Function reference • crestr

Reconstructing Functions for running the CREST reconstructions.
`crest.get_modern_data()`	Extract distributions from the database
`crest.set_modern_data()`	Format a `crestObj` with private data.
`crest.calibrate()`	Fit the species and proxy `pdfs`
`crest.reconstruct()`	Reconstruct climate from fossil data
`crest()`	A wrapper for all the crest functions.
`loo()`	Performs the leave-one-out analysis
Plotting Functions for generating plots.
`eqearth_get_ext()`	Calculates the extent of the plot in the equal earth projection.
`explore_calibration_dataset()`	Extract distributions from the database
`isColourStr()`	Test if `R` can interpret a string as a colour
`makeTransparent()`	Wrapper function of to add transparency to a colour.
`plot(<crestObj>)`	Plot the reconstructions.
`plot_climateSpace()`	Plot the studied climate space.
`plot_combinedPDFs()`	Plot representing how the `pdfs` combine to produce the reconstruction.
`plot_diagram()`	Plot stratigraphic data as polygons or barplots.
`plot_loo()`	Plot the results of the leave-one-out analysis.
`plot_map_eqearth()`	Plots raster data in equal earth projection.
`plot_scatterPDFs()`	Plot the pdf optima and uncertainty ranges in a climate biplot
`plot_taxaCharacteristics()`	Plot the distribution and responses of the studied taxa
`plot_violinPDFs()`	Plot the pdfs as violins
CrestObj Manipulation Functions for creating, reading and modifying crestObj objects.
`copy_crest()`	Copy crest data to the clipboard.
`createPSE()`	Creates a spreadsheet with the format required for a PSE.
`crestObj()`	Create a `crestObj` object.
`crest.simplify()`	Simplify a crestObj into a dataframe.
`crop()`	Crop the dataset obtained from `crest.get_modern_data`
`export()`	Export the results
`export_pdfs()`	Export the pdfs fitted for the different taxa.
`excludeTaxa()`	Excludes the list of taxa from the reconstructions.
`getSpeciesdiversity()`	Calculates how many species compose the response of each taxon.
`includeTaxa()`	Includes the list of taxa into the reconstructions.
`is.crestObj()`	Test if x is a crestObj.
`pdf_ranges()`	Calculate the climate tolerance of the taxa from their pdfs.
`PSE_log()`	Displays the log of the proxy-species association
`taxonComposition()`	Return the size of the distribution of each composing species of each taxon
Citing sources Functions for generating the list of references to cite when publishing reconstructions.
`cite_climate_data()`	Returns the references associated with the climate data used to fit the `pdfs`.
`cite_crest()`	Returns the list of references associated to the reconstruction.
`cite_distrib_data()`	Returns the references associated with the GBIF data used to fit the `pdfs`.
`cite_method()`	Returns the references associated with the development of CREST.
Database Functions for querying the calibration data database.
`accBasinNames()`	Return the list of oceans and seas.
`accClimateVariables()`	Describes all the variables available in the database.
`accCountryNames()`	Return the list of the continents and associated countries.
`accRealmNames()`	Return the list of the realms and associated biomes and ecoregions.
`climate_from_xy()`	Extract The climate values associated to a set of coordinates.
`close_db_connection()`	Disconnect the database connection.
`connect_online()`	Connect to the gbif4crest calibration database
`connect_local_sqlite3()`	Connect to the gbif4crest calibration database
`dbDownload()`	Download the gbif4crest_02 dataset from figShare.
`dbRequest()`	Connect to the gbif4crest database
`dbSubset()`	Create a subset of the global calibration dataset
`getClimateSpace()`	Extract the distribution of the studied climate gradient(s) across the study area.
`getDistribTaxa()`	Extract taxonID(s) corresponding to the taxonomic description
`getTaxonID()`	Extract taxonID(s) corresponding to the taxonomic description
`getTaxonomy()`	Extract taxonID(s) corresponding to the taxonomic description
`testConnection()`	Test if a connection can be established with the calibration data
Modelling functions Functions used model the data. Not to be used.
`calib_clim_space()`	Calibrate the distribution of the modern climate space.
`check_coordinates()`	Check if the coordinates are correct.
`colour_theme()`	Returns a vector of colours
`convert2percentages()`	Convert abundance data into percentage data.
`convert2presenceAbsence()`	Convert data into presence/absence data.
`find.original.name()`	Returns the name of the function argument in the global environment
`fit_pdfsp()`	Fit the species `pdfs`.
`fit_xrange()`	Define the climate gradient to fit the `pdfs`.
`get_taxa_type()`	Returns the taxa type corresponding to the index.
`getTaxaTypeFromTaxID()`	Returns the taxa type corresponding to the taxID.
`meanPositiveValues()`	Calculate the mean of all strictly positive values.
`normalise()`	Normalises the percentages
Datasets
`M1`	A shapefile of the world's country borders. Use 'M1 <- terra::unwrap(M1)' to render the object usable in R.
`crest_ex`	Example dataset to run the CREST method for the first time.
`crest_ex_pse`	Example dataset to Extract data from the example database.
`crest_ex_selection`	Example dataset to associate taxa with climate variables.
`reconstr`	A `crestObj` ran with the example dataset.

Reference

Reconstructing

Plotting

CrestObj Manipulation

Citing sources

Database

Modelling functions

Datasets