Working with the Neotoma Paleoecology Database

Documentation for package ‘neotoma2’ version 1.0.10

Help Pages

-- A --

add_chronology	Add a new chronology into an existing collectionunit.
add_chronology-method	Add a new chronology into an existing collectionunit.
as.data.frame	as.data.frame
as.data.frame-method	as.data.frame
author-class	An S4 class for the authors of a Neotoma publication.
authors-class	An S4 class for the authors of a Neotoma publication.
author_classes	An S4 class for the authors of a Neotoma publication.

-- C --

c	c - Combine 'neotoma2' objects
c-method	c - Combine 'neotoma2' objects
cash	cash
cash-method	cash
cash-set	cash-set
cash-set-method	cash-set
check_contacts	Check contact information for a record against Neotoma contributors
check_contacts.contacts	Check contact information for a record against Neotoma contributors
chroncontrols	chroncontrols
chroncontrols-method	Recover information about the chron controls for a collectionunit.
chroncontrols-method	Recover information about the chron controls for a collectionunit.
chronologies	Obtain the chronology from a record or multiple records.
chronologies-class	S4 class for 'chronologies' information
chronologies-method	Extract 'chronologies' from a 'site's or 'collunits' object.
chronologies-method	Obtain the chronology from a record or multiple records.
chronologies_classes	S4 class for 'chronologies' information
chronology-class	S4 class for 'chronologies' information
cite_data	Generate a data citation from a Neotoma2 object.
cite_data-method	Obtain data citations from multiple records.
cite_data-method	Generate a data citation from a Neotoma2 object.
clean	clean Neotoma objects to remove duplicates and empty objects.
clean.collunits	clean Neotoma objects to remove duplicates and empty objects.
clean.datasets	clean Neotoma objects to remove duplicates and empty objects.
clean.sites	clean Neotoma objects to remove duplicates and empty objects.
collunit-class	S4 class for collection units information.
collunits	Extract collection units from a sites object
collunits-class	S4 class for collection units information.
collunits-method	Extract 'collunits' from a 'sites' object.
collunits-method	Extract collection units from a sites object
collunits_classes	S4 class for collection units information.
contact-class	An S4 class for multi-contact information from the Neotoma Paleoecology Database.
contacts-class	An S4 class for multi-contact information from the Neotoma Paleoecology Database.
contacts_classes	An S4 class for multi-contact information from the Neotoma Paleoecology Database.
coordinates	Obtain coordinates from a sites object.
coordinates-method	Return the latitude and longitude of sites

-- D --

dataset-class	S4 class for 'datasets' information
datasets	Extract datasets from a sites object.
datasets-class	S4 class for 'datasets' information
datasets-method	Extract 'datasets' from a 'sites' or 'collunits' object.
datasets-method	Extract datasets from a sites object.
doi	Obtain the DOI for publications or datasets.
doi-method	Obtain dataset DOIs from records.
doi-method	Obtain the DOI for publications or datasets.

-- F --

filter	Apply a 'filter' for Neotoma sites objects.
filter.data.frame	Apply a 'filter' for Neotoma sites objects.
filter.NULL	Apply a 'filter' for Neotoma sites objects.
filter.sites	Apply a 'filter' for Neotoma sites objects.

