Package: neotoma 1.7.7

Simon J. Goring

neotoma: Access to the Neotoma Paleoecological Database Through R

NOTE: This package is deprecated. Please use the neotoma2 package described at https://github.com/NeotomaDB/neotoma2. Access paleoecological datasets from the Neotoma Paleoecological Database using the published API (<http://wnapi.neotomadb.org/>), only containing datasets uploaded prior to June 2020. The functions in this package access various pre-built API functions and attempt to return the results from Neotoma in a usable format for researchers and the public.

Authors:Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek [ctb], Karthik Ram [aut], Luke Sosalla [ctb]

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neotoma.pdf |neotoma.html✨
neotoma/json (API)
NEWS

# Install 'neotoma' in R:
install.packages('neotoma', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ropensci/neotoma/issues

Pkgdown:https://docs.ropensci.org

Datasets:
  • pollen.equiv - A table to convert the pollen taxa identified by investigators to standardized lists.
  • taxon.list - Neotoma taxon list

On CRAN:

neotomaneotoma-apisneotoma-databasensfpaleoecology

5.04 score 30 stars 145 scripts 142 downloads 1 mentions 23 exports 87 dependencies

Last updated 2 years agofrom:fd935c440b (on master). Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 15 2024
R-4.5-winNOTEDec 15 2024
R-4.5-linuxNOTEDec 15 2024
R-4.4-winNOTEDec 15 2024
R-4.4-macNOTEDec 15 2024
R-4.3-winNOTEDec 15 2024
R-4.3-macNOTEDec 15 2024

Exports:agesbindbrowsecompile_downloadscompile_taxacountsdepthsget_chroncontrolget_closestget_contactget_datasetget_downloadget_geochronget_publicationget_siteget_tableget_taxaparam_checkplot_leafletread_baconread.tiliataxawrite_agefile

Dependencies:analogueaskpassassertthatbase64encbrglmbslibcachemclassclassIntcliclustercolorspacecrosstalkcurlDBIdigestdplyre1071evaluatefansifarverfastmapfontawesomefsgenericsgluehighrhtmltoolshtmlwidgetshttrjquerylibjsonliteKernSmoothknitrlabelinglatticelazyevalleafletleaflet.providerslifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpermutepillarpkgconfigplyrpngprincurveprofileModelproxyR6rappdirsrasterRColorBrewerRcppreshape2rlangrmarkdowns2sassscalessfspstringistringrsysterratibbletidyselecttinytexunitsutf8vctrsveganviridisLitewithrwkxfunxml2yaml

Readme and manuals

Help Manual

Help pageTopics
Access proxy age dataages ages.download ages.download_list
Function to bind objects together into a longer object.bind
Open a browser window to display a Neotoma dataset within the Neotoma Explorerbrowse
Open a browser window to display a Neotoma dataset within the Neotoma Explorerbrowse.dataset
Open a browser window to display a Neotoma dataset within the Neotoma Explorerbrowse.dataset_list
Open a browser window to display a Neotoma dataset within the Neotoma Explorerbrowse.default
Open a browser window to display a Neotoma dataset within the Neotoma Explorerbrowse.download
Open a browser window to display a Neotoma dataset within the Neotoma Explorerbrowse.download_list
Compile download objectscompile_downloads
Function to convert assemblage taxa to standardized lists.compile_taxa
Access proxy count datacounts counts.download counts.download_list
Extracts the depth values from a `download` objectdepths depths.default depths.download depths.download_list
A class for download objects.download
Function to return chronological control tables used to build age models.get_chroncontrol
Function to return chronological control tables from a 'dataset'.get_chroncontrol.dataset
Function to return chronological control tables from a 'dataset_list'.get_chroncontrol.dataset_list
Function to return chronological control tables from a chronologic ID.get_chroncontrol.default
Function to return chronological control tables from a 'download' object.get_chroncontrol.download
Function to return chronological control tables from a 'download_list' object.get_chroncontrol.download_list
Find the closest dataset records to a site, dataset or long/lat pair in Neotomaget_closest
Get contact information.get_contact
Obtain dataset information from the Neotoma Paleoecological Database or an existing object.get_dataset
Obtain dataset information from the Neotoma Paleoecological Database or an existing object.get_dataset.default
Obtain dataset information from an existing 'download' object.get_dataset.download
Obtain dataset information from a 'download_list'.get_dataset.download_list
Obtain dataset information from an object of class 'geochronologic'.get_dataset.geochronologic
Obtain dataset information from an object of class 'geochronologic_list'.get_dataset.geochronologic_list
Obtain dataset information from a vector of dataset IDs.get_dataset.integer
Obtain dataset information from a vector of dataset IDs.get_dataset.numeric
Obtain dataset information from an existing 'site' object.get_dataset.site
Function to return full download records using 'site's, 'dataset's, or dataset IDs.get_download
Function to return full download records using a 'dataset'.get_download.dataset
Function to return full download records using a 'dataset_list'.get_download.dataset_list
Function to return full download records using 'numeric' dataset IDs.get_download.default
Function to return full download records using a 'site'.get_download.site
Function to return geochronological data from records.get_geochron
A function to get publications for sites or datasets in the Neotoma Database using the API.get_publication
A function to get publications for datasets in the Neotoma Database using the API.get_publication.dataset
A function to get publications for dataset_lists in the Neotoma Database using the API.get_publication.dataset_list
A function to get publications for sites or datasets in the Neotoma Database using the API.get_publication.default
A function to get publications for downloads in the Neotoma Database using the API.get_publication.download
A function to get publications for datasets in the Neotoma Database using the API.get_publication.download_list
Return Site Information.get_site
Return Site Information from a numeric list of site ids.get_site.dataset
Return Site Information from a 'dataset_list'get_site.dataset_list
Return Site Information.get_site.default
Return Site Information from a 'download'get_site.download
Return Site Information from a 'download_list'get_site.download_list
Return Site Information from a 'geochronologic'get_site.geochronologic
Return Site Information from a 'geochronologic_list'get_site.geochronologic_list
Return Site Information from a vector of integers.get_site.integer
Return Site information from a vector of numeric elements.get_site.numeric
Get Neotoma value tables.get_table
Get taxon information from Neotoma.get_taxa
A list of all the geopolitical entities in the Neotoma database.gp.table
Leaflet plots for neotoma data.plot_leaflet
A table to convert the pollen taxa identified by investigators to standardized lists.pollen.equiv
Function to read in defined Bacon outputs.read_bacon
Read proxy data from Tilia TLX filesread.tilia
Palaeoecological stratigraphic diagramsStratiplot.download
Palaeoecological stratigraphic diagramsStratiplot.download_list
Access proxy taxonomic datataxa taxa.download taxa.download_list
Neotoma taxon listtaxon.list
Write age control file to disk formatted for either Bacon or Clamwrite_agefile