R/derive_adeg_params.R
In epijim/admiral: ADaM in R Asset Library
Defines functions
compute_rr
derive_param_rr
compute_qtc
default_qtc_paramcd
derive_param_qtc
Documented in
compute_qtc
compute_rr
default_qtc_paramcd
derive_param_qtc
derive_param_rr
#' Adds a Parameter for Corrected QT
#'
#' Adds a record for corrected QT using either Bazett's, Fridericia's or Sagie's
#' formula for each by group (e.g., subject and visit) where the source parameters
#' are available.
#'
#' @param dataset Input dataset
#'
#' The variables specified by the `by_vars` and the `unit_var` parameter,
#' `PARAMCD`, and `AVAL` are expected.
#'
#' The variable specified by `by_vars` and `PARAMCD` must be a unique key of
#' the input dataset after restricting it by the filter condition (`filter`
#' parameter) and to the parameters specified by `qt_code` and `rr_code`.
#'
#'
#' @param by_vars Grouping variables
#'
#' Permitted Values: list of variables
#'
#' @param method Method used to QT correction
#'
#' Permitted Values: `"Bazett"`, `"Fridericia"`, `"Sagie"`
#'
#' @param qt_code QT parameter code
#'
#' The observations where `PARAMCD` equals the specified value are considered
#' as the QT interval assessments. It is expected that QT is measured in msec.
#'
#' Permitted Values: character value
#'
#' @param rr_code RR parameter code
#'
#' The observations where `PARAMCD` equals the specified value are considered
#' as the RR interval assessments. It is expected that RR is measured in msec.
#'
#' Permitted Values: character value
#'
#' @param get_unit_expr An expression providing the unit of the parameter
#'
#' The result is used to check the units of the input parameters.
#'
#' Permitted Values: A variable of the input dataset or a function call
#'
#' @inheritParams derive_derived_param
#'
#' @seealso [compute_qtc()]
#'
#' @author Stefan Bundfuss
#'
#' @return The input dataset with the new parameter added
#'
#' @keywords derivation adeg
#'
#' @export
#'
#' @examples
#' adeg <- tibble::tribble(
#' ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT,
#' "01-701-1015", "HR", "Heart Rate (beats/min)", 70.14, "beats/min", "BASELINE",
#' "01-701-1015", "QT", "QT Duration (msec)", 370, "msec", "WEEK 2",
#' "01-701-1015", "HR", "Heart Rate (beats/min)", 62.66, "beats/min", "WEEK 1",
#' "01-701-1015", "RR", "RR Duration (msec)", 710, "msec", "WEEK 2",
#' "01-701-1028", "HR", "Heart Rate (beats/min)", 85.45, "beats/min", "BASELINE",
#' "01-701-1028", "QT", "QT Duration (msec)", 480, "msec", "WEEK 2",
#' "01-701-1028", "QT", "QT Duration (msec)", 350, "msec", "WEEK 3",
#' "01-701-1028", "HR", "Heart Rate (beats/min)", 56.54, "beats/min", "WEEK 3",
#' "01-701-1028", "RR", "RR Duration (msec)", 842, "msec", "WEEK 2",
#' )
#'
#' derive_param_qtc(
#' adeg,
#' by_vars = vars(USUBJID, VISIT),
#' method = "Bazett",
#' set_values_to = vars(
#' PARAMCD = "QTCBR",
#' PARAM = "QTcB - Bazett's Correction Formula Rederived (msec)",
#' AVALU = "msec"
#' ),
#' get_unit_expr = AVALU
#' )
#'
#' derive_param_qtc(
#' adeg,
#' by_vars = vars(USUBJID, VISIT),
#' method = "Fridericia",
#' set_values_to = vars(
#' PARAMCD = "QTCFR",
#' PARAM = "QTcF - Fridericia's Correction Formula Rederived (msec)",
#' AVALU = "msec"
#' ),
#' get_unit_expr = extract_unit(PARAM)
#' )
