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Create an EpiTrax object from data file

Source: R/epitrax.R
create_epitrax_from_file.Rd

create_epitrax_from_file reads an EpiTrax data file and creates a structured object containing the data along with commonly used metadata and empty report lists.

Usage

create_epitrax_from_file(filepath = NULL, num_yrs = 5)

Arguments

filepath

Optional filepath. EpiTrax 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

An object of class epitrax containing:

  • data: The validated and formatted EpiTrax data

  • diseases: Vector of unique diseases in the dataset

  • yrs: Vector of years in the dataset

  • report_year: Most recent year in the dataset

  • report_month: Most recent month in report_year

  • internal_reports: Empty list to store internal reports

  • public_reports: Empty list to store public reports

See also

read_epitrax_data() which this function wraps and setup_epitrax() which wraps this function

Examples

if (interactive()) {
  # Interactive file chooser:
  create_epitrax_from_file()
}

# Using sample data included with package
data_file <- system.file("sample_data/sample_epitrax_data.csv",
                         package = "epitraxr")
epitrax <- create_epitrax_from_file(data_file)

# Access components
head(epitrax$data)
#>     disease month year counts
#> 1 Influenza     8 2020      1
#> 2 Influenza    12 2019      1
#> 3 Influenza     7 2021      1
#> 4  COVID-19     7 2024      1
#> 5 Influenza     6 2020      1
#> 6 Influenza     4 2022      1
epitrax$diseases
#> [1] "Influenza"  "COVID-19"   "Measles"    "Chickenpox" "Syphilis"  
epitrax$report_year
#> [1] 2024