-- G --

getids	Get object IDs
getids.collunit	Get object IDs
getids.collunits	Get object IDs
getids.site	Get object IDs
getids.sites	Get object IDs
get_contacts	Get 'contact' information for Neotoma contributors
get_contacts.default	Get 'contact' information for Neotoma contributors
get_contacts.numeric	Get 'contact' information for Neotoma contributors
get_datasets	get_datasets
get_datasets.default	get_datasets
get_datasets.NULL	get_datasets
get_datasets.numeric	get_datasets
get_datasets.site	get_datasets
get_datasets.sites	get_datasets
get_documentation	get_documentation
get_downloads	get_downloads
get_downloads.NULL	get_downloads
get_downloads.numeric	get_downloads
get_downloads.sites	get_downloads
get_manual	get_manual
get_publications	Get publication information for Neotoma records
get_publications.default	Get publication information for Neotoma records
get_publications.numeric	Get publication information for Neotoma records
get_publications.publication	Get publication information for Neotoma records
get_publications.publications	Get publication information for Neotoma records
get_publications.sites	Get publication information for Neotoma records
get_sites	get_sites
get_sites.default	get_sites
get_sites.NULL	get_sites
get_sites.numeric	get_sites
get_speleothems	get_speleothems
get_speleothems.numeric	get_speleothems
get_speleothems.sites	get_speleothems
get_stats	get_stats
get_table	Get table record from Neotoma
get_taxa	get_taxa
get_taxa.default	get_taxa
get_taxa.numeric	get_taxa
get_taxon	get_taxon
get_taxon.default	get_taxon
get_taxon.numeric	get_taxon

-- L --

length	length
length-method	length

-- M --

missingOrNULL-class

c Method - Combine objects, including NULL

-- N --

names	Get a 'neotoma2' object's slot names
names-method	Get a 'neotoma2' object's slot names

-- P --

pingNeotoma	pingNeotoma
plot	Plot site coordinates using a basic plot.
plot-method	Plot site coordinates using a basic plot.
plotLeaflet	plotLeaflet
plotLeaflet-method	plotLeaflet
plotLeaflet-method	plotLeaflet
publication-class	An S4 class for Neotoma 'publications'.
publications-class	An S4 class for Neotoma 'publications'.
publications_classes	An S4 class for Neotoma 'publications'.

-- R --

repositories-class	S4 class for 'repository' information
repositories_classes	S4 class for 'repository' information
repository-class	S4 class for 'repository' information

-- S --

sample-class	S4 class for 'samples' information
samples	Obtain samples from a record or multiple records.
samples-class	S4 class for 'samples' information
samples-method	samples
samples-method	Obtain samples from a record or multiple records.
samples_classes	S4 class for 'samples' information
set_chronology	set chronology information for a new record.
set_collunit	set Site Information for Fossil Sites
set_contact	Set contact information for a new record.
set_dataset	set Site Information for Fossil Sites
set_default	Set the default chronology within a collectionunit.
set_default-method	Change the default age model for a record.
set_publication	Create a new publication (or publication set)
set_sample	set Sample Information
set_server	Set Neotoma API Source or Server
set_site	set Site Information for Fossil Sites
set_speleothem	Set Speleothem
show	Display a 'sites' object or nested slots.
show-method	Display a 'sites' object or nested slots.
site-class	An S4 class for 'sites' information
sites-class	An S4 class for 'sites' information
sites_classes	An S4 class for 'sites' information
specimen-class	S4 class for 'specimens' information
specimens-class	S4 class for 'specimens' information
specimens_classes	S4 class for 'specimens' information
speleothem-class	S4 class for 'speleothem' information
speleothemdetails	Obtain speleothems and samples from a record or multiple records.
speleothemdetails-method	speleothemdetails
speleothemdetails-method	Obtain speleothems and samples from a record or multiple records.
speleothems	Obtain speleothems from a record or multiple records.
speleothems-class	S4 class for 'speleothem' information
speleothems-method	speleothems
speleothems-method	Obtain speleothems from a record or multiple records.
speleothems_classes	S4 class for 'speleothem' information
sub-method	sub
sub-sub	sub-sub
sub-sub-method	sub-sub
sub-subset	sub-subset
sub-subset-method	sub-subset
subset	subset
subset-method	subset
summary-method	Summary of objects within a sites object.

-- T --

taxa	taxa
taxa-class	S4 class for taxa information
taxa-method	Extract taxonomic data from a set of sites.
taxa-method	taxa
taxa_classes	S4 class for taxa information
taxon-class	S4 class for taxa information
toWide	toWide

-- misc --

$-method	cash
$<--method	cash-set
[	sub
[-method	sub
[<--method	subset
[[-method	sub-sub
[[<--method	sub-subset