# Working with the Neotoma Paleoecology Database

## Documentation for package ‘neotoma2’ version 1.0.6

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D F G L M N P R S T W misc

## -- 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.data.frame-method | as.data.frame taxa
as.data.frame-method | as.data.frame taxon
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
c-method | c Method - Combine taxa 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
get_taxa | get_taxa
get_taxa.default | Get Taxa Default
get_taxon | get_taxon
get_taxon.default | Get Taxa Default
get_taxon.numeric | Get Taxa Numeric

## -- 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
length-method | Length Method taxa

## -- 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
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
show-method | Show Taxa Method
show-method | Show Taxon Method
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-class | S4 class for taxa information
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.
taxon-class | S4 class for specimen information
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
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 | $ for taxa
$-method | $
$<--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 | Assign taxon 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 | Get or remove taxa 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 | Assign taxon field by numeric index
[<--method | Assign taxon 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 | Slicer
[[<--method | Insert collunit
[[<--method | Insert dataset
[[<--method | Assign value to an element in a publication list.
[[<--method | Insert site
[[<--method | Insert specimen
[[<--method | Insert taxon