#'
#' derive_param_qtc(
#' adeg,
#' by_vars = vars(USUBJID, VISIT),
#' method = "Sagie",
#' set_values_to = vars(
#' PARAMCD = "QTLCR",
#' PARAM = "QTlc - Sagie's Correction Formula Rederived (msec)",
#' AVALU = "msec"
#' ),
#' get_unit_expr = extract_unit(PARAM)
#' )
derive_param_qtc <- function(dataset,
by_vars,
method,
set_values_to = default_qtc_paramcd(method),
qt_code = "QT",
rr_code = "RR",
get_unit_expr,
filter = NULL) {
assert_vars(by_vars)
assert_data_frame(
dataset,
required_vars = vars(!!!by_vars, PARAMCD, AVAL)
)
assert_character_scalar(method, values = c("Bazett", "Fridericia", "Sagie"))
assert_varval_list(set_values_to, required_elements = "PARAMCD")
assert_param_does_not_exist(dataset, quo_get_expr(set_values_to$PARAMCD))
assert_character_scalar(qt_code)
assert_character_scalar(rr_code)
get_unit_expr <- assert_expr(enquo(get_unit_expr))
filter <- assert_filter_cond(enquo(filter), optional = TRUE)
assert_unit(
dataset,
param = qt_code,
required_unit = "msec",
get_unit_expr = !!get_unit_expr
)
assert_unit(
dataset,
param = rr_code,
required_unit = "msec",
get_unit_expr = !!get_unit_expr
)
derive_derived_param(
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
)
}
#' Get Default Parameter Code for Corrected QT
#'
#' @param method Method used to QT correction
#'
#' Permitted Values: `"Bazett"`, `"Fridericia"`, `"Sagie"`
#'
#' @author Thomas Neitmann
#'
#' @export
#'
#' @keywords user_utility
#'
#' @examples
#' default_qtc_paramcd("Sagie")
default_qtc_paramcd <- function(method) {
assert_character_scalar(method, values = c("Bazett", "Fridericia", "Sagie"))
paramcd <- c(Bazett = "QTCBR", Fridericia = "QTCFR", Sagie = "QTLCR")
vars(PARAMCD = !!paramcd[[method]])
}
#' Compute Corrected QT
#'
#' Computes corrected QT using Bazett's, Fridericia's or Sagie's formula.
#'
#' @param qt QT interval
#'
#' A numeric vector is expected. It is expected that QT is measured in msec.
#'
#' @param rr RR interval
#'
#' A numeric vector is expected. It is expected that RR is measured in msec.
#'
#' @inheritParams derive_param_qtc
#'
#' @author Stefan Bundfuss
#'
#' @return QT interval in msec
#'
#' @details
#' Depending on the chosen `method` one of the following formulae is used.
#'
#' *Bazett*: \deqn{\frac{QT}{\sqrt{\frac{RR}{1000}}}}{QT/\sqrt(RR/1000)}
#'
#' *Fridericia*: \deqn{\frac{QT}{\sqrt[3]{\frac{RR}{1000}}}}{QT/(RR/1000)^(1/3)}
#'
#' *Sagie*: \deqn{1000\left(\frac{QT}{1000} + 0.154\left(1 - \frac{RR}{1000}\right)\right)}{
#' 1000(QT/1000 + 0.154(1 - RR/1000))}
#'
#' @keywords computation adeg
#'
#' @export
#'
#' @examples
#' compute_qtc(qt = 350, rr = 56.54, method = "Bazett")
#'
#' compute_qtc(qt = 350, rr = 56.54, method = "Fridericia")
#'
#' compute_qtc(qt = 350, rr = 56.54, method = "Sagie")
compute_qtc <- function(qt, rr, method) {
assert_numeric_vector(qt)
assert_numeric_vector(rr)
assert_character_scalar(method, values = c("Bazett", "Fridericia", "Sagie"))
formulae <- alist(
Bazett = qt / sqrt(rr / 1000),
Fridericia = qt / (rr / 1000) ^ (1 / 3),
Sagie = 1000 * (qt / 1000 + 0.154 * (1 - rr / 1000))
)
eval(formulae[[method]])
}
#' Adds a Parameter for Derived RR
#'
#' Adds a record for derived RR based on heart rate for each by group (e.g.,
#' subject and visit) where the source parameters are available.
