$,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
$,taxa-method           $ for taxa
$,taxon-method          $
$<-,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
$<-,taxon-method        Assign taxon field by numeric index
[,collunits,numeric-method
                        Get or remove sites by numeric index
[,datasets,numeric-method
                        Get or remove datasets by numeric index
[,site,character-method
                        Get site field by character index
[,site,numeric-method   Get site field by numeric index
[,sites,numeric-method
                        Get or remove sites by numeric index
[,taxa,numeric-method   Get or remove taxa 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
[<-,sample,character,ANY,ANY-method
                        Assign sample 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
[<-,taxon,character,ANY,ANY-method
                        Assign taxon field by numeric index
[<-,taxon,numeric,ANY,ANY-method
                        Assign taxon field by numeric index
[[,chronologies,numeric-method
                        Extract
[[,collunits,numeric-method
                        Slicer
[[,contacts,numeric-method
                        Extract or Replace Parts of an Object
[[,datasets,numeric-method
                        Slicer
[[,publications,numeric-method
                        Obtain one of the elements within a publication
                        list.
[[,samples,numeric-method
                        Slicer
[[,sites,numeric-method
                        Slicer
[[,taxa,numeric-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.
[[<-,samples,ANY,ANY,ANY-method
                        Insert sample
[[<-,sites,ANY,ANY,ANY-method
                        Insert site
[[<-,taxa,ANY,ANY,ANY-method
                        Insert taxon
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,taxa-method
                        as.data.frame taxa
as.data.frame,taxon-method
                        as.data.frame taxon
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_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,samples-method        c Method - Combine datasets objects
c,sites-method          c Method - Combine sites objects
c,taxa-method           c Method - Combine taxa objects
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.
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.
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.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_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
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,taxa-method      Length Method taxa
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,taxon-method      Get slot names
pingNeotoma             pingNeotoma
plot,sites-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,taxa-method        Show Taxa Method
show,taxon-method       Show Taxon Method
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-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.
taxa-class              S4 class for taxa information
taxon-class             S4 class for specimen information
toWide                  toWide
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,taxa-method   write CSV
