Title:	Working with the Neotoma Paleoecology Database
Date:	2025-07-14
Version:	1.0.7
URL:	https://github.com/NeotomaDB/neotoma2
BugReports:	https://github.com/NeotomaDB/neotoma2/issues
Description:	Access and manipulation of data using the Neotoma Paleoecology Database. https://api.neotomadb.org/api-docs/.
License:	MIT + file LICENSE
Encoding:	UTF-8
RoxygenNote:	7.3.2
Suggests:	testthat, knitr, pkgdown, rmarkdown, ggplot2, Bchron, covr
Imports:	rlang, magrittr, sf, digest, geojsonsf, purrr, lubridate, httr, jsonlite, methods, dplyr, gtools, leaflet, assertthat, stringr, progress, uuid, utils, tidyr
VignetteBuilder:	knitr
NeedsCompilation:	no
Packaged:	2025-07-14 23:39:00 UTC; sedv8808
Author:	Dominguez Vidana Socorro [aut, cre], Simon Goring [aut]
Maintainer:	Dominguez Vidana Socorro <s.dominguez@ht-data.com>
Repository:	CRAN
Date/Publication:	2025-07-15 03:30:02 UTC

Replace part of an object

Description

Assign values to slots within a chronology object.

Usage

## S4 replacement method for signature 'chronology'
x$name <- value

Arguments

Value

reassigned chronology object

Assign collunit field by numeric index

Description

Assign collunit field by numeric index

Usage

## S4 replacement method for signature 'collunit'
x$name <- value

Arguments

Value

assign a new value to a slot

Assign dataset field by numeric index

Description

Assign dataset field by numeric index

Usage

## S4 replacement method for signature 'dataset'
x$name <- value

Arguments

Value

Assign new dataset by numeric index

Assign site field by numeric index

Description

Assign site field by numeric index

Usage

## S4 replacement method for signature 'site'
x$name <- value

Arguments

Value

site object with reassigned values

Assign taxon field by numeric index

Description

Assign taxon field by numeric index

Usage

## S4 replacement method for signature 'taxon'
x$name <- value

Arguments

Value

Assign new taxon by numeric index

Extract

Description

Obtain chronology slots across all chronology elements within a chronologies object.

Usage

## S4 method for signature 'chronologies'
x$name

Arguments

Value

A multiple chronologies

Extract

Description

Extract chronology metadata by slot name.

Usage

## S4 method for signature 'chronology'
x$name

Arguments

Value

value of the slot name

$

Description

Obtain slots of a collunit without using at-mark

Usage

## S4 method for signature 'collunit'
x$name

Arguments

Value

null prints element of a slot

$ for collunits

Description

Obtain slots of a collunit without using at-mark

Usage

## S4 method for signature 'collunits'
x$name

Arguments

Value

null prints element of a slot

Extract or Replace Parts of an Object

Description

Extract or Replace Parts of an Object

Usage

## S4 method for signature 'contact'
x$name

Arguments

Value

value in the selected slot

Extract or Replace Parts of an Object

Description

Extract or Replace Parts of an Object

Usage

## S4 method for signature 'contacts'
x$name

Arguments

Value

object value from the slot

$

Description

Obtain slots of a dataset without using at-mark

Usage

## S4 method for signature 'dataset'
x$name

Arguments

Value

Obtain a dataset's slot value using $

$ for datasets

Description

Obtain slots of a dataset without using at-mark

Usage

## S4 method for signature 'datasets'
x$name

Arguments

Value

Obtain a datasets' slot value using $

Extract an element from a publication

Description

Extract an element from a publication

Usage

## S4 method for signature 'publication'
x$name

Arguments

Value

value in the selected slot

$

Description

Obtain slots of a sample without using at-mark

Usage

## S4 method for signature 'sample'
x$name

Arguments

Value

value at selected slot

$ for samples

Description

Obtain slots of a site without using at-mark

Usage

## S4 method for signature 'samples'
x$name

Arguments

Value

value at selected slot

$

Description

Obtain slots of a site without using at-mark

Usage

## S4 method for signature 'site'
x$name

Arguments

Value

value at chosen slot in the site object

$ for sites

Description

Obtain slots of a site without using at-mark

Usage

## S4 method for signature 'sites'
x$name

Arguments

Value

value at chosen slot in the site object

$ for taxa

Description

Obtain slots of a taxon without using at-mark

Usage

## S4 method for signature 'taxa'
x$name

Arguments

Value

Obtain a taxa' slot value using $

$

Description

Obtain slots of a taxon without using at-mark

Usage

## S4 method for signature 'taxon'
x$name

Arguments

Value

Obtain a taxon's slot value using $

Pipe operator

Description

See magrittr::%>% for details.

Usage

lhs %>% rhs

Value

NULL; allows using tidyverse pipe operator.

Assign collunit field by numeric index

Description

Assign collunit field by numeric index

Usage

## S4 replacement method for signature 'collunit,character,ANY,ANY'
x[i] <- value

Arguments

Value

sliced element

Assign collunit field by numeric index

Description

Assign collunit field by numeric index

Usage

## S4 replacement method for signature 'collunit,numeric,ANY,ANY'
x[i] <- value

Arguments

Value

sliced value

Assign dataset field by numeric index

Description

Assign dataset field by numeric index

Usage

## S4 replacement method for signature 'dataset,character,ANY,ANY'
x[i] <- value

Arguments

Value

dataset slot with new assigned character value

Assign dataset field by numeric index

Description

Assign dataset field by numeric index

Usage

## S4 replacement method for signature 'dataset,numeric,ANY,ANY'
x[i] <- value

Arguments

Value

dataset slot with new assigned numeric value

Assign sample field by numeric index

Description

Assign sample field by numeric index

Usage

## S4 replacement method for signature 'sample,character,ANY,ANY'
x[i] <- value

Arguments

Value

sample object with reassigned character values

Assign site field by numeric index

Description

Assign site field by numeric index

Usage

## S4 replacement method for signature 'site,character,ANY,ANY'
x[i] <- value

Arguments

Value

site object with reassigned character values

Assign site field by numeric index

Description

Assign site field by numeric index

Usage

## S4 replacement method for signature 'site,numeric,ANY,ANY'
x[i] <- value

Arguments

Value

sites object with reassigned numeric values

Assign taxon field by numeric index

Description

Assign taxon field by numeric index

Usage

## S4 replacement method for signature 'taxon,character,ANY,ANY'
x[i] <- value

Arguments

Value

taxon slot with new assigned character value

Assign taxon field by numeric index

Description

Assign taxon field by numeric index

Usage

## S4 replacement method for signature 'taxon,numeric,ANY,ANY'
x[i] <- value

Arguments

Value

taxon slot with new assigned numeric value

Get or remove sites by numeric index

Description

Retrieve sites by numeric index

Usage

## S4 method for signature 'collunits,numeric'
x[i]

Arguments

Value

null used for side effects. Printing a data.frame

Get or remove datasets by numeric index

Description

Get or remove datasets by numeric index

Usage

## S4 method for signature 'datasets,numeric'
x[i]

Arguments

Value

Get or remove datasets by numeric index

Get site field by character index

Description

Get site field by character index

Usage

## S4 method for signature 'site,character'
x[i]

Arguments

Value

sliced site object

Get site field by numeric index

Description

Get site field by numeric index

Usage

## S4 method for signature 'site,numeric'
x[i]

Arguments

Value

sliced site object

Get or remove sites by numeric index

Description

Get or remove sites by numeric index

Usage

## S4 method for signature 'sites,numeric'
x[i]

Arguments

Value

sliced site object

Get or remove taxa by numeric index

Description

Get or remove taxa by numeric index

Usage

## S4 method for signature 'taxa,numeric'
x[i]

Arguments

Value

Get or remove taxa by numeric index

Insert collunit

Description

Obtain one of the elements within a collunits list

Usage

## S4 replacement method for signature 'collunits,ANY,ANY,ANY'
x[[i]] <- value

Arguments

Value

Modified collunits

Insert dataset

Description

Obtain one of the elements within a datasets list

Usage

## S4 replacement method for signature 'datasets,ANY,ANY,ANY'
x[[i]] <- value

Arguments

Value

One dataset slot's value

Assign value to an element in a publication list.

