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Closes #2510 enhance derive param computed #2544

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Nov 7, 2024
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Closes #2510 enhance derive param computed #2544

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77a1b9c
#2510 enhance_derive_param_computed: enhance keep_nas argument
bundfussr Oct 29, 2024
b99d063
#2510 enhance_derive_param_computed: style files
bundfussr Oct 29, 2024
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#2510 enhance_derive_param_computed: add note if no records were adde…
bundfussr Oct 30, 2024
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#2510 enhance_derive_param_computed: fix links
bundfussr Oct 30, 2024
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Merge branch 'main' into 2510_enhance_derive_param_computed
bundfussr Nov 6, 2024
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Merge branch 'main' into 2510_enhance_derive_param_computed
bundfussr Nov 7, 2024
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5 changes: 5 additions & 0 deletions NEWS.md
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Expand Up @@ -12,6 +12,11 @@

## Updates of Existing Functions

- The `keep_nas` argument of `derive_param_computed()` was enhanced such that it
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is now possible to specify a list of variables for which `NA`s are acceptable.
I.e., records are added even if some of the specified variables are `NA`.
(#2510)

## Breaking Changes

- The following function arguments are entering the next phase of the deprecation process: (#2487)
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79 changes: 61 additions & 18 deletions R/derive_param_computed.R
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Expand Up @@ -117,13 +117,18 @@
#' @param keep_nas Keep observations with `NA`s
#'
#' If the argument is set to `TRUE`, observations are added even if some of
#' the values contributing to the computed value are `NA`.
#' the values contributing to the computed value are `NA` (see Example 1b).
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#'
#' If the argument is set to a list of variables, observations are added even
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#' if some of specified variables are `NA` (see Example 1c).
#'
#' @details For each group (with respect to the variables specified for the
#' `by_vars` parameter) an observation is added to the output dataset if the
#' filtered input dataset (`dataset`) or the additional dataset
#' (`dataset_add`) contains exactly one observation for each parameter code
#' specified for `parameters`.
#' specified for `parameters` and all contributing values like `AVAL.SYSBP`
#' are not `NA`. The `keep_nas` can be used to specify variables for which
#' `NA`s are acceptable. See also Example 1b and 1c.
#'
#' For the new observations the variables specified for `set_values_to` are
#' set to the provided values. The values of the other variables of the input
Expand All @@ -145,17 +150,18 @@
#'
#' # Example 1a: Derive MAP
#' advs <- tribble(
#' ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT,
#' "01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 51, "mmHg", "BASELINE",
#' "01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 50, "mmHg", "WEEK 2",
#' "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "mmHg", "BASELINE",
#' "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "mmHg", "WEEK 2",
#' "01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 79, "mmHg", "BASELINE",
#' "01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 80, "mmHg", "WEEK 2",
#' "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 130, "mmHg", "BASELINE",
#' "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 132, "mmHg", "WEEK 2"
#' ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~VISIT,
#' "01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 51, "BASELINE",
#' "01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 50, "WEEK 2",
#' "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "BASELINE",
#' "01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "WEEK 2",
#' "01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 79, "BASELINE",
#' "01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 80, "WEEK 2",
#' "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 130, "BASELINE",
#' "01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", NA, "WEEK 2"
#' ) %>%
#' mutate(
#' AVALU = "mmHg",
#' ADT = case_when(
#' VISIT == "BASELINE" ~ as.Date("2024-01-10"),
#' VISIT == "WEEK 2" ~ as.Date("2024-01-24")
Expand All @@ -176,8 +182,8 @@
#' )
#' )
#'
#' # Example 1b: Using option `keep_nas = TRUE` to derive MAP in the case where some/all values
#' # of a variable used in the computation are missing
#' # Example 1b: Using option `keep_nas = TRUE` to derive MAP in the case where some/all
#' # values of a variable used in the computation are missing
#'
#' derive_param_computed(
#' advs,
Expand All @@ -194,6 +200,24 @@
#' keep_nas = TRUE
#' )
#'
#' # Example 1c: Using option `keep_nas = exprs(ADTF)` to derive MAP in the case where
#' # some/all values of a variable used in the computation are missing but ignoring ADTF
#'
#' derive_param_computed(
#' advs,
#' by_vars = exprs(USUBJID, VISIT),
#' parameters = c("SYSBP", "DIABP"),
#' set_values_to = exprs(
#' AVAL = (AVAL.SYSBP + 2 * AVAL.DIABP) / 3,
#' PARAMCD = "MAP",
#' PARAM = "Mean Arterial Pressure (mmHg)",
#' AVALU = "mmHg",
#' ADT = ADT.SYSBP,
#' ADTF = ADTF.SYSBP
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#' ),
#' keep_nas = exprs(ADTF)
#' )
#'
#' # Example 2: Derive BMI where height is measured only once
#' advs <- tribble(
#' ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT,
Expand Down Expand Up @@ -303,7 +327,17 @@ derive_param_computed <- function(dataset = NULL,
if (!is.null(set_values_to$PARAMCD) && !is.null(dataset)) {
assert_param_does_not_exist(dataset, set_values_to$PARAMCD)
}
assert_logical_scalar(keep_nas)
if (typeof(keep_nas) == "list") {
assert_vars(keep_nas)
} else {
assert_logical_scalar(
keep_nas,
message = paste(
"Argument {.arg {arg_name}} must be either {.val {TRUE}}, {.val {FALSE}},",
"or a list of {.cls symbol}, but is {.obj_type_friendly {arg}}."
)
)
}

