Package 'neotoma2'

Title: Working with the Neotoma Paleoecology Database
Description: Access and manipulation of data using the Neotoma Paleoecology Database. <https://api.neotomadb.org/api-docs/>. Examples in functions that require API access are not executed during CRAN checks. Vignettes do not execute as to avoid API calls during CRAN checks.
Authors: Dominguez Vidana Socorro [aut, cre] (ORCID: <https://orcid.org/0000-0002-7926-4935>), Simon Goring [aut] (ORCID: <https://orcid.org/0000-0002-2700-4605>)
Maintainer: Dominguez Vidana Socorro <[email protected]>
License: MIT + file LICENSE
Version: 1.0.11
Built: 2026-04-13 08:21:58 UTC
Source: https://github.com/neotomadb/neotoma2

Help Index

sub

Description

sub

Usage

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

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

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

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

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

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

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

Arguments

x

The sites object
i

The numeric index

Value

sliced site object

sub-sub

Description

Obtain one of the elements within a sites, collectionunits, datasets, etc... Neotoma objects.

Usage

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

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

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

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

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

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

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

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

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

Arguments

x

Neotoma2 nested object
i

iteration in nested list

Value

sliced site object

Examples

## Not run: 
some_site <- get_sites(sitename = "Site%", limit=3)
some_site[[2]]

## End(Not run)

sub-subset

Description

Obtain one of the elements within a nested neotoma2 object

Usage

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

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

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

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

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

## S4 replacement method for signature 'speleothems'
x[[i]] <- value

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

Arguments

x

neotoma2 object
i

iteration in neotoma2 object
value

The value to be used

Value

sites object with reassigned values

subset

Description

subset

Usage

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

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

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

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

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

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

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

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

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

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

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

Arguments

x

A neotoma2 object.
i

The column indicator.
value

The value to be used.

Value

site object with reassigned character values

cash

Description

Obtain slots of a neotoma2 without using at-mark

Usage

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Arguments

x

neotoma2 object
name

name of the slot

Value

value at chosen slot in the site object

cash-set

Description

cash-set

Usage

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

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

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

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

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

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

Arguments

x

A neotoma2 object.
name

name of the slot
value

The value to be used.

Value

neotoma2 object with reassigned values

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

add_chronology(object, x, y)

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

Arguments

object

A collection unit object
x

A chronology object generated using set_chronology()
y

A data.frame of sample ages, with required columns: "analysisunitid", "age", "agetype", "ageolder", and "ageyounger".

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 https://open.neotomadb.org/EPD_binder/complex_workflow.html documentation online.

Value

chronologies with new added chronology

Author(s)

Socorro Dominguez [email protected]

as.data.frame

Description

Returns neotoma2 object's data as a data.frame.

Usage

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Arguments

x

neotoma2 object

Value

data.frame object

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)
}

c - Combine neotoma2 objects

Description

c - Combine neotoma2 objects

Usage

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

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

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

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

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

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

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

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

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

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

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

Arguments

x

neotoma2 object or NULL
y

neotoma2 object or NULL

Value

concatenated and cleaned sites 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, ...)

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

Arguments

x

contacts A contacts object associated with a set of names.
...

Additional parameters associated with the call.
similarity

The similarity score between matched records (from 0 - 1).

Value

contacts object

Author(s)

Simon Goring [email protected]

chroncontrols

Description

Show the samples table

Usage

chroncontrols(x)

Arguments

x

Sites object to extract chroncontrols table from

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

x

site object

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

x

sites object

Value

data.frame with chronological controls

Author(s)

Socorro Dominguez [email protected]

Obtain the chronology from a record or multiple records.

Description

Obtain the chronology from a record or multiple records.

Usage

chronologies(x)

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

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

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

Arguments

x

sites object that contains chronologies

Value

chronologies object with all chronologies used.

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. The individual chronology classes are grouped into an S4 chronologies class.

Value

object of class chronologies

Extract chronologies from a sites or collunits object.

Description

Extract chronologies from a sites or collunits object.

Usage

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

Arguments

x

A sites or collunits object

Value

chronologies from a collunit object

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)

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

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

Arguments

x

Object with DOIs associated to it.

Value

data.frame with citation data

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

x

sites object

Value

data.frame object with citation information.

Examples

## Not run: 
# Get datasets metadata from API
ds <- get_datasets(1)

## End(Not run)

clean Neotoma objects to remove duplicates and empty objects.