Description

Assign value to an element in a publication list.

Usage

## S4 replacement method for signature 'publications,ANY,ANY,ANY'
x[[i]] <- value

Arguments

Value

publications with new assigned value.

Insert sample

Description

Obtain one of the elements within a samples list

Usage

## S4 replacement method for signature 'samples,ANY,ANY,ANY'
x[[i]] <- value

Arguments

Value

samples object with reassigned values

Insert site

Description

Obtain one of the elements within a sites list

Usage

## S4 replacement method for signature 'sites,ANY,ANY,ANY'
x[[i]] <- value

Arguments

Value

sites object with reassigned values

Insert taxon

Description

Obtain one of the elements within a taxa list

Usage

## S4 replacement method for signature 'taxa,ANY,ANY,ANY'
x[[i]] <- value

Arguments

Value

One taxon slot's value

Extract

Description

Obtain one of the elements within a chronologies list either by element order or by element name.

Usage

## S4 method for signature 'chronologies,numeric'
x[[i]]

Arguments

Value

selected chronology object

Slicer

Description

Obtain one of the elements within a collunits list

Usage

## S4 method for signature 'collunits,numeric'
x[[i]]

Arguments

Value

sliced collunits object

Extract or Replace Parts of an Object

Description

Extract or Replace Parts of an Object

Usage

## S4 method for signature 'contacts,numeric'
x[[i]]

Arguments

Value

sliced contacts

Slicer

Description

Obtain one of the elements within a datasets list

Usage

## S4 method for signature 'datasets,numeric'
x[[i]]

Arguments

Value

sliced dataset object

Obtain one of the elements within a publication list.

Description

Obtain one of the elements within a publication list.

Usage

## S4 method for signature 'publications,numeric'
x[[i]]

Arguments

Value

selected publications object from index

Slicer

Description

Obtain one of the elements within a samples list

Usage

## S4 method for signature 'samples,numeric'
x[[i]]

Arguments

Value

samples sliced object

Slicer

Description

Obtain one of the elements within a sites list

Usage

## S4 method for signature 'sites,numeric'
x[[i]]

Arguments

Value

sliced site object

Examples

some_site <- get_sites(sitename = "Site%", limit=3)
some_site[[2]]

Slicer

Description

Obtain one of the elements within a taxa list

Usage

## S4 method for signature 'taxa,numeric'
x[[i]]

Arguments

Value

sliced taxa object

Add a new chronology to a collection unit.

Description

Add a new chronology to a collection unit.

Usage

add_chronology(object, x, y)

Arguments

Value

chronology object defined by user,

Add a new chronology into an existing collectionunit.

Description

Given a collunit, add a new chronology object to the unit with both the chronology metadata and the age information (as y)

Usage

## S4 method for signature 'collunit,chronology,data.frame'
add_chronology(object, x, y)

Arguments

Details

When undertaking analysis we may wish to add a new chronology to existing records within Neotoma. To do this we must first build the chronology, but also link it to existing analysis units within the collection unit. For examples from this function, see the Complex Workflows documentation online.

Value

chronologies with new added chronology

Convert a publication author to a data.frame

Description

Convert a publication author to a data.frame

Usage

## S4 method for signature 'authors'
as.data.frame(x)

Arguments

Value

data.frame with publications metadata

as.data.frame chronologies

Description

Convert all slots within each chronology within a chronologies object to a data.frame.

Usage

## S4 method for signature 'chronologies'
as.data.frame(x)

Arguments

Value

data.frame with chronologies metadata

Create a data.frame from a chronology object.

Description

Convert all slots within a chronology to a data.frame.

Usage

## S4 method for signature 'chronology'
as.data.frame(x)

Arguments

Value

data.frame

as.data.frame site

Description

show as dataframe

Usage

## S4 method for signature 'collunit'
as.data.frame(x)

Arguments

Value

data.frame object with a collection units metadata

as.data.frame collunits

Description

show as dataframe as prep to save as csv

Usage

## S4 method for signature 'collunits'
as.data.frame(x)

Arguments

Value

data.frame of multiple collection units metadata.

Transform a contacts object to a data.frame()

Description

Transform a contacts object to a data.frame()

Usage

## S4 method for signature 'contact'
as.data.frame(x)

Arguments

Value

data.frame object with contact metadata

Transform a contacts object to a data.frame()

Description

Transform a contacts object to a data.frame()

Usage

## S4 method for signature 'contacts'
as.data.frame(x)

Arguments

Value

data.frame object with multiple contacts metadata

as.data.frame dataset

Description

show as dataframe as prep to save as csv

Usage

## S4 method for signature 'dataset'
as.data.frame(x)

Arguments

Value

data.frame with dataset metadata

as.data.frame datasets

Description

show as dataframe as prep to save as csv

Usage

## S4 method for signature 'datasets'
as.data.frame(x)

Arguments

Value

data.frame with datasets metadata

Convert a publication to a data.frame

Description

Convert a publication to a data.frame

Usage

## S4 method for signature 'publication'
as.data.frame(x)

Arguments

Value

data.frame with publications' metadata.

Convert publications to a data.frame

Description

Convert publications to a data.frame

Usage

## S4 method for signature 'publications'
as.data.frame(x)

Arguments

Value

data.frame with publications' metadata.

as.data.frame site

Description

show as dataframe as prep to save as csv

Usage

## S4 method for signature 'site'
as.data.frame(x)

Arguments

Value

data.frame object with site metadata

as.data.frame sites

Description

shows object as data.frame

Usage

## S4 method for signature 'sites'
as.data.frame(x)

Arguments

Value

data.frame object with sites metadata

as.data.frame taxa

Description

show as dataframe as prep to save as csv

Usage

## S4 method for signature 'taxa'
as.data.frame(x)

Arguments

Value

data.frame with taxa metadata

as.data.frame taxon

Description

show as dataframe as prep to save as csv

Usage

## S4 method for signature 'taxon'
as.data.frame(x)

Arguments

Value

data.frame with taxon metadata

as.list sites

Description

show as dataframe as prep to save as csv

Usage

## S4 method for signature 'sites'
as.list(x)

Arguments

Value

list object with sites metadata

An S4 class for the authors of a Neotoma publication.

Description

This class combines the S4 class contact with a numeric author order. This allows us to reuse contact objects, and to assign the authorship order within a publication. The full set of authors for a publication are represented by the authors object.

Value

object of class author

Examples

{
simon <- new("contact", familyname = "Goring", givennames = "Simon J.")
firstauthor <- new("author", author = simon, order = 1)
}

An S4 class for a set of Neotoma author objects.

Description

The S4 authors are a set of individual author objects that are then associated with a single S4 publication class.

Value

object of class authors

Examples

{
simon <- new("contact", familyname = "Goring", givennames = "Simon J.")
socorro <- new("contact", familyname = "Dominguez", givennames = "Socorro")
first_author <- new("author", author = simon, order = 1)
second_author <- new("author", author = socorro, order = 2)
author_list <- new("authors", authors = list(first_author, second_author))
}

Build a specimen objects.

Description

A helper function to build a specimen object from a list returned by the Neotoma API call. The function is not exported, but called from the get_specimens() call.

Usage

build_specimen(x)

Arguments

Value

A simple specimen object

c Method - Combine chronologies objects

Description

c Method - Combine chronologies objects

Usage

## S4 method for signature 'chronologies'
c(x, y)

Arguments

Value

concatenated chronologies

c Method - Combine collunits objects

Description

c Method - Combine collunits objects

Usage

## S4 method for signature 'collunits'
c(x, y)

Arguments

Value

concatenated collection units without duplicates

c Method - Combine contacts objects

Description

c Method - Combine contacts objects

Usage

## S4 method for signature 'contact'
c(x, y)

Arguments

Value

contacts concatenated object

c Method - Combine contacts objects

Description

c Method - Combine contacts objects

Usage

## S4 method for signature 'contacts'
c(x, y)

Arguments

Value

concatenated and clean objects

c Method - Combine datasets objects

Description

c Method - Combine datasets objects

Usage

## S4 method for signature 'datasets'
c(x, y)

Arguments

Value

concatenated datasets object

c Method for NULL values

Description

c Method for NULL values

c Method for NULL values

Usage

## S4 method for signature 'missingOrNULL'
c(x = "missingORNULL", y)

## S4 method for signature 'missingOrNULL'
c(x = "missingORNULL", y)

Arguments

Value

concatenated collunits object

list of concatenated items when the first object is NULL

Combine publication objects.

