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Add New Variable(s) to the Input dataset Based on Variables from Another dataset

Source: R/derive_vars_merged_vaccine.R
derive_vars_merged_vaccine.Rd

Add new variables to the input dataset based on variables from another dataset. The variables to be added to the output dataset will be based on input variables passed on ex_vars argument.

Usage

derive_vars_merged_vaccine(
  dataset,
  dataset_ex,
  by_vars_sys,
  by_vars_adms,
  ex_vars
)

Arguments

dataset

Input dataset which should have been combined with the supplementary(if exists).

The variables specified by the by_vars argument inside the derive_vars_mergedare expected.

dataset_ex

ex dataset(combined with suppex) to merge with the input dataset.

The variables specified by the ex_vars argument are expected.

by_vars_sys

Grouping variables for systemic events.

by_vars_adms

Grouping variables for administration site events.

ex_vars

Variables to be added to the output dataset from EX dataset

Value

The dataset with variables added from the EX dataset.

Details

The input dataset will be merged with EX dataset for "ADMINISTRATION SITE" and "SYSTEMIC" categories separately and these datasets will be bound together as the final output dataset.

This function is intended to add only EX variables to the input dataset and user is expected to handle if any pre-processing is required.

Only the variables passed to the ex_vars will be added in the output dataset

If the input dataset has multiple vaccination for a subject at same visit then this function will not merge ex dataset and will return the dataset.

See also

Other der_var: derive_var_aval_adis(), derive_vars_crit(), derive_vars_event_flag(), derive_vars_max_flag(), derive_vars_params(), derive_vars_vaxdt()

Author

Vikram S

Examples


library(tibble)
library(admiral)
library(dplyr)
library(pharmaversesdtm)

derive_vars_merged_vaccine(
  dataset = face_vaccine,
  dataset_ex = ex_vaccine,
  by_vars_sys = exprs(USUBJID, FATPTREF = EXLNKGRP),
  by_vars_adms = exprs(USUBJID, FATPTREF = EXLNKGRP, FALOC = EXLOC, FALAT = EXLAT),
  ex_vars = exprs(EXTRT, EXDOSE, EXDOSU, EXSTDTC, EXENDTC)
) %>%
  select(USUBJID, FATPTREF, FALOC, FALAT, EXTRT, EXDOSE, EXDOSU, EXSTDTC, EXENDTC) %>%
  head(10)
#> # A tibble: 10 × 9
#>    USUBJID  FATPTREF      FALOC        FALAT EXTRT EXDOSE EXDOSU EXSTDTC EXENDTC
#>    <chr>    <chr>         <chr>        <chr> <chr>  <dbl> <chr>  <chr>   <chr>  
#>  1 ABC-1001 VACCINATION 1 DELTOID MUS… LEFT  VACC…      1 SYRIN… 2021-1… 2021-1…
#>  2 ABC-1001 VACCINATION 1 DELTOID MUS… LEFT  VACC…      1 SYRIN… 2021-1… 2021-1…
#>  3 ABC-1001 VACCINATION 1 DELTOID MUS… LEFT  VACC…      1 SYRIN… 2021-1… 2021-1…
#>  4 ABC-1001 VACCINATION 1 DELTOID MUS… LEFT  VACC…      1 SYRIN… 2021-1… 2021-1…
#>  5 ABC-1001 VACCINATION 1 DELTOID MUS… LEFT  VACC…      1 SYRIN… 2021-1… 2021-1…
#>  6 ABC-1001 VACCINATION 1 DELTOID MUS… LEFT  VACC…      1 SYRIN… 2021-1… 2021-1…
#>  7 ABC-1001 VACCINATION 1 DELTOID MUS… LEFT  VACC…      1 SYRIN… 2021-1… 2021-1…
#>  8 ABC-1001 VACCINATION 1 DELTOID MUS… LEFT  VACC…      1 SYRIN… 2021-1… 2021-1…
#>  9 ABC-1001 VACCINATION 1 DELTOID MUS… LEFT  VACC…      1 SYRIN… 2021-1… 2021-1…
#> 10 ABC-1001 VACCINATION 1 DELTOID MUS… LEFT  VACC…      1 SYRIN… 2021-1… 2021-1…

derive_vars_merged_vaccine(
  dataset = face_vaccine,
  dataset_ex = ex_vaccine,
  by_vars_sys = exprs(USUBJID, FATPTREF = EXLNKGRP),
  by_vars_adms = exprs(USUBJID, FATPTREF = EXLNKGRP, FALOC = EXLOC, FALAT = EXLAT),
  ex_vars = exprs(EXTRT, EXDOSE, EXDOSU, EXSTDTC, EXENDTC)
)
#> # A tibble: 307 × 35
#>    STUDYID DOMAIN USUBJID  FASEQ FALNKGRP    FALAT FALNKID FALOC FATESTCD FATEST
#>    <chr>   <chr>  <chr>    <int> <chr>       <chr> <chr>   <chr> <chr>    <chr> 
#>  1 ABC     FACE   ABC-1001     8 VACCINATIO… LEFT  VACCIN… DELT… OCCUR    Occur…
#>  2 ABC     FACE   ABC-1001     9 VACCINATIO… LEFT  VACCIN… DELT… OCCUR    Occur…
#>  3 ABC     FACE   ABC-1001    10 VACCINATIO… LEFT  VACCIN… DELT… SEV      Sever…
#>  4 ABC     FACE   ABC-1001    11 VACCINATIO… LEFT  VACCIN… DELT… OCCUR    Occur…
#>  5 ABC     FACE   ABC-1001    12 VACCINATIO… LEFT  VACCIN… DELT… SEV      Sever…
#>  6 ABC     FACE   ABC-1001    13 VACCINATIO… LEFT  VACCIN… DELT… OCCUR    Occur…
#>  7 ABC     FACE   ABC-1001    14 VACCINATIO… LEFT  VACCIN… DELT… SEV      Sever…
#>  8 ABC     FACE   ABC-1001    15 VACCINATIO… LEFT  VACCIN… DELT… OCCUR    Occur…
#>  9 ABC     FACE   ABC-1001    16 VACCINATIO… LEFT  VACCIN… DELT… SEV      Sever…
#> 10 ABC     FACE   ABC-1001    17 VACCINATIO… LEFT  VACCIN… DELT… OCCUR    Occur…
#> # ℹ 297 more rows
#> # ℹ 25 more variables: FAOBJ <chr>, FACAT <chr>, FASCAT <chr>, FAEVAL <chr>,
#> #   FAORRES <chr>, FAORRESU <chr>, EPOCH <chr>, FADTC <chr>, FADY <dbl>,
#> #   FATPT <chr>, FATPTNUM <dbl>, FATPTREF <chr>, FARFTDTC <chr>,
#> #   FAEVLINT <chr>, FAEVINTX <chr>, FASTAT <chr>, FAREASND <chr>,
#> #   FASTRESC <chr>, FASTRESN <dbl>, FASTRESU <chr>, EXTRT <chr>, EXDOSE <dbl>,
#> #   EXDOSU <chr>, EXSTDTC <chr>, EXENDTC <chr>