#'
#' The analysis value of the new parameter is derived as
#' \deqn{\frac{60000}{HR}}{60000 / HR}
#'
#' @param dataset Input dataset
#'
#' The variables specified by the `by_vars` parameter, `PARAMCD`, and `AVAL`
#' are expected.
#'
#' The variable specified by `by_vars` and `PARAMCD` must be a unique key of
#' the input dataset after restricting it by the filter condition (`filter`
#' parameter) and to the parameters specified by `hr_code`.
#'
#' @param hr_code HR parameter code
#'
#' The observations where `PARAMCD` equals the specified value are considered
#' as the heart rate assessments.
#'
#' Permitted Values: character value
#'
#' @inheritParams derive_derived_param
#'
#' @inheritParams derive_param_qtc
#'
#' @author Stefan Bundfuss
#'
#' @return The input dataset with the new parameter added
#'
#' @keywords derivation adeg
#'
#' @export
#'
#' @examples
#' adeg <- tibble::tribble(
#' ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT,
#' "01-701-1015", "HR", "Heart Rate", 70.14, "beats/min", "BASELINE",
#' "01-701-1015", "QT", "QT Duration", 370, "msec", "WEEK 2",
#' "01-701-1015", "HR", "Heart Rate", 62.66, "beats/min", "WEEK 1",
#' "01-701-1015", "RR", "RR Duration", 710, "msec", "WEEK 2",
#' "01-701-1028", "HR", "Heart Rate", 85.45, "beats/min", "BASELINE",
#' "01-701-1028", "QT", "QT Duration", 480, "msec", "WEEK 2",
#' "01-701-1028", "QT", "QT Duration", 350, "msec", "WEEK 3",
#' "01-701-1028", "HR", "Heart Rate", 56.54, "beats/min", "WEEK 3",
#' "01-701-1028", "RR", "RR Duration", 842, "msec", "WEEK 2"
#' )
#'
#' derive_param_rr(
#' adeg,
#' by_vars = vars(USUBJID, VISIT),
#' set_values_to = vars(
#' PARAMCD = "RRR",
#' PARAM = "RR Duration Rederived (msec)",
#' AVALU = "msec"
#' ),
#' get_unit_expr = AVALU
#' )
derive_param_rr <- function(dataset,
by_vars,
set_values_to = vars(PARAMCD = "RRR"),
hr_code = "HR",
get_unit_expr,
filter = NULL) {
assert_vars(by_vars)
assert_data_frame(
dataset,
required_vars = vars(!!!by_vars, PARAMCD, AVAL)
)
assert_varval_list(set_values_to, required_elements = "PARAMCD", optional = TRUE)
assert_param_does_not_exist(dataset, quo_get_expr(set_values_to$PARAMCD))
assert_character_scalar(hr_code)
get_unit_expr <- assert_expr(enquo(get_unit_expr))
filter <- assert_filter_cond(enquo(filter), optional = TRUE)
assert_unit(
dataset,
param = hr_code,
required_unit = "beats/min",
get_unit_expr = !!get_unit_expr
)
derive_derived_param(
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
)
}
#' Compute RR Interval From Heart Rate
#'
#' Computes RR interval from heart rate.
#'
#' @param hr Heart rate
#'
#' A numeric vector is expected. It is expected that heart rate is measured in
#' beats/min.
