R/derive_diam_to_sev_records.R
derive_diam_to_sev_records.RdTo derive the severity records from the diameter records.
derive_diam_to_sev_records(
dataset,
filter_add = NULL,
diam_code = "DIAMETER",
faobj_values = c("REDNESS", "SWELLING"),
testcd_sev = "SEV",
test_sev = "Severity/Intensity",
none = 0,
mild = 2,
mod = 5,
sev = 10
)Input data set
The variables USUBJID,FAOBJ,AVAL, AVALC, FATESTCD and FATEST are expected
for Input data set.
filter for the dataset.
Diameter record filter
Permitted Value: A character vector or scalar.
Helps to filter the diameter records to derive the severity records by
passing the FATESTCD value for diameter which is corresponding to the
specified events in faobj_values.
Event filter
Permitted Value: A character vector or Scalar.
Helps to filter the events (Redness and Swelling) which has diameter records
to derive severity records by passing the events from FAOBJ.
To assign FATESTCD value for severity
Permitted Value: A character scalar
Assign the value for FATESTCD variable to indicate the severity records.
Ignore the argument if you want to set the default value (SEV).
FATEST Value for severity
Permitted Value: A Character scalar
Assign the value for FATEST variable to indicate the severity records.
Ignore the argument if you want to set the default value.
Pass the lower limit for grade "NONE"
Permitted Value: A numeric vector
The none and the following arguments (mild, mode and sev) will be
used for assigning the diameter limit to derive the AVALC (severity grade).
Assign the lower limit to derive the Severity Grade (AVALC).
For Example: User passing 0 to none and 2 to mild, 0 will act as lower limit and 2 will act
as upper limit.
Note: Use the limit reference to pass the values to these arguments
Since the condition was coded like this,
NONE : none < AVAL <= mild
MILD : mild < AVAL <= mod
MODERATE : mod < AVAL <= sev
SEVERE : sev < AVAL
User should pass the values as numeric scalar. Refer the default values.
Pass the lower limit for grade "MILD"
Permitted Value: A numeric vector
Pass the lower limit for grade "MODERATE"
Permitted Value: A numeric vector
Pass the lower limit for grade "SEVERE"
Permitted Value: A numeric vector
The Input data with the new severity records for Redness and swelling which
is specified in faobj_values and AVAL, AVALC will be derived and FATESTCD,
FATEST will be changed as per the values.
Basically, This function will derive and create the severity records from the
diameter record for the particular events specified in the faobj_values that user wants.
If you want to derive the Severity from diameter, even though you have the severity in SDTM data.
This function will re-derive the severity and remove the derived SDTM severity records.
Other der_rec:
derive_fever_records()
library(dplyr)
#>
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#>
#> filter, lag
#> The following objects are masked from ‘package:base’:
#>
#> intersect, setdiff, setequal, union
library(admiral)
library(tibble)
input <- tribble(
~USUBJID, ~FAOBJ, ~AVAL, ~AVALC, ~ATPTREF, ~FATEST, ~FATESTCD,
"XYZ1001", "REDNESS", 7.5, "7.5", "VACCINATION 1", "Diameter", "DIAMETER",
"XYZ1001", "REDNESS", 3.5, "3.5", "VACCINATION 1", "Diameter", "DIAMETER",
"XYZ1001", "REDNESS", 2, "2", "VACCINATION 1", "Diameter", "DIAMETER",
"XYZ1001", "REDNESS", 1.8, "1.8", "VACCINATION 1", "Diameter", "DIAMETER",
"XYZ1001", "REDNESS", 1.4, "1.4", "VACCINATION 1", "Diameter", "DIAMETER",
"XYZ1002", "REDNESS", 11.1, "11.1", "VACCINATION 2", "Diameter", "DIAMETER",
"XYZ1002", "REDNESS", 7.4, "7.4", "VACCINATION 2", "Diameter", "DIAMETER",
"XYZ1002", "REDNESS", 6, "6", "VACCINATION 2", "Diameter", "DIAMETER",
"XYZ1002", "REDNESS", 2.1, "2.1", "VACCINATION 2", "Diameter", "DIAMETER",
"XYZ1002", "REDNESS", 1.1, "1.1", "VACCINATION 2", "Diameter", "DIAMETER",
"XYZ1001", "SWELLING", 5.5, "5.5", "VACCINATION 1", "Diameter", "DIAMETER",
"XYZ1001", "SWELLING", 2.5, "2.5", "VACCINATION 1", "Diameter", "DIAMETER",
"XYZ1001", "SWELLING", 2, "2", "VACCINATION 1", "Diameter", "DIAMETER",
"XYZ1001", "SWELLING", 1.8, "1.8", "VACCINATION 1", "Diameter", "DIAMETER",
"XYZ1001", "SWELLING", 1.4, "1.4", "VACCINATION 1", "Diameter", "DIAMETER",
"XYZ1002", "SWELLING", 10.1, "10.1", "VACCINATION 2", "Diameter", "DIAMETER",
"XYZ1002", "SWELLING", 7.1, "7.1", "VACCINATION 2", "Diameter", "DIAMETER",
"XYZ1002", "SWELLING", 5, "5", "VACCINATION 2", "Diameter", "DIAMETER",
"XYZ1002", "SWELLING", 1.8, "1.8", "VACCINATION 2", "Diameter", "DIAMETER",
"XYZ1002", "SWELLING", 1.4, "1.4", "VACCINATION 2", "Diameter", "DIAMETER"
)
derive_diam_to_sev_records(
dataset = input,
faobj_values = c("REDNESS", "SWELLING"),
diam_code = "DIAMETER",
testcd_sev = "SEV",
test_sev = "Severity"
)
#> # A tibble: 40 × 8
#> USUBJID FAOBJ AVAL AVALC ATPTREF FATEST FATESTCD FASEQ
#> <chr> <chr> <dbl> <chr> <chr> <chr> <chr> <int>
#> 1 XYZ1001 REDNESS 2 MODERATE VACCINATION 1 Severity SEV NA
#> 2 XYZ1001 REDNESS 1 MILD VACCINATION 1 Severity SEV NA
#> 3 XYZ1001 REDNESS 0 NONE VACCINATION 1 Severity SEV NA
#> 4 XYZ1001 REDNESS 0 NONE VACCINATION 1 Severity SEV NA
#> 5 XYZ1001 REDNESS 0 NONE VACCINATION 1 Severity SEV NA
#> 6 XYZ1002 REDNESS 3 SEVERE VACCINATION 2 Severity SEV NA
#> 7 XYZ1002 REDNESS 2 MODERATE VACCINATION 2 Severity SEV NA
#> 8 XYZ1002 REDNESS 2 MODERATE VACCINATION 2 Severity SEV NA
#> 9 XYZ1002 REDNESS 1 MILD VACCINATION 2 Severity SEV NA
#> 10 XYZ1002 REDNESS 0 NONE VACCINATION 2 Severity SEV NA
#> # ℹ 30 more rows