admiralvaccine (version 0.6.0)

derive_diam_to_sev_records: Creating Severity Records From Diameter

Description

To derive the severity records from the diameter records.

Usage

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
)

Value

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.

Arguments

dataset

Input data set

The variables USUBJID,FAOBJ,AVAL, AVALC, FATESTCD and FATEST are expected for Input data set.

filter_add

filter for the dataset.

diam_code

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.

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.

testcd_sev

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).

test_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.

none

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.

mild

Pass the lower limit for grade "MILD"

Permitted Value: A numeric vector

mod

Pass the lower limit for grade "MODERATE"

Permitted Value: A numeric vector

sev

Pass the lower limit for grade "SEVERE"

Permitted Value: A numeric vector

Author

Arjun Rubalingam

See Also

Other der_rec: derive_fever_records()

Examples

library(dplyr)
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"
)