## 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.

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.

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

dbRequest()

Connect to the gbif4crest database

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

## 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.

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.