Description

Combine publication objects.

Usage

## S4 method for signature 'publications'
c(x, y)

Arguments

Value

concatenated publications object

c Method - Combine datasets objects

Description

c Method - Combine datasets objects

Usage

## S4 method for signature 'samples'
c(x, y)

Arguments

Value

concatenated samples object

c Method - Combine sites objects

Description

c Method - Combine sites objects

Usage

## S4 method for signature 'sites'
c(x, y)

Arguments

Value

concatenated and cleaned sites object

c Method - Combine taxa objects

Description

c Method - Combine taxa objects

Usage

## S4 method for signature 'taxa'
c(x, y)

Arguments

Value

concatenated taxa object

Check contact information for a record against Neotoma contributors

Description

Uses the Neotoma API to search and access information about individuals who have contributed to the data in the Neotoma Paleoecology Database

Usage

check_contacts(x, ...)

Arguments

Value

contacts object

Get contact information for Neotoma contributors

Description

Get contact information for Neotoma contributors

Usage

## S3 method for class 'contacts'
check_contacts(x, similarity = 0.5, ...)

Arguments

Value

contacts object

chroncontrols

Description

Show the samples table

Usage

chroncontrols(x)

Arguments

Value

data.frame with chroncontrols information

Recover information about the chron controls for a collectionunit.

Description

For a site that includes collection units with chronologies return the chronological controls that are used in building the chronology.

Usage

## S4 method for signature 'site'
chroncontrols(x)

Arguments

Value

data.frame with chronological controls

Recover information about the chron controls for a collectionunit.

Description

For all sites that includes collection units with chronologies return the chronological controls that are used in building the chronology.

Usage

## S4 method for signature 'sites'
chroncontrols(x)

Arguments

Value

data.frame with chronological controls

Obtain the chronology from a record or multiple records.

Description

Obtain the chronology from a record or multiple records.

Usage

chronologies(x)

Arguments

Value

chronologies object with all chronologies used.

Extract chronologies from a collunit object.

Description

Extract chronologies from a collunit object.

Usage

## S4 method for signature 'collunit'
chronologies(x)

Arguments

Value

chronologies from a collunit object

Extract chronologies from a collunits object.

Description

Extract chronologies from a collunits object.

Usage

## S4 method for signature 'collunits'
chronologies(x)

Arguments

Value

chronologies from a collunits object

Extract chronologies from a site object.

Description

Extract chronologies from a site object.

Usage

## S4 method for signature 'site'
chronologies(x)

Arguments

Value

chronologies from a site object

Extract chronologies from a sites object.

Description

Extract chronologies from a sites object.

Usage

## S4 method for signature 'sites'
chronologies(x)

Arguments

Value

chronologies from a sites object

S4 class for chronologies information

Description

The grouped class for chronologies from the Neotoma Paleoecology Database.

Value

object of class chronologies

S4 class for chronologies information

Description

The class for chronologies from the Neotoma Paleoecology Database. A single collection unit may have one or more chronology. These individual chronology classes are then grouped into an S4 chronologies class.

Value

object of class chronology

Generate a data citation from a Neotoma2 object.

Description

The function, applied to a data object with a valid dataset, will return a properly formatted data citation for the record.

Usage

cite_data(x)

Arguments

Value

data.frame with citation data

Obtain data citations from a single record.

Description

Given complete dataset objects in Neotoma (must have used get_datasets() or get_downloads()), return a formatted citation for the record, including the dataset DOI.

Usage

## S4 method for signature 'site'
cite_data(x)

Arguments

Value

data.frame object with citation information.

Examples

ds <- get_datasets(1)
cite_data(ds)

Obtain data citations from multiple records.

Description

Given complete dataset objects in Neotoma (must have used get_datasets() or get_downloads()), return a formatted citation for the record, including the dataset DOI.

Usage

## S4 method for signature 'sites'
cite_data(x)

Arguments

Value

data.frame object with citation information.

Examples

{
ds <- get_datasets(1)
cite_data(ds)
}

S4 class for collection units information.

Description

A collection unit represents a collection event from within a site. For example, a lake sediment core, or a single dig site within an archaeological site.

Value

object of class collunit

Extract collection units from a sites object

Description

Extract collection units from a sites object

Usage

collunits(object)

Arguments

Value

collunits detail from a sites object

Extract collunits from a site object.

Description

Extract collunits from a site object.

Usage

## S4 method for signature 'site'
collunits(object)

Arguments

Value

collunits from a site object

Extract collunits from a sites object.

Description

Extract collunits from a sites object.

Usage

## S4 method for signature 'sites'
collunits(object)

Arguments

Value

collunits from a sites object

An S4 class for Neotoma Collection Units

Description

Holds Collection unit information from the Neotoma Paleoecology Database. @returns object of class collunits

An S4 class for Neotoma contacts

Description

The object that contains the contact information for an individual, along with associated metadata.

Value

object of class contact

Examples

new("contact", familyname = "Goring", givennames = "Simon J.")

An S4 class for multi-contact information from the Neotoma Paleoecology Database.

Description

An unordered list of individual S4 contact objects.

Value

object of class contacts

Examples

{
# Create two contact objects and associate them within a contacts object.
simon <- new("contact", familyname = "Goring", givennames = "Simon J.")
socorro <- new("contact", familyname = "Dominguez", givennames = "Socorro")
packagers <- new("contacts", contacts = list(simon, socorro))
packagers
}

Obtain coordinates from a sites object.

Description

Obtain coordinates from a sites object.

Usage

coordinates(obj, ...)

Arguments

Value

dataframe with coordinate values

Return the latitude and longitude of sites

Description

Return the latitude and longitude of sites

Usage

## S4 method for signature 'sites'
coordinates(obj, ...)

Arguments

Value

data.frame object with site coordinates.

S4 class for dataset information

Description

The standard object class for datasets from the Neotoma Paleoecology Database.

Value

object of class dataset

Extract datasets from a sites object.

Description

If the sites object contains datasets, then the datasets will be returned. If the sites object does not contain datasets then the user can apply get_datasets() to the object.

Usage

datasets(object)

Arguments

Value

datasets object specific to the metadata contained in datasets

Extract datasets from a collunit object.

Description

Extract datasets from a collunit object.

Usage

## S4 method for signature 'collunit'
datasets(object)

Arguments

Value

datasets from a collunit object

Extract datasets from a collunits object.

Description

Extract datasets from a collunits object.

Usage

## S4 method for signature 'collunits'
datasets(object)

Arguments

Value

datasets from a collunits object

Extract datasets from a site object.

Description

Extract datasets from a site object.

Usage

## S4 method for signature 'site'
datasets(object)

Arguments

Value

datasets from a site object

Extract datasets from a sites object.

Description

Extract datasets from a sites object.

Usage

## S4 method for signature 'sites'
datasets(object)

Arguments

Value

datasets from a sites object

S4 class for datasets information

Description

The grouped class for datasets from the Neotoma Paleoecology Database.

Value

object of class datasets

Obtain the DOI for publications or datasets.

Description

Obtain the DOI for publications or datasets.

Usage

doi(x)

Arguments

Value

doi object with DOI information

Get a publication DOI.

Description

Get a publication DOI.

Usage

## S4 method for signature 'publication'
doi(x)

Arguments

Value

DOI from a publication

Obtain dataset DOIs from records.

Description

Given complete dataset objects in Neotoma (must have used get_datasets() or get_downloads()), return the dataset DOI for the record.

Usage

## S4 method for signature 'site'
doi(x)

Arguments

Value

data.frame object with DOIs information.

Examples

{
ds <- get_datasets(1)
doi(ds)
}

Obtain dataset DOIs from records.

Description

Given complete dataset objects in Neotoma (must have used get_datasets() or get_downloads()), return the dataset DOI for the record.

Usage

## S4 method for signature 'sites'
doi(x)

Arguments

Value

data.frame object with DOIs information.

Examples

{
ds <- get_datasets(1)
doi(ds)
}

Apply a filter for Neotoma sites objects.

