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Derive Baseline Variables

Source: R/derive_var_base.R
derive_var_base.Rd

Derive baseline variables, e.g. BASE or BNRIND, in a BDS dataset.

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

Usage

derive_var_base(
  dataset,
  by_vars,
  source_var = AVAL,
  new_var = BASE,
  filter = ABLFL == "Y"
)

Arguments

dataset

Input dataset

The variables specified by the by_vars and source_var arguments are expected to be in the dataset.

by_vars

Grouping variables

Grouping variables uniquely identifying a set of records for which to calculate new_var.

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

source_var

The column from which to extract the baseline value, e.g. AVAL

new_var

The name of the newly created baseline column, e.g. BASE

filter

The condition used to filter dataset for baseline records.

By default ABLFL == "Y"

Value

A new data.frame containing all records and variables of the input dataset plus the new_var variable

Details

For each by_vars group, the baseline record is identified by the condition specified in filter which defaults to ABLFL == "Y". Subsequently, every value of the new_var variable for the by_vars group is set to the value of the source_var variable of the baseline record. In case there are multiple baseline records within by_vars an error is issued.

See also

BDS-Findings Functions that returns variable appended to dataset: derive_basetype_records(), derive_var_analysis_ratio(), derive_var_anrind(), derive_var_atoxgr_dir(), derive_var_atoxgr(), derive_var_chg(), derive_var_ontrtfl(), derive_var_pchg(), derive_var_shift()

Examples

library(tibble)

dataset <- tribble(
  ~STUDYID, ~USUBJID,   ~PARAMCD, ~AVAL,   ~AVALC,      ~AVISIT, ~ABLFL,  ~ANRIND,
  "TEST01",  "PAT01",  "PARAM01", 10.12,       NA,   "Baseline",    "Y", "NORMAL",
  "TEST01",  "PAT01",  "PARAM01", 9.700,       NA,      "Day 7",    "N",    "LOW",
  "TEST01",  "PAT01",  "PARAM01", 15.01,       NA,     "Day 14",    "N",   "HIGH",
  "TEST01",  "PAT01",  "PARAM02", 8.350,       NA,   "Baseline",    "Y",    "LOW",
  "TEST01",  "PAT01",  "PARAM02",    NA,       NA,      "Day 7",    "N",       NA,
  "TEST01",  "PAT01",  "PARAM02", 8.350,       NA,     "Day 14",    "N",    "LOW",
  "TEST01",  "PAT01",  "PARAM03",    NA,    "LOW",   "Baseline",    "Y",       NA,
  "TEST01",  "PAT01",  "PARAM03",    NA,    "LOW",      "Day 7",    "N",       NA,
  "TEST01",  "PAT01",  "PARAM03",    NA, "MEDIUM",     "Day 14",    "N",       NA,
  "TEST01",  "PAT01",  "PARAM04",    NA,   "HIGH",   "Baseline",    "Y",       NA,
  "TEST01",  "PAT01",  "PARAM04",    NA,   "HIGH",      "Day 7",    "N",       NA,
  "TEST01",  "PAT01",  "PARAM04",    NA, "MEDIUM",     "Day 14",    "N",       NA
)

## Derive `BASE` variable from `AVAL`
derive_var_base(
  dataset,
  by_vars = exprs(USUBJID, PARAMCD),
  source_var = AVAL,
  new_var = BASE
)
#> # A tibble: 12 × 9
#>    STUDYID USUBJID PARAMCD  AVAL AVALC  AVISIT   ABLFL ANRIND  BASE
#>    <chr>   <chr>   <chr>   <dbl> <chr>  <chr>    <chr> <chr>  <dbl>
#>  1 TEST01  PAT01   PARAM01 10.1  NA     Baseline Y     NORMAL 10.1 
#>  2 TEST01  PAT01   PARAM01  9.7  NA     Day 7    N     LOW    10.1 
#>  3 TEST01  PAT01   PARAM01 15.0  NA     Day 14   N     HIGH   10.1 
#>  4 TEST01  PAT01   PARAM02  8.35 NA     Baseline Y     LOW     8.35
#>  5 TEST01  PAT01   PARAM02 NA    NA     Day 7    N     NA      8.35
#>  6 TEST01  PAT01   PARAM02  8.35 NA     Day 14   N     LOW     8.35
#>  7 TEST01  PAT01   PARAM03 NA    LOW    Baseline Y     NA     NA   
#>  8 TEST01  PAT01   PARAM03 NA    LOW    Day 7    N     NA     NA   
#>  9 TEST01  PAT01   PARAM03 NA    MEDIUM Day 14   N     NA     NA   
#> 10 TEST01  PAT01   PARAM04 NA    HIGH   Baseline Y     NA     NA   
#> 11 TEST01  PAT01   PARAM04 NA    HIGH   Day 7    N     NA     NA   
#> 12 TEST01  PAT01   PARAM04 NA    MEDIUM Day 14   N     NA     NA   