Description

Function that removes duplicate objects such as sites, datasets, or collection units. When we pull in a large number of objects, or overlapping searches, we can run into a problem where we have multiple instances of the same site, but with different datasets. This function attempts to gather all objects together:

  • Before: {site: 1, dataset: 1}, {site: 1, dataset: 2}

  • After: {site: 1, dataset: [1, 2]} So the site is gathered, and the datasets are now part of an array of datasets.

Usage

clean(x, verbose = TRUE, ...)

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

## S3 method for class 'collunits'
clean(x, verbose = TRUE, ...)

## S3 method for class 'datasets'
clean(x, verbose = TRUE, ...)

Arguments

x

sites, datasets, collunits that may have duplicates.
verbose

parameter to prints out progress bar
...

Additional parameters associated with the call.

Value

clean neotoma objects without duplicates after concatenation

Author(s)

Simon Goring [email protected]

Examples

## Not run: 
tryCatch({
  alex <- get_sites(sitename = "Alex%")
  alex2 <- get_sites(24)
  c <- c(alex, alex2) #uncleaned
}, error = function(e) {
  message("Neotoma server not responding. Try again later.")
})

## End(Not run)

Extract collection units from a sites object

Description

Extract collection units from a sites object

Usage

collunits(object)

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

Arguments

object

A sites object

Value

collunits detail from a sites object

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 collunits

Extract collunits from a sites object.

Description

Extract collunits from a sites object.

Usage

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

Arguments

object

A sites object

Value

collunits from a sites object

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 contact

Examples

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

Obtain coordinates from a sites object.

Description

Obtain coordinates from a sites object.

Usage

coordinates(obj, ...)

Arguments

obj

A sites object
...

Additional parameters associated with the call.

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

obj

A sites object
...

Additional parameters associated with the call.

Value

data.frame object with site coordinates.

S4 class for datasets information

Description

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

Value

object of class datasets

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)

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

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

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

Arguments

object

A sites object

Value

datasets object specific to the metadata contained in datasets

Extract datasets from a sites or collunits object.

Description

Extract datasets from a sites or collunits object.

Usage

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

Arguments

object

A sites orcollunits object

Value

datasets object

Obtain the DOI for publications or datasets.

Description

Obtain the DOI for publications or datasets.

Usage

doi(x)

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

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

Arguments

x

Object with DOIs associated to it.

Value

doi object with DOI information

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

x

a Neotoma2 site object

Value

data.frame object with DOIs information.

Examples

## Not run: 
# Get datasets metadata from API and retrieve DOIs
ds <- get_datasets(1)
doi(ds)

## End(Not run)

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(.data, ..., .by = NULL, .preserve = FALSE)

## S3 method for class ''NULL''
filter(.data, ...)

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

## S3 method for class 'data.frame'
filter(.data, ..., .by = NULL, .preserve = FALSE)

Arguments

.data

A site, dataset, download, or data frame
...

Additional arguments passed to filter()
.by

(only used for filtering data.frame objects)
.preserve

(only used for filtering data.frame objects)

Value

filtered sites object

Author(s)

Simon Goring [email protected]

Socorro Dominguez [email protected]

Examples

## Not run: 
# Download 10 sites, but only keep the sites that are close to sea level.
tryCatch({
 some_sites <- get_sites(sitename = "Lake%", limit = 3)
  site_subset <- some_sites %>% filter(altitude < 100)
}, error = function(e) {
  message("Neotoma server not responding. Try again later.")
})
# Download 10 sites, get all associated datasets, but keep only
# sites/datasets that are of datasettype "pollen":
tryCatch({
  sites <- get_sites(limit = 10) %>%
    get_datasets()
  pollen_subset <- sites %>% filter(datasettype == "pollen")
}, error = function(e) {
  message("Neotoma server not responding. Try again later.") 
})

## End(Not run)

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, ...)

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

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

Arguments

x

integer A contact ID
...

(contactname) A full or partial name for an individual contributor to the database. (familyname) The full or partial last name for an individual contributor to the database. (status) The current status of the contributor (active or retired)

Value

contacts object

Author(s)

Simon Goring [email protected]

Socorro Dominguez [email protected]

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, ...)

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

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

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

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

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

Arguments

x

A single datasetid, or a vector of unique dataset ids.
...

accepted arguments, see details for more information.

