )
   )
 }
 
@@ -269,6 +273,8 @@ compute_qtc <- function(qt, rr, method) {
 #'
 #'   Permitted Values: character value
 #'
+#' @inheritParams derive_param_map
+#'
 #' @inheritParams derive_param_computed
 #'
 #' @inheritParams derive_param_qtc
@@ -339,8 +345,10 @@ derive_param_rr <- function(dataset,
     filter = !!filter,
     parameters = c(hr_code),
     by_vars = by_vars,
-    analysis_value = compute_rr(!!sym(paste0("AVAL.", hr_code))),
-    set_values_to = set_values_to
+    set_values_to = exprs(
+      AVAL = compute_rr(!!sym(paste0("AVAL.", hr_code))),
+      !!!set_values_to
+    )
   )
 }
 

diff --git a/R/derive_advs_params.R b/R/derive_advs_params.R
@@ -36,6 +36,14 @@
 #'
 #'   *Permitted Values:* character value
 #'
+#' @param set_values_to Variables to be set
+#'
+#' The specified variables are set to the specified values for the new
+#' observations. For example `exprs(PARAMCD = "MAP")` defines the parameter code
+#' for the new parameter.
+#'
+#' *Permitted Values*: List of variable-value pairs
+#'
 #' @inheritParams derive_param_computed
 #'
 #' @inheritParams derive_param_qtc
@@ -148,8 +156,10 @@ derive_param_map <- function(dataset,
     filter = !!filter,
     parameters = c(sysbp_code, diabp_code, hr_code),
     by_vars = by_vars,
-    analysis_value = !!analysis_value,
-    set_values_to = set_values_to
+    set_values_to = exprs(
+      AVAL = !!analysis_value,
+      !!!set_values_to
+    )
   )
 }
 
@@ -271,6 +281,8 @@ compute_map <- function(diabp, sysbp, hr = NULL) {
 #'
 #'   *Permitted Values:* list of variables
 #'
+#' @inheritParams derive_param_map
+#'
 #' @inheritParams derive_param_computed
 #'
 #' @inheritParams derive_param_qtc
@@ -423,8 +435,10 @@ derive_param_bsa <- function(dataset,
     filter = !!filter,
     parameters = parameters,
     by_vars = by_vars,
-    analysis_value = !!bsa_formula,
-    set_values_to = set_values_to,
+    set_values_to = exprs(
+      AVAL = !!bsa_formula,
+      !!!set_values_to
+    ),
     constant_parameters = constant_parameters,
     constant_by_vars = constant_by_vars
   )
@@ -572,6 +586,8 @@ compute_bsa <- function(height = height,
 #'
 #'   *Permitted Values:* list of variables
 #'
+#' @inheritParams derive_param_map
+#'
 #' @inheritParams derive_param_computed
 #'
 #' @inheritParams derive_param_qtc
@@ -710,8 +726,10 @@ derive_param_bmi <- function(dataset,
     filter = !!filter,
     parameters = parameters,
     by_vars = by_vars,
-    analysis_value = !!bmi_formula,
-    set_values_to = set_values_to,
+    set_values_to = exprs(
+      AVAL = !!bmi_formula,
+      !!!set_values_to
+    ),
     constant_parameters = constant_parameters,
     constant_by_vars = constant_by_vars
   )