Description

The filter function takes a sites object and allows a user to filter on a number of properties. Since a sites object is a nested object (it contains collection units, datasets, samples, etc.) the degree to which filtering occurs depends on the amount of data contained within the sites object. Filtering parameters include:

• siteid A numeric site identifier from the Neotoma Database.

• sitename The character string sitename.

• lat A numeric latitude value.

• long A numeric longitude value.

• altitude The elevation of the site. Note that some sites do not include elevation information. For these an NA value appears, and they would be removed when using an elevation filter.

• datasetid A numeric datasetid from Neotoma.

• database A character string naming the constituent database from which the dataset is drawn.

• datasettype A character string representing one of the many dataset types within Neotoma.

• age_range_old A dataset-level parameter indicating the oldest date covered by the dataset chronology.

• age_range_young A dataset-level parameter indicating the youngest date covered by the dataset chronology.

• notes Free-form dataset notes provided by the dataset PI(s), analysts or data stewards.

• collectionunitid A numeric collection unit identifier from Neotoma.

• handle A character string identifying the collection unit. These are often shorter form names (originally a default 8 character length).

• collectionunitname A character string identifying the collection unit name.

• colldate The date on which the collection unit was sampled. Many of these are empty.

• location A free-form character string indicating the location of the collection unit within the site.

• waterdepth A numeric depth at which the core was obtained.

• collunittype A character string for the collection unit type.

• collectiondevice A fixed vocabulary term for the collection device.

• depositionalenvironment A fixed vocabulary name for the depositional environment.

Usage

filter(x, ...)

Arguments

Value

filtered sites object

Apply a filter for Neotoma sites objects.

Description

The filter function takes a sites object and allows a user to filter on a number of properties. Since a sites object is a nested object (it contains collection units, datasets, samples, etc.) the degree to which filtering occurs depends on the amount of data contained within the sites object. Filtering parameters include:

• siteid A numeric site identifier from the Neotoma Database.

• sitename The character string sitename.

• lat A numeric latitude value.

• long A numeric longitude value.

• altitude The elevation of the site. Note that some sites do not include elevation information. For these an NA value appears, and they would be removed when using an elevation filter.

• datasetid A numeric datasetid from Neotoma.

• database A character string naming the constituent database from which the dataset is drawn.

• datasettype A character string representing one of the many dataset types within Neotoma.

• age_range_old A dataset-level parameter indicating the oldest date covered by the dataset chronology.

• age_range_young A dataset-level parameter indicating the youngest date covered by the dataset chronology.

• notes Free-form dataset notes provided by the dataset PI(s), analysts or data stewards.

• collectionunitid A numeric collection unit identifier from Neotoma.

• handle A character string identifying the collection unit. These are often shorter form names (originally a default 8 character length).

• collectionunitname A character string identifying the collection unit name.

• colldate The date on which the collection unit was sampled. Many of these are empty.

• location A free-form character string indicating the location of the collection unit within the site.

• waterdepth A numeric depth at which the core was obtained.

• collunittype A character string for the collection unit type.

• collectiondevice A fixed vocabulary term for the collection device.

• depositionalenvironment A fixed vocabulary name for the depositional environment.

Usage

## S3 method for class 'sites'
filter(x, ...)

Arguments

Value

filtered sites object

Examples

# Download 100 sites, but only keep the sites that are close to sea level.
some_sites <- get_sites(sitename = "Lake%", limit = 3)
site_subset <- some_sites %>% filter(altitude < 100)
# Download 100 sites, get all associated datasets, but keep only
# sites/datasets that are of datasettype "pollen":
sites <- get_sites(limit = 1) %>%
  get_datasets()
pollen_subset <- sites %>% filter(datasettype == "pollen")

Get contact information for Neotoma contributors

Description

Uses the Neotoma API to search and access information about individuals who have contributed to the data in the Neotoma Paleoecology Database

Usage

get_contacts(x = NA, ...)

Arguments

Value

contacts object

Get contact information for Neotoma contributors

Description

Uses the Neotoma API to search and access information about individuals who have contributed to the data in the Neotoma Paleoecology Database

Usage

## Default S3 method:
get_contacts(x, ...)

Arguments

Value

contacts object

Get contact information for Neotoma contributors

Description

Uses the Neotoma API to search and access information about individuals who have contributed to the data in the Neotoma Paleoecology Database

Usage

## S3 method for class 'numeric'
get_contacts(x, ...)

Arguments

Value

contacts object

get_datasets

Description

The get_datasets() function is a wrapper for the Neotoma datasets API endpoint. The function takes parameters defined by the user and returns dataset information supplied by the Neotoma Paleoecological Database. The user may define all or none of the possible fields.

Usage

get_datasets(x = NA, ...)

Arguments

Details

A dataset is an element nested within neotoma2 site objects. The get_datasets() call returns a list of individual site objects with collunits (collection units) that contain valid, matching dataset elements. So, get_sites() returns only site metadata. get_datasets() returns site metadata, plus metadata about the individual datasets present at that site. The get_datasets() function searches for each site within Neotoma that matches the query parameters, and returns them as a sites object, a list of site objects, plus returns all the additional metadata for the datasets at that site. The get_datasets() command wraps the Neotoma API (api.neotomadb.org) call for datasets. The call itself uses a SQL query which accepts any one of the following parameters:

• siteid The unique site ID (integer) in Neotoma. Can be passed as a vector of site IDs.

• sitename The site name, or approximate match using the % wildcard.

• database The constituent database for the record. See get_table("constituentdatabases")

• datasettype Neotoma contains data for a number of dataset types. This returns a subset of data types. For a complete list of available dataset types, run neotoma2::get_table('datasettypes')

• altmin The minimum altitude range for site elevation (in meters).

• altmax The maximum altitude range for site elevation (in meters).

• datasetid The unique dataset ID (integer) in Neotoma. Can be passed as a vector of dataset IDs.

• doi The dataset DOI for a dataset contained within a site. Can be passed as a vector of DOIs.

• gpid The geopolitical name or identifier containing a site. Can be passed as a vector of names.

• keywords Keywords for samples within a set of sites. For example "modern" indicates a sample within the record uses the keyword "modern".

• contacts Contact names or IDs associated with a site.

• ageyoung A minimum spanning age for the record, in years before radiocarbon present (1950).

• ageold A maximum spanning age for the record, in years before radiocarbon present (1950).

• ageof An age which must be contained within the range of sample ages for a site.

• taxa The names of taxa which must be present within samples in a record.

• all_data The API only downloads the first 25 records of the query. For the complete records, use all_data=TRUE

Value

The function returns either a single item of class "try-error" describing the reason for failure (either misdefined parameters or an error from the Neotoma API), or list of site objects, each containing one or more collunit objects, with fully populated datasets elements.

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

Examples

# To find all datasets with a min altitude of 12 and a max altitude of 25:
sites_12to25 <- get_datasets(altmin=12, altmax=25)
# To find all datasets in Brazil
brazil <- '{"type": "Polygon",
"coordinates": [[
 [-73.125, -9.102096738726443],
 [-56.953125,-33.137551192346145],
 [-36.5625,-7.710991655433217],
 [-68.203125,13.923403897723347],
 [-73.125,-9.102096738726443]]]}'
brazil_datasets <- get_datasets(loc = brazil[1], limit=2)
# To obtain the dataset metadata:
datasets(brazil_datasets)
# There is insufficient metadata at this point to obtain information
# about taxa present at the site. We must use get_downloads() to
# obtain the full set of sample information:
# This fails: taxa(brazil_datasets)

Get Dataset Default

Description

Get Dataset Default

Usage

## Default S3 method:
get_datasets(x, ...)

Arguments

Value

sites object with full metadata up to the dataset level

Get Dataset Numeric

Description

Get Dataset Numeric

Usage

## S3 method for class 'numeric'
get_datasets(x, ...)

Arguments

Value

sites object with full metadata up to the dataset level

Examples

allds <- get_datasets(1:3)

Get Dataset from a site object.

Description

Get Dataset from a site object.

Usage

## S3 method for class 'site'
get_datasets(x, ...)

Arguments

Value

sites object with full metadata up to the dataset level

Examples

random_sites <- get_sites(1)
allds <- get_datasets(random_sites, limit=3)

Get Dataset from a sites object.

