gatoRs (Geographic and Taxonomic Occurrence R-Based Scrubbing) provides users with tools to streamline the downloading and processing biodiversity data.
Historically, many names may have been used to refer to your taxa of interest. For example, specimen representing Galax urceolata (Diapensiaceae) can be found under the scientific name Galax aphylla, despite the latter being invalidated over 50 years ago (see more here). Since synonyms are common, we designed gatoRs retrieve biodiversity records based on a list of names, however the user must supply the synonym list.
There are many databases available to compile synonym lists for plant species including:
Many R packages have been developed to access these databases including:
With gators_download() you can obtain biodiversity records for your species of interest from both GBIF and iDigBio. This function is innovative in how it searches iDigBio. Unlike spocc::occ(), we do not query the iDigBio API using the scientific name field, as this will only return exact matches. Instead, we designed a “pseudo-fuzzy match” to search all fields for partial matches to the supplied scientific names. Additionally, the columns returned have been handpicked to aid in processing records for investigations of species distributions (see more gators_download()).
After you identify synonyms, create a list of all possible names for your species of interest with the first name in the list as the accepted name (ex. c("Galax urceolata", "Galax aphylla")). Note, the first name in your list will be used to identify the GBIF species code when gbif_match = "code".
Example:
library(gatoRs)
galaxdf <- gators_download(synonyms.list = c("Galax urceolata", "Galax aphylla"),
write.file = TRUE,
filename = "base_folder/my_file.csv", # Location to save file - must end in .csv
gbif.match = "fuzzy",
idigbio.filter = TRUE)We downloaded 7742 observations for Galax urceolata in the example above. Of these observations, only those with locality information will be helpful when investigating this species distribution.
Locality information can be redacted or skewed due to protect threatened taxa, often locality information will be provided upon request or can be identified through georeferencing. We created functions to aid in this process.
Locality information can be redacted or skewed due to protect threatened taxa; often locality information will be provided to aid research upon request.
To find data that needs to be manually received by an institution via a permit (or removed from the data set), use needed_records(). After receiving the data from herbaria, manually merge the obtained records with your original data set.
Example:
redacted_info <- needed_records(galaxdf)Some records may be missing latitude and longitude values, however locality information can be used to assign coordinates to the record through georeferencing.
To find data lacking coordinates but containing locality information, use need_to_georeference(). You should georeference these records and then manually merge the obtain records with your original data set.
Example:
to_georeference <- need_to_georeference(galaxdf)After receiving the data from herbaria or through georeferencing, you will want to merge the obtained records with your original data set.
Note, the following steps will only work if columns are equivalent between the two data sets you hope to merge. If the columns are not equivalent, we recommend bcd::bcd_standardize_datasets()
Example:
# Avoid duplicates by removing the records you are about to merge
dfsub <- remove_missing(galaxdf)
# Use gator_merge to merge the main data set with retrieved records
dfnew <- gators_merge(dfsub, retrieved_records)
# Version control - save a copy prior to any additional processing!!
write.csv(dfnew, "data/merged_data_Galax_urceolata_YYYYMMDD.csv") ## Version control!
# Set gatordf equal to the newly merged data set
gatordf <- dfnewHere we walk through each cleaning function, however we also created a simple one-step option full_clean(), see below.
To find data containing scientific names corresponding to your desired species, use taxa_clean(). Use your downloaded data from the first step as input, as well as a synonyms list, the accepted name, and the filter option (exact, fuzzy, or interactive).
Example:
galaxdf <- taxa_clean(df = galaxdf,
synonyms.list = c("Galax urceolata", "Galax aphylla"),
taxa.filter = "fuzzy",
accepted.name = "Galax urceolata") # creates a new column with accepted name for easy comparisonHere we remove any records with missing coordinates, impossible coordinates, coordinates at (0,0), and any that are flagged as skewed. The skewed records can be identified with the remove_skewed() function and row value for the ‘InformationWitheld’ column. We also provide the option to round the provided latitude and longitude values to a specified number of decimal places.
galaxdf <- basic_locality_clean(df = galaxdf,
remove.zero = TRUE, # Records at (0,0) are removed
precision = TRUE, # latitude and longitude are rounded
digits = 2, # round to 2 decimal places
remove.skewed = TRUE)To find records that may have problematic coordinates, use process_flagged(). This function can either automate the process of finding and removing problematic points (interactive = FALSE) or allow for manual inspection. The latter will let you manually remove points deemed improper by viewing the points on a graph.
This function utilizes CoordinateCleaner::clean_coordinates().
Example:
galaxdf <- process_flagged(galaxdf, interactive = TRUE)