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Adds a Parameter Computed from the Analysis Value of Other Parameters

Source: R/derive_param_computed.R
derive_param_computed.Rd

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 $$MAP = \frac{SYSBP + 2 DIABP}{3}$$

Usage

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

Arguments

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

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 exprs(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 (parameters that are measured only once) are merged to the other parameters using the specified variables. (Refer to Example 2)

Permitted Values: list of variables

constant_parameters

Required constant parameter codes

It is expected that all the parameter codes (PARAMCD) which are required to derive the new parameter and are measured only once are specified here. For example if BMI should be derived and height is measured only once while weight is measured at each visit. Height could be specified in the constant_parameters parameter. (Refer to Example 2)

Permitted Values: A character vector of PARAMCD values

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.

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 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.

See also

BDS-Findings Functions for adding Parameters/Records: default_qtc_paramcd(), derive_expected_records(), derive_extreme_event(), derive_extreme_records(), derive_locf_records(), derive_param_bmi(), derive_param_bsa(), derive_param_doseint(), derive_param_exist_flag(), derive_param_exposure(), derive_param_extreme_event(), derive_param_framingham(), derive_param_map(), derive_param_qtc(), derive_param_rr(), derive_param_wbc_abs(), derive_summary_records()

Examples

library(tibble)

# Example 1: 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"
)

derive_param_computed(
  advs,
  by_vars = exprs(USUBJID, VISIT),
  parameters = c("SYSBP", "DIABP"),
  analysis_value = (AVAL.SYSBP + 2 * AVAL.DIABP) / 3,
  set_values_to = exprs(
    PARAMCD = "MAP",
    PARAM = "Mean Arterial Pressure (mmHg)",
    AVALU = "mmHg"
  )
)
#> # A tibble: 12 x 6
#>    USUBJID     PARAMCD PARAM                            AVAL AVALU VISIT   
#>    <chr>       <chr>   <chr>                           <dbl> <chr> <chr>   
#>  1 01-701-1015 DIABP   Diastolic Blood Pressure (mmHg)  51   mmHg  BASELINE
#>  2 01-701-1015 DIABP   Diastolic Blood Pressure (mmHg)  50   mmHg  WEEK 2  
#>  3 01-701-1015 SYSBP   Systolic Blood Pressure (mmHg)  121   mmHg  BASELINE
#>  4 01-701-1015 SYSBP   Systolic Blood Pressure (mmHg)  121   mmHg  WEEK 2  
#>  5 01-701-1028 DIABP   Diastolic Blood Pressure (mmHg)  79   mmHg  BASELINE
#>  6 01-701-1028 DIABP   Diastolic Blood Pressure (mmHg)  80   mmHg  WEEK 2  
#>  7 01-701-1028 SYSBP   Systolic Blood Pressure (mmHg)  130   mmHg  BASELINE
#>  8 01-701-1028 SYSBP   Systolic Blood Pressure (mmHg)  132   mmHg  WEEK 2  
#>  9 01-701-1015 MAP     Mean Arterial Pressure (mmHg)    74.3 mmHg  BASELINE
#> 10 01-701-1015 MAP     Mean Arterial Pressure (mmHg)    73.7 mmHg  WEEK 2  
#> 11 01-701-1028 MAP     Mean Arterial Pressure (mmHg)    96   mmHg  BASELINE
#> 12 01-701-1028 MAP     Mean Arterial Pressure (mmHg)    97.3 mmHg  WEEK 2  

# Example 2: Derive BMI where height is measured only once
advs <- 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_param_computed(
  advs,
  by_vars = exprs(USUBJID, VISIT),
  parameters = "WEIGHT",
  analysis_value = AVAL.WEIGHT / (AVAL.HEIGHT / 100)^2,
  set_values_to = exprs(
    PARAMCD = "BMI",
    PARAM = "Body Mass Index (kg/m^2)",
    AVALU = "kg/m^2"
  ),
  constant_parameters = c("HEIGHT"),
  constant_by_vars = exprs(USUBJID)
)
#> # A tibble: 14 x 6
#>    USUBJID     PARAMCD PARAM                     AVAL AVALU  VISIT    
#>    <chr>       <chr>   <chr>                    <dbl> <chr>  <chr>    
#>  1 01-701-1015 HEIGHT  Height (cm)              147   cm     SCREENING
#>  2 01-701-1015 WEIGHT  Weight (kg)               54   kg     SCREENING
#>  3 01-701-1015 WEIGHT  Weight (kg)               54.4 kg     BASELINE 
#>  4 01-701-1015 WEIGHT  Weight (kg)               53.1 kg     WEEK 2   
#>  5 01-701-1028 HEIGHT  Height (cm)              163   cm     SCREENING
#>  6 01-701-1028 WEIGHT  Weight (kg)               78.5 kg     SCREENING
#>  7 01-701-1028 WEIGHT  Weight (kg)               80.3 kg     BASELINE 
#>  8 01-701-1028 WEIGHT  Weight (kg)               80.7 kg     WEEK 2   
#>  9 01-701-1015 BMI     Body Mass Index (kg/m^2)  25.0 kg/m^2 SCREENING
#> 10 01-701-1015 BMI     Body Mass Index (kg/m^2)  25.2 kg/m^2 BASELINE 
#> 11 01-701-1015 BMI     Body Mass Index (kg/m^2)  24.6 kg/m^2 WEEK 2   
#> 12 01-701-1028 BMI     Body Mass Index (kg/m^2)  29.5 kg/m^2 SCREENING
#> 13 01-701-1028 BMI     Body Mass Index (kg/m^2)  30.2 kg/m^2 BASELINE 
#> 14 01-701-1028 BMI     Body Mass Index (kg/m^2)  30.4 kg/m^2 WEEK 2