#'
#' @author Stefan Bundfuss
#'
#' @return RR interval in msec:
#' \deqn{\frac{60000}{HR}}{60000 / HR}
#'
#' @keywords computation adeg
#'
#' @export
#'
#' @examples
#' compute_rr(hr = 70.14)
compute_rr <- function(hr) {
assert_numeric_vector(hr)
60000 / hr
}
epijim/admiral documentation built on Feb. 13, 2022, 12:15 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions compute_rr derive_param_rr compute_qtc default_qtc_paramcd derive_param_qtc
Documented in compute_qtc compute_rr default_qtc_paramcd derive_param_qtc derive_param_rr
#' Adds a Parameter for Corrected QT
#'
#' Adds a record for corrected QT using either Bazett's, Fridericia's or Sagie's
#' formula for each by group (e.g., subject and visit) where the source parameters
#' are available.
#'
#' @param dataset Input dataset
#'
#' The variables specified by the `by_vars` and the `unit_var` parameter,
#' `PARAMCD`, and `AVAL` are expected.
#'
#' The variable specified by `by_vars` and `PARAMCD` must be a unique key of
#' the input dataset after restricting it by the filter condition (`filter`
#' parameter) and to the parameters specified by `qt_code` and `rr_code`.
#'
#'
#' @param by_vars Grouping variables
#'
#' Permitted Values: list of variables
#'
#' @param method Method used to QT correction
#'
#' Permitted Values: `"Bazett"`, `"Fridericia"`, `"Sagie"`
#'
#' @param qt_code QT parameter code
#'
#' The observations where `PARAMCD` equals the specified value are considered
#' as the QT interval assessments. It is expected that QT is measured in msec.
#'
#' Permitted Values: character value
#'
#' @param rr_code RR parameter code
#'
#' The observations where `PARAMCD` equals the specified value are considered
#' as the RR interval assessments. It is expected that RR is measured in msec.
#'
#' Permitted Values: character value
#'
#' @param get_unit_expr An expression providing the unit of the parameter
#'
#' The result is used to check the units of the input parameters.
#'
#' Permitted Values: A variable of the input dataset or a function call
#'
#' @inheritParams derive_derived_param
#'
#' @seealso [compute_qtc()]
#'
#' @author Stefan Bundfuss
#'
#' @return The input dataset with the new parameter added
#'
#' @keywords derivation adeg
#'
#' @export
#'
#' @examples
#' adeg <- tibble::tribble(
#' ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT,
#' "01-701-1015", "HR", "Heart Rate (beats/min)", 70.14, "beats/min", "BASELINE",
#' "01-701-1015", "QT", "QT Duration (msec)", 370, "msec", "WEEK 2",
#' "01-701-1015", "HR", "Heart Rate (beats/min)", 62.66, "beats/min", "WEEK 1",
#' "01-701-1015", "RR", "RR Duration (msec)", 710, "msec", "WEEK 2",
#' "01-701-1028", "HR", "Heart Rate (beats/min)", 85.45, "beats/min", "BASELINE",
#' "01-701-1028", "QT", "QT Duration (msec)", 480, "msec", "WEEK 2",
#' "01-701-1028", "QT", "QT Duration (msec)", 350, "msec", "WEEK 3",
#' "01-701-1028", "HR", "Heart Rate (beats/min)", 56.54, "beats/min", "WEEK 3",
#' "01-701-1028", "RR", "RR Duration (msec)", 842, "msec", "WEEK 2",
#' )
#'
#' derive_param_qtc(
#' adeg,
#' by_vars = vars(USUBJID, VISIT),
#' method = "Bazett",
#' set_values_to = vars(
#' PARAMCD = "QTCBR",
#' PARAM = "QTcB - Bazett's Correction Formula Rederived (msec)",
#' AVALU = "msec"
#' ),
#' get_unit_expr = AVALU
#' )
#'
#' derive_param_qtc(
#' adeg,
#' by_vars = vars(USUBJID, VISIT),
#' method = "Fridericia",
#' set_values_to = vars(
#' PARAMCD = "QTCFR",
