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Closes #1228 produce bmi records for more visits #1957

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merged 8 commits into from
Jun 28, 2023
Merged

Closes #1228 produce bmi records for more visits #1957

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c048d03
feat: #1228 Produce BMI records for more visits: Add constant_height …
jeffreyad Jun 13, 2023
c84a877
feat: #1228 Produce BMI records for more visits: Update to use consta…
jeffreyad Jun 15, 2023
cabc201
docs: #1228 Produce BMI records for more visits: Fix typo in NEWS
jeffreyad Jun 15, 2023
e272bf5
feat: #1228 Produce BMI records for more visits: Update ADVS template…
jeffreyad Jun 15, 2023
5ac774d
Merge branch 'devel' into 1228_Produce_BMI_records_for_more_visits@devel
jeffreyad Jun 16, 2023
7c286dc
Merge branch 'devel' into 1228_Produce_BMI_records_for_more_visits@devel
bms63 Jun 23, 2023
a1d3050
Merge branch 'devel' into 1228_Produce_BMI_records_for_more_visits@devel
jeffreyad Jun 26, 2023
022c8fa
doc: #1228 Produce BMI records for more visits: Add backticks to vari…
jeffreyad Jun 28, 2023
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138 changes: 117 additions & 21 deletions R/derive_advs_params.R
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Original file line number Diff line number Diff line change
Expand Up @@ -255,6 +255,15 @@ compute_map <- function(diabp, sysbp, hr = NULL) {
#'
#' Permitted Values: character value
#'
#' @param constant_height HEIGHT parameter is constant
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#'
#' If the HEIGHT value is considered constant (e.g. measured once at screening),
#' the values of BSA will be calculated for each WEIGHT value.
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#'
#' Permitted Values: logical scalar
#'
#' Default Values: FALSE
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#'
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#' @inheritParams derive_param_computed
#'
#' @inheritParams derive_param_qtc
Expand Down Expand Up @@ -305,14 +314,29 @@ compute_map <- function(diabp, sysbp, hr = NULL) {
#' ),
#' get_unit_expr = extract_unit(PARAM)
#' )
#'
#' derive_param_bsa(
#' advs,
#' by_vars = exprs(USUBJID, VISIT),
#' method = "Mosteller",
#' set_values_to = exprs(
#' PARAMCD = "BSA",
#' PARAM = "Body Surface Area (m^2)"
#' ),
#' get_unit_expr = extract_unit(PARAM),
#' constant_height = TRUE,
#' constant_by_vars = exprs(USUBJID)
#' )
derive_param_bsa <- function(dataset,
by_vars,
method,
set_values_to = exprs(PARAMCD = "BSA"),
height_code = "HEIGHT",
weight_code = "WEIGHT",
get_unit_expr,
filter = NULL) {
filter = NULL,
constant_height = FALSE,
constant_by_vars = NULL) {
assert_vars(by_vars)
assert_data_frame(dataset, required_vars = exprs(!!!by_vars, PARAMCD, AVAL))
assert_character_scalar(
Expand All @@ -328,6 +352,8 @@ derive_param_bsa <- function(dataset,
assert_character_scalar(weight_code)
get_unit_expr <- assert_expr(enexpr(get_unit_expr))
filter <- assert_filter_cond(enexpr(filter), optional = TRUE)
assert_vars(constant_by_vars, optional = TRUE)
assert_logical_scalar(constant_height)

assert_unit(
dataset,
Expand All @@ -350,14 +376,33 @@ derive_param_bsa <- function(dataset,
)
)

derive_param_computed(
dataset,
filter = !!filter,
parameters = c(height_code, weight_code),
by_vars = by_vars,
analysis_value = !!bsa_formula,
set_values_to = set_values_to
)
if (constant_height == FALSE) {
derive_param_computed(
dataset,
filter = !!filter,
parameters = c(height_code, weight_code),
by_vars = by_vars,
analysis_value = !!bsa_formula,
set_values_to = set_values_to
)
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} else {
if (is.null(constant_by_vars)) {
abort(
"constant_by_vars is expected when constant_height is TRUE"
)
} else {
derive_param_computed(
dataset,
filter = !!filter,
parameters = c(weight_code),
by_vars = by_vars,
analysis_value = !!bsa_formula,
set_values_to = set_values_to,
constant_parameters = c(height_code),
constant_by_vars = constant_by_vars
)
}
}
}

