derive_derived_param: Adds a Parameter Computed from the Analysis Value of Other...
In epijim/admiral: ADaM in R Asset Library

Description Usage Arguments Details Value Author(s) Examples

Adds a parameter computed from the analysis value of other parameters. It is expected that the analysis value of the new parameter is defined by an expression using the analysis values of other parameters. For example mean arterial pressure (MAP) can be derived from systolic (SYSBP) and diastolic blood pressure (DIABP) with the formula

MAP = (SYSBP + 2 DIABP) / 3

derive_derived_param(
  dataset,
  by_vars,
  parameters,
  analysis_value,
  set_values_to,
  filter = NULL,
  constant_by_vars = NULL,
  constant_parameters = NULL
)

`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 `parameters`.
`by_vars`	Grouping variables For each group defined by `by_vars` an observation is added to the output dataset. Permitted Values: list of variables
`parameters`	Required parameter codes It is expected that all parameter codes (`PARAMCD`) which are required to derive the new parameter are specified for this parameter or the `constant_parameters` parameter. Permitted Values: A character vector of `PARAMCD` values
`analysis_value`	Definition of the analysis value An expression defining the analysis value (`AVAL`) of the new parameter is expected. The analysis values of the parameters specified by `parameters` can be accessed using `AVAL.<parameter code>`, e.g., `AVAL.SYSBP`. Permitted Values: An unquoted expression
`set_values_to`	Variables to be set The specified variables are set to the specified values for the new observations. For example `vars(PARAMCD = "MAP")` defines the parameter code for the new parameter. Permitted Values: List of variable-value pairs
`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: a condition
`constant_by_vars`	By variables for constant parameters The constant parameters are merged to the other parameters using the specified variables. This is useful if some parameters were measured only once. For example if BMI should be derived and height is measured only once while weight is measured at each visit. Height could be specified for the constant parameters. Permitted Values: list of variables
`constant_parameters`	Required constant parameter codes It is expected that all parameter codes (`PARAMCD`) which are required to derive the new parameter are specified for this parameter or the `parameters` parameter. Permitted Values: A character vector of `PARAMCD` values

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 contains exactly one observation for each parameter code specified for parameters.

For the new observations AVAL is set to the value specified by analysis_value and the variables specified for set_values_to are set to the provided values. The values of the other variables of the input dataset are set to NA.

The input dataset with the new parameter added

Stefan Bundfuss

# derive MAP
advs <- tibble::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"
)

derive_derived_param(
  advs,
  by_vars = vars(USUBJID, VISIT),
  parameters = c("SYSBP", "DIABP"),
  analysis_value = (AVAL.SYSBP + 2 * AVAL.DIABP) / 3,
  set_values_to = vars(
    PARAMCD = "MAP",
    PARAM = "Mean Arterial Pressure (mmHg)",
    AVALU = "mmHg"
  )
)

# derive BMI where height is measured only once
advs <- tibble::tribble(
  ~USUBJID, ~PARAMCD, ~PARAM, ~AVAL, ~AVALU, ~VISIT,
  "01-701-1015", "HEIGHT", "Height (cm)", 147, "cm", "SCREENING",
  "01-701-1015", "WEIGHT", "Weight (kg)", 54.0, "kg", "SCREENING",
  "01-701-1015", "WEIGHT", "Weight (kg)", 54.4, "kg", "BASELINE",
  "01-701-1015", "WEIGHT", "Weight (kg)", 53.1, "kg", "WEEK 2",
  "01-701-1028", "HEIGHT", "Height (cm)", 163, "cm", "SCREENING",
  "01-701-1028", "WEIGHT", "Weight (kg)", 78.5, "kg", "SCREENING",
  "01-701-1028", "WEIGHT", "Weight (kg)", 80.3, "kg", "BASELINE",
  "01-701-1028", "WEIGHT", "Weight (kg)", 80.7, "kg", "WEEK 2"
)

derive_derived_param(
  advs,
  by_vars = vars(USUBJID, VISIT),
  parameters = "WEIGHT",
  analysis_value = AVAL.WEIGHT / (AVAL.HEIGHT / 100)^2,
  set_values_to = vars(
    PARAMCD = "BMI",
    PARAM = "Body Mass Index (kg/m^2)",
    AVALU = "kg/m^2"
  ),
  constant_parameters = c("HEIGHT"),
  constant_by_vars = vars(USUBJID)
)