Man pages for mchevalier2/crestr
A Probabilistic Approach to Reconstruct Past Climates Using Palaeoecological Datasets
| 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... |
| calib_clim_space | Calibrate the distribution of the modern climate space. |
| check_coordinates | Check if the coordinates are correct. |
| cite_climate_data | Returns the references associated with the climate data used... |
| cite_crest | Returns the list of references associated to the... |
| cite_distrib_data | Returns the references associated with the GBIF data used to... |
| cite_method | Returns the references associated with the development of... |
| climate_from_xy | Extract The climate values associated to a set of... |
| close_db_connection | Disconnect the database connection. |
| colour_theme | Returns a vector of colours |
| connect_local_sqlite3 | Connect to the gbif4crest calibration database |
| connect_online | Connect to the gbif4crest calibration database |
| convert2percentages | Convert abundance data into percentage data. |
| convert2presenceAbsence | Convert data into presence/absence data. |
| copy_crest | Copy crest data to the clipboard. |
| createPSE | Creates a spreadsheet with the format required for a PSE. |
| crest | A wrapper for all the crest functions. |
| crest.calibrate | Fit the species and proxy 'pdfs' |
| 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. |
| crest.get_modern_data | Extract distributions from the database |
| crestObj | Create a 'crestObj' object. |
| crest.reconstruct | Reconstruct climate from fossil data |
| crest.set_modern_data | Format a 'crestObj' with private data. |
| crest.simplify | Simplify a crestObj into a dataframe. |
| crop | Crop the dataset obtained from 'crest.get_modern_data' |
| dbDownload | Download the gbif4crest_02 dataset from figShare. |
| dbRequest | Connect to the gbif4crest database |
| dbSubset | Create a subset of the global calibration dataset |
| dot-ecoid2names | Return biogeographical units associated with a ecoID. |
| dot-geopoid2names | Return geopolitical units associated with a geopoID. |
| eqearth_get_ext | Calculates the extent of the plot in the equal earth... |
| excludeTaxa | Excludes the list of taxa from the reconstructions. |
| explore_calibration_dataset | Extract distributions from the database |
| export | Export the results |
| export_pdfs | Export the pdfs fitted for the different taxa. |
| find.original.name | Returns the name of the function argument in the global... |
| fit_pdfsp | Fit the species 'pdfs'. |
| fit_xrange | Define the climate gradient to fit the 'pdfs'. |
| f_locid | Calculates a unique identifier from coordinates. |
| getBasinNames | Return the list of oceans and seas. |
| getClimateSpace | Extract the distribution of the studied climate gradient(s)... |
| getCountryNames | Return the list of the continents and associated countries. |
| getDistribTaxa | Extract taxonID(s) corresponding to the taxonomic description |
| getRealmNames | Return the list of the realms and associated biomes and... |
| getResol | Calculates a unique identifier from coordinates. |
| getSpeciesdiversity | Calculates how many species compose the response of each... |
| get_taxa_type | Returns the taxa type corresponding to the index. |
| getTaxaTypeFromTaxID | Returns the taxa type corresponding to the taxID. |
| getTaxonID | Extract taxonID(s) corresponding to the taxonomic description |
| getTaxonomy | Extract taxonID(s) corresponding to the taxonomic description |
| identifyDatabase | Identify the calibration database used. |
| includeTaxa | Includes the list of taxa into the reconstructions. |
| isColourStr | Test if 'R' can interpret a string as a colour |
| is.crestObj | Test if x is a crestObj. |
| loo | Performs the leave-one-out analysis |
| M1 | A shapefile of the world's country borders. Use 'M1 <-... |
| makeTransparent | Wrapper function of to add transparency to a colour. |
| meanPositiveValues | Calculate the mean of all strictly positive values. |
| normalise | Normalises the percentages |
| pdf_ranges | Calculate the climate tolerance of the taxa from their pdfs. |
| plot_climateSpace | Plot the studied climate space. |
| plot_combinedPDFs | Plot representing how the 'pdfs' combine to produce the... |
| plot.crestObj | Plot the reconstructions. |
| 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... |
| plot_taxaCharacteristics | Plot the distribution and responses of the studied taxa |
| plot_violinPDFs | Plot the pdfs as violins |
| PSE_log | Displays the log of the proxy-species association |
| reconstr | A 'crestObj' ran with the example dataset. |
| taxonComposition | Return the size of the distribution of each composing species... |
| testConnection | Test if a connection can be established with the calibration... |