parameters <- assert_parameters_argument(parameters)
constant_parameters <- assert_parameters_argument(constant_parameters, optional = TRUE)
Expand Down Expand Up @@ -346,17 +380,26 @@ derive_param_computed <- function(dataset = NULL,
hori_data <- inner_join(hori_data, hori_const_data, by = vars2chr(constant_by_vars))
}

# add analysis value (AVAL) and parameter variables, e.g., PARAMCD
if (!keep_nas) {
# keep only observations where all analysis values are available
if (isFALSE(keep_nas) || typeof(keep_nas) == "list") {
# keep only observations where the specified analysis values are available
if (typeof(keep_nas) == "list") {
na_vars <- discard(
analysis_vars_chr,
~ str_detect(., paste0("^(", paste(vars2chr(keep_nas), collapse = "|"), ")\\."))
)
} else {
na_vars <- analysis_vars_chr
}
hori_data <- filter(
hori_data,
!!!parse_exprs(map_chr(
analysis_vars_chr,
na_vars,
~ str_c("!is.na(", .x, ")")
))
)
}

# add computed variables like AVAL and constant variables like PARAMCD
hori_data <- hori_data %>%
process_set_values_to(set_values_to) %>%
select(-all_of(analysis_vars_chr[str_detect(analysis_vars_chr, "\\.")]))
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1 change: 1 addition & 0 deletions _pkgdown.yml
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@@ -1,6 +1,7 @@
url: https://pharmaverse.github.io/admiral

template:
math-rendering: mathjax
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is this intentional? Just checking!?! :)

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Yes, I rendered the documentation with pkgdown 2.1.1 and noticed that formulas are no longer rendered correctly. Adding this line fixes the issues.

bootstrap: 5
params:
bootswatch: flatly
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50 changes: 37 additions & 13 deletions man/derive_param_computed.Rd
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Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

15 changes: 13 additions & 2 deletions tests/testthat/_snaps/derive_param_computed.md
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@@ -1,12 +1,23 @@
# assert_parameters_argument Test 10: error if argument is of wrong type
# derive_param_computed Test 11: error if keep_nas is invalid

Code
derive_param_computed(advs, by_vars = exprs(USUBJID, AVISIT), parameters = c(
"SYSBP", "DIABP"), set_values_to = exprs(AVAL = (AVAL.SYSBP + 2 *
AVAL.DIABP) / 3, PARAMCD = "MAP", PARAM = "Mean Arterial Pressure (mmHg)"),
keep_nas = 3)
Condition
Error in `derive_param_computed()`:
! Argument `keep_nas` must be either TRUE, FALSE, or a list of <symbol>, but is a number.

# assert_parameters_argument Test 12: error if argument is of wrong type

Code
assert_parameters_argument(myparameters <- c(1, 2, 3))
Condition
Error in `assert_parameters_argument()`:
! `myparameters <- c(1, 2, 3)` must be a character vector or a list of expressions but it is a double vector.

