Adds a Parameter for Corrected QT (an ECG measurement)

Source: R/derive_param_qtc.R

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.

Note: This is a wrapper function for the more generic derive_param_computed().

derive_param_qtc(
  dataset,
  by_vars,
  method,
  set_values_to = default_qtc_paramcd(method),
  qt_code = "QT",
  rr_code = "RR",
  get_unit_expr,
  filter = NULL
)

Arguments

dataset

Input dataset

The variables specified by the by_vars and get_unit_expr arguments are expected to be in the dataset. PARAMCD, and AVAL are expected as well.

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 argument) and to the parameters specified by qt_code and rr_code.

Default value

none

by_vars

Grouping variables

Only variables specified in by_vars will be populated in the newly created records.

Permitted values

list of variables created by exprs(), e.g., exprs(USUBJID, VISIT)

Default value

none

method

Method used to QT correction

See compute_qtc() for details.

Permitted values

"Bazett", "Fridericia", "Sagie"

Default value

none

set_values_to

Variables to be set

The specified variables are set to the specified values for the new observations. For example exprs(PARAMCD = "MAP") defines the parameter code for the new parameter.

Permitted values

List of variable-value pairs

Default value

exprs(PARAMCD = "MAP")

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 ms or msec.

Permitted values

character value

Default value

"QT"

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 ms or msec.

Permitted values

character value

Default value

"RR"

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

An expression which is evaluable in the input dataset and results in a character value

Default value

none

filter

Filter condition

The specified condition is applied to the input dataset before deriving the new parameter, i.e., only observations fulfilling the condition are taken into account.

Permitted values

an unquoted condition, e.g., AVISIT == "BASELINE"

Default value

NULL

Value

The input dataset with the new parameter added. Note, a variable will only be populated in the new parameter rows if it is specified in by_vars.

Examples

library(tibble)

adeg <- 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 (ms)",         370, "ms",        "WEEK 2",
  "01-701-1015", "HR",     "Heart Rate (beats/min)", 62.66, "beats/min", "WEEK 1",
  "01-701-1015", "RR",     "RR Duration (ms)",         710, "ms",        "WEEK 2",
  "01-701-1028", "HR",     "Heart Rate (beats/min)", 85.45, "beats/min", "BASELINE",
  "01-701-1028", "QT",     "QT Duration (ms)",         480, "ms",        "WEEK 2",
  "01-701-1028", "QT",     "QT Duration (ms)",         350, "ms",        "WEEK 3",
  "01-701-1028", "HR",     "Heart Rate (beats/min)", 56.54, "beats/min", "WEEK 3",
  "01-701-1028", "RR",     "RR Duration (ms)",         842, "ms",        "WEEK 2"
)

derive_param_qtc(
  adeg,
  by_vars = exprs(USUBJID, VISIT),
  method = "Bazett",
  set_values_to = exprs(
    PARAMCD = "QTCBR",
    PARAM = "QTcB - Bazett's Correction Formula Rederived (ms)",
    AVALU = "ms"
  ),
  get_unit_expr = AVALU
)
#> # A tibble: 11 × 6
#>    USUBJID     PARAMCD PARAM                                    AVAL AVALU VISIT
#>    <chr>       <chr>   <chr>                                   <dbl> <chr> <chr>
#>  1 01-701-1015 HR      Heart Rate (beats/min)                   70.1 beat… BASE…
#>  2 01-701-1015 QT      QT Duration (ms)                        370   ms    WEEK…
#>  3 01-701-1015 HR      Heart Rate (beats/min)                   62.7 beat… WEEK…
#>  4 01-701-1015 RR      RR Duration (ms)                        710   ms    WEEK…
#>  5 01-701-1028 HR      Heart Rate (beats/min)                   85.4 beat… BASE…
#>  6 01-701-1028 QT      QT Duration (ms)                        480   ms    WEEK…
#>  7 01-701-1028 QT      QT Duration (ms)                        350   ms    WEEK…
#>  8 01-701-1028 HR      Heart Rate (beats/min)                   56.5 beat… WEEK…
#>  9 01-701-1028 RR      RR Duration (ms)                        842   ms    WEEK…
#> 10 01-701-1015 QTCBR   QTcB - Bazett's Correction Formula Red… 439.  ms    WEEK…
#> 11 01-701-1028 QTCBR   QTcB - Bazett's Correction Formula Red… 523.  ms    WEEK…