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 [email protected]

Examples

## Not run: 
tryCatch({
  random_sites <- get_sites(1)
  allds <- get_datasets(random_sites, limit=3)
}, error = function(e) {
   message("Neotoma server not responding. Try again later.")
})
# To find all datasets with a min altitude of 12 and a max altitude of 25:
tryCatch({
  sites_12to25 <- get_datasets(altmin=12, altmax=25)
}, error = function(e) {
  message("Neotoma server not responding. Try again later.")
})
# 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]]]}'
tryCatch({
  brazil_datasets <- get_datasets(loc = brazil[1], limit=2)
}, error = function(e) {
  message("Neotoma server not responding. Try again later.")
})

## End(Not run)

get_documentation

Description

Open up the Neotoma R homepage.

Usage

get_documentation()

Author(s)

Socorro Dominguez [email protected]

Examples

## Not run: 
if (interactive()) {
 get_documentation()
}

## End(Not run)

get_downloads

Description

Download sites objects up to datum and chronology detail level.

Usage

get_downloads(x = NA, ...)

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

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

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

Arguments

x

Use a single number to extract site information
...

accepted arguments: sites, datasets
verbose

Status bar of items being downloaded

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:

siteid

site ID number
sitename

site's name
location

sf object that describes site's location
description
collunits

limited information on collunits

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

collunitid

collection unit ID number
handle

collection unit's handle
collunitname

collection unit's name
colldate

date in collection unit
substrate

substrate
location

sf object that describes site's location
datasets

detailed information regarding dataset

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

datasetid

dataset ID number
datasetname

site's name
datasettype

type of data found
location

sf object that describes site's location
notes

notes on the dataset
taxa table

taxa table
pi list

P.I. info
analyst

analyst info
metadata

dataset metadata

Author(s)

Socorro Dominguez [email protected]

Examples

## Not run: 
# To find the downloads object of dataset 24:
tryCatch({
  downloads24 <- get_downloads(24)
}, error = function(e) {
 message("Neotoma server not responding. Try again later.")
})
# 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]]]}'
tryCatch({
  brazil_datasets <- get_datasets(loc = brazil[1])
  brazil_downloads <- get_downloads(brazil_datasets)
}, error = function(e) {
  message("Neotoma server not responding. Try again later.")
})

## End(Not run)

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 [email protected]

Examples

## Not run: 
# 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()
}

## End(Not run)

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, ...)

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

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

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

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

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

Arguments

x

integer A contact ID
...

publicationid The unique numeric identifier associated with a publication in Neotoma. datasetid A unique identifier for a Neotoma dataset that is associated with a publication. familyname The full or partial last name for an individual author. pubtype The publication type, from get_tables("publicationtypes"). year The year the publication was released. search A plain text search string used to search the citation.

Value

publications object

Examples

## Not run: 
# How old are the papers in Neotoma that include the term "mammut"?
tryCatch({
  mammoth_papers <- get_publications(search="mammut") %>%
    as.data.frame()
  hist(as.numeric(mammoth_papers$year))
}, error = function(e) {
 message("Neotoma server not responding. Try again later.")
})
# We want the paper identified in Neotoma as 666:
tryCatch({
get_publications(666)
}, error = function(e) {
message("Neotoma server not responding. Try again later.")
})
# Take a publication object and purposely degrade the metadata:
tryCatch({
  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]]
}, error = function(e) {
 message("Neotoma server not responding. Try again later.")
})

## End(Not run)

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, ...)

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

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

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

Arguments

x

Use a single integer or vector of integers representing unique Neotoma site identifiers (siteids) to extract site information.
...

accepted arguments, see details for more information.

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 [email protected]

Examples

## Not run: 
## Find sites with a min altitude of 12m and a max altitude of 25m
sites_12to25 <- get_sites(altmin=12, altmax=25)
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])

## End(Not run)

get_speleothems

Description

get_speleothems

Usage

get_speleothems(x = NA, ...)

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

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

Arguments

x

A dataset ID or vector of dataset IDs
...

accepted arguments

Details

Experimental function: API and behavior may change. The get_speleothems() command wraps the Neotoma API (api.neotomadb.org) call for speleothems. The call itself uses a SQL query which accepts any one of the following parameters:

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

  • sites A sites R object.

