$,chronologies-method   Extract
$,chronology-method     Extract
$,collunit-method       $
$,collunits-method      $ for collunits
$,contact-method        Extract or Replace Parts of an Object
$,contacts-method       Extract or Replace Parts of an Object
$,dataset-method        $
$,datasets-method       $ for datasets
$,publication-method    Extract an element from a 'publication'
$,sample-method         $
$,samples-method        $ for samples
$,site-method           $
$,sites-method          $ for sites
$,specimen-method       $
$,specimens-method      $ for specimens
$<-,chronology-method   Replace part of an object
$<-,collunit-method     Assign collunit field by numeric index
$<-,dataset-method      Assign dataset field by numeric index
$<-,site-method         Assign site field by numeric index
$<-,specimen-method     Assign specimen field by numeric index
[,collunits,numeric,ANY-method
                        Get or remove sites by numeric index
[,datasets,numeric,ANY-method
                        Get or remove datasets by numeric index
[,site,character,ANY-method
                        Get site field by character index
[,site,numeric,ANY-method
                        Get site field by numeric index
[,sites,numeric,ANY-method
                        Get or remove sites by numeric index
[,specimens,numeric,ANY-method
                        Get or remove specimens by numeric index
[<-,collunit,character,ANY,ANY-method
                        Assign collunit field by numeric index
[<-,collunit,numeric,ANY,ANY-method
                        Assign collunit field by numeric index
[<-,dataset,character,ANY,ANY-method
                        Assign dataset field by numeric index
[<-,dataset,numeric,ANY,ANY-method
                        Assign dataset field by numeric index
[<-,site,character,ANY,ANY-method
                        Assign site field by numeric index
[<-,site,numeric,ANY,ANY-method
                        Assign site field by numeric index
[<-,specimen,character,ANY,ANY-method
                        Assign specimen field by numeric index
[<-,specimen,numeric,ANY,ANY-method
                        Assign specimen field by numeric index
[[,chronologies,numeric,ANY-method
                        Extract
[[,collunits,numeric,ANY-method
                        Slicer
[[,contacts,numeric,ANY-method
                        Extract or Replace Parts of an Object
[[,datasets,numeric,ANY-method
                        Slicer
[[,publications,numeric,ANY-method
                        Obtain one of the elements within a publication
                        list.
[[,samples,numeric,ANY-method
                        Slicer
[[,sites,numeric,ANY-method
                        Slicer
[[,specimens,numeric,ANY-method
                        Slicer
[[<-,collunits,ANY,ANY,ANY-method
                        Insert collunit
[[<-,datasets,ANY,ANY,ANY-method
                        Insert dataset
[[<-,publications,ANY,ANY,ANY-method
                        Assign value to an element in a publication
                        list.
[[<-,sites,ANY,ANY,ANY-method
                        Insert site
[[<-,specimens,ANY,ANY,ANY-method
                        Insert specimen
add_chronology          Add a new chronology to a collection unit.
add_chronology,collunit,chronology,data.frame-method
                        Add a new chronology into an existing
                        collectionunit.
as.data.frame,authors-method
                        Convert a publication author to a 'data.frame'
as.data.frame,chronologies-method
                        as.data.frame chronologies
as.data.frame,chronology-method
                        Create a data.frame from a chronology object.
as.data.frame,collunit-method
                        as.data.frame site
as.data.frame,collunits-method
                        as.data.frame collunits
as.data.frame,contact-method
                        Transform a contacts object to a data.frame()
as.data.frame,contacts-method
                        Transform a contacts object to a data.frame()
as.data.frame,dataset-method
                        as.data.frame dataset
as.data.frame,datasets-method
                        as.data.frame datasets
as.data.frame,publication-method
                        Convert a 'publication' to a 'data.frame'
as.data.frame,publications-method
                        Convert publications to a 'data.frame'
as.data.frame,site-method
                        as.data.frame site
as.data.frame,sites-method
                        as.data.frame sites
as.data.frame,specimen-method
                        as.data.frame specimen
as.data.frame,specimens-method
                        as.data.frame specimens
as.list,sites-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.
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,chronologies-method   c Method - Combine chronologies objects
c,collunits-method      c Method - Combine collunits objects
c,contact-method        c Method - Combine contacts objects
c,contacts-method       c Method - Combine contacts objects
c,datasets-method       c Method - Combine datasets objects
c,missingOrNULL-method
                        c Method for NULL values
c,publications-method   Combine publication objects.
c,sites-method          c Method - Combine sites objects
c,specimens-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,site-method
                        Recover information about the chron controls
                        for a collectionunit.
chroncontrols,sites-method
                        Recover information about the chron controls
                        for a collectionunit.
chronologies            Obtain the chronology from a record or multiple
                        records.
chronologies,collunit-method
                        Extract 'chronologies' from a 'collunit'
                        object.
chronologies,collunits-method
                        Extract 'chronologies' from a 'collunits'
                        object.
chronologies,site-method
                        Extract 'chronologies' from a 'site' object.
