Automated flagging of common spatial and temporal errors in biological and palaeontological collection data, for the use in conservation, ecology and palaeontology.
I’ve just started using CoordinateCleaner to flag and remove problematic records from the Gbif package. So I apologize in advance if my following comment is due to my unfamiliarity with this package.
From a given input (GBIF records of species occurrence), I ran the clean_coordinates function as follows:
flags<-clean_coordinates(gbif_data_df,
lon = "decimalLongitude",
lat = "decimalLatitude",
countries = "countryCode2",
species = "species",
tests = c("capitals", "centroids", "duplicated", "equal", "gbif", "institutions", "outliers", "zeros"))
Here, I obtained the following results in my R console:
Testing coordinate validity
Flagged 0 records.
Testing equal lat/lon
Flagged 0 records.
Testing zero coordinates
Flagged 0 records.
Testing country capitals
Flagged 10 records.
Testing country centroids
Flagged 3 records.
Testing geographic outliers
Flagged 44 records.
Testing GBIF headquarters, flagging records around Copenhagen
Flagged 0 records.
Testing biodiversity institutions
Flagged 0 records.
Flagged 10 of 12187 records, EQ = 0
If the 3 "centroids" flagged records seems to be comprised within the 10 "country capitals" records, I don't understand why the "geographic outliers" flagged records are not shown in the summary, nor in the "flags" object.
Dear all,
I’ve just started using CoordinateCleaner to flag and remove problematic records from the Gbif package. So I apologize in advance if my following comment is due to my unfamiliarity with this package.
From a given input (GBIF records of species occurrence), I ran the clean_coordinates function as follows:
Here, I obtained the following results in my R console:
If the 3 "centroids" flagged records seems to be comprised within the 10 "country capitals" records, I don't understand why the "geographic outliers" flagged records are not shown in the summary, nor in the "flags" object.
Thank you for your attention to this matter,
Léa