Value

sites object with speleothem data

Author(s)

Socorro Dominguez [email protected]

Examples

## Not run: 
## Find speleothems by numeric datasetid:
speleo <- get_speleothems(c(2,5))

## End(Not run)

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 = 0, end = 1, type = "dsdbmonth")

Arguments

start

The starting month (from present == 0) for which to generate the summary. Default is 0 (the current month).
end

The ending month (from present == 0) for which to generate the summary. Default is 1 (one month ago).
type

A character string indicating the type of summary to return. Options are dsdbmonth (the number of datasets in the Neotoma Database added per month), rawbymonth (the number of datasets, sites, publications, authors, countries and observations added per month), and dstypemonth (the number of datasets added per dataset type per month). Default is dsdbmonth.

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 [email protected]

Simon Goring [email protected]

Examples

## Not run: 
tryCatch({
last_month <- get_stats(start = 0, end = 1, type = "dsdbmonth")
}, error = function(e) {
 message("Neotoma server not responding. Try again later.")
})

## End(Not run)

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

x

Table name (consult https://open.neotomadb.org/dbschema/ for a complete list of table names.
limit

Default 25 records
offset

Default 0.

Value

selected table values from the Database.

Examples

## Not run: 
# Returns only the first 25 specimen records.
someSpec <- get_table('specimens')

## End(Not run)

get_taxa

Description

a sites object with sites that contain the requested taxa.

Usage

get_taxa(x = NA, ...)

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

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

Arguments

x

A taxon ID to extract site information
...

accepted arguments, see details for more information.

Details

The get_taxa function searches for a sites within Neotoma that contain the requested taxa. The get_taxa command wraps the Neotoma API'. The call itself accepts any one of the following parameters:

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

Value

A Neotoma2 sites object with datasets with the requested taxa.

Author(s)

Socorro Dominguez [email protected]

get_taxon

Description

a taxon object with detailed information

Usage

get_taxon(x = NA, ...)

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

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

Arguments

x

taxon ID
...

accepted arguments, see details for more information.

Details

A taxa may have one or more taxa associated with it. The get_taxon function searches for taxa detail data within Neotoma while the get_taxa function searches for sites that contain the requested taxa. The function searches for each taxon by using a SQL query which accepts any one of the following parameters:

  • taxonid The unique taxon ID (integer) in Neotoma. Can be passed as a vector of taxa IDs.

  • taxonname Taxon name or partial name. You can pass wildcard characters using %.

  • taxagroup The taxonomic grouping the taxon belongs to, from the Neotoma taxagrouptypes table.

  • ecolgroup The ecological group of interest for the Neotoma taxon (from the Neotoma ecolgrouptypes table)

  • status The taxonomic extinction status of the taxon, either extinct (1, True) or extant (0, False).

Value

A Neotoma2 taxa object with datasets with the requested taxa.

Author(s)

Socorro Dominguez [email protected]

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)

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

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

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

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

Arguments

x

A Neotoma2 sites or collunits object.
order

sort items by siteid, collunitid, datasetid

Value

data.frame containing siteid, datasetid, and collunitid

Author(s)

Simon Goring [email protected]

Examples

## Not run: 
marion <- get_sites(sitename = "Marion Lake")
collunitids <- getids(collunits(marion))

## End(Not run)

length

Description

length

Usage

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

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

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

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

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

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

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

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

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

Arguments

x

neotoma2 object

Value

int representing length of a neotoma2 object

c Method - Combine objects, including NULL

Description

c Method - Combine objects, including NULL

Get a neotoma2 object's slot names

Description

Get all names for elements' slots within a collunit object.

Usage

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

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

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

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

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

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

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

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

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

Arguments

x

A neotoma2 object.

Value

NULL.

pingNeotoma

Description

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

Usage

pingNeotoma(server = "neotoma")

Arguments

server

One of localhost:PORT (where PORT is a valid numeric port), neotoma or dev.

Value

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

Examples

## Not run: 
test_connection <- pingNeotoma("neotoma")

## End(Not run)

Plot site coordinates using a basic plot.

Description

Plot site coordinates using a basic plot.

Usage

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

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

Arguments

x

sites object
y

Ignored.
...

Additional parameters associated with the call.

Value

plot object with site coordinates.

plotLeaflet

Description

Plot sites on a leaflet map

Usage

plotLeaflet(object)

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

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

Arguments

object

Sites object to plot

Value

leaflet map with site markers

Author(s)

Socorro Dominguez [email protected]

plotLeaflet

Description

Plot sites on a leaflet map

Usage

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

Arguments

object

Sites object to plot

Value

leaflet map

Examples

## Not run: 
# Note that by default the limit for queries is 25 records:
tryCatch({
modernSites <- get_sites(keyword = "Modern")
plotLeaflet(modernSites)
}, error = function(e) {
 message("Neotoma server not responding. Try again later.")
})

## End(Not run)

An S4 class for Neotoma publications.

