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Convert WDDS disease data to PHAROS data

Source: R/wdds_to_pharos.R
wdds_to_pharos.Rd

As of 11 September 2025, WDDS and the PHAROS data model are not fully aligned. This function converts data that conforms to WDDS into the PHAROS data model. See wdds_to_pharos_map for the data model crosswalk.

Usage

wdds_to_pharos(wdds_disease_data)

Arguments

wdds_disease_data

Data frame. A Disease Data set that conforms to the wdds data standard.

Value

Data frame. A tabular data set that conforms to the PHAROS data model.

See also

Other Standards Mapping: na_to_blank(), translate_to_dcmi(), wdds_to_dcmi()

Examples


wdds_to_pharos(wdds_disease_data = wddsWizard::minimal_disease_data)
#> `sampleCollectionMethod` does not map perfectly to `Collection method or tissue`. Please review those entries.
#> # A tibble: 3 × 13
#>   `Animal ID` `Collection day` `Collection month` `Collection year`
#>   <chr>       <chr>            <chr>              <chr>            
#> 1 d           1                12                 1                
#> 2 e           1                10                 2024             
#> 3 f           1                1                  2025             
#> # ℹ 9 more variables: `Detection method` <chr>, `Detection outcome` <chr>,
#> #   `Detection target` <chr>, `Host species` <chr>, Latitude <chr>,
#> #   Longitude <chr>, Pathogen <chr>, `Collection method or tissue` <chr>,
#> #   `Sample ID` <chr>

# data must be written to CSV then uploaded to PHAROS