#1968 compute_multiple_vars: fix R-CMD checks

pharmaverse · Jul 28, 2023 · 2abae76 · 2abae76
1 parent e8c533f
commit 2abae76
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Showing 10 changed files with 60 additions and 40 deletions.
diff --git a/R/derive_adeg_params.R b/R/derive_adeg_params.R
@@ -153,12 +153,14 @@ 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
+    )
   )
 }
 
@@ -336,8 +338,10 @@ 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
@@ -154,8 +154,10 @@ 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
+    )
   )
 }
 
@@ -427,8 +429,10 @@ 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
   )
@@ -712,8 +716,10 @@ 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
   )

diff --git a/R/derive_param_computed.R b/R/derive_param_computed.R
@@ -162,6 +162,7 @@
 #'
 #' @examples
 #' library(tibble)
+#' library(dplyr)
 #' library(lubridate)
 #'
 #' # Example 1: Derive MAP
@@ -438,14 +439,14 @@ assert_parameters_argument <- function(parameters, optional = TRUE) {
 #'
 #'   *Permitted Values:* A character vector of `PARAMCD` values or a list of expressions
 #'
-#' @param analysis_value
+#' @param set_values_to
 #'
 #'   All variables of the form `<variable>.<parameter>` like `AVAL.WEIGHT` are
 #'   added to the input dataset. They are set to the value of the variable for
 #'   the parameter. E.g., `AVAL.WEIGHT` is set to the value of `AVAL` where
 #'   `PARAMCD == "WEIGHT"`.
 #'
-#'   *Permitted Values:* An unquoted expression
+#'   *Permitted Values:* A list of expressions
 #'
 #' @param filter Filter condition used for restricting the input dataset
 #'
@@ -536,7 +537,7 @@ get_hori_data <- function(dataset,
   )
 
   # horizontalize data, e.g., AVAL for PARAMCD = "PARAMx" -> AVAL.PARAMx
-  analysis_vars <- flatten(map(set_values_to, extract_vars))
+  analysis_vars <- flatten(map(unname(set_values_to), extract_vars))
   analysis_vars_chr <- vars2chr(analysis_vars)
   multi_dot_names <- str_count(analysis_vars_chr, "\\.") > 1
   if (any(multi_dot_names)) {

diff --git a/R/derive_param_framingham.R b/R/derive_param_framingham.R
@@ -271,7 +271,9 @@ derive_param_framingham <- function(dataset,
       diabetfl,
       trthypfl
     ),
-    analysis_value = !!analysis_value,
-    set_values_to = set_values_to
+    set_values_to = exprs(
+      AVAL = !!analysis_value,
+      !!!set_values_to
+    )
   )
 }
diff --git a/R/derive_param_wbc_abs.R b/R/derive_param_wbc_abs.R
@@ -159,8 +159,10 @@ derive_param_wbc_abs <- function(dataset,
         diff_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
+      )
     ) %>%
     filter(PARAMCD == !!set_values_to$PARAMCD) %>%
     select(-starts_with("temp_"))

diff --git a/inst/templates/ad_adex.R b/inst/templates/ad_adex.R
@@ -214,13 +214,17 @@ adex <- adex %>%
     variable_params = list(
       params(
         parameters = c("TDOSE", "TDURD"),
-        analysis_value = (AVAL.TDOSE / AVAL.TDURD),
-        set_values_to = exprs(PARAMCD = "AVDDSE")
+        set_values_to = exprs(
+          AVAL = (AVAL.TDOSE / AVAL.TDURD),
+          PARAMCD = "AVDDSE"
+        )
       ),
       params(
         parameters = c("PDOSE", "PDURD"),
-        analysis_value = (AVAL.PDOSE / AVAL.PDURD),
-        set_values_to = exprs(PARAMCD = "PAVDDSE")
+        set_values_to = exprs(
+          AVAL = (AVAL.PDOSE / AVAL.PDURD),
+          PARAMCD = "PAVDDSE"
+        )
       )
     ),
     by_vars = exprs(

diff --git a/man/derive_param_computed.Rd b/man/derive_param_computed.Rd
diff --git a/man/get_hori_data.Rd b/man/get_hori_data.Rd
diff --git a/tests/testthat/test-derive_advs_params.R b/tests/testthat/test-derive_advs_params.R
@@ -434,8 +434,8 @@ test_that("derive_param_bmi Test 38: Derive BMI where height is measured only on
     input,
     by_vars = exprs(USUBJID, VISIT),
     parameters = "WEIGHT",
-    analysis_value = AVAL.WEIGHT / (AVAL.HEIGHT / 100)^2,
     set_values_to = exprs(
+      AVAL = AVAL.WEIGHT / (AVAL.HEIGHT / 100)^2,
       PARAMCD = "BMI",
       PARAM = "Body Mass Index (kg/m^2)",
       AVALU = "kg/m^2"
@@ -859,11 +859,11 @@ test_that("derive_param_bsa Test 51: Derive BSA where height is measured only on
     input,
     by_vars = exprs(USUBJID, VISIT),
     parameters = "WEIGHT",
-    analysis_value = compute_bsa(
-      height = AVAL.HEIGHT, weight = AVAL.WEIGHT,
-      method = "Mosteller"
-    ),
     set_values_to = exprs(
+      AVAL = compute_bsa(
+        height = AVAL.HEIGHT, weight = AVAL.WEIGHT,
+        method = "Mosteller"
+      ),
       PARAMCD = "BSA",
       PARAM = "Body Surface Area (m^2)",
       AVALU = "m^2"

diff --git a/vignettes/bds_finding.Rmd b/vignettes/bds_finding.Rmd
@@ -1018,8 +1018,8 @@ advs_ex3 <- derive_param_computed(
   advs,
   by_vars = exprs(USUBJID, VISIT, ATPT),
   parameters = c("SYSBP", "DIABP"),
-  analysis_value = (AVAL.SYSBP - AVAL.DIABP) / 3 + AVAL.DIABP,
   set_values_to = exprs(
+    AVAL = (AVAL.SYSBP - AVAL.DIABP) / 3 + AVAL.DIABP,
     PARAMCD = "MAP2",
     PARAM = "Mean Arterial Pressure 2 (mmHg)"
   )