| Get or remove sites by numeric index | [,collunits,numeric-method |
| Get or remove sites by numeric index | [,collunits,numeric,ANY-method |
| Get or remove datasets by numeric index | [,datasets,numeric-method |
| Get or remove datasets by numeric index | [,datasets,numeric,ANY-method |
| Get site field by character index | [,site,character-method |
| Get site field by character index | [,site,character,ANY-method |
| Get site field by numeric index | [,site,numeric-method |
| Get site field by numeric index | [,site,numeric,ANY-method |
| Get or remove sites by numeric index | [,sites,numeric-method |
| Get or remove sites by numeric index | [,sites,numeric,ANY-method |
| Get or remove specimens by numeric index | [,specimens,numeric-method |
| Get or remove specimens by numeric index | [,specimens,numeric,ANY-method |
| Extract | [[,chronologies,numeric-method |
| Extract | [[,chronologies,numeric,ANY-method |
| Slicer | [[,collunits,numeric-method |
| Slicer | [[,collunits,numeric,ANY-method |
| Extract or Replace Parts of an Object | [[,contacts,numeric-method |
| Extract or Replace Parts of an Object | [[,contacts,numeric,ANY-method |
| Slicer | [[,datasets,numeric-method |
| Slicer | [[,datasets,numeric,ANY-method |
| Obtain one of the elements within a publication list. | [[,publications,numeric-method |
| Obtain one of the elements within a publication list. | [[,publications,numeric,ANY-method |
| Slicer | [[,samples,numeric-method |
| Slicer | [[,samples,numeric,ANY-method |
| Slicer | [[,sites,numeric-method |
| Slicer | [[,sites,numeric,ANY-method |
| Slicer | [[,specimens,numeric-method |
| Slicer | [[,specimens,numeric,ANY-method |
| Insert collunit | [[<-,collunits,ANY,ANY,ANY-method |
| Insert dataset | [[<-,datasets,ANY,ANY,ANY-method |
| Assign value to an element in a publication list. | [[<-,publications,ANY,ANY,ANY-method |
| Insert site | [[<-,sites,ANY,ANY,ANY-method |
| Insert specimen | [[<-,specimens,ANY,ANY,ANY-method |
| Assign collunit field by numeric index | [<-,collunit,character,ANY,ANY-method |
| Assign collunit field by numeric index | [<-,collunit,numeric,ANY,ANY-method |
| Assign dataset field by numeric index | [<-,dataset,character,ANY,ANY-method |
| Assign dataset field by numeric index | [<-,dataset,numeric,ANY,ANY-method |
| Assign site field by numeric index | [<-,site,character,ANY,ANY-method |
| Assign site field by numeric index | [<-,site,numeric,ANY,ANY-method |
| Assign specimen field by numeric index | [<-,specimen,character,ANY,ANY-method |
| Assign specimen field by numeric index | [<-,specimen,numeric,ANY,ANY-method |
| Extract | $,chronologies-method |
| Extract | $,chronology-method |
| $ | $,collunit-method |
| $ for collunits | $,collunits-method |
| Extract or Replace Parts of an Object | $,contact-method |
| Extract or Replace Parts of an Object | $,contacts-method |
| $ | $,dataset-method |
| $ for datasets | $,datasets-method |
| Extract an element from a 'publication' | $,publication-method |
| $ | $,sample-method |
| $ for samples | $,samples-method |
| $ | $,site-method |
| $ for sites | $,sites-method |
| $ | $,specimen-method |
| $ for specimens | $,specimens-method |
| Replace part of an object | $<-,chronology-method |
| Assign collunit field by numeric index | $<-,collunit-method |
| Assign dataset field by numeric index | $<-,dataset-method |
| Assign site field by numeric index | $<-,site-method |
| Assign specimen field by numeric index | $<-,specimen-method |
| Add a new chronology to a collection unit. | add_chronology |
| Add a new chronology into an existing collectionunit. | add_chronology,collunit,chronology,data.frame-method |
| Convert a publication author to a 'data.frame' | as.data.frame,authors-method |
| as.data.frame chronologies | as.data.frame,chronologies-method |
| Create a data.frame from a chronology object. | as.data.frame,chronology-method |
| as.data.frame site | as.data.frame,collunit-method |
| as.data.frame collunits | as.data.frame,collunits-method |
| Transform a contacts object to a data.frame() | as.data.frame,contact-method |
| Transform a contacts object to a data.frame() | as.data.frame,contacts-method |
| as.data.frame dataset | as.data.frame,dataset-method |
| as.data.frame datasets | as.data.frame,datasets-method |
| Convert a 'publication' to a 'data.frame' | as.data.frame,publication-method |
| Convert publications to a 'data.frame' | as.data.frame,publications-method |
| as.data.frame site | as.data.frame,site-method |
| as.data.frame sites | as.data.frame,sites-method |
| as.data.frame specimen | as.data.frame,specimen-method |
| as.data.frame specimens | as.data.frame,specimens-method |
| as.list sites | as.list,sites-method |
| An S4 class for the authors of a Neotoma publication. | author-class |
| An S4 class for a set of Neotoma author objects. | authors-class |