## Derive `BASEC` variable from `AVALC`
derive_var_base(
  dataset,
  by_vars = exprs(USUBJID, PARAMCD),
  source_var = AVALC,
  new_var = BASEC
)
#> # A tibble: 12 × 9
#>    STUDYID USUBJID PARAMCD  AVAL AVALC  AVISIT   ABLFL ANRIND BASEC
#>    <chr>   <chr>   <chr>   <dbl> <chr>  <chr>    <chr> <chr>  <chr>
#>  1 TEST01  PAT01   PARAM01 10.1  NA     Baseline Y     NORMAL NA   
#>  2 TEST01  PAT01   PARAM01  9.7  NA     Day 7    N     LOW    NA   
#>  3 TEST01  PAT01   PARAM01 15.0  NA     Day 14   N     HIGH   NA   
#>  4 TEST01  PAT01   PARAM02  8.35 NA     Baseline Y     LOW    NA   
#>  5 TEST01  PAT01   PARAM02 NA    NA     Day 7    N     NA     NA   
#>  6 TEST01  PAT01   PARAM02  8.35 NA     Day 14   N     LOW    NA   
#>  7 TEST01  PAT01   PARAM03 NA    LOW    Baseline Y     NA     LOW  
#>  8 TEST01  PAT01   PARAM03 NA    LOW    Day 7    N     NA     LOW  
#>  9 TEST01  PAT01   PARAM03 NA    MEDIUM Day 14   N     NA     LOW  
#> 10 TEST01  PAT01   PARAM04 NA    HIGH   Baseline Y     NA     HIGH 
#> 11 TEST01  PAT01   PARAM04 NA    HIGH   Day 7    N     NA     HIGH 
#> 12 TEST01  PAT01   PARAM04 NA    MEDIUM Day 14   N     NA     HIGH 

## Derive `BNRIND` variable from `ANRIND`
derive_var_base(
  dataset,
  by_vars = exprs(USUBJID, PARAMCD),
  source_var = ANRIND,
  new_var = BNRIND
)
#> # A tibble: 12 × 9
#>    STUDYID USUBJID PARAMCD  AVAL AVALC  AVISIT   ABLFL ANRIND BNRIND
#>    <chr>   <chr>   <chr>   <dbl> <chr>  <chr>    <chr> <chr>  <chr> 
#>  1 TEST01  PAT01   PARAM01 10.1  NA     Baseline Y     NORMAL NORMAL
#>  2 TEST01  PAT01   PARAM01  9.7  NA     Day 7    N     LOW    NORMAL
#>  3 TEST01  PAT01   PARAM01 15.0  NA     Day 14   N     HIGH   NORMAL
#>  4 TEST01  PAT01   PARAM02  8.35 NA     Baseline Y     LOW    LOW   
#>  5 TEST01  PAT01   PARAM02 NA    NA     Day 7    N     NA     LOW   
#>  6 TEST01  PAT01   PARAM02  8.35 NA     Day 14   N     LOW    LOW   
#>  7 TEST01  PAT01   PARAM03 NA    LOW    Baseline Y     NA     NA    
#>  8 TEST01  PAT01   PARAM03 NA    LOW    Day 7    N     NA     NA    
#>  9 TEST01  PAT01   PARAM03 NA    MEDIUM Day 14   N     NA     NA    
#> 10 TEST01  PAT01   PARAM04 NA    HIGH   Baseline Y     NA     NA    
#> 11 TEST01  PAT01   PARAM04 NA    HIGH   Day 7    N     NA     NA    
#> 12 TEST01  PAT01   PARAM04 NA    MEDIUM Day 14   N     NA     NA