Description

A publication is liked to an individual Neotoma dataset object They are grouped using an S4 publications class. This publications class allows a single dataset to have one or more publication classes associated with it.

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)
           }

S4 class for repository information

Description

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

Value

object of class repository

Obtain samples from a record or multiple records.

Description

Obtain samples from a record or multiple records.

Usage

samples(x)

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

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

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

Arguments

x

sites object

Value

data.frame with record information at sample level

S4 class for samples information

Description

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

Value

object of class sample

samples

Description

Obtain all samples within a sites object

Usage

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

Arguments

x

sites object

Value

data.frame with sample records

Author(s)

Socorro Dominguez [email protected]

Simon Goring [email protected]

Examples

## Not run: 
# Get full data download from API and create a long table with samples data.
dw <- get_downloads(1)
pollen <- samples(dw)

## End(Not run)

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

x

Object to be set as a chronology
chronologyid

An optional value. Will be assigned a unique identifier if not provided.
notes

Additional notes about the chronology. For more modern models, often the function call to Bacon or Bchron is added here.
contact

A contacts object, identifying the individual(s) who created the chronology
agemodel

A string representing the age model name, for example "Crummy linear interpolation".
ageboundolder

The ageboundolder is assigned the oldest sample age rounded up to the nearest 10
ageboundyounger

The ageboundyounger is assigned the oldest sample age rounded up to the nearest 10
isdefault

Defines whether the model is the default for the collection unit for a particular model age type.
dateprepared

The date at which the age model was prepared.
modelagetype

The age type for the model. For validation, the models should be one of the valid Neotoma agetypes: https://api.neotomadb.org/v2.0/data/dbtables?table=agetypes
chronologyname

A valid name for the chronology.
chroncontrols

A data.frame containing the chronological controls for the age model.

Value

chronology object

Author(s)

Socorro Dominguez [email protected]

Simon Goring [email protected]

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_,
  speleothems = NULL
)

Arguments

x

object to be set as collunit
collectionunitid

collection unit identifier
notes

notes
handle

handle
colldate

collection date
location

location of the collection unit
waterdepth

depth at where the sample is taken
gpslocation

location with GPS
collunittype

type of collection unit
collectiondevice

device used to collect the sample
collectionunitname

name of the collection unit
depositionalenvironment

depositional environment
datasets

datasets that the collection unit has
chronologies

chronologies taken from the collection unit
defaultchronology

best chronology model identifier to be used with this collection unit
speleothems

speleothems associated with the collection unit

Value

collunit object

Author(s)

Socorro Dominguez [email protected]

Simon Goring [email protected]

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_,
  contactname = 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

x

Object to be set as a contact
contactid

An arbitrary Contact identification number.
familyname

Family or surname name of a person.
leadinginitials

Leading initials for given or forenames without spaces (e.g. G.G.).
givennames

Given or forenames of a person (e.g. George Gaylord). Initials with spaces are used if full given names are not known (e.g. G. G).
contactname

Full name of a person (e.g. George Gaylord Simpson).
suffix

Suffix of a person’s name (e.g. Jr., III).
ORCID

A unique ORCID (see https://orcid.org).
title

A person’s title (e.g. Dr., Prof., Prof. Dr).
institution

The institution where an individual works.
email

An individuals email address
phone

Their phone number
contactstatus

Are they "active" or "retired"?
fax

Do people still use fax machines?
url

Their homepage
address

A physical address
notes

Notes about the individual

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,
  recdatecreated = as.Date(character(1)),
  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

x

object to be set as dataset,
datasetid

dataset identifier
datasetname

name of the dataset
database

dataset where the dataset came from
doi

DOI
recdatecreated

date the dataset was created
datasettype

type the dataset belongs to
age_range_old

age range old
age_range_young

age range young
age_units

age units
notes

notes
pi_list

pi list
samples

taxa objects
specimens

specimens slot

Value

dataset object

Author(s)

Socorro Dominguez [email protected]

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

x

A chronologies object.
n

The particular chronology to be used as the default.

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

x

A chronologies object.
n

The particular chronology to be used as the default.

