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Locality Cleaning - Find possibly problematic occurrence records

Source: R/process_flagged.R
process_flagged.Rd

The process_flagged() function allows you to visualize and inspect possible problematic points, as well as manually remove these points, if desired. By default, this function is interactive. When running the function interactively you can hover over a point to see the record's scientific name, and click on a point to see the record's coordinates.The interactive option plots flagged points in red and non-flagged points in blue.

Usage

process_flagged(
  df,
  interactive = TRUE,
  latitude = "latitude",
  longitude = "longitude",
  scientific.name = "scientificName"
)

Arguments

df

Data frame of occurrence records returned from gators_download().

interactive

Default = TRUE. The interactive option allows for a visual display of possible problematic points and the ability to manually remove these points. Setting interactive = FALSE will automatically remove these points from the data frame.

latitude

Default = "latitude". The name of the latitude column in the data frame.

longitude

Default = "longitude". The name of the longitude column in the data frame.

scientific.name

Default = "scientificName". The name of the scientificName column in the data frame.

Value

Return cleaned data frame. Information about the columns in the returned data frame can be found in the documentation for gators_download().

Details

This function is a wrapper to visualize results for the CoordinateCleaner::clean_coordinates() function. Briefly, CoordinateCleaner::clean_coordinates() flags records with coordinates that are unlikely valid, spatial outliers, or in certain locations including the ocean, state capitals, country centroids, the GBIF headquarters, and biodiversity institutions (including botanical gardens, museums, herbaria, etc.). This function requires packages CoordinateCleaner, leaflet, and magrittr. This function requires interactive user input.

Examples

# \donttest{
cleaned_data <- process_flagged(data, interactive = FALSE)
#> Testing coordinate validity
#> Flagged 0 records.
#> Testing equal lat/lon
#> Flagged 0 records.
#> Testing zero coordinates
#> Flagged 0 records.
#> Testing country capitals
#> Flagged 0 records.
#> Testing country centroids
#> Flagged 0 records.
#> Testing sea coordinates
#> Reading layer `ne_50m_land' from data source `/tmp/Rtmpgu44v2/ne_50m_land.shp' using driver `ESRI Shapefile'
#> Simple feature collection with 1420 features and 3 fields
#> Geometry type: MULTIPOLYGON
#> Dimension:     XY
#> Bounding box:  xmin: -180 ymin: -89.99893 xmax: 180 ymax: 83.59961
#> Geodetic CRS:  WGS 84
#> Flagged 0 records.
#> Testing geographic outliers
#> Testing GBIF headquarters, flagging records around Copenhagen
#> Flagged 0 records.
#> Testing biodiversity institutions
#> Flagged 0 records.
#> Flagged 0 of 8 records, EQ = 0.
# }