chronologies,sites-method
                        Extract 'chronologies' from a 'sites' object.
chronologies-class      S4 class for chronologies information
chronology-class        S4 class for chronologies information
cite_data               Generate a data citation from a Neotoma2
                        object.
cite_data,site-method   Obtain data citations from a single record.
cite_data,sites-method
                        Obtain data citations from multiple records.
clean                   clean Neotoma objects to remove duplicates and
                        empty objects.
clean.collunits         clean sites objects to remove duplicates.
clean.datasets          clean sites objects to remove duplicates.
clean.sites             clean sites objects to remove duplicates.
cleanNULL               Clean NULL values
collunit-class          S4 class for collection units information.
collunits               Extract collection units from a sites object
collunits,site-method   Extract 'collunits' from a 'site' object.
collunits,sites-method
                        Extract 'collunits' from a 'sites' object.
collunits-class         An S4 class for Neotoma Collection Units
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,sites-method
                        Return the latitude and longitude of sites
dataset-class           S4 class for dataset information
datasets                Extract datasets from a sites object.
datasets,collunit-method
                        Extract 'datasets' from a 'collunit' object.
datasets,collunits-method
                        Extract 'datasets' from a 'collunits' object.
datasets,site-method    Extract 'datasets' from a 'site' object.
datasets,sites-method   Extract 'datasets' from a 'sites' object.
datasets-class          S4 class for datasets information
doi                     Obtain the DOI for publications or datasets.
doi,publication-method
                        Get a publication DOI.
doi,site-method         Obtain dataset DOIs from records.
doi,sites-method        Obtain dataset DOIs from records.
filter                  Apply a filter for Neotoma sites objects.
filter.sites            Apply a filter for Neotoma sites objects.
fix_null                Fix null values from API responses
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.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_table               Get table record from Neotoma
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
length,chronologies-method
                        Length Method chronologies
length,collunits-method
                        Length Method collunits
length,datasets-method
                        Length Method datasets
length,publications-method
                        Get the number of publications in a
                        publications object.
length,samples-method   Length Method samples
length,sites-method     Length Method Sites
length,specimens-method
                        Length Method specimens
missingOrNULL-class     c Method - Combine objects, including NULL
names,collunit-method   Get slot names
names,contact-method    Get names of contacts slots
names,dataset-method    Get slot names
names,publication-method
                        Get slot names for a publication object.
names,publications-method
                        Get slot names for a publication object.
names,site-method       Get slot names
names,specimen-method   Get slot names
newURL                  Format API call to Neotoma from call arguments
parseURL                parseURL
parse_location          parse_location
parse_site              parse_site
parsebody               parse_body
pingNeotoma             pingNeotoma
plot,sites,ANY-method   Plot site coordinates using a basic plot.
plotLeaflet             plotLeaflet
plotLeaflet,site-method
                        plotLeaflet
plotLeaflet,sites-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.
repositories-class      S4 class for repositories information
repository-class        S4 class for repository information
sample-class            S4 class for dataset information
samples                 Obtain samples from a record or multiple
                        records.
samples,collunit-method
                        samples
samples,collunits-method
                        Get samples from a collectionunit or set of
                        collection units:
samples,site-method     samples
samples,sites-method    samples
samples-class           S4 class for the set of samples
selectMatch             Select the best match for an object.
selectMatch,publication,logical-method
                        Select the best match (between a local record
                        and a Neotoma match)
selectMatch,publication,numeric-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,chronologies-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,collunit-method    Show the collection unit information
show,collunits-method   Show the collection unit information
show,contact-method     Show contact object
show,contacts-method    Show a contacts object.
show,dataset-method     Show Dataset Method
show,datasets-method    Show Datasets object as a dataframe
show,publication-method
                        Print publications to screen.
show,publications-method
                        Show the contents of a publication object.
show,site-method        Show a site object as a dataframe
show,sites-method       Show sites objects as a dataframe
show,specimen-method    Show Specimen Method
show,specimens-method   Show Specimens object as a dataframe
showMatch               Show matches for objects.
showMatch,publication-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,collunit-method
                        specimens
specimens,collunits-method
                        specimens
specimens,site-method   specimens
specimens,sites-method
                        specimens
specimens-class         S4 class for specimens information
summary,sites-method    Summary of objects within a sites object.
taxa                    taxa
taxa,collunit-method    Extract taxonomic data from a set of sites.
taxa,collunits-method   Extract taxonomic data from a set of sites.
taxa,site-method        Extract taxonomic data from a single site.
taxa,sites-method       Extract taxonomic data from a set of sites.
testNull                Clear NULL values and replace with value
                        predefined value.
toJSON                  toJSON
toJSON,sites-method     toJSON
toWide                  toWide
use_na                  Change NA values from logic to a prescribed
                        type.
write.csv,chronologies-method
                        write CSV
write.csv,collunits-method
                        write CSV
write.csv,datasets-method
                        write CSV
write.csv,sites-method
                        write CSV
write.csv,specimens-method
                        write CSV