| build_chron | build_chron |
| Build a collection unit from the API response | build_collunits |
| Build a dataset object from a JSON list representation. | build_dataset |
| Build a samples 'data.frame' from Neotoma API JSON | build_sample |
| Build a 'site' from the Neotoma API response. | build_sites |
| Build a specimen objects. | build_specimen |
| c Method - Combine chronologies objects | c,chronologies-method |
| c Method - Combine collunits objects | c,collunits-method |
| c Method - Combine contacts objects | c,contact-method |
| c Method - Combine contacts objects | c,contacts-method |
| c Method - Combine datasets objects | c,datasets-method |
| c Method for NULL values | c,missingOrNULL-method |
| Combine publication objects. | c,publications-method |
| c Method - Combine sites objects | c,sites-method |
| c Method - Combine specimens objects | c,specimens-method |
| check_args | check_args |
| Check contact information for a record against Neotoma contributors | check_contacts |
| Get contact information for Neotoma contributors | check_contacts.contacts |
| chroncontrols | chroncontrols |
| Recover information about the chron controls for a collectionunit. | chroncontrols,site-method |
| Recover information about the chron controls for a collectionunit. | chroncontrols,sites-method |
| Obtain the chronology from a record or multiple records. | chronologies |
| S4 class for chronologies information | chronologies-class |
| Extract 'chronologies' from a 'collunit' object. | chronologies,collunit-method |
| Extract 'chronologies' from a 'collunits' object. | chronologies,collunits-method |
| Extract 'chronologies' from a 'site' object. | chronologies,site-method |
| Extract 'chronologies' from a 'sites' object. | chronologies,sites-method |
| S4 class for chronologies information | chronology-class |
| Generate a data citation from a Neotoma2 object. | cite_data |
| Obtain data citations from a single record. | cite_data,site-method |
| Obtain data citations from multiple records. | cite_data,sites-method |
| S4 class for collection units information. | collunit-class |
| Extract collection units from a sites object | collunits |
| An S4 class for Neotoma Collection Units | collunits-class |
| Extract 'collunits' from a 'site' object. | collunits,site-method |
| Extract 'collunits' from a 'sites' object. | collunits,sites-method |
| An S4 class for Neotoma contacts | contact-class |
| An S4 class for multi-contact information from the Neotoma Paleoecology Database. | contacts-class |
| Obtain coordinates from a sites object. | coordinates |
| Return the latitude and longitude of sites | coordinates,sites-method |
| S4 class for dataset information | dataset-class |
| Extract datasets from a sites object. | datasets |
| S4 class for datasets information | datasets-class |
| Extract 'datasets' from a 'collunit' object. | datasets,collunit-method |
| Extract 'datasets' from a 'collunits' object. | datasets,collunits-method |
| Extract 'datasets' from a 'site' object. | datasets,site-method |
| Extract 'datasets' from a 'sites' object. | datasets,sites-method |
| Obtain the DOI for publications or datasets. | doi |
| Get a publication DOI. | doi,publication-method |
| Obtain dataset DOIs from records. | doi,site-method |
| Obtain dataset DOIs from records. | doi,sites-method |
| Apply a filter for Neotoma sites objects. | filter |
| Apply a filter for Neotoma sites objects. | filter.sites |
| Get contact information for Neotoma contributors | get_contacts |
| Get contact information for Neotoma contributors | get_contacts.default |
| Get contact information for Neotoma contributors | get_contacts.numeric |
| get_datasets | get_datasets |
| Get Dataset Default | get_datasets.default |
| Get Dataset Numeric | get_datasets.numeric |
| Get Dataset from a 'site' object. | get_datasets.site |
| Get Dataset from a 'sites' object. | get_datasets.sites |
| get_downloads | get_downloads |
| get_downloads JSON | get_downloads.character |
| get_downloads | get_downloads.numeric |
| get_downloads sites | get_downloads.sites |
| get_manual | get_manual |
| Get publication information for Neotoma records | get_publications |
| Get publication information from Neotoma | get_publications.default |
| Get publications using their unique identifier. | get_publications.numeric |
| Update information for a publications object. | get_publications.publication |
| Update metadata for a set of publication objects. | get_publications.publications |
| get_sites | get_sites |
| get_sites | get_sites.default |
| Get Site Information for Fossil Sites | get_sites.numeric |
| Get Site Information for Fossil Sites from a Set of Sites | get_sites.sites |
| get_specimens | get_specimens |
| Get Specimen datasetid | get_specimens.default |
| Get Specimen Numeric | get_specimens.numeric |
