vignettes/Comparison_other_software.Rmd
Comparison_other_software.Rmd##Background Erroneous database entries and problematic geographic
coordinates are a central issue in biogeography and there is a set of
tools available to address different dimensions of the problem.
CoordinateCleaner focuses on the fast and reproducible flagging of large
amounts of records, and additional functions to detect dataset-level and
fossil-specific biases. In the R-environment the scrubr and biogeo offer
cleaning approaches complementary to CoordinateCleaner. The scrubr
package combines basic geographic cleaning (comparable to cc_dupl,
cc_zero and cc_count in CoordinateCleaner) but adds options to clean
taxonomic names (See also taxize) and date
information. biogeo includes some basic automated geographic cleaning
(similar to cc_val, cc_count and
cc_outl) but rather focusses on correcting suspicious
coordinates on a manual basis using environmental information.
Table 1. Function by function comparison of CoordinateCleaner, scrubr and biogeo.
| Functionality | CoordinateCleaner 2.0-2 | scrubr 0.1.1 | biogeo 1.0 | Percent overlap |
|---|---|---|---|---|
| Missing coordinates | cc_val | coord_incomplete | missingvalsexclude | 100% |
| Coordinates outside CRS | cc_val | coord_impossible | - | 100% |
| Duplicated records | cc_dupl | dedup | duplicatesexclude | The aim is identical, methods differ |
| 0/0 coordinates | cc_zero | coord_unlikely | - | 100% |
| Identical lon/lat | cc_equ | - | - | 0% |
| Country capitals | cc_cap | - | - | 0% |
| Political unit centroids | cc_cen | - | - | 0% |
| Coordinates in-congruent with additional location information | cc_count | coord_within | errorcheck, quickclean | 100% |
| Coordinates assigned to GBIF headquarters | cc_gbif | - | - | 0% |
| Coordinates assigned to the location of biodiversity institutions | cc_inst | - | - | 0% |
| Coordinates outside natural range | cc_iucn | - | - | 0% |
| Spatial outliers | cc_outl | - | outliers | 50%, biogeo uses environmental distance |
| Coordinates within the ocean | cc_sea | - | - | 0% |
| Coordinates in urban area | cc_urb | - | - | 0% |
| Coordinate conversion error | dc_ddmm | - | - | 0% |
| Rounded coordinates/rasterized collection | dc_round | - | precisioncheck | 20%, biogeo test for predefined rasters |
| Fossils: invalid age range | tc_equal | - | - | 0% |
| Fossils: excessive age range | tc_range | - | - | 0% |
| Fossils: temporal outlier | tc_outl | - | - | 0% |
| Fossils: PyRate interface | WritePyrate | - | - | 0% |
| Wrapper functions to run all test | CleanCoordinates, CleanCoordinatesDS, CleanCoordinatesFOS | - | - | 0% |
| Database of biodiversity institutions | institutions | - | - | 0% |
| Taxonomic cleaning | - | tax_no_epithet | - | 0% |
| Missing date | - | date_missing | - | 0% |
| Add date | - | date_create | - | 0% |
| Date format | - | date_standardize | - | 0% |
| Reformatting coordinate annotation | - | - | a large set of functions | 0 % |
| Correcting coordinates using guessing and environmental distance | - | - | a large set of functions | 0 % |