Process ECOTOX search results by converting character to dates where relevant

The function search_ecotox() returns fields from the ECOTOX database as is. Fields that represent dates are usually formatted as "%m\%d\%Y". Unfortunately, this format is not consistently used throughout the database. process_ecotox_dates() takes a data.frame returned by search_ecotox(), locates date columns, represented by text, sanitises the text and converts them to Date objects. It will sanitise the date fields as much as possible. It will correct most dates. Dates without a specified calender year, a date range, illegal date format (even after sanitation) are returned as NA.

Usage

process_ecotox_dates(x, .fns = as_date_ecotox, ..., .names = NULL)

Arguments

x

A data.frame obtained with search_ecotox(), for which the dates need to be processed.

.fns

Function to convert character to Date. By default as_date_ecotox() is used which also sanitises the input. You can also use as.Date() if you don't want the sanitation step. You can also write a custom function.

...

Arguments passed to .fns.

.names

A 'glue' specification used to rename the date columns. By default it is "{.col}", which will overwrite existing text columns with date columns. You can for instance add a suffix with "{.col}_date" if you want to rename the resulting date columns.

Value

Returns a data.frame in which the columns containing date information is converted from the character format from the database to actual date objects ( "POSIXlt" and "POSIXct").

See also

Other ecotox-sanitisers: as_date_ecotox(), as_numeric_ecotox(), as_unit_ecotox(), mixed_to_single_unit(), process_ecotox_numerics(), process_ecotox_units()

Author

Pepijn de Vries

Examples

if (check_ecotox_availability()) {
  df <- search_ecotox(
    list(
      latin_name    = list(
        terms          = c("Skeletonema", "Daphnia"),
        method         = "contains"
      ),
      chemical_name = list(
        terms          = "benzene",
        method         = "exact"
      )
    ), list_ecotox_fields("full"))

  df_dat <-
    process_ecotox_dates(df, warn = FALSE)
}