#' Compute Body Surface Area (BSA)
Expand Down Expand Up @@ -486,6 +531,15 @@ compute_bsa <- function(height = height,
#'
#' Permitted Values: character value
#'
#' @param constant_height HEIGHT parameter is constant
#'
#' If the HEIGHT value is considered constant (e.g. measured once at screening),
#' the values of BSA will be calculated for each WEIGHT value.
#'
#' Permitted Values: logical scalar
#'
#' Default Values: FALSE
#'
#' @inheritParams derive_param_computed
#'
#' @inheritParams derive_param_qtc
Expand Down Expand Up @@ -530,13 +584,30 @@ compute_bsa <- function(height = height,
#' ),
#' get_unit_expr = extract_unit(PARAM)
#' )
#'
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#' # Example 2: Derive BMI where height is measured only once
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#' derive_param_bmi(
#' advs,
#' by_vars = exprs(USUBJID, AVISIT),
#' weight_code = "WEIGHT",
#' height_code = "HEIGHT",
#' set_values_to = exprs(
#' PARAMCD = "BMI",
#' PARAM = "Body Mass Index (kg/m^2)"
#' ),
#' get_unit_expr = extract_unit(PARAM),
#' constant_height = TRUE,
#' constant_by_vars = exprs(USUBJID)
#' )
derive_param_bmi <- function(dataset,
by_vars,
set_values_to = exprs(PARAMCD = "BMI"),
weight_code = "WEIGHT",
height_code = "HEIGHT",
get_unit_expr,
filter = NULL) {
filter = NULL,
constant_height = FALSE,
constant_by_vars = NULL) {
assert_vars(by_vars)
assert_data_frame(dataset, required_vars = exprs(!!!by_vars, PARAMCD, AVAL))
assert_varval_list(set_values_to, required_elements = "PARAMCD")
Expand All @@ -545,6 +616,9 @@ derive_param_bmi <- function(dataset,
assert_character_scalar(height_code)
get_unit_expr <- assert_expr(enexpr(get_unit_expr))
filter <- assert_filter_cond(enexpr(filter), optional = TRUE)
assert_vars(constant_by_vars, optional = TRUE)
assert_logical_scalar(constant_height)


assert_unit(
dataset,
Expand All @@ -559,17 +633,39 @@ derive_param_bmi <- function(dataset,
get_unit_expr = !!get_unit_expr
)

derive_param_computed(
dataset,
filter = !!filter,
parameters = c(weight_code, height_code),
by_vars = by_vars,
analysis_value = compute_bmi(
height = !!sym(paste0("AVAL.", height_code)),
weight = !!sym(paste0("AVAL.", weight_code))
),
set_values_to = set_values_to
)
if (constant_height == FALSE) {
derive_param_computed(
dataset,
filter = !!filter,
parameters = c(weight_code, height_code),
by_vars = by_vars,
analysis_value = compute_bmi(
height = !!sym(paste0("AVAL.", height_code)),
weight = !!sym(paste0("AVAL.", weight_code))
),
set_values_to = set_values_to
)
} else {
if (is.null(constant_by_vars)) {
abort(
"constant_by_vars is expected when constant_height is TRUE"
)
} else {
derive_param_computed(
dataset,
filter = !!filter,
parameters = c(weight_code),
by_vars = by_vars,
analysis_value = compute_bmi(
height = !!sym(paste0("AVAL.", height_code)),
weight = !!sym(paste0("AVAL.", weight_code))
),
set_values_to = set_values_to,
constant_parameters = c(height_code),
constant_by_vars = constant_by_vars
)
}
}
}

#' Compute Body Mass Index (BMI)
Expand Down
35 changes: 34 additions & 1 deletion man/derive_param_bmi.Rd
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33 changes: 32 additions & 1 deletion man/derive_param_bsa.Rd
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