BeeBDC (version 1.2.0)

summaryFun: Create or update the .summary flag column

Description

Using all flag columns (column names starting with "."), this function either creates or updates the .summary flag column which is FALSE when ANY of the flag columns are FALSE. Columns can be excluded and removed after creating the .summary column. Additionally, the occurrence dataset can be filtered to only those where .summary = TRUE at the end of the function.

Usage

summaryFun(
  data = NULL,
  dontFilterThese = NULL,
  onlyFilterThese = NULL,
  removeFilterColumns = FALSE,
  filterClean = FALSE
)

Value

Returns a data frame or tibble of the input data but modified based on the above parameters.

Arguments

data

A data frame or tibble. Occurrence records to use as input.

dontFilterThese

A character vector of flag columns to be ignored in the creation or updating of the .summary column. Cannot be specified with onlyFilterThese.

onlyFilterThese

A character vector. The inverse of dontFilterThese, where columns identified here will be filtered and no others. Cannot be specified with dontFilterThese.

removeFilterColumns

Logical. If TRUE all columns starting with "." will be removed in the output data. This only makes sense to use when filterClean = TRUE. Default = FALSE.

filterClean

Logical. If TRUE, the data will be filtered to only those occurrence where .summary = TRUE (i.e., completely clean according to the used flag columns). Default = FALSE.

Examples

# Read in example data
data(beesFlagged)

# To only update the .summary column
beesFlagged_out <- summaryFun(
    data = beesFlagged,
    dontFilterThese = c(".gridSummary", ".lonFlag", ".latFlag", ".uncer_terms", ".unLicensed"),
    removeFilterColumns = FALSE,
    filterClean = FALSE)
  # View output
table(beesFlagged_out$.summary, useNA = "always")

# Now filter to only the clean data and remove the flag columns
beesFlagged_out <- summaryFun(
  data = BeeBDC::beesFlagged,
  dontFilterThese = c(".gridSummary", ".lonFlag", ".latFlag", ".uncer_terms", ".unLicensed"),
  removeFilterColumns = TRUE,
  filterClean = TRUE)
# View output
table(beesFlagged_out$.summary, useNA = "always")