Working with the Neotoma Paleoecology Database

Documentation for package ‘neotoma2’ version 1.0.4

Help Pages

-- A --

add_chronology	Add a new chronology to a collection unit.
add_chronology-method	Add a new chronology into an existing collectionunit.
as.data.frame-method	Convert a publication author to a 'data.frame'
as.data.frame-method	as.data.frame chronologies
as.data.frame-method	Create a data.frame from a chronology object.
as.data.frame-method	as.data.frame site
as.data.frame-method	as.data.frame collunits
as.data.frame-method	Transform a contacts object to a data.frame()
as.data.frame-method	Transform a contacts object to a data.frame()
as.data.frame-method	as.data.frame dataset
as.data.frame-method	as.data.frame datasets
as.data.frame-method	Convert a 'publication' to a 'data.frame'
as.data.frame-method	Convert publications to a 'data.frame'
as.data.frame-method	as.data.frame site
as.data.frame-method	as.data.frame sites
as.data.frame-method	as.data.frame specimen
as.data.frame-method	as.data.frame specimens
as.list-method	as.list sites
author-class	An S4 class for the authors of a Neotoma publication.
authors-class	An S4 class for a set of Neotoma author objects.

-- B --

build_chron	build_chron
build_collunits	Build a collection unit from the API response
build_dataset	Build a dataset object from a JSON list representation.
build_sample	Build a samples 'data.frame' from Neotoma API JSON
build_sites	Build a 'site' from the Neotoma API response.
build_specimen	Build a specimen objects.

-- C --

c-method	c Method - Combine chronologies objects
c-method	c Method - Combine collunits objects
c-method	c Method - Combine contacts objects
c-method	c Method - Combine contacts objects
c-method	c Method - Combine datasets objects
c-method	c Method for NULL values
c-method	Combine publication objects.
c-method	c Method - Combine sites objects
c-method	c Method - Combine specimens objects
check_args	check_args
check_contacts	Check contact information for a record against Neotoma contributors
check_contacts.contacts	Get contact information for 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 'collunit' object.
chronologies-method	Extract 'chronologies' from a 'collunits' object.
chronologies-method	Extract 'chronologies' from a 'site' object.
chronologies-method	Extract 'chronologies' from a 'sites' object.
chronology-class	S4 class for chronologies information
cite_data	Generate a data citation from a Neotoma2 object.
cite_data-method	Obtain data citations from a single record.
cite_data-method	Obtain data citations from multiple records.
collunit-class	S4 class for collection units information.
collunits	Extract collection units from a sites object
collunits-class	An S4 class for Neotoma Collection Units
collunits-method	Extract 'collunits' from a 'site' object.
collunits-method	Extract 'collunits' from a 'sites' object.
contact-class	An S4 class for Neotoma contacts
contacts-class	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 dataset information
datasets	Extract datasets from a sites object.
datasets-class	S4 class for datasets information
datasets-method	Extract 'datasets' from a 'collunit' object.
datasets-method	Extract 'datasets' from a 'collunits' object.
datasets-method	Extract 'datasets' from a 'site' object.
datasets-method	Extract 'datasets' from a 'sites' object.
doi	Obtain the DOI for publications or datasets.
doi-method	Get a publication DOI.
doi-method	Obtain dataset DOIs from records.
doi-method	Obtain dataset DOIs from records.

-- F --

filter	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 from a single collectionunit.
getids.collunits	Get object IDs from collectionunits.
getids.site	Get object IDs from a site object.
getids.sites	Get object IDs from sites
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 Dataset Default
get_datasets.numeric	Get Dataset Numeric
get_datasets.site	Get Dataset from a 'site' object.
get_datasets.sites	Get Dataset from a 'sites' object.
get_downloads	get_downloads
get_downloads.character	get_downloads JSON
get_downloads.numeric	get_downloads
get_downloads.sites	get_downloads sites
get_manual	get_manual
get_publications	Get publication information for Neotoma records
get_publications.default	Get publication information from Neotoma
get_publications.numeric	Get publications using their unique identifier.
get_publications.publication	Update information for a publications object.
get_publications.publications	Update metadata for a set of publication objects.
get_sites	get_sites
get_sites.default	get_sites
get_sites.numeric	Get Site Information for Fossil Sites
get_sites.sites	Get Site Information for Fossil Sites from a Set of Sites
get_specimens	get_specimens
get_specimens.default	Get Specimen datasetid
get_specimens.numeric	Get Specimen Numeric
get_specimens.sites	Get Specimen Sites
get_stats	get_stats
get_table	Get table record from Neotoma