| Get Specimen Sites | get_specimens.sites |
| get_stats | get_stats |
| Get table record from Neotoma | get_table |
| Get object IDs | getids |
| Get object IDs from a single collectionunit. | getids.collunit |
| Get object IDs from collectionunits. | getids.collunits |
| Get object IDs from a site object. | getids.site |
| Get object IDs from sites | getids.sites |
| Length Method chronologies | length,chronologies-method |
| Length Method collunits | length,collunits-method |
| Length Method datasets | length,datasets-method |
| Get the number of publications in a publications object. | length,publications-method |
| Length Method samples | length,samples-method |
| Length Method Sites | length,sites-method |
| Length Method specimens | length,specimens-method |
| c Method - Combine objects, including NULL | missingOrNULL-class |
| Get slot names | names,collunit-method |
| Get names of contacts slots | names,contact-method |
| Get slot names | names,dataset-method |
| Get slot names for a publication object. | names,publication-method |
| Get slot names for a publication object. | names,publications-method |
| Get slot names | names,site-method |
| Get slot names | names,specimen-method |
| Format API call to Neotoma from call arguments | newURL |
| parse_site | parse_site |
| parseURL | parseURL |
| pingNeotoma | pingNeotoma |
| Plot site coordinates using a basic plot. | plot,sites-method |
| Plot site coordinates using a basic plot. | plot,sites,ANY-method |
| plotLeaflet | plotLeaflet |
| plotLeaflet | plotLeaflet,site-method |
| plotLeaflet | plotLeaflet,sites-method |
| An S4 class for a single Neotoma publication. | publication-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. | publications-class |
| S4 class for repositories information | repositories-class |
| S4 class for repository information | repository-class |
| S4 class for dataset information | sample-class |
| Obtain samples from a record or multiple records. | samples |
| S4 class for the set of samples | samples-class |
| samples | samples,collunit-method |
| Get samples from a collectionunit or set of collection units: | samples,collunits-method |
| samples | samples,site-method |
| samples | samples,sites-method |
| Select the best match for an object. | selectMatch |
| Select the best match (between a local record and a Neotoma match) | selectMatch,publication,logical-method |
| Select the best match (between a local record and a Neotoma match) | selectMatch,publication,numeric-method |
| set chronology information for a new record. | set_chronology |
| set Site Information for Fossil Sites | set_collunit |
| Set contact information for a new record. | set_contact |
| set Site Information for Fossil Sites | set_dataset |
| Set the default chronology within a collectionunit. | set_default |
| Change the default age model for a record. | set_default,chronologies-method |
| Create a new publication (or publication set) | set_publications |
| set Sample Information | set_sample |
| Set Neotoma API Source or Server | set_server |
| set Site Information for Fossil Sites | set_site |
| Show the collection unit information | show,collunit-method |
| Show the collection unit information | show,collunits-method |
| Show contact object | show,contact-method |
| Show a contacts object. | show,contacts-method |
| Show Dataset Method | show,dataset-method |
| Show Datasets object as a dataframe | show,datasets-method |
| Print publications to screen. | show,publication-method |
| Show the contents of a publication object. | show,publications-method |
| Show a site object as a dataframe | show,site-method |
| Show sites objects as a dataframe | show,sites-method |
| Show Specimen Method | show,specimen-method |
| Show Specimens object as a dataframe | show,specimens-method |
| Show matches for objects. | showMatch |
| Show matched publication objects. | showMatch,publication-method |
| An S4 class for site information | site-class |
| An S4 class for multi-site information | sites-class |
| S4 class for specimen information | specimen-class |
| Obtain specimens from a record or multiple records. | specimens |
| S4 class for specimens information | specimens-class |
| specimens | specimens,collunit-method |
| specimens | specimens,collunits-method |
| specimens | specimens,site-method |
| specimens | specimens,sites-method |
| Summary of objects within a sites object. | summary,sites-method |
| taxa | taxa |
| Extract taxonomic data from a set of sites. | taxa,collunit-method |
| Extract taxonomic data from a set of sites. | taxa,collunits-method |
| Extract taxonomic data from a single site. | taxa,site-method |
| Extract taxonomic data from a set of sites. | taxa,sites-method |
| toJSON | toJSON |
| toJSON | toJSON,sites-method |
| toWide | toWide |
| write CSV | 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 |
