Skip to contents

Read in EpiTrax data

Source: R/data.R
read_epitrax_data.Rd

'read_epitrax_data' reads EpiTrax data from a CSV, validates, and formats it. It also filters rows older than given number of years. The input file must contain the columns:

  • patient_mmwr_year (integer)

  • patient_mmwr_week (integer)

  • patient_disease (character)

Usage

read_epitrax_data(filepath = NULL, num_yrs = 5)

Arguments

filepath

Optional filepath. Data file should be a CSV. If this parameter is NULL, the user will be prompted to choose a file interactively.

num_yrs

Integer. Number of years of data to keep. Defaults to 5.

Value

The validated and formatted EpiTrax data from the input file.

Details

See the example file here: system.file("sample_data/sample_epitrax_data.csv", package = "epitraxr")

Examples

if (FALSE) { # \dontrun{
# Interactive file chooser:
read_epitrax_data()
} # }

# Using a file path:
data <- read_epitrax_data(
 filepath = system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr"),
 num_yrs = 3
)
head(data)
#>      disease month year counts
#> 3  Influenza     7 2021      1
#> 4   COVID-19     7 2024      1
#> 6  Influenza     4 2022      1
#> 7   COVID-19     6 2021      1
#> 9    Measles     4 2023      1
#> 11 Influenza     4 2021      1