Using the gbif4crest database

There are two ways to access and use the gbif4crest calibration dataset, which are illustrated here with a simple PSE file.

crest_ex_pse
#>   Level      Family    Genus Species ProxyName
#> 1     3 Randomaceae Randomus  Taxon1    Taxon1
#> 2     3 Randomaceae Randomus  Taxon2    Taxon2
#> 3     3 Randomaceae Randomus  Taxon3    Taxon3
#> 4     3 Randomaceae Randomus  Taxon4    Taxon4
#> 5     3 Randomaceae Randomus  Taxon5    Taxon5
#> 6     3 Randomaceae Randomus  Taxon6    Taxon6
#> 7     3 Randomaceae Randomus  Taxon7    Taxon7

The cloud-based option (online)

The first option consists in using the default option: connecting to the online gbif4crest. This is the simplest option and users only have to provide the name of the database to the field dbname = "gbif4crest_02".

reconstr <- crest.get_modern_data(  pse = PSE,
                                    taxaType = 1,
                                    climate = c("bio1", "bio12"),
                                    # The name of the online database
                                    dbname = "crest_example",
                                    verbose = FALSE
)

tapply(reconstr$modelling$taxonID2proxy[,1], reconstr$modelling$taxonID2proxy[,2], length)
#> Taxon1 Taxon2 Taxon3 Taxon4 Taxon5 Taxon6 
#>      1      1      1      1      1      1

The SQLite3 option (offline) [only in crestr v > 1.1.0]

This option is usually much faster but it requires downloading the full database in a zipped format from [here]. Once unzipped, the file, which is about ~23Gb, should be saved in a location of interest.

reconstr <- crest.get_modern_data(  pse = PSE,
                                    taxaType = 1,
                                    climate = c("bio1", "bio12"),
                                    # The full path to the local database
                                    # Or place the database in the working
                                    #   directory.
                                    dbname = "path/to/gbif4crest_02.sqlite3",
                                    verbose = FALSE
)

The local calibration database file can be saved anywhere and named in any way. The file extension ‘.sqlite3’ is, however, the only difference between the online and the offline options. It is thus crucial to call the file database.sqlite3 to orient the package in the right direction.