Description

Get Dataset from a sites object.

Usage

## S3 method for class 'sites'
get_datasets(x, ...)

Arguments

Value

sites object with full metadata up to the dataset level

Examples

random_sites <- get_sites(1)
allds <- get_datasets(random_sites, limit=3)

get_downloads

Description

Information for Fossil Datasets

Usage

get_downloads(x = NA, verbose = TRUE, ...)

Arguments

Details

The get_downloads() command wraps the Neotoma API (api.neotomadb.org) call for downloads. The call itself uses a SQL query which accepts any one of the following parameters:

• datasetid The unique dataset ID (integer) in Neotoma. Can be passed as a vector of dataset IDs.

• all_data The API only downloads the first 25 records of the query. For the complete records, use all_data=TRUE

Value

The function returns either a single item of class "try-error" describing the reason for failure (either misdefined parameters or an error from the Neotoma API), or a table of sites, with rows corresponding to the number of individual sites and datasets returned by the Neotoma API. Each "site" object contains 6 parameters that can be accessed as well:

Each "collection unit" embedded in the "sites" object contains 6 parameters that can be accessed as well:

Each "dataset" nested in the "collection unit" contains the following detail of information:

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

Examples

# To find the downloads object of dataset 24:
downloads24 <- get_downloads(24)

# To find all downloads in Brazil
brazil <- '{"type": "Polygon",
"coordinates": [[
 [-73.125, -9.102096738726443],
 [-56.953125,-33.137551192346145],
 [-36.5625,-7.710991655433217],
 [-68.203125,13.923403897723347],
 [-73.125,-9.102096738726443]]]}'
brazil_datasets <- get_datasets(loc = brazil[1])
brazil_downloads <- get_downloads(brazil_datasets)

get_downloads

Description

get_downloads

Usage

## S3 method for class 'numeric'
get_downloads(x, ...)

Arguments

Value

The function returns either a single item of class "try-error" describing the reason for failure (either misdefined parameters or an error from the Neotoma API), or a table of sites, with rows corresponding to the number of individual sites and datasets returned by the Neotoma API.

get_downloads sites

Description

get_downloads sites

Usage

## S3 method for class 'sites'
get_downloads(x, verbose = TRUE, ...)

Arguments

Value

The function returns either a single item of class "try-error" describing the reason for failure (either misdefined parameters or an error from the Neotoma API), or a table of sites, with rows corresponding to the number of individual sites and datasets returned by the Neotoma API.

get_manual

Description

Open up the Neotoma manual homepage.

Usage

get_manual()

Value

NULL side effect for opening browser with the manual

Author(s)

Simon Goring goring@wisc.edu

Examples

{
# This call does not work from `source()` calls or in testing.
# interactive() just lets us know you are interacting with the console:
if (interactive()) {
 get_manual()
}
}

Get publication information for Neotoma records

Description

Uses the Neotoma API to search and access information about publications associated with data in the Neotoma Paleoecology Database

Usage

get_publications(x = NA, ...)

Arguments

Value

publications object

Examples

# How old are the papers in Neotoma that include the term "mammut"?
mammoth_papers <- get_publications(search="mammut") %>%
  as.data.frame()
hist(as.numeric(mammoth_papers$year))

Get publication information from Neotoma

Description

Get publication information from Neotoma

Usage

## Default S3 method:
get_publications(...)

Arguments

Value

publications object

Examples

# How old are the papers in Neotoma that include the term "mammut"?
mammoth_papers <- get_publications(search="mammut") %>%
  as.data.frame()
hist(as.numeric(mammoth_papers$year))

Get publications using their unique identifier.

Description

Get publications using their unique identifier.

Usage

## S3 method for class 'numeric'
get_publications(x, ...)

Arguments

Value

publications object

Examples

{
# We want the paper identified in Neotoma as 666:
get_publications(666)
}

Update information for a publications object.

Description

This works for records without publicationids. We assume that data with publicationids is correct.

Usage

## S3 method for class 'publication'
get_publications(x, ...)

Arguments

Value

updated publication object

Examples

# Take a publication object and purposely degrade the metadata:
bad_pub <- get_publications(666)
# Note this only changes the reported year, not the citation string.
bad_pub[[1]]@year <- "1923"
bad_pub[[1]]@publicationid <- NA_integer_
updated_pubs <- get_publications(bad_pub[[1]])
attr(updated_pubs, "matches")
# we see the proper citation in the record:
updated_pubs <- attr(updated_pubs, "matches")[[3]]

Update metadata for a set of publication objects.

Description

Update metadata for a set of publication objects.

Usage

## S3 method for class 'publications'
get_publications(x, ...)

Arguments

Value

publications object

Examples

# Take a publication object and purposely degrade the metadata:
bad_pub <- get_publications(c(666, 667, 668))
# Note this only changes the reported year, not the citation string.
bad_pub[[1]]@year <- "1923"
bad_pub[[1]]@publicationid <- NA_integer_
updated_pubs <- get_publications(bad_pub)
# Only the first publication object has any matches. It's the only one
# that is missing its publicaitonid.
attr(updated_pubs[[1]], "matches")
attr(updated_pubs[[2]], "matches")
# we see the proper citation in the record:
updated_pubs[[1]] <- attr(updated_pubs[[1]], "matches")[[1]]

get_sites

Description

The get_sites() function is a wrapper for the Neotoma sites API endpoint. The function takes parameters defined by the user and returns a list of site information supplied by the Neotoma Paleoecological Database. The user may define all or none of the possible fields.

Usage

get_sites(x = NA, ...)

Arguments

Details

A site object in Neotoma is a physical location at which one or more collection units are located. Each collection unit may have one or more datasets within it, defined by the dataset type. The get_sites() function searches for each site within Neotoma that matches the query parameters, and returns them as a sites object, a list of site objects. The get_sites() command wraps the Neotoma API (api.neotomadb.org) call for sites. The call itself uses a SQL query which accepts any one of the following parameters:

• siteid The unique site ID (integer) in Neotoma. Can be passed as a vector of site IDs.

• sitename The site name, or approximate match using the % wildcard.

• database The constituent database for the record. See get_table("constituentdatabases")

• altmin The minimum altitude range for site elevation (in meters).

• altmax The maximum altitude range for site elevation (in meters).

• datasetid The unique dataset ID (integer) in Neotoma. Can be passed as a vector of dataset IDs.

• datasettype Neotoma contains data for a number of datasettypes. This returns a subset of data types. For a complete list of available datasettypes, run neotoma2::get_table('datasettypes')

• doi The dataset DOI for a dataset contained within a site. Can be passed as a vector of DOIs.

• gpid The geopolitical name or identifier containing a site. Can be passed as a vector of names.

• keywords Keywords for samples within a set of sites. For example "modern" indicates a sample within the record uses the keyword "modern".

• contacts Contact names or IDs associated with a site.

• ageyoung A minimum spanning age for the record, in years before radiocarbon present (1950).

• ageold A maximum spanning age for the record, in years before radiocarbon present (1950).

• ageof An age which must be contained within the range of sample ages for a site.

• taxa The names of taxa which must be present within samples in a record.

• all_data The API only downloads the first 25 records of the query. For the complete records, use all_data=TRUE This call will then return a data object that contains site metadata for one or more sites, along with limited metadata describing the collection units and datasets located at that site.

Value

The function returns either a single item of class "try-error" describing the reason for failure (either misdefined parameters or an error from the Neotoma API), or a table of sites, with rows corresponding to the number of individual sites returned by the Neotoma API. Each "site" object contains 6 parameters that can be accessed as well: siteid, sitename, location, altitude, description, limited collection units information.

• loc An sf object that describes site's location.