# get_hori_data Test 11: error if variables with more than one dot
# get_hori_data Test 13: error if variables with more than one dot

Code
get_hori_data(input, parameters = exprs(SYSBP, DIABP), by_vars = exprs(USUBJID,
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99 changes: 95 additions & 4 deletions tests/testthat/test-derive_param_computed.R
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Expand Up @@ -399,18 +399,109 @@ test_that("derive_param_computed Test 9: compute multiple variables, keep_nas",
)
})

## Test 10: specify variables for keep_nas ----
test_that("derive_param_computed Test 10: specify variables for keep_nas", {
advs <- tibble::tribble(
~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVISIT,
"01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 51, "BASELINE",
"01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 50, "WEEK 2",
"01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "BASELINE",
"01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "WEEK 2",
"01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 79, "BASELINE",
"01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 80, "WEEK 2",
"01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 130, "BASELINE",
"01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", NA, "WEEK 2"
) %>%
mutate(
ADT = case_when(
AVISIT == "BASELINE" ~ as.Date("2024-01-10"),
AVISIT == "WEEK 2" ~ as.Date("2024-01-24")
),
ADTF = NA_character_
)

expected <- bind_rows(
advs,
tibble::tribble(
~USUBJID, ~AVISIT, ~AVAL,
"01-701-1015", "BASELINE", (121 + 2 * 51) / 3,
"01-701-1015", "WEEK 2", (121 + 2 * 50) / 3,
"01-701-1028", "BASELINE", (130 + 2 * 79) / 3
) %>%
mutate(
PARAMCD = "MAP",
PARAM = "Mean Arterial Pressure (mmHg)",
ADT = case_when(
AVISIT == "BASELINE" ~ as.Date("2024-01-10"),
AVISIT == "WEEK 2" ~ as.Date("2024-01-24")
),
ADTF = NA_character_
)
)

actual <- derive_param_computed(
advs,
by_vars = exprs(USUBJID, AVISIT),
parameters = c("SYSBP", "DIABP"),
set_values_to = exprs(
AVAL = (AVAL.SYSBP + 2 * AVAL.DIABP) / 3,
PARAMCD = "MAP",
PARAM = "Mean Arterial Pressure (mmHg)",
ADT = ADT.SYSBP,
ADTF = ADTF.SYSBP
),
keep_nas = exprs(ADTF)
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)

expect_dfs_equal(
base = expected,
compare = actual,
keys = c("USUBJID", "PARAMCD", "AVISIT")
)
})

## Test 11: error if keep_nas is invalid ----
test_that("derive_param_computed Test 11: error if keep_nas is invalid", {
advs <- tibble::tribble(
~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVISIT,
"01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 51, "BASELINE",
"01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 50, "WEEK 2",
"01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "BASELINE",
"01-701-1015", "SYSBP", "Systolic Blood Pressure (mmHg)", 121, "WEEK 2",
"01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 79, "BASELINE",
"01-701-1028", "DIABP", "Diastolic Blood Pressure (mmHg)", 80, "WEEK 2",
"01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", 130, "BASELINE",
"01-701-1028", "SYSBP", "Systolic Blood Pressure (mmHg)", NA, "WEEK 2"
)

expect_snapshot(
derive_param_computed(
advs,
by_vars = exprs(USUBJID, AVISIT),
parameters = c("SYSBP", "DIABP"),
set_values_to = exprs(
AVAL = (AVAL.SYSBP + 2 * AVAL.DIABP) / 3,
PARAMCD = "MAP",
PARAM = "Mean Arterial Pressure (mmHg)"
),
keep_nas = 3
),
error = TRUE
)
})

# assert_parameters_argument ----
## Test 10: error if argument is of wrong type ----
test_that("assert_parameters_argument Test 10: error if argument is of wrong type", {
## Test 12: error if argument is of wrong type ----
test_that("assert_parameters_argument Test 12: error if argument is of wrong type", {
expect_snapshot(
assert_parameters_argument(myparameters <- c(1, 2, 3)),
error = TRUE
)
})

# get_hori_data ----
## Test 11: error if variables with more than one dot ----
test_that("get_hori_data Test 11: error if variables with more than one dot", {
## Test 13: error if variables with more than one dot ----
test_that("get_hori_data Test 13: error if variables with more than one dot", {
input <- tibble::tribble(
~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT,
"01-701-1015", "DIABP", "Diastolic Blood Pressure (mmHg)", 51, "mmHg", "BASELINE",
Expand Down
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