derive_param_qtc(
  adeg,
  by_vars = exprs(USUBJID, VISIT),
  method = "Fridericia",
  set_values_to = exprs(
    PARAMCD = "QTCFR",
    PARAM = "QTcF - Fridericia's Correction Formula Rederived (ms)",
    AVALU = "ms"
  ),
  get_unit_expr = extract_unit(PARAM)
)
#> # A tibble: 11 × 6
#>    USUBJID     PARAMCD PARAM                                    AVAL AVALU VISIT
#>    <chr>       <chr>   <chr>                                   <dbl> <chr> <chr>
#>  1 01-701-1015 HR      Heart Rate (beats/min)                   70.1 beat… BASE…
#>  2 01-701-1015 QT      QT Duration (ms)                        370   ms    WEEK…
#>  3 01-701-1015 HR      Heart Rate (beats/min)                   62.7 beat… WEEK…
#>  4 01-701-1015 RR      RR Duration (ms)                        710   ms    WEEK…
#>  5 01-701-1028 HR      Heart Rate (beats/min)                   85.4 beat… BASE…
#>  6 01-701-1028 QT      QT Duration (ms)                        480   ms    WEEK…
#>  7 01-701-1028 QT      QT Duration (ms)                        350   ms    WEEK…
#>  8 01-701-1028 HR      Heart Rate (beats/min)                   56.5 beat… WEEK…
#>  9 01-701-1028 RR      RR Duration (ms)                        842   ms    WEEK…
#> 10 01-701-1015 QTCFR   QTcF - Fridericia's Correction Formula… 415.  ms    WEEK…
#> 11 01-701-1028 QTCFR   QTcF - Fridericia's Correction Formula… 508.  ms    WEEK…

derive_param_qtc(
  adeg,
  by_vars = exprs(USUBJID, VISIT),
  method = "Sagie",
  set_values_to = exprs(
    PARAMCD = "QTLCR",
    PARAM = "QTlc - Sagie's Correction Formula Rederived (ms)",
    AVALU = "ms"
  ),
  get_unit_expr = extract_unit(PARAM)
)
#> # A tibble: 11 × 6
#>    USUBJID     PARAMCD PARAM                                    AVAL AVALU VISIT
#>    <chr>       <chr>   <chr>                                   <dbl> <chr> <chr>
#>  1 01-701-1015 HR      Heart Rate (beats/min)                   70.1 beat… BASE…
#>  2 01-701-1015 QT      QT Duration (ms)                        370   ms    WEEK…
#>  3 01-701-1015 HR      Heart Rate (beats/min)                   62.7 beat… WEEK…
#>  4 01-701-1015 RR      RR Duration (ms)                        710   ms    WEEK…
#>  5 01-701-1028 HR      Heart Rate (beats/min)                   85.4 beat… BASE…
#>  6 01-701-1028 QT      QT Duration (ms)                        480   ms    WEEK…
#>  7 01-701-1028 QT      QT Duration (ms)                        350   ms    WEEK…
#>  8 01-701-1028 HR      Heart Rate (beats/min)                   56.5 beat… WEEK…
#>  9 01-701-1028 RR      RR Duration (ms)                        842   ms    WEEK…
#> 10 01-701-1015 QTLCR   QTlc - Sagie's Correction Formula Rede… 415.  ms    WEEK…
#> 11 01-701-1028 QTLCR   QTlc - Sagie's Correction Formula Rede… 504.  ms    WEEK…