• description

• collunits limited information on collunits

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

Examples

## Find sites with a min altitude of 12m and a max altitude of 25m
sites_12to25 <- get_sites(altmin=12, altmax=25)
## Return all sites, using a minimum altitude of 2500m (returns >500 sites):
sites_2500 <- get_sites(altmin=2500, all_data = TRUE)
## To find sites in Brazil
brazil <- '{"type": "Polygon",
"coordinates": [[
 [-73.125, -9.102096738726443],
 [-56.953125,-33.137551192346145],
 [-36.5625,-7.710991655433217],
 [-68.203125,13.923403897723347],
 [-73.125,-9.102096738726443]]]}'
brazil_sites <- get_sites(loc = brazil[1])

# Finding all sites with Liliaceae pollen in 1000 year bins:
lilysites <- c()
for (i in seq(0, 10000, by = 1000)) {
  lily <- get_sites(taxa=c("Liliaceae"),
                    ageyoung = i - 500,
                    ageold = i + 500,
                    all_data = TRUE)
  lilysites <- c(lilysites, length(lily))
}

get_sites

Description

get_sites

Usage

## Default S3 method:
get_sites(...)

Arguments

Value

The function returns either a single item of class "try-error" describing the reason for failure (either misdefined parameters or an error from the Neotoma API), or a table of sites, with rows corresponding to the number of individual sites returned by the Neotoma API. Each "site" object contains 6 parameters that can be accessed as well: siteid, sitename, location, altitude, description, limited collection units information.

• loc An sf object that describes site's location.

• collunits limited information on collunits

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

Get Site Information for Fossil Sites

Description

Get Site Information for Fossil Sites

Usage

## S3 method for class 'numeric'
get_sites(x, ...)

Arguments

Value

The function returns either a single item of class "try-error" describing the reason for failure (either misdefined parameters or an error from the Neotoma API), or a table of sites, with rows corresponding to the number of individual sites returned by the Neotoma API. Each "site" object contains 6 parameters that can be accessed as well: siteid, sitename, location, altitude, description, limited collection units information.

• loc An sf object that describes site's location.

• collunits limited information on collunits

Examples

{
## Find all sites by numeric siteid:
sites <- get_sites(seq(1,3))
}

get_stats

Description

Returns a count of sites, datasets, publications and other objects added to Neotoma during the requested time period.

Usage

get_stats(start, end)

Arguments

Details

This function returns summaries about the data holdings within Neotoma using the existing Neotoma API's summary endpoint. This can provide information about recent uploads (the number of new sites uploaded within the last month, for example), or can be used to provide information about the overall number of sites/datasets (using an arbitrarily high value for end).

Value

data.frame with summary statistics

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

Simon Goring goring@wisc.edu

Examples

last_month <- get_stats(start = 0, end = 1)

Get table record from Neotoma

Description

Call Neotoma and return a table (with limits & offsets for large tables)

Usage

get_table(x, limit = 25, offset = 0)

Arguments

Value

selected table values from the Database

Examples

{
# Returns only the first 25 specimen records.
someSpec <- get_table('specimens')
}

get_taxa

Description

a sites object with the requested taxa.

Usage

get_taxa(x = NA, ...)

Arguments

Value

A Neotoma2 sites object with datasets with the requested taxa.

Get Taxa Default

Description

Get Taxa Default

Usage

## Default S3 method:
get_taxa(x, ...)

Arguments

Value

sites object containing the requested taxa

get_taxon

Description

a sites object with the requested taxa.

Usage

get_taxon(x = NA, ...)

Arguments

Value

A Neotoma2 sites object with datasets with the requested taxa.

Get Taxa Default

Description

Get Taxa Default

Usage

## Default S3 method:
get_taxon(x, ...)

Arguments

Value

sites object containing the requested taxa

Get Taxa Numeric

Description

Get Taxa Numeric

Usage

## S3 method for class 'numeric'
get_taxon(x, ...)

Arguments

Value

sites object with requested taxa

Examples

allds <- get_datasets(1:3)

Get object IDs

Description

This function parses a site object, from site to dataset level and returns a data.frame that contains the site, collectionunit and dataset IDs for each element within the site.

Usage

getids(x, order = TRUE)

Arguments

Value

data.frame containing siteid, datasetid, and collunitid

Get object IDs from a single collectionunit.

Description

From a collectionunit object, return the collectionunit and dataset ids.

Usage

## S3 method for class 'collunit'
getids(x, order = TRUE)

Arguments

Value

data.frame containing siteid, datasetid, and collunitid

Examples

marion <- get_sites(sitename = "Marion Lake") 
collunitids <- getids(collunits(marion)[[1]])

Get object IDs from collectionunits.

Description

From a set of collectionunit objects, return the collectionunit and dataset ids.

Usage

## S3 method for class 'collunits'
getids(x, order = TRUE)

Arguments

Value

data.frame containing siteid, datasetid, and collunitid

Examples

marion <- get_sites(sitename = "Marion Lake")
collunitids <- getids(collunits(marion))

Get object IDs from a site object.

Description

Get object IDs from a site object.

Usage

## S3 method for class 'site'
getids(x, order = TRUE)

Arguments

Value

data.frame containing siteid, datasetid, and collunitid

Get object IDs from sites

Description

Get object IDs from sites

Usage

## S3 method for class 'sites'
getids(x, order = TRUE)

Arguments

Value

data.frame containing siteid, datasetid, and collunitid

Length Method chronologies

Description

Length Method chronologies

Usage

## S4 method for signature 'chronologies'
length(x)

Arguments

Value

integer describing length

Length Method collunits

Description

Length Method collunits

Usage

## S4 method for signature 'collunits'
length(x)

Arguments

Value

length of a collunits object

Length Method datasets

Description

Length Method datasets

Usage

## S4 method for signature 'datasets'
length(x)

Arguments

Value

int that showcases the length of a datasets object

Get the number of publications in a publications object.

Description

Get the number of publications in a publications object.

Usage

## S4 method for signature 'publications'
length(x)

Arguments

Value

int of the length of the publications object

Length Method samples

Description

Length Method samples

Usage

## S4 method for signature 'samples'
length(x)

Arguments

Value

int representing the length of ⁠samples object⁠

Length Method Sites

Description

Length Method Sites

Usage

## S4 method for signature 'sites'
length(x)

Arguments

Value

int with the length of sites object

Length Method taxa

Description

Length Method taxa

Usage

## S4 method for signature 'taxa'
length(x)

Arguments

Value

int that showcases the length of a taxa object

c Method - Combine objects, including NULL

Description

c Method - Combine objects, including NULL

c Method - Combine objects, including NULL

Get slot names

Description

Get all names for named elements within a collunit object.

Usage

## S4 method for signature 'collunit'
names(x)

Arguments

Value

NULL. Shows the names of the slots

Get names of contacts slots

Description

Get names of contacts slots

Usage

## S4 method for signature 'contact'
names(x)

Arguments

Value

names of slots

Get slot names

Description

Get all names for named elements within a dataset object.

Usage

## S4 method for signature 'dataset'
names(x)

Arguments

Value

list with all names of dataset slots

Get slot names for a publication object.

Description

Get slot names for a publication object.

Usage

## S4 method for signature 'publication'
names(x)

Arguments

Value

string with publication slots' names

Get slot names for a publication object.

Description

Get slot names for a publication object.

Usage

## S4 method for signature 'publications'
names(x)

Arguments

Value

string with publications slots' names

Get slot names

Description

Get all names for named elements within a site object.

Usage

## S4 method for signature 'site'
names(x)

Arguments

Value

names of the slots of a site object

Get slot names

Description

Get all names for named elements within a taxon object.

Usage

## S4 method for signature 'taxon'
names(x)

Arguments

Value

list with all names of taxon slots

pingNeotoma

Description

A quick function to test whether or not the Neotoma Database API is currently running.

Usage

pingNeotoma(server = "neotoma")

Arguments

Value

A valid HTTP status code or returns an error if a connection is refused.

Examples

{
test_connection <- pingNeotoma("neotoma")
}

Plot site coordinates using a basic plot.

Description

Plot site coordinates using a basic plot.

Usage

## S4 method for signature 'sites'
plot(x, y, ...)

Arguments

Value

plot object with site coordinates.

plotLeaflet

Description

Plot sites on a leaflet map

Usage

plotLeaflet(object)

Arguments

Value

leaflet map with site markers

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

plotLeaflet

Description

Plot a site on a leaflet map

Usage

## S4 method for signature 'site'
plotLeaflet(object)

Arguments

Value

leaflet map

Examples

modernSites <- get_sites(keyword = "Modern")
plotLeaflet(modernSites[[1]])

plotLeaflet

Description

Plot sites on a leaflet map

Usage

## S4 method for signature 'sites'
plotLeaflet(object)

Arguments

Value

leaflet map

Examples

# Note that by default the limit for queries is 25 records:
modernSites <- get_sites(keyword = "Modern")
plotLeaflet(modernSites)

An S4 class for a single Neotoma publication.

