Package: neotoma2 1.0.11

Dominguez Vidana Socorro

neotoma2: Working with the Neotoma Paleoecology Database

Access and manipulation of data using the Neotoma Paleoecology Database. <https://api.neotomadb.org/api-docs/>. Examples in functions that require API access are not executed during CRAN checks. Vignettes do not execute as to avoid API calls during CRAN checks.

Authors:Dominguez Vidana Socorro [aut, cre], Simon Goring [aut]

neotoma2_1.0.11.tar.gz
neotoma2_1.0.11.zip(r-4.7)neotoma2_1.0.11.zip(r-4.6)neotoma2_1.0.11.zip(r-4.5)
neotoma2_1.0.11.tgz(r-4.6-any)neotoma2_1.0.11.tgz(r-4.5-any)
neotoma2_1.0.11.tar.gz(r-4.6-any)
neotoma2_1.0.11.tgz(r-4.5-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
neotoma2/json (API)

# Install 'neotoma2' in R:

install.packages('neotoma2', repos = c('https://neotomadb.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/neotomadb/neotoma2/issues

On CRAN:

earthcube neotoma nsf paleoecology

7.45 score 9 stars 90 scripts 365 downloads 46 exports 84 dependencies

Last updated from:b1e0e3fd74. Checks:8 OK, 1 NOTE. Indexed: yes.

The latest version of this package failed to build. Look at thebuild logs for more information.

Target	Result	Time
linux-devel-x86_64	OK	178
source / vignettes	OK	233
linux-release-x86_64	OK	177
macos-release-arm64	OK	179
macos-oldrel-arm64	OK	208
windows-devel	NOTE	126
windows-release	OK	113
windows-oldrel	OK	121
wasm-release	OK	153

Exports:%>%add_chronology as.data.frame check_contacts chroncontrols chronologies cite_data clean collunits coordinates datasets doi filter get_contacts get_datasets get_documentation get_downloads get_manual get_publications get_sites get_speleothems get_stats get_table get_taxa get_taxon getids getids.sites pingNeotoma plot plotLeaflet samples set_chronology set_collunit set_contact set_dataset set_default set_publication set_sample set_server set_site set_speleothem speleothemdetails speleothems summary taxa toWide

Dependencies:askpass assertthat base64enc bslib cachem class classInt cli cpp11 crayon crosstalk curl DBI digest dplyr e1071 evaluate farver fastmap fontawesome fs generics geojsonsf geometries glue highr hms htmltools htmlwidgets httr jquerylib jsonify jsonlite KernSmooth knitr labeling lattice lazyeval leaflet leaflet.providers lifecycle magrittr MASS memoise mime openssl pillar pkgconfig png prettyunits progress proxy purrr R6 rapidjsonr rappdirs raster RColorBrewer Rcpp rlang rmarkdown s2 sass scales sf sfheaders sp stringi stringr sys terra tibble tidyr tidyselect tinytex units utf8 uuid vctrs viridisLite withr wk xfun yaml

