Man pages for neotoma2
Working with the Neotoma Paleoecology Database
| 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. |
| cash-chronologies-method | Extract |
| cash-chronology-method | Extract |
| cash-collunit-method | $ |
| cash-collunits-method | $ for collunits |
| cash-contact-method | Extract or Replace Parts of an Object |
| cash-contacts-method | Extract or Replace Parts of an Object |
| cash-dataset-method | $ |
| cash-datasets-method | $ for datasets |
| cash-publication-method | Extract an element from a 'publication' |
| cash-sample-method | $ |
| cash-samples-method | $ for samples |
| cash-set-chronology-method | Replace part of an object |
| cash-set-collunit-method | Assign collunit field by numeric index |
| cash-set-dataset-method | Assign dataset field by numeric index |
| cash-set-site-method | Assign site field by numeric index |
| cash-set-specimen-method | Assign specimen field by numeric index |
| cash-site-method | $ |
| cash-sites-method | $ for sites |
| cash-specimen-method | $ |
| cash-specimens-method | $ for specimens |
| 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 |
| check_args | check_args |
| check_contacts | Check contact information for a record against Neotoma... |
| check_contacts.contacts | Get contact information for Neotoma contributors |
| chroncontrols | chroncontrols |
| chroncontrols-site-method | Recover information about the chron controls for a... |
| chroncontrols-sites-method | Recover information about the chron controls for a... |
| chronologies | Obtain the chronology from a record or multiple records. |
| chronologies-class | S4 class for chronologies information |
| 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. |
| 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. |
| cleanNULL | Clean NULL values |
| clean.sites | clean sites objects to remove duplicates. |
| c-missingOrNULL-method | c Method for NULL values |
| 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-site-method | Extract 'collunits' from a 'site' object. |
| collunits-sites-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... |
| coordinates | Obtain coordinates from a sites object. |
| coordinates-sites-method | Return the latitude and longitude of sites |
| c-publications-method | Combine publication objects. |
| c-sites-method | c Method - Combine sites objects |
| c-specimens-method | c Method - Combine specimens objects |
| dataset-class | S4 class for dataset information |
| datasets | Extract datasets from a sites object. |
| datasets-class | S4 class for datasets information |
| 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. |
| 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 |
| 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_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 |
| 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 |
| parsebody | parse_body |
| parse_location | parse_location |
| parse_site | parse_site |
| parseURL | parseURL |
| pingNeotoma | pingNeotoma |
| pipe | Pipe operator |
| plotLeaflet | plotLeaflet |
| plotLeaflet-site-method | plotLeaflet |
| plotLeaflet-sites-method | plotLeaflet |
| plot-sites-ANY-method | Plot site coordinates using a basic plot. |
| publication-class | An S4 class for a single Neotoma publication. |
| publications-class | An S4 class for multi-publication information from the... |
| 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-class | S4 class for the set of samples |
| 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 |
| selectMatch | Select the best match for an object. |
| selectMatch-publication-logical-method | Select the best match (between a local record and a Neotoma... |
| selectMatch-publication-numeric-method | Select the best match (between a local record and a Neotoma... |
| 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 |
| showMatch | Show matches for objects. |
| showMatch-publication-method | Show matched publication objects. |
| 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 |
| 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-collunit-method | specimens |
| specimens-collunits-method | specimens |
| specimens-site-method | specimens |
| specimens-sites-method | specimens |
| sub-collunits-numeric-ANY-method | Get or remove sites by numeric index |
| sub-datasets-numeric-ANY-method | Get or remove datasets by numeric index |
| subset-collunit-character-ANY-ANY-method | Assign collunit field by numeric index |
| subset-collunit-numeric-ANY-ANY-method | Assign collunit field by numeric index |
| subset-dataset-character-ANY-ANY-method | Assign dataset field by numeric index |
| subset-dataset-numeric-ANY-ANY-method | Assign dataset field by numeric index |
| subset-site-character-ANY-ANY-method | Assign site field by numeric index |
| subset-site-numeric-ANY-ANY-method | Assign site field by numeric index |
| subset-specimen-character-ANY-ANY-method | Assign specimen field by numeric index |
| subset-specimen-numeric-ANY-ANY-method | Assign specimen field by numeric index |
| sub-site-character-ANY-method | Get site field by character index |
| sub-site-numeric-ANY-method | Get site field by numeric index |
| sub-sites-numeric-ANY-method | Get or remove sites by numeric index |
| sub-specimens-numeric-ANY-method | Get or remove specimens by numeric index |
| sub-sub-chronologies-numeric-ANY-method | Extract |
| sub-sub-collunits-numeric-ANY-method | Slicer |
| sub-sub-contacts-numeric-ANY-method | Extract or Replace Parts of an Object |
| sub-sub-datasets-numeric-ANY-method | Slicer |
| sub-sub-publications-numeric-ANY-method | Obtain one of the elements within a publication list. |
| sub-sub-samples-numeric-ANY-method | Slicer |
| sub-subset-collunits-ANY-ANY-ANY-method | Insert collunit |
| sub-subset-datasets-ANY-ANY-ANY-method | Insert dataset |
| sub-subset-publications-ANY-ANY-ANY-method | Assign value to an element in a publication list. |
| sub-subset-sites-ANY-ANY-ANY-method | Insert site |
| sub-subset-specimens-ANY-ANY-ANY-method | Insert specimen |
| sub-sub-sites-numeric-ANY-method | Slicer |
| sub-sub-specimens-numeric-ANY-method | Slicer |
| 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 |