Description

A publication is liked to an individual Neotoma dataset object They are grouped using an S4 publications class.

Value

object of class publication

Examples

{
simon <- new("contact", familyname = "Goring", givennames = "Simon J.")
socorro <- new("contact", familyname = "Dominguez", givennames = "Socorro")
first_author <- new("author", author = simon, order = 1)
second_author <- new("author", author = socorro, order = 2)
author_list <- new("authors", authors = list(first_author, second_author))
pub <- new("publication",
           articletitle = "Top or bottom: Best toast spreading surfaces.",
           journal = "Peanut Butter Science",
           year = "2022",
           volume = "2",
           author = author_list)
           }

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.

Description

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.

Value

object of class publications

S4 class for repositories information

Description

The grouped class for repositories from the Neotoma Paleoecology Database.

Value

object of class repositories

S4 class for repository information

Description

The standard object class for repository from the Neotoma Paleoecology Database.

Value

object of class repository

S4 class for dataset information

Description

The standard object class for samples from the Neotoma Paleoecology Database.

Value

object of class sample

Obtain samples from a record or multiple records.

Description

Obtain samples from a record or multiple records.

Usage

samples(x)

Arguments

Value

data.frame with record information at sample level

samples

Description

Obtain elements from collunit

Usage

## S4 method for signature 'collunit'
samples(x)

Arguments

Value

data.frame with sample records

Get samples from a collectionunit or set of collection units:

Description

Obtain elements from collunits

Usage

## S4 method for signature 'collunits'
samples(x)

Arguments

Value

data.frame with sample records

samples

Description

Obtain elements on the samples level

Usage

## S4 method for signature 'site'
samples(x)

Arguments

Value

data.frame with sample records

Examples

marion <- get_sites(sitename = "Marion Lake") %>%
  get_datasets() %>%
  filter(datasettype == "pollen") %>%
  get_downloads()
pollen <- samples(marion)

samples

Description

Obtain all samples within a sites object

Usage

## S4 method for signature 'sites'
samples(x)

Arguments

Value

data.frame with sample records

Examples

{
dw <- get_downloads(1)
pollen <- samples(dw)
}

S4 class for the set of samples

Description

The grouped class for samples from the Neotoma Paleoecology Database.

Value

object of class samples

Select the best match for an object.

Description

Select the best match for an object.

Usage

selectMatch(x, n)

Arguments

Value

attr Select the match between a local record and a Neotoma match

Select the best match (between a local record and a Neotoma match)

Description

Select the best match (between a local record and a Neotoma match)

Usage

## S4 method for signature 'publication,logical'
selectMatch(x, n)

Arguments

Value

the best match to the selected publication.

Select the best match (between a local record and a Neotoma match)

Description

Select the best match (between a local record and a Neotoma match)

Usage

## S4 method for signature 'publication,numeric'
selectMatch(x, n)

Arguments

Value

the best match to the selected publication.

set chronology information for a new record.

Description

Create a new chronology for a record. Within Neotoma all chronologies have unique numeric identifiers. Within R, because of the need to use the identifiers across objects, and because we want to avoid conflicts between naming systems, a universally unique identifier (UUID) is created for the object ID.

Function to create new chronology objects for personal analysis. The new object will not be uploaded to the database.

Usage

set_chronology(
  x = NA,
  chronologyid = NA_integer_,
  notes = NA_character_,
  contact = list(),
  agemodel = NA_character_,
  ageboundolder = NA_integer_,
  ageboundyounger = NA_integer_,
  isdefault = NA_integer_,
  dateprepared = as.Date(character(0)),
  modelagetype = NA_character_,
  chronologyname = NA_character_,
  chroncontrols = data.frame(0)
)

Arguments

Value

chronology object

set Site Information for Fossil Sites

Description

Function to create new collection unit objects for personal analysis. The new object will not be uploaded to the database.

Usage

set_collunit(
  x = NA,
  collectionunitid = NA_integer_,
  notes = NA_character_,
  handle = NA_character_,
  colldate = as.Date(character(1)),
  location = NA_character_,
  waterdepth = NA_integer_,
  gpslocation = st_as_sf(st_sfc()),
  collunittype = NA_character_,
  collectiondevice = NA_character_,
  collectionunitname = NA_character_,
  depositionalenvironment = NA_character_,
  datasets = NULL,
  chronologies = NULL,
  defaultchronology = NA_integer_
)

Arguments

Value

collunit object

Examples

{
# Create a collunit
my_collunit <- set_collunit(notes = "my lake")
}

Set contact information for a new record.

Description

Create a new contact for a record. Within Neotoma all chronologies have unique numeric identifiers. Within R, because of the need to use the indentifiers across objects, and because we want to avoid conflicts between naming systems, a universally unique identifier (UUID) is created for the object ID.This is not to be updated to the database.

Usage

set_contact(
  x = NA,
  contactid = NA_integer_,
  familyname = NA_character_,
  leadinginitials = NA_character_,
  givennames = NA_character_,
  suffix = NA_character_,
  ORCID = NA_character_,
  title = NA_character_,
  institution = NA_character_,
  email = NA_character_,
  phone = NA_character_,
  contactstatus = NA_character_,
  fax = NA_character_,
  url = NA_character_,
  address = NA_character_,
  notes = NA_character_
)

Arguments

Value

contact object

set Site Information for Fossil Sites

Description

Function to create new dataset objects for personal analysis. The new object will not be uploaded to the database.

Usage

set_dataset(
  x = NA,
  datasetid = NA_integer_,
  datasetname = NA_character_,
  database = NA_character_,
  doi = NA,
  datasettype = NA_character_,
  age_range_old = NA_integer_,
  age_range_young = NA_integer_,
  age_units = NA_character_,
  notes = NA_character_,
  pi_list = NA,
  samples = NULL,
  specimens = NULL
)

Arguments

Value

dataset object

Examples

{
# Create a dataset
my_dataset <- set_dataset(database = "EPD",
                    datasettype = "pollen",
                    notes = "my lake")
}

Set the default chronology within a collectionunit.

Description

Set the default chronology within a collectionunit.

Usage

set_default(x, n)

Arguments

Value

sites object with new default chronology

Change the default age model for a record.

Description

Change the default age model for a record.

Usage

## S4 method for signature 'chronologies'
set_default(x, n)

Arguments

Value

chronologies object with a new defaulted chronology

Create a new publication (or publication set)

Description

A function to create new publication objects by hand.

Usage

set_publications(
  publicationid = NA_integer_,
  publicationtypeid = NA_integer_,
  publicationtype = NA_character_,
  year = NA_character_,
  citation = NA_character_,
  articletitle = NA_character_,
  journal = NA_character_,
  volume = NA_character_,
  issue = NA_character_,
  pages = NA_character_,
  citationnumber = NA_character_,
  doi = NA_character_,
  booktitle = NA_character_,
  numvolumes = NA_character_,
  edition = NA_character_,
  volumetitle = NA_character_,
  seriestitle = NA_character_,
  seriesvolume = NA_character_,
  publisher = NA_character_,
  url = NA_character_,
  city = NA_character_,
  state = NA_character_,
  country = NA_character_,
  originallanguage = NA_character_,
  notes = NA_character_,
  author = NULL
)

Arguments

Value

publication object

set Sample Information

Description

Function to create new samples objects for analysis. The new object will not be uploaded to the database.

Usage

set_sample(
  x = NA,
  ages = list(),
  igsn = NA_character_,
  datum = data.frame(),
  depth = NA_integer_,
  sampleid = NA_integer_,
  thickness = NA_integer_,
  samplename = NA_character_,
  sampleanalyst = list(),
  analysisunitid = NA_integer_,
  analysisunitname = NA_character_
)

Arguments

Value

sample object

Examples

{
# Set an empty sample
my_sample <- set_sample()
}

Set Neotoma API Source or Server

Description

Choose to pull Neotoma data from the main Neotoma server, the development server or from a local instance of the API.