The neotoma2 R Package

Rendered fromneotoma2-package.Rmdusingknitr::rmarkdown

Last update: 2025-12-14
Started: 2020-06-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
sub	sub,collunits-method sub,datasets-method sub,speleothems-method sub,taxa-method [ [,collunits,numeric-method [,datasets,numeric-method [,site,character-method [,site,numeric-method [,sites,numeric-method [,speleothems,numeric-method [,taxa,numeric-method
sub-sub	sub-sub sub-sub,collunits-method sub-sub,contacts-method sub-sub,datasets-method sub-sub,publications-method sub-sub,samples-method sub-sub,speleothems-method sub-sub,taxa-method [[,chronologies,numeric-method [[,collunits,numeric-method [[,contacts,numeric-method [[,datasets,numeric-method [[,publications,numeric-method [[,samples,numeric-method [[,sites,numeric-method [[,speleothems,numeric-method [[,taxa,numeric-method
sub-subset	sub-subset sub-subset,collunits-method sub-subset,datasets-method sub-subset,publications-method sub-subset,samples-method sub-subset,speleothems-method sub-subset,taxa-method [[<-,collunits-method [[<-,datasets-method [[<-,publications-method [[<-,samples-method [[<-,sites-method [[<-,speleothems-method [[<-,taxa-method
subset	subset subset,collunit-method subset,dataset-method subset,sample-method subset,speleothem-method subset,taxon-method [<-,collunit,character-method [<-,collunit,numeric-method [<-,dataset,character-method [<-,dataset,numeric-method [<-,sample,character-method [<-,site,character-method [<-,site,numeric-method [<-,speleothem,character-method [<-,speleothem,numeric-method [<-,taxon,character-method [<-,taxon,numeric-method
cash	$,chronologies-method $,chronology-method $,collunit-method $,collunits-method $,contact-method $,contacts-method $,dataset-method $,datasets-method $,publication-method $,sample-method $,samples-method $,site-method $,sites-method $,speleothem-method $,speleothems-method $,taxa-method $,taxon-method cash cash,collunit-method cash,collunits-method cash,contact-method cash,contacts-method cash,dataset-method cash,datasets-method cash,publication-method cash,sample-method cash,samples-method cash,speleothem-method cash,speleothems-method cash,taxa-method cash,taxon-method
cash-set	$<-,chronology-method $<-,collunit-method $<-,dataset-method $<-,site-method $<-,speleothem-method $<-,taxon-method cash-set cash-set,collunit-method cash-set,dataset-method cash-set,speleothem-method cash-set,taxon-method
Add a new chronology into an existing collectionunit.	add_chronology add_chronology,collunit,chronology,data.frame-method add_chronology,collunit-method
as.data.frame	as.data.frame as.data.frame,authors-method as.data.frame,chronologies-method as.data.frame,chronology-method as.data.frame,collunit-method as.data.frame,collunits-method as.data.frame,contact-method as.data.frame,contacts-method as.data.frame,dataset-method as.data.frame,datasets-method as.data.frame,publication-method as.data.frame,publications-method as.data.frame,site-method as.data.frame,sites-method as.data.frame,speleothem-method as.data.frame,speleothems-method as.data.frame,taxa-method as.data.frame,taxon-method
An S4 class for the authors of a Neotoma publication.	author-class authors-class author_classes
c - Combine 'neotoma2' objects	c c,chronologies-method c,collunits-method c,contact-method c,contacts-method c,datasets-method c,missingOrNULL-method c,publications-method c,samples-method c,sites-method c,speleothems-method c,taxa-method
Check contact information for a record against Neotoma contributors	check_contacts check_contacts.contacts
chroncontrols	chroncontrols
Recover information about the chron controls for a collectionunit.	chroncontrols,site-method
Recover information about the chron controls for a collectionunit.	chroncontrols,sites-method
Obtain the chronology from a record or multiple records.	chronologies chronologies,collunits-method chronologies,site-method chronologies,sites-method
S4 class for 'chronologies' information	chronologies-class chronologies_classes chronology-class
Extract 'chronologies' from a 'site's or 'collunits' object.	chronologies,collunit-method
Generate a data citation from a Neotoma2 object.	cite_data cite_data,NULL-method cite_data,site-method
Obtain data citations from multiple records.	cite_data,sites-method
clean Neotoma objects to remove duplicates and empty objects.	clean clean.collunits clean.datasets clean.sites
Extract collection units from a sites object	collunits collunits,site-method
S4 class for collection units information.	collunit-class collunits-class collunits_classes
Extract 'collunits' from a 'sites' object.	collunits,sites-method