#' PARAM = "QTcF - Fridericia's Correction Formula Rederived (msec)",
#' AVALU = "msec"
#' ),
#' get_unit_expr = extract_unit(PARAM)
#' )
#'
#' derive_param_qtc(
#' adeg,
#' by_vars = vars(USUBJID, VISIT),
#' method = "Sagie",
#' set_values_to = vars(
#' PARAMCD = "QTLCR",
#' PARAM = "QTlc - Sagie's Correction Formula Rederived (msec)",
#' AVALU = "msec"
#' ),
#' get_unit_expr = extract_unit(PARAM)
#' )
derive_param_qtc <- function(dataset,
by_vars,
method,
set_values_to = default_qtc_paramcd(method),
qt_code = "QT",
rr_code = "RR",
get_unit_expr,
filter = NULL) {
assert_vars(by_vars)
assert_data_frame(
dataset,
required_vars = vars(!!!by_vars, PARAMCD, AVAL)
)
assert_character_scalar(method, values = c("Bazett", "Fridericia", "Sagie"))
assert_varval_list(set_values_to, required_elements = "PARAMCD")
assert_param_does_not_exist(dataset, quo_get_expr(set_values_to$PARAMCD))
assert_character_scalar(qt_code)
assert_character_scalar(rr_code)
get_unit_expr <- assert_expr(enquo(get_unit_expr))
filter <- assert_filter_cond(enquo(filter), optional = TRUE)
assert_unit(
dataset,
param = qt_code,
required_unit = "msec",
get_unit_expr = !!get_unit_expr
)
assert_unit(
dataset,
param = rr_code,
required_unit = "msec",
get_unit_expr = !!get_unit_expr
)
derive_derived_param(
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
)
}
#' Get Default Parameter Code for Corrected QT
#'
#' @param method Method used to QT correction
#'
#' Permitted Values: `"Bazett"`, `"Fridericia"`, `"Sagie"`
#'
#' @author Thomas Neitmann
#'
#' @export
#'
#' @keywords user_utility
#'
#' @examples
#' default_qtc_paramcd("Sagie")
default_qtc_paramcd <- function(method) {
assert_character_scalar(method, values = c("Bazett", "Fridericia", "Sagie"))
paramcd <- c(Bazett = "QTCBR", Fridericia = "QTCFR", Sagie = "QTLCR")
vars(PARAMCD = !!paramcd[[method]])
}
#' Compute Corrected QT
#'
#' Computes corrected QT using Bazett's, Fridericia's or Sagie's formula.
#'
#' @param qt QT interval
#'
#' A numeric vector is expected. It is expected that QT is measured in msec.
#'
#' @param rr RR interval
#'
#' A numeric vector is expected. It is expected that RR is measured in msec.
#'
#' @inheritParams derive_param_qtc
#'
#' @author Stefan Bundfuss
#'
#' @return QT interval in msec
#'
#' @details
#' Depending on the chosen `method` one of the following formulae is used.
#'
#' *Bazett*: \deqn{\frac{QT}{\sqrt{\frac{RR}{1000}}}}{QT/\sqrt(RR/1000)}
#'
#' *Fridericia*: \deqn{\frac{QT}{\sqrt[3]{\frac{RR}{1000}}}}{QT/(RR/1000)^(1/3)}
#'
#' *Sagie*: \deqn{1000\left(\frac{QT}{1000} + 0.154\left(1 - \frac{RR}{1000}\right)\right)}{
#' 1000(QT/1000 + 0.154(1 - RR/1000))}
#'
#' @keywords computation adeg
#'
#' @export
#'
#' @examples
#' compute_qtc(qt = 350, rr = 56.54, method = "Bazett")
#'
#' compute_qtc(qt = 350, rr = 56.54, method = "Fridericia")
#'
#' compute_qtc(qt = 350, rr = 56.54, method = "Sagie")
compute_qtc <- function(qt, rr, method) {
assert_numeric_vector(qt)
assert_numeric_vector(rr)
assert_character_scalar(method, values = c("Bazett", "Fridericia", "Sagie"))
formulae <- alist(
Bazett = qt / sqrt(rr / 1000),
Fridericia = qt / (rr / 1000) ^ (1 / 3),
Sagie = 1000 * (qt / 1000 + 0.154 * (1 - rr / 1000))
)
eval(formulae[[method]])
}
#' Adds a Parameter for Derived RR
#'
#' Adds a record for derived RR based on heart rate for each by group (e.g.,
#' subject and visit) where the source parameters are available.