Usage

set_server(server = "neotoma")

Arguments

Value

NULL modifies how to talk to the API (local, dev, server)

Examples

# The user is running the API locally using the node/express API
# cloned from github: https://github.com/NeotomaDB/api_nodetest
set_server(server = "local")
# The user switches back to the remote api server.
set_server(server = "neotoma")

set Site Information for Fossil Sites

Description

set Site Information for Fossil Sites

Usage

set_site(
  x = NA,
  siteid = NA_integer_,
  sitename = NA_character_,
  geography = st_as_sf(st_sfc()),
  altitude = NA_integer_,
  geopolitical = list(),
  area = NA_integer_,
  notes = NA_character_,
  description = NA_character_,
  collunits = NULL
)

Arguments

Value

site object

Examples

{
# Create a site called "My Lake", to
x = sf::st_as_sf(sf::st_sfc(sf::st_point(c(5,5))))
my_site <- set_site(sitename = "My Lake",
                    geography = x,
                    description = "my lake",
                    altitude = 30)
}

Show the collection unit information

Description

Show the collection unit information

Usage

## S4 method for signature 'collunit'
show(object)

Arguments

Value

null used for side effects. Printing a data.frame

Show the collection unit information

Description

Show the collection unit information

Usage

## S4 method for signature 'collunits'
show(object)

Arguments

Value

null used for side effects. Printing a data.frame

Show contact object

Description

Show contact object

Show a contact object

Usage

## S4 method for signature 'contact'
show(object)

## S4 method for signature 'contact'
show(object)

Arguments

Value

null - side effect for printing contact object

Null - prints a data.frame

Show a contacts object.

Description

Show a contacts object.

Usage

## S4 method for signature 'contacts'
show(object)

Arguments

Value

null - side effect for printing contacts object

Show Dataset Method

Description

Show Dataset Method

Usage

## S4 method for signature 'dataset'
show(object)

Arguments

Value

null - side effect, prints a data.frame with dataset metadata

Show Datasets object as a dataframe

Description

Show Datasets object as a dataframe

Usage

## S4 method for signature 'datasets'
show(object)

Arguments

Value

null - side effect, prints a data.frame with datasets metadata

Print publications to screen.

Description

Print publications to screen.

Usage

## S4 method for signature 'publication'
show(object)

Arguments

Value

NULL - side effect function of printing a data.frame

Show the contents of a publication object.

Description

Show the contents of a publication object.

Usage

## S4 method for signature 'publications'
show(object)

Arguments

Value

NULL - side effect function of printing a data.frame

Show a site object as a dataframe

Description

Convert a Neotoma package site object into a data.frame() returning the siteid, sitename, latitude, longitude and altitude of the site.

Usage

## S4 method for signature 'site'
show(object)

Arguments

Value

NULL - side effect for printing a data.frame object

Show sites objects as a dataframe

Description

Return a set of site objects as a single data.frame().

Usage

## S4 method for signature 'sites'
show(object)

Arguments

Value

NULL - side effect for printing a data.frame object

Show Taxa Method

Description

Show Taxa Method

Usage

## S4 method for signature 'taxa'
show(object)

Arguments

Value

null - side effect, prints a data.frame with taxon metadata

Show Taxon Method

Description

Show Taxon Method

Usage

## S4 method for signature 'taxon'
show(object)

Arguments

Value

null - side effect, prints a data.frame with taxon metadata

Show matches for objects.

Description

Show matches for objects.

Usage

showMatch(x)

Arguments

Value

data.frame that marks if a site exists in another sites object

Show matched publication objects.

Description

Show matched publication objects.

Usage

## S4 method for signature 'publication'
showMatch(x)

Arguments

Value

NULL printed matches with other publications

An S4 class for site information

Description

The standard object class for sites from the Neotoma Paleoecology Database.

Value

object of class site

An S4 class for multi-site information

Description

The standard object class for multi-sites from the Neotoma Paleoecology Database.from @returns object of class sites

S4 class for specimen information

Description

The standard object class for specimen from the Neotoma Paleoecology Database.

Value

object of class specimen

S4 class for specimens information

Description

The grouped class for specimens from the Neotoma Paleoecology Database.

Value

object of class specimens

Summary of objects within a sites object.

Description

This function summarizes a sites object, from site level and returns a data.frame that contains the site ID, sitename, collectionunit ID, count of chronologies, count of datasets and types of datasets within the site.

Usage

## S4 method for signature 'sites'
summary(object, ...)

Arguments

Value

data.frame object with site summary information

taxa

Description

Show the samples table

Usage

taxa(object)

Arguments

Value

data.frame with taxa records

Extract taxonomic data from a set of sites.

Description

Extract taxonomic data from a set of sites.

Usage

## S4 method for signature 'collunit'
taxa(object)

Arguments

Value

A data.frame reporting the taxa/data objects, units, elements and other features within a set of records.

Extract taxonomic data from a set of sites.

Description

Extract taxonomic data from a set of sites.

Usage

## S4 method for signature 'collunits'
taxa(object)

Arguments

Value

A data.frame reporting the taxa/data objects, units, elements and other features within a set of records.

Extract taxonomic data from a single site.

Description

Extract taxonomic data from a single site.

Usage

## S4 method for signature 'site'
taxa(object)

Arguments

Value

A data.frame reporting the taxa/data objects, units, elements and other features within a set of records.

Examples

somesites <- get_sites(datasettype = "pollen", limit = 3) %>%
  get_downloads()
diatomtaxa <- taxa(somesites[[1]])

Extract taxonomic data from a set of sites.

Description

From a sites object,

Usage

## S4 method for signature 'sites'
taxa(object)

Arguments

Value

A data.frame reporting the taxa/data objects, units, elements and other features within a set of records.

Examples

somesites <- get_sites(datasettype = "diatom", limit = 3) %>%
  get_downloads()
diatomtaxa <- taxa(somesites)
common_taxa <- diatomtaxa %>%
  dplyr::filter(sites == 3)
  

S4 class for taxa information

Description

Taxa class for taxa information from the Neotoma Paleoecology Database.

Value

object of class taxon

S4 class for specimen information

Description

Taxon class for single taxon information from the Neotoma Paleoecology Database.

Value

object of class taxon

toWide

Description

Obtain a wide table with information regarding of samples grouped by variablename and depth/age.

Usage

toWide(
  x,
  variablenames = c(),
  ecologicalgroups = c(),
  elementtypes = c(),
  unit = c(),
  groupby = "age",
  operation = "prop"
)

Arguments

Value

wide data.frame obtained from long samples data.frame

Examples

fourcorners <- '{"type": "Polygon",
"coordinates": [[
[-109.36060497194846, 37.69552879956651],
[-107.813845732192, 37.69552879956651],
[-107.813845732192, 36.80303716260222],
[-109.36060497194846, 36.80303716260222], 
[-109.36060497194846, 37.69552879956651]
]]}'

# Download all vertebrate localities within a bounding box.
fc_sites <- neotoma2::get_sites(loc = fourcorners[1])
fc_ds <- neotoma2::get_datasets(fc_sites) %>% 
neotoma2::filter(datasettype=="vertebrate fauna")

fc_dl <- neotoma2::get_downloads(fc_ds)
fc_dl1 <- fc_dl[[1]]

fc_smp <- samples(fc_dl1)
toWide(fc_smp, ecologicalgroups=c('AVES', 'RODE'), 
elementtypes='bone/tooth', unit='present/absent')

write CSV

Description

write CSV

Usage

## S4 method for signature 'chronologies'
write.csv(x, ...)

Arguments

Value

null, called for side effects

write CSV

Description

write CSV

Usage

## S4 method for signature 'collunits'
write.csv(x, ...)

Arguments

Value

null side effect for saving a CSV file.

write CSV

Description

write CSV

Usage

## S4 method for signature 'datasets'
write.csv(x, ...)

Arguments

Value

null -side effect for printing a CSV file

write CSV

Description

write CSV

Usage

## S4 method for signature 'sites'
write.csv(x, ...)

Arguments

Value

NULL side effect from saving a csv file

write CSV

Description

write CSV

Usage

## S4 method for signature 'taxa'
write.csv(x, ...)

Arguments

Value

null -side effect for printing a CSV file