Creating Fever Records — derive_fever_records • admiralvaccine

Creating Fever records from the VS SDTM dataset.

Usage

derive_fever_records(dataset, dataset_source, filter_source, faobj)

Arguments

dataset: Input Dataset Input dataset is expected to have variables USUBJID and FAOBJ.
dataset_source: Source Dataset - SDTM Vital Sign (VS) Source Dataset (VS) is expected to have temperature records.
filter_source: Filter condition for Source dataset.
faobj: FAOBJ Value for fever records in output dataset.

Value

The output dataset contains records with FATESTCD = "OCCUR" for FAOBJ = FEVER records.

Details

Check if FAOBJ = FEVER record is present in input dataset, if not then use SDTM.VS to get FEVER records. With temperature values from VSSTRESN we decide if FEVER has occurred or not (FAORRES = "Y"/"N"). Since records are derived, these FEVER records are considered DTYPE = "DERIVED" if FAOBJ = FEVER record is present, then input dataset will be made as output with no further analysis.

The temperature value greater or equal 38° C will be considered as FEVER records.

See also

Other der_rec: derive_diam_to_sev_records()

Author

Dhivya Kanagaraj

Examples

library(tibble)
library(dplyr)
library(admiraldev)
#> 
#> Attaching package: ‘admiraldev’
#> The following objects are masked from ‘package:dplyr’:
#> 
#>     anti_join, filter_if, inner_join, left_join
library(admiral)

input <- tribble(
  ~USUBJID, ~FAOBJ, ~FATESTCD, ~FACAT, ~FASCAT, ~FATPT,
  "ABC101", "REDNESS", "SEV", "REACTOGENICITY", "ADMINISTRATIVE SITE", "DAY 1",
  "ABC101", "REDNESS", "DIAM", "REACTOGENICITY", "ADMINISTRATIVE SITE", "DAY 2",
  "ABC101", "VOMITTING", "SEV", "REACTOGENICITY", "SYSTEMIC", "DAY 1",
  "ABC101", "FATIQUE", "OCCUR", "REACTOGENICITY", "SYSTEMIC", "DAY 3"
)

vs <- tribble(
  ~USUBJID, ~VSTESTCD, ~VSCAT, ~VSSTRESN, ~VSSTRESU, ~VSTPT,
  "ABC101", "TEMP", "REACTOGENICITY", 38.3, "C", "DAY 1",
  "ABC101", "TEMP", "REACTOGENICITY", 38, "C", "DAY 2",
  "ABC101", "TEMP", "REACTOGENICITY", 36, "C", "DAY 3",
  "ABC101", "TEMP", "REACTOGENICITY", 37, "C", "DAY 4",
  "ABC101", "TEMP", "REACTOGENICITY", 39, "C", "DAY 5",
  "ABC101", "TEMP", "REACTOGENICITY", 39, "C", "DAY 6",
  "ABC101", "TEMP", "REACTOGENICITY", 38, "C", "DAY 7"
)

derive_fever_records(
  dataset = input,
  dataset_source = vs,
  filter_source = VSCAT == "REACTOGENICITY" & VSTESTCD == "TEMP",
  faobj = "FEVER"
)
#> # A tibble: 11 × 10
#>    USUBJID FAOBJ    FATESTCD FACAT FASCAT FATPT FATEST FAORRES FASTRESC VSSTRESN
#>    <chr>   <chr>    <chr>    <chr> <chr>  <chr> <chr>  <chr>   <chr>       <dbl>
#>  1 ABC101  REDNESS  SEV      REAC… ADMIN… DAY 1 NA     NA      NA           NA  
#>  2 ABC101  REDNESS  DIAM     REAC… ADMIN… DAY 2 NA     NA      NA           NA  
#>  3 ABC101  VOMITTI… SEV      REAC… SYSTE… DAY 1 NA     NA      NA           NA  
#>  4 ABC101  FATIQUE  OCCUR    REAC… SYSTE… DAY 3 NA     NA      NA           NA  
#>  5 ABC101  FEVER    OCCUR    REAC… SYSTE… DAY 1 Occur… Y       Y            38.3
#>  6 ABC101  FEVER    OCCUR    REAC… SYSTE… DAY 2 Occur… Y       Y            38  
#>  7 ABC101  FEVER    OCCUR    REAC… SYSTE… DAY 3 Occur… N       N            36  
#>  8 ABC101  FEVER    OCCUR    REAC… SYSTE… DAY 4 Occur… N       N            37  
#>  9 ABC101  FEVER    OCCUR    REAC… SYSTE… DAY 5 Occur… Y       Y            39  
#> 10 ABC101  FEVER    OCCUR    REAC… SYSTE… DAY 6 Occur… Y       Y            39  
#> 11 ABC101  FEVER    OCCUR    REAC… SYSTE… DAY 7 Occur… Y       Y            38