Working with the Neotoma Paleoecology Database
Get object IDs from collectionunits.
Get object IDs
Get object IDs from a site object.
Get object IDs from sites
Length Method chronologies
Length Method collunits
Length Method datasets
Get the number of publications in a publications object.
Length Method samples
Length Method Sites
Length Method specimens
c Method - Combine objects, including NULL
Get slot names
Get names of contacts slots
Get slot names
Get slot names for a publication object.
Get slot names for a publication object.
Get slot names
Get slot names
Format API call to Neotoma from call arguments
parse_site
parse_body
An S4 class for the authors of a Neotoma publication.
An S4 class for a set of Neotoma author objects.
build_chron
Build a collection unit from the API response
Build a dataset object from a JSON list representation.
Build a samples data.frame from Neotoma API JSON
Build a site from the Neotoma API response.
Build a specimen objects.
c Method - Combine chronologies objects
c Method - Combine collunits objects
c Method - Combine contacts objects
c Method - Combine contacts objects
c Method - Combine datasets objects
c Method for NULL values
Combine publication objects.
c Method - Combine sites objects
c Method - Combine specimens objects
Extract
Extract
$
$ for collunits
Extract or Replace Parts of an Object
Extract or Replace Parts of an Object
$
$ for datasets
Extract an element from a publication
$
$ for samples
Replace part of an object
Assign collunit field by numeric index
Assign dataset field by numeric index
Assign site field by numeric index
Assign specimen field by numeric index
$
$ for sites
$
$ for specimens
check_args
Get contact information for Neotoma contributors
Check contact information for a record against Neotoma contributors
Recover information about the chron controls for a collectionunit.
Recover information about the chron controls for a collectionunit.
chroncontrols
S4 class for chronologies information
Extract chronologies from a collunit object.
Extract chronologies from a collunits object.
Extract chronologies from a site object.
Extract chronologies from a sites object.
Obtain the chronology from a record or multiple records.
S4 class for chronologies information
Obtain data citations from a single record.
Obtain data citations from multiple records.
Generate a data citation from a Neotoma2 object.
S4 class for collection units information.
An S4 class for Neotoma Collection Units
Extract collunits from a site object.
Extract collunits from a sites object.
Extract collection units from a sites object
An S4 class for Neotoma contacts
An S4 class for multi-contact information from the Neotoma Paleoecolog...
Return the latitude and longitude of sites
Obtain coordinates from a sites object.
S4 class for dataset information
S4 class for datasets information
Extract datasets from a collunit object.
Extract datasets from a collunits object.
Extract datasets from a site object.
Extract datasets from a sites object.
Extract datasets from a sites object.
Get a publication DOI.
Obtain dataset DOIs from records.
Obtain dataset DOIs from records.
Obtain the DOI for publications or datasets.
parseURL
pingNeotoma
Pipe operator
Plot site coordinates using a basic plot.
plotLeaflet
plotLeaflet
plotLeaflet
Assign value to an element in a publication list.
Insert site
Insert specimen
Assign collunit field by numeric index
Assign collunit field by numeric index
Assign dataset field by numeric index
Assign dataset field by numeric index
Assign site field by numeric index
Assign site field by numeric index
Assign specimen field by numeric index
Assign specimen field by numeric index
Summary of objects within a sites object.
Extract taxonomic data from a set of sites.
Extract taxonomic data from a set of sites.
Extract taxonomic data from a single site.
Extract taxonomic data from a set of sites.
taxa
toJSON
toJSON
Apply a filter for Neotoma sites objects.
Get table record from Neotoma
Get object IDs from a single collectionunit.
Show matches for objects.
as.data.frame collunits
An S4 class for site information
Transform a contacts object to a data.frame()
Transform a contacts object to a data.frame()
as.data.frame dataset
as.data.frame datasets
Convert a publication to a data.frame
Convert publications to a data.frame
as.data.frame site
as.data.frame sites
as.data.frame specimen
as.data.frame specimens
as.list sites
An S4 class for multi-site information
S4 class for specimen information
S4 class for specimens information
specimens
specimens
specimens
specimens
Obtain specimens from a record or multiple records.
Get or remove sites by numeric index
Get or remove datasets by numeric index
Get site field by character index
Get site field by numeric index
Get or remove sites by numeric index
Get or remove specimens by numeric index
Insert dataset
Extract
Slicer
Extract or Replace Parts of an Object
Slicer
Obtain one of the elements within a publication list.
Slicer
Slicer
Slicer
Insert collunit
Convert a publication author to a data.frame
as.data.frame chronologies
Create a data.frame from a chronology object.
as.data.frame site
Add a new chronology into an existing collectionunit.
Add a new chronology to a collection unit.
Apply a filter for Neotoma sites objects.
Get contact information for Neotoma contributors
Get contact information for Neotoma contributors
Get contact information for Neotoma contributors
Get Dataset Default
Get Dataset Numeric
get_datasets
Get Dataset from a site object.
Get Dataset from a sites object.
get_downloads JSON
get_downloads
get_downloads
get_downloads sites
get_manual
Get publication information from Neotoma
Get publications using their unique identifier.
Update information for a publications object.
Update metadata for a set of publication objects.
Get publication information for Neotoma records
get_sites
Get Site Information for Fossil Sites
get_sites
Get Site Information for Fossil Sites from a Set of Sites
Get Specimen datasetid
Get Specimen Numeric
get_specimens
Get Specimen Sites
get_stats
An S4 class for a single Neotoma publication.
An S4 class for multi-publication information from the Neotoma Paleoec...
S4 class for repositories information
S4 class for repository information
S4 class for dataset information
S4 class for the set of samples
samples
Get samples from a collectionunit or set of collection units:
samples
samples
Obtain samples from a record or multiple records.
Select the best match (between a local record and a Neotoma match)
Select the best match (between a local record and a Neotoma match)
Select the best match for an object.
Create a new publication (or publication set)
set chronology information for a new record.
set Site Information for Fossil Sites
Set contact information for a new record.
set Site Information for Fossil Sites
Change the default age model for a record.
Set the default chronology within a collectionunit.
Show Specimens object as a dataframe
Show matched publication objects.
set Sample Information
Set Neotoma API Source or Server
set Site Information for Fossil Sites
Show the collection unit information
Show the collection unit information
Show contact object
Show a contacts object.
Show Dataset Method
Show Datasets object as a dataframe
Print publications to screen.
Show the contents of a publication object.
Show a site object as a dataframe
Show sites objects as a dataframe
Show Specimen Method
toWide
write CSV
write CSV
write CSV
write CSV
write CSV
Access and manipulation of data using the Neotoma Paleoecology Database. <https://api.neotomadb.org/api-docs/>.