-- L --

length-method	Length Method chronologies
length-method	Length Method collunits
length-method	Length Method datasets
length-method	Get the number of publications in a publications object.
length-method	Length Method samples
length-method	Length Method Sites
length-method	Length Method specimens

-- M --

missingOrNULL-class

c Method - Combine objects, including NULL

-- N --

names-method	Get slot names
names-method	Get names of contacts slots
names-method	Get slot names
names-method	Get slot names for a publication object.
names-method	Get slot names for a publication object.
names-method	Get slot names
names-method	Get slot names
newURL	Format API call to Neotoma from call arguments

-- P --

parseURL	parseURL
parse_site	parse_site
pingNeotoma	pingNeotoma
plot-method	Plot site coordinates using a basic plot.
plotLeaflet	plotLeaflet
plotLeaflet-method	plotLeaflet
plotLeaflet-method	plotLeaflet
publication-class	An S4 class for a single Neotoma publication.
publications-class	An S4 class for multi-publication information from the Neotoma Paleoecology Database. This S4 class allows a single dataset to have one or more publication classes associated with it.

-- R --

repositories-class	S4 class for repositories information
repository-class	S4 class for repository information

-- S --

sample-class	S4 class for dataset information
samples	Obtain samples from a record or multiple records.
samples-class	S4 class for the set of samples
samples-method	samples
samples-method	Get samples from a collectionunit or set of collection units:
samples-method	samples
samples-method	samples
selectMatch	Select the best match for an object.
selectMatch-method	Select the best match (between a local record and a Neotoma match)
selectMatch-method	Select the best match (between a local record and a Neotoma match)
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_publications	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
show-method	Show the collection unit information
show-method	Show the collection unit information
show-method	Show contact object
show-method	Show a contacts object.
show-method	Show Dataset Method
show-method	Show Datasets object as a dataframe
show-method	Print publications to screen.
show-method	Show the contents of a publication object.
show-method	Show a site object as a dataframe
show-method	Show sites objects as a dataframe
show-method	Show Specimen Method
show-method	Show Specimens object as a dataframe
showMatch	Show matches for objects.
showMatch-method	Show matched publication objects.
site-class	An S4 class for site information
sites-class	An S4 class for multi-site information
specimen-class	S4 class for specimen information
specimens	Obtain specimens from a record or multiple records.
specimens-class	S4 class for specimens information
specimens-method	specimens
specimens-method	specimens
specimens-method	specimens
specimens-method	specimens
summary-method	Summary of objects within a sites object.

-- T --

taxa	taxa
taxa-method	Extract taxonomic data from a set of sites.
taxa-method	Extract taxonomic data from a set of sites.
taxa-method	Extract taxonomic data from a single site.
taxa-method	Extract taxonomic data from a set of sites.
toJSON	toJSON
toJSON-method	toJSON
toWide	toWide

-- W --

write.csv-method	write CSV
write.csv-method	write CSV
write.csv-method	write CSV
write.csv-method	write CSV
write.csv-method	write CSV

-- misc --

$-method	Extract
$-method	Extract
$-method	$
$-method	$ for collunits
$-method	Extract or Replace Parts of an Object
$-method	Extract or Replace Parts of an Object
$-method	$
$-method	$ for datasets
$-method	Extract an element from a 'publication'
$-method	$
$-method	$ for samples
$-method	$
$-method	$ for sites
$-method	$
$-method	$ for specimens
$<--method	Replace part of an object
$<--method	Assign collunit field by numeric index
$<--method	Assign dataset field by numeric index
$<--method	Assign site field by numeric index
$<--method	Assign specimen field by numeric index
[-method	Get or remove sites by numeric index
[-method	Get or remove datasets by numeric index
[-method	Get site field by character index
[-method	Get site field by numeric index
[-method	Get or remove sites by numeric index
[-method	Get or remove specimens by numeric index
[<--method	Assign collunit field by numeric index
[<--method	Assign collunit field by numeric index
[<--method	Assign dataset field by numeric index
[<--method	Assign dataset field by numeric index
[<--method	Assign site field by numeric index
[<--method	Assign site field by numeric index
[<--method	Assign specimen field by numeric index
[<--method	Assign specimen field by numeric index
[[-method	Extract
[[-method	Slicer
[[-method	Extract or Replace Parts of an Object
[[-method	Slicer
[[-method	Obtain one of the elements within a publication list.
[[-method	Slicer
[[-method	Slicer
[[-method	Slicer
[[<--method	Insert collunit
[[<--method	Insert dataset
[[<--method	Assign value to an element in a publication list.
[[<--method	Insert site
[[<--method	Insert specimen