#'
#' The analysis value of the new parameter is derived as
#' \deqn{\frac{60000}{HR}}{60000 / HR}
#'
#' @param dataset Input dataset
#'
#' The variables specified by the `by_vars` parameter, `PARAMCD`, and `AVAL`
#' are expected.
#'
#' The variable specified by `by_vars` and `PARAMCD` must be a unique key of
#' the input dataset after restricting it by the filter condition (`filter`
#' parameter) and to the parameters specified by `hr_code`.
#'
#' @param hr_code HR parameter code
#'
#' The observations where `PARAMCD` equals the specified value are considered
#' as the heart rate assessments.
#'
#' Permitted Values: character value
#'
#' @inheritParams derive_derived_param
#'
#' @inheritParams derive_param_qtc
#'
#' @author Stefan Bundfuss
#'
#' @return The input dataset with the new parameter added
#'
#' @keywords derivation adeg
#'
#' @export
#'
#' @examples
#' adeg <- tibble::tribble(
#' ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT,
#' "01-701-1015", "HR", "Heart Rate", 70.14, "beats/min", "BASELINE",
#' "01-701-1015", "QT", "QT Duration", 370, "msec", "WEEK 2",
#' "01-701-1015", "HR", "Heart Rate", 62.66, "beats/min", "WEEK 1",
#' "01-701-1015", "RR", "RR Duration", 710, "msec", "WEEK 2",
#' "01-701-1028", "HR", "Heart Rate", 85.45, "beats/min", "BASELINE",
#' "01-701-1028", "QT", "QT Duration", 480, "msec", "WEEK 2",
#' "01-701-1028", "QT", "QT Duration", 350, "msec", "WEEK 3",
#' "01-701-1028", "HR", "Heart Rate", 56.54, "beats/min", "WEEK 3",
#' "01-701-1028", "RR", "RR Duration", 842, "msec", "WEEK 2"
#' )
#'
#' derive_param_rr(
#' adeg,
#' by_vars = vars(USUBJID, VISIT),
#' set_values_to = vars(
#' PARAMCD = "RRR",
#' PARAM = "RR Duration Rederived (msec)",
#' AVALU = "msec"
#' ),
#' get_unit_expr = AVALU
#' )
derive_param_rr <- function(dataset,
by_vars,
set_values_to = vars(PARAMCD = "RRR"),
hr_code = "HR",
get_unit_expr,
filter = NULL) {
assert_vars(by_vars)
assert_data_frame(
dataset,
required_vars = vars(!!!by_vars, PARAMCD, AVAL)
)
assert_varval_list(set_values_to, required_elements = "PARAMCD", optional = TRUE)
assert_param_does_not_exist(dataset, quo_get_expr(set_values_to$PARAMCD))
assert_character_scalar(hr_code)
get_unit_expr <- assert_expr(enquo(get_unit_expr))
filter <- assert_filter_cond(enquo(filter), optional = TRUE)
assert_unit(
dataset,
param = hr_code,
required_unit = "beats/min",
get_unit_expr = !!get_unit_expr
)
derive_derived_param(
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
)
}
#' Compute RR Interval From Heart Rate
#'
#' Computes RR interval from heart rate.
#'
#' @param hr Heart rate
#'
#' A numeric vector is expected. It is expected that heart rate is measured in
#' beats/min.
#'
#' @author Stefan Bundfuss
#'
#' @return RR interval in msec:
#' \deqn{\frac{60000}{HR}}{60000 / HR}
#'
#' @keywords computation adeg
#'
#' @export
#'
#' @examples
#' compute_rr(hr = 70.14)
compute_rr <- function(hr) {
assert_numeric_vector(hr)
60000 / hr
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.