An S4 class for multi-contact information from the Neotoma Paleoecology Database.	contact-class contacts-class contacts_classes
Obtain coordinates from a sites object.	coordinates
Return the latitude and longitude of sites	coordinates,sites-method
S4 class for 'datasets' information	dataset-class datasets-class
Extract datasets from a sites object.	datasets datasets,collunit-method datasets,site-method datasets,sites-method
Extract 'datasets' from a 'sites' or 'collunits' object.	datasets,collunits-method
Obtain the DOI for publications or datasets.	doi doi,publication-method doi,site-method
Obtain dataset DOIs from records.	doi,sites-method
Apply a 'filter' for Neotoma sites objects.	filter filter.data.frame filter.NULL filter.sites
Get 'contact' information for Neotoma contributors	get_contacts get_contacts.default get_contacts.numeric
get_datasets	get_datasets get_datasets.default get_datasets.NULL get_datasets.numeric get_datasets.site get_datasets.sites
get_documentation	get_documentation
get_downloads	get_downloads get_downloads.NULL get_downloads.numeric get_downloads.sites
get_manual	get_manual
Get publication information for Neotoma records	get_publications get_publications.default get_publications.numeric get_publications.publication get_publications.publications get_publications.sites
get_sites	get_sites get_sites.default get_sites.NULL get_sites.numeric
get_speleothems	get_speleothems get_speleothems.numeric get_speleothems.sites
get_stats	get_stats
Get table record from Neotoma	get_table
get_taxa	get_taxa get_taxa.default get_taxa.numeric
get_taxon	get_taxon get_taxon.default get_taxon.numeric
Get object IDs	getids getids.collunit getids.collunits getids.site getids.sites
length	length length,chronologies-method length,collunits-method length,contacts-method length,datasets-method length,publications-method length,samples-method length,sites-method length,speleothems-method length,taxa-method
c Method - Combine objects, including NULL	missingOrNULL-class
Get a 'neotoma2' object's slot names	names names,collunit-method names,contact-method names,dataset-method names,publication-method names,publications-method names,site-method names,sites-method names,speleothem-method names,taxon-method
pingNeotoma	pingNeotoma
Plot site coordinates using a basic plot.	plot plot,site-method plot,sites-method
plotLeaflet	plotLeaflet plotLeaflet,ANY-method plotLeaflet,site-method
plotLeaflet	plotLeaflet,sites-method
An S4 class for Neotoma 'publications'.	publication-class publications-class publications_classes
S4 class for 'repository' information	repositories-class repositories_classes repository-class
Obtain samples from a record or multiple records.	samples samples,collunit-method samples,collunits-method samples,site-method
S4 class for 'samples' information	sample-class samples-class samples_classes
samples	samples,sites-method
set chronology information for a new record.	set_chronology
set Site Information for Fossil Sites	set_collunit
Set contact information for a new record.	set_contact
set Site Information for Fossil Sites	set_dataset
Set the default chronology within a collectionunit.	set_default
Change the default age model for a record.	set_default,chronologies-method
Create a new publication (or publication set)	set_publication
set Sample Information	set_sample
Set Neotoma API Source or Server	set_server
set Site Information for Fossil Sites	set_site
Set Speleothem	set_speleothem
Display a 'sites' object or nested slots.	show show,collunit-method show,collunits-method show,contact-method show,contacts-method show,dataset-method show,datasets-method show,publication-method show,publications-method show,site-method show,sites-method show,speleothem-method show,speleothems-method show,taxa-method show,taxon-method
An S4 class for 'sites' information	site-class sites-class sites_classes
S4 class for 'specimens' information	specimen-class specimens-class specimens_classes
Obtain speleothems and samples from a record or multiple records.	speleothemdetails speleothemdetails,collunit-method speleothemdetails,collunits-method speleothemdetails,site-method
speleothemdetails	speleothemdetails,sites-method
Obtain speleothems from a record or multiple records.	speleothems speleothems,collunit-method speleothems,collunits-method speleothems,site-method
S4 class for 'speleothem' information	speleothem-class speleothems-class speleothems_classes
speleothems	speleothems,sites-method
Summary of objects within a sites object.	summary,sites-method
taxa	taxa taxa,collunit-method taxa,collunits-method taxa,site-method
S4 class for taxa information	taxa-class taxa_classes taxon-class
Extract taxonomic data from a set of sites.	taxa,sites-method
toWide	toWide