R: Working with the Neotoma Paleoecology Database

# Working with the Neotoma Paleoecology Database

## Documentation for package ‘neotoma2’ version 1.0.12

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

## Help Pages

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

## -- 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