Processes a GBIF data cube and (if applicable) an associated taxonomic information file. If your cube includes a taxonomic info file it is likely a previous generation cube and should be processed using 'process_cube_old'. The taxonomic info file must reside in the same directory as your cube and share a base file name (e.g., 'cubes/my_mammals_cube.csv', 'cubes/my_mammals_info.csv'). If your cube does NOT include a taxonomic info file then it is likely a current generation cube and should be processed using the standard process_cube function The API used to generate the current generation cubes is very flexible and allows user-specified column names. Therefore, please check that the column names of your cube match the Darwin Core standard expected by the process_cube function. If they do not, you may need to enter them manually. The function will return an error if it cannot find all required columns.
Usage
process_cube(
cube_name,
grid_type = c("automatic", "eea", "mgrs", "eqdgc", "custom", "none"),
first_year = NULL,
last_year = NULL,
force_gridcode = FALSE,
cols_year = NULL,
cols_yearMonth = NULL,
cols_cellCode = NULL,
cols_occurrences = NULL,
cols_scientificName = NULL,
cols_minCoordinateUncertaintyInMeters = NULL,
cols_minTemporalUncertainty = NULL,
cols_kingdom = NULL,
cols_family = NULL,
cols_species = NULL,
cols_kingdomKey = NULL,
cols_familyKey = NULL,
cols_speciesKey = NULL,
cols_familyCount = NULL,
cols_sex = NULL,
cols_lifeStage = NULL
)
process_cube_old(
cube_name,
tax_info = NULL,
datasets_info = NULL,
first_year = 1600,
last_year = NULL
)Arguments
- cube_name
The location and name of a data cube file (e.g., 'inst/extdata/europe_species_cube.csv').
- grid_type
Specify which grid reference system your cube uses. By default the function will attempt to determine this automatically and return an error if it fails. If you want to perform analysis on a cube with custom grid codes (e.g. output from the gcube package) or a cube without grid codes, select 'custom' or 'none', respectively.
- first_year
(Optional) The first year of occurrences to include. If not specified, uses a default of 1600 to prevent false records (e.g. with year = 0).
- last_year
(Optional) The final year of occurrences to include. If not specified, uses the latest year present in the cube.
- force_gridcode
Force the function to assume a specific grid reference system. This may cause unexpected downstream issues, so it is not recommended. If you are getting errors related to grid cell codes, check to make sure they are valid.
- cols_year
The name of the column containing the year of occurrence (if something other than 'year'). This column is required unless you have a yearMonth column.
- cols_yearMonth
The name of the column containing the year and month of occurrence (if present and if other than 'yearMonth'). Use this if only if you do not have a year column. The b3gbi package does not use month data, so the function will convert your yearMonth column to a year column.
- cols_cellCode
The name of the column containing the grid reference codes (if other than 'cellCode'). This column is required.
- cols_occurrences
The name of the column containing the number of occurrence (if other than 'occurrences'). This column is required.
- cols_scientificName
The name of the column containing the scientific name of the species (if other than 'scientificName'). Note that it is not necessary to have both a species column and a scientificName column. One or the other is sufficient.
- cols_minCoordinateUncertaintyInMeters
The name of the column containing the minimum coordinate uncertainty of the occurrences (if other than 'minCoordinateUncertaintyinMeters').
- cols_minTemporalUncertainty
The name of the column containing the minimum temporal uncertainty of the occurrences (if other than 'minTemporalUncertainty').
- cols_kingdom
The name of the column containing the kingdom the occurring species belongs to (if other than 'kingdom'). This column is optional.
- cols_family
The name of the column containing the family the occurring species belongs to (if other than 'family'). This column is optional.
- cols_species
The name of the column containing the name of the occurring species (if other than 'species'). Note that it is not necessary to have both a species column and a scientificName column. One or the other is sufficient.
- cols_kingdomKey
The name of the column containing the kingdom key of the occurring species (if other than 'kingdomKey'). This column is optinal.
- cols_familyKey
The name of the column containing the family key of the occurring species (if other than 'familykey'). This column is optional.
- cols_speciesKey
The name of the column containing the species key of the occurring species (if other than 'speciesKey'). This column is required, but note that if you have a 'taxonKey' column you can provide it as the speciesKey.
- cols_familyCount
The name of the column containing the occurrence count by family. This column is optional.
- cols_sex
The name of the column containing the sex of the observed individuals. This column is optional.
- cols_lifeStage
the name of the column containing the life stage of the observed individuals. This column is optional.
- tax_info
The location and name of an associated taxonomic info file (e.g., 'inst/extdata/europe_species_info.csv').
- datasets_info
The location and name of an associated dataset info file (e.g., 'inst/extdata/europe_species_datasets.csv').
Examples
if (FALSE) { # \dontrun{
cube_name <- system.file("extdata", "europe_species_cube.csv", package = "b3gbi")
tax_info <- system.file("extdata", "europe_species_info.csv", package = "b3gbi")
europe_example_cube <- process_cube(cube_name, tax_info)
europe_example_cube
} # }