Working with the Neotoma Paleoecology Database


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Documentation for package ‘neotoma2’ version 1.0.2

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

-- A --

add_chronology Add a new chronology to a collection unit.
add_chronology-method Add a new chronology into an existing collectionunit.
as.data.frame-method Convert a publication author to a 'data.frame'
as.data.frame-method as.data.frame chronologies
as.data.frame-method Create a data.frame from a chronology object.
as.data.frame-method as.data.frame site
as.data.frame-method as.data.frame collunits
as.data.frame-method Transform a contacts object to a data.frame()
as.data.frame-method Transform a contacts object to a data.frame()
as.data.frame-method as.data.frame dataset
as.data.frame-method as.data.frame datasets
as.data.frame-method Convert a 'publication' to a 'data.frame'
as.data.frame-method Convert publications to a 'data.frame'
as.data.frame-method as.data.frame site
as.data.frame-method as.data.frame sites
as.data.frame-method as.data.frame specimen
as.data.frame-method as.data.frame specimens
as.list-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.

-- B --

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 --

c-method c Method - Combine chronologies objects
c-method c Method - Combine collunits objects
c-method c Method - Combine contacts objects
c-method c Method - Combine contacts objects
c-method c Method - Combine datasets objects
c-method c Method for NULL values
c-method Combine publication objects.
c-method c Method - Combine sites objects
c-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-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 'collunit' object.
chronologies-method Extract 'chronologies' from a 'collunits' object.
chronologies-method Extract 'chronologies' from a 'site' object.
chronologies-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-method Obtain data citations from a single record.
cite_data-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-class An S4 class for Neotoma Collection Units
collunits-method Extract 'collunits' from a 'site' object.
collunits-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 Paleoecology Database.
coordinates Obtain coordinates from a sites object.
coordinates-method Return the latitude and longitude of sites

-- D --

dataset-class S4 class for dataset information
datasets Extract datasets from a sites object.
datasets-class S4 class for datasets information
datasets-method Extract 'datasets' from a 'collunit' object.
datasets-method Extract 'datasets' from a 'collunits' object.
datasets-method Extract 'datasets' from a 'site' object.
datasets-method Extract 'datasets' from a 'sites' object.
doi Obtain the DOI for publications or datasets.
doi-method Get a publication DOI.
doi-method Obtain dataset DOIs from records.
doi-method Obtain dataset DOIs from records.

-- F --

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

-- G --

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_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

-- L --

length-method Length Method chronologies
length-method Length Method collunits
length-method Length Method datasets
length-method Get the number of publications in a publications object.
length-method Length Method samples
length-method Length Method Sites
length-method Length Method specimens

-- M --

missingOrNULL-class c Method - Combine objects, including NULL

-- N --

names-method Get slot names
names-method Get names of contacts slots
names-method Get slot names
names-method Get slot names for a publication object.
names-method Get slot names for a publication object.
names-method Get slot names
names-method Get slot names
newURL Format API call to Neotoma from call arguments

-- P --

parsebody parse_body
parseURL parseURL
parse_location parse_location
parse_site parse_site
pingNeotoma pingNeotoma
plot-method Plot site coordinates using a basic plot.
plotLeaflet plotLeaflet
plotLeaflet-method plotLeaflet
plotLeaflet-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.

-- R --

repositories-class S4 class for repositories information
repository-class S4 class for repository information

-- S --

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-method samples
samples-method Get samples from a collectionunit or set of collection units:
samples-method samples
samples-method samples
selectMatch Select the best match for an object.
selectMatch-method Select the best match (between a local record and a Neotoma match)
selectMatch-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-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-method Show the collection unit information
show-method Show the collection unit information
show-method Show contact object
show-method Show a contacts object.
show-method Show Dataset Method
show-method Show Datasets object as a dataframe
show-method Print publications to screen.
show-method Show the contents of a publication object.
show-method Show a site object as a dataframe
show-method Show sites objects as a dataframe
show-method Show Specimen Method
show-method Show Specimens object as a dataframe
showMatch Show matches for objects.
showMatch-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-class S4 class for specimens information
specimens-method specimens
specimens-method specimens
specimens-method specimens
specimens-method specimens
summary-method Summary of objects within a sites object.

-- T --

taxa taxa
taxa-method Extract taxonomic data from a set of sites.
taxa-method Extract taxonomic data from a set of sites.
taxa-method Extract taxonomic data from a single site.
taxa-method Extract taxonomic data from a set of sites.
testNull Clear NULL values and replace with value predefined value.
toJSON toJSON
toJSON-method toJSON
toWide toWide

-- U --

use_na Change NA values from logic to a prescribed type.

-- W --

write.csv-method write CSV
write.csv-method write CSV
write.csv-method write CSV
write.csv-method write CSV
write.csv-method write CSV

-- misc --

$-method Extract
$-method Extract
$-method $
$-method $ for collunits
$-method Extract or Replace Parts of an Object
$-method Extract or Replace Parts of an Object
$-method $
$-method $ for datasets
$-method Extract an element from a 'publication'
$-method $
$-method $ for samples
$-method $
$-method $ for sites
$-method $
$-method $ for specimens
$<--method Replace part of an object
$<--method Assign collunit field by numeric index
$<--method Assign dataset field by numeric index
$<--method Assign site field by numeric index
$<--method Assign specimen field by numeric index
[-method Get or remove sites by numeric index
[-method Get or remove datasets by numeric index
[-method Get site field by character index
[-method Get site field by numeric index
[-method Get or remove sites by numeric index
[-method Get or remove specimens by numeric index
[<--method Assign collunit field by numeric index
[<--method Assign collunit field by numeric index
[<--method Assign dataset field by numeric index
[<--method Assign dataset field by numeric index
[<--method Assign site field by numeric index
[<--method Assign site field by numeric index
[<--method Assign specimen field by numeric index
[<--method Assign specimen field by numeric index
[[-method Extract
[[-method Slicer
[[-method Extract or Replace Parts of an Object
[[-method Slicer
[[-method Obtain one of the elements within a publication list.
[[-method Slicer
[[-method Slicer
[[-method Slicer
[[<--method Insert collunit
[[<--method Insert dataset
[[<--method Assign value to an element in a publication list.
[[<--method Insert site
[[<--method Insert specimen