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Closes #2091 fixing deprecation messaging in derive_param_doseint() #2092

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merged 4 commits into from
Sep 11, 2023
Merged

Closes #2091 fixing deprecation messaging in derive_param_doseint() #2092

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1d72836
feat: #2091 did that work?
Sep 10, 2023
f8eab87
chore: #2091 address errors
Sep 10, 2023
17ae615
fixed deprecation warning
StefanThoma Sep 11, 2023
9853f5b
deprecation for analysis_var
StefanThoma Sep 11, 2023
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19 changes: 11 additions & 8 deletions R/derive_param_computed.R
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Original file line number Diff line number Diff line change
Expand Up @@ -293,14 +293,6 @@ derive_param_computed <- function(dataset = NULL,
constant_parameters = NULL,
keep_nas = FALSE) {
assert_vars(by_vars)
if (!missing(analysis_var)) {
deprecate_warn(
"0.12.0",
"derive_param_computed(analysis_var = )",
"derive_param_computed(set_values_to = )"
)
}
analysis_var <- assert_symbol(enexpr(analysis_var))
Comment on lines -296 to -303
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I think we should not remove this part because otherwise the following does not issue a deprecation warning.

> derive_param_computed(
+   advs,
+   by_vars = exprs(USUBJID, VISIT),
+   parameters = c("SYSBP", "DIABP"),
+   analysis_var = CHR,
+   set_values_to = exprs(
+     AVAL = (AVAL.SYSBP + 2 * AVAL.DIABP) / 3,
+     PARAMCD = "MAP",
+     PARAM = "Mean Arterial Pressure (mmHg)",
+     AVALU = "mmHg"
+   )
+ )

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I was a bit confused by analysis_var and analysis_value, but I think I fixed it now, hopefully!

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Have you committed your fix?

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Will be up in a minute, still running check()

assert_vars(constant_by_vars, optional = TRUE)
assert_data_frame(dataset, required_vars = by_vars, optional = TRUE)
assert_data_frame(dataset_add, optional = TRUE)
Expand All @@ -310,6 +302,16 @@ derive_param_computed <- function(dataset = NULL,
assert_param_does_not_exist(dataset, set_values_to$PARAMCD)
}
assert_logical_scalar(keep_nas)
### BEGIN DEPRECATION
if (!missing(analysis_var)) {
deprecate_warn(
"0.12.0",
"derive_param_computed(analysis_var = )",
"derive_param_computed(set_values_to = )"
)
}
analysis_var <- assert_symbol(enexpr(analysis_var))

if (!missing(analysis_value)) {
deprecate_warn(
"0.12.0",
Expand All @@ -318,6 +320,7 @@ derive_param_computed <- function(dataset = NULL,
)
set_values_to <- exprs(!!analysis_var := !!enexpr(analysis_value), !!!set_values_to)
}
### END DEPRECATION

parameters <- assert_parameters_argument(parameters)
constant_parameters <- assert_parameters_argument(constant_parameters, optional = TRUE)
Expand Down
5 changes: 3 additions & 2 deletions R/derive_param_doseint.R
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Original file line number Diff line number Diff line change
Expand Up @@ -131,6 +131,8 @@ derive_param_doseint <- function(dataset,
aval_tadm <- sym(paste0("AVAL.", tadm_code))
aval_tpdm <- sym(paste0("AVAL.", tpadm_code))

analysis_value <- exprs(AVAL = !!aval_tadm / !!aval_tpdm * 100)

# handle 0 doses planned if needed
if (zero_doses == "100") {
update_aval <- exprs(
Expand All @@ -151,7 +153,6 @@ derive_param_doseint <- function(dataset,
filter = !!filter,
parameters = c(tadm_code, tpadm_code),
by_vars = by_vars,
analysis_value = (!!aval_tadm / !!aval_tpdm * 100),
set_values_to = expr_c(set_values_to, update_aval)
set_values_to = expr_c(set_values_to, analysis_value, update_aval)
)
}