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_pkgdown.yml
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_pkgdown.yml
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template:
params:
bootswatch: flatly
figures:
dev: ragg::agg_png
dpi: 96
dev.args: []
fig.ext: png
fig.width: 7.2916667
fig.height: ~
fig.retina: 2
fig.asp: 1
bg: NA
navbar:
structure:
left:
- home
- how
- start
- data
- calibration
- reference
- community
- vignettes
right:
- news
- github
components:
home:
icon: fas fa-home fa-lg
href: index.html
how:
text: How it works
href: articles/theory.html
start:
text: Get started
href: articles/get-started.html
data:
text: Prepare your data
href: articles/technicalities.html
calibration:
text: Calibration data
href: articles/calibration-data.html
reference:
text: Reference
href: reference/index.html
community:
text: Community
href: articles/community.html
vignettes:
text: Vignettes
menu:
- text: Using the _gbif4crest_ database
href: articles/databasing-with-crestr.html
- text: Understanding warnings
href: articles/warnings.html
- text: MD96-2048 Reconstruction
href: articles/limpopo.html
news:
text: News
href: news/index.html
github:
icon: fab fa-github fa-lg
href: https://github.com/mchevalier2/crestr/
twitter:
icon: "fab fa-twitter fa-lg"
href: https://twitter.com/ChevalierManu
reference:
- title: "Reconstructing"
desc: "Functions for running the CREST reconstructions."
contents:
- '`crest.get_modern_data`'
- '`crest.set_modern_data`'
- '`crest.calibrate`'
- '`crest.reconstruct`'
- '`crest`'
- '`loo`'
- title: "Plotting"
desc: "Functions for generating plots."
contents:
- '`eqearth_get_ext`'
- '`explore_calibration_dataset`'
- '`isColourStr`'
- '`makeTransparent`'
- '`plot.crestObj`'
- '`plot_climateSpace`'
- '`plot_combinedPDFs`'
- '`plot_diagram`'
- '`plot_loo`'
- '`plot_map_eqearth`'
- '`plot_scatterPDFs`'
- '`plot_taxaCharacteristics`'
- '`plot_violinPDFs`'
- title: "CrestObj Manipulation"
desc: "Functions for creating, reading and modifying crestObj objects."
contents:
- '`copy_crest`'
- '`createPSE`'
- '`crestObj`'
- '`crest.simplify`'
- '`crop`'
- '`export`'
- '`export_pdfs`'
- '`excludeTaxa`'
- '`getSpeciesdiversity`'
- '`includeTaxa`'
- '`is.crestObj`'
- '`pdf_ranges`'
- '`PSE_log`'
- '`taxonComposition`'
- title: "Citing sources"
desc: "Functions for generating the list of references to cite when publishing reconstructions."
contents:
- '`cite_climate_data`'
- '`cite_crest`'
- '`cite_distrib_data`'
- '`cite_method`'
- title: "Database"
desc: "Functions for querying the calibration data database."
contents:
- '`accBasinNames`'
- '`accClimateVariables`'
- '`accCountryNames`'
- '`accRealmNames`'
- '`climate_from_xy`'
- '`close_db_connection`'
- '`connect_online`'
- '`connect_local_sqlite3`'
- '`dbDownload`'
- '`dbRequest`'
- '`dbSubset`'
- '`getClimateSpace`'
- '`getDistribTaxa`'
- '`getTaxonID`'
- '`getTaxonomy`'
- '`testConnection`'
- title: "Modelling functions"
desc: "Functions used model the data. Not to be used."
contents:
- '`calib_clim_space`'
- '`check_coordinates`'
- '`colour_theme`'
- '`convert2percentages`'
- '`convert2presenceAbsence`'
- '`find.original.name`'
- '`fit_pdfsp`'
- '`fit_xrange`'
- '`get_taxa_type`'
- '`getTaxaTypeFromTaxID`'
- '`meanPositiveValues`'
- '`normalise`'
- title: "Datasets"
contents:
- '`M1`'
- '`crest_ex`'
- '`crest_ex_pse`'
- '`crest_ex_selection`'
- '`reconstr`'