Creating PARAMCD from lookup dataset and assigning PARAM,PARAMN,PARCAT1,
PARCAT2 variables
derive_vars_params(dataset, lookup_dataset, merge_vars)Input dataset
Input dataset is expected to have variables USUBJID,FAOBJ,
FACAT, FATESTCD and FATEST
lookup dataset containing PARAMCD values for every
unique FATESTCD and FAOBJ
lookup dataset is expected to have variables FATEST, PARAMCD,
FATESTCD, FAOBJ and one entry for every unique
FATESTCD and FAOBJ
List of Variables need to be merged from lookup dataset
The output dataset contains all observations and variables of the
input dataset along with PARAM,PARAMCD,PARCAT1,PARCAT2,PARAMN
A lookup dataset is required with PARAMCD values for every combination
of FATEST & FAOBJ.
PARAMCD PARAMN PARAMN PARCAT1 PARCAT2 values can be assigned
from lookup dataset.
if `PARAMN` not assigned in lookup dataset then
`PARAMN` is assigned with a unique number for every unique PARAM value.
if `PARAM` value not assigned in lookup dataset then
`PARAM` value is a combination of `FAOBJ` `FATEST` `FASTRESU` `FALOC`
`FADIR` `FALAT`
if `PARCAT1` value not assigned in lookup dataset then
`PARCAT1` is assigned as `FACAT`
if `PARCAT2` value not assigned in lookup dataset then
`PARCAT2` is assigned as `FASCAT`Other der_var:
derive_var_aval_adis(),
derive_vars_crit(),
derive_vars_event_flag(),
derive_vars_max_flag(),
derive_vars_merged_vaccine(),
derive_vars_vaxdt()
library(admiral)
library(tibble)
library(dplyr)
lookup_dataset <- tibble::tribble(
~FATESTCD, ~PARAMCD, ~PARAMN, ~FATEST, ~FAOBJ,
"SEV", "SEVREDN", 1, "Severity", "Redness",
"DIAMETER", "DIARE", 2, "Diameter", "Redness",
"MAXDIAM", "MDIRE", 3, "Maximum Diameter cm", "Redness",
"MAXTEMP", "MAXTEMP", 4, "Maximum Temperature", "Fever",
"OCCUR", "OCFEVER", 5, "Occurrence Indicator", "Fever",
"OCCUR", "OCERYTH", 6, "Occurrence Indicator", "Erythema",
"SEV", "SEVPAIN", 7, "Severity", "Pain at Injection site",
"OCCUR", "OCPAIN", 8, "Occurrence Indicator", "Pain at Injection site",
"OCCUR", "OCSWEL", 9, "Occurrence Indicator", "Swelling"
)
input <- tibble::tribble(
~USUBJID, ~FACAT, ~FASCAT, ~FATESTCD, ~FAOBJ, ~FATEST, ~FALOC, ~FALAT,
"ABC101", "REACTO", "ADMIN", "SEV", "Redness", "Severity", "ARM", "LEFT",
"ABC101", "REACTO", "ADMIN", "DIAMETER", "Redness", "Diameter", "ARM", "RIGHT",
"ABC101", "REACTO", "ADMIN", "MAXDIAM", "Redness", "Maximum Diameter", NA, NA,
"ABC101", "REACTO", "SYSTEMIC", "MAXTEMP", "Fever", "Maximum Temp", NA, NA,
"ABC101", "REACTO", "SYSTEMIC", "OCCUR", "Fever", "Occurrence", NA, NA,
"ABC101", "REACTO", "ADMIN", "OCCUR", "Erythema", "Occurrence", NA, NA,
"ABC101", "REACTO", "ADMIN", "SEV", "Swelling", "Severity", NA, NA,
"ABC101", "REACTO", "ADMIN", "OCCUR", "Swelling", "Occurrence", NA, NA,
"ABC101", "REACTO", "ADMIN", "OCCUR", "Swelling", "Occurrence", NA, NA
)
derive_vars_params(
dataset = input,
lookup_dataset = lookup_dataset,
merge_vars = exprs(PARAMCD, PARAMN)
)
#> # A tibble: 9 × 13
#> USUBJID FACAT FASCAT FATESTCD PARAM FAOBJ FATEST FALOC FALAT PARAMCD PARAMN
#> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl>
#> 1 ABC101 REACTO ADMIN SEV Redn… Redn… Sever… ARM LEFT SEVREDN 1
#> 2 ABC101 REACTO ADMIN DIAMETER Redn… Redn… Diame… ARM RIGHT DIARE 2
#> 3 ABC101 REACTO ADMIN MAXDIAM Redn… Redn… Maxim… NA NA MDIRE 3
#> 4 ABC101 REACTO SYSTEMIC MAXTEMP Feve… Fever Maxim… NA NA MAXTEMP 4
#> 5 ABC101 REACTO SYSTEMIC OCCUR Feve… Fever Occur… NA NA OCFEVER 5
#> 6 ABC101 REACTO ADMIN OCCUR Eryt… Eryt… Occur… NA NA OCERYTH 6
#> 7 ABC101 REACTO ADMIN SEV Swel… Swel… Sever… NA NA NA NA
#> 8 ABC101 REACTO ADMIN OCCUR Swel… Swel… Occur… NA NA OCSWEL 9
#> 9 ABC101 REACTO ADMIN OCCUR Swel… Swel… Occur… NA NA OCSWEL 9
#> # ℹ 2 more variables: PARCAT1 <chr>, PARCAT2 <chr>