count_cases {AEenrich}

Convert data on the report level to aggregated data.

Description

The count_cases function is used to convert data on the report level to aggregated data, grouping by specified covariates.

Usage

count_cases(
  data,
  drug.case = drug.case,
  drug.control = NULL,
  covar_disc = NULL,
  covar_cont = NULL,
  breaks = NULL,
  cores = detectCores(),
  min_AE = 10
)

Arguments

data

a data.frame with at least 3 columns, consisting data on the report level, having ID, Drug type and AE name as the first 3 columns with covariates(optional) followed. The order of columns is not interchangeable.

drug.case

a character string for the target drug of interest.

drug.control

a character string for the reference drug. If NULL(default), all other drugs combined are the reference.

covar_disc

a character vector of categorical covariates.

covar_cont

a character vector of continuous covariates.

breaks

a list consists of vectors used for creating specific bins to transform continuous covariates into categorical. Breaks Should have the same length as covar_cont. Given a vector of non-decreasing breakpoints in breaks[i], find the interval containing each element of covar_cont[i]; i.e., for each index j in breaks[i], value j is assigned to covar_cont[i] if and only if breaks[i][j] ⁠<= covar_cont[i] < breaks[i][j+1]⁠.

cores

the number of cores to use for parallel execution.

min_AE

the minimum number of cases required to start counting for a specific AE. Default 10.

Value

A data.frame consists of aggregated data.

The returned data.frame contains the following columns:

• DRUG_TYPE: type of the drug, DrugYes for target drug and DrugNo for referenced drug

• AE_NAME: the name of the adverse event

• AEyes: number of observations that have this AE

• AEno: number of observations that do not have this AE

• covariates: covariates specifed by user

Examples

# count_cases(data = covid1, drug.case = "COVID19", drug.control = "OTHER",
#             covar_cont = c("AGE"), covar_disc = c("SEX"),
#             breaks = list(c(16,30,50,65,120)))