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_publication(
  x = NA,
  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

x

"publications" object to be updated.
publicationid

ID of publication
publicationtypeid

ID of kind of publication
publicationtype

A text string identifying the publication type within the Neotoma database.
year

The year of publication.
citation

A full text citation for the article.
articletitle

The title of the article.
journal

The journal in which the article was published.
volume

The journal volume.
issue

The journal issue.
pages

The pages of the journal.
citationnumber

How many times has the paper been cited?
doi

A DOI for the record.
booktitle

The title of the book (if the publication is a book)
numvolumes

The number of book volumes (if a series)
edition

The book edition.
volumetitle

The title of the volume (in a published series)
seriestitle

The title of the series.
seriesvolume

The series volume.
publisher

The publisher.
url

Publication URL
city

City of publication.
state

State of publication.
country

Country of publication.
originallanguage

Original language of publication.
notes

Publication notes.
author

name of the author of publication.

Value

publication object

Author(s)

Simon Goring [email protected]

Socorro Dominguez [email protected]

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

x

Object to be set as a sample
ages

ages
igsn

IGSN character
datum

dataframe of datum
depth

integer representing depth
sampleid

ID for sample
thickness

thickness of core
samplename

sample's name
sampleanalyst

Analyst's contact name
analysisunitid

Which analysis unit it is
analysisunitname

Analysis Unit's name

Value

sample object

Author(s)

Socorro Dominguez [email protected]

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

server

One of local (when the API is running locally on port 3005), neotoma or dev.

Value

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

Author(s)

Simon Goring [email protected]

Examples

## Not run: 
# 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")

## End(Not run)

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 = sf::st_as_sf(sf::st_sfc()),
  altitude = NA_integer_,
  geopolitical = list(),
  area = NA_integer_,
  notes = NA_character_,
  description = NA_character_,
  collunits = NULL
)

Arguments

x

Object to be set as a site
siteid

The unique ⁠site id⁠ for a site. If this site is new to Neotoma then leave the ID as NA.
sitename

Name of a site.
geography

A sf object representing the site location, either as a polygon or point.
altitude

altitude/elevation of the site.
geopolitical

The geopolitical unit in which the site is located.
area

The area of the site or depositional basin in ha. Can be calculated from the polygon.
notes

additional information of the site
description

Function to create new site objects. The new object will not be uploaded to the database.
collunits

Collection units in the site

Value

site object

Author(s)

Socorro Dominguez [email protected]

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)
}

Set Speleothem

Description

Set Speleothem

Usage

set_speleothem(
  x = NA,
  entityid = NA_integer_,
  entityname = NA_character_,
  siteid = NA_integer_,
  collectionunitid = NA_integer_,
  dripheight = NA_integer_,
  monitoring = FALSE,
  geology = NA_character_,
  relativeage = NA_character_,
  speleothemtype = NA_character_,
  dripheightunits = NA_character_,
  entitycovertype = NA_character_,
  entrancedistance = NA_integer_,
  landusecovertype = NA_character_,
  speleothemdriptype = NA_character_,
  landusecoverpercent = NA_integer_,
  vegetationcovertype = NA_character_,
  entitycoverthickness = NA_integer_,
  entrancedistanceunits = NA_character_,
  vegetationcoverpercent = NA_integer_
)

Arguments

x

Object to be set as a speleothem
entityid

The speleothem entity ID.
entityname

Name of the speleothem entity.
siteid

The unique site ID for a site.
collectionunitid

The unique collection unit ID for a collection unit.
dripheight

drip height
monitoring

Is the speleothem being monitored? TRUE/FALSE
geology

rock type of the speleothem
relativeage

relative age of the speleothem
speleothemtype

type of speleothem
dripheightunits

Units for drip height
entitycovertype

type of cover around the speleothem
entrancedistance

distance from cave entrance
landusecovertype

type of land use cover around the speleothem
speleothemdriptype

type of speleothem drip
landusecoverpercent

land use cover percent
vegetationcovertype

type of vegetation cover around the speleothem
entitycoverthickness

thickness of the entity cover
entrancedistanceunits

Units for distance from cave entrance
vegetationcoverpercent

vegetation cover percent

Value

speleothem object

Author(s)

Socorro Dominguez [email protected]

Display a sites object or nested slots.

Description

Display a sites object or nested slots.

Usage

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Arguments

object

sites, datasets, collunits, contacts object

An S4 class for sites information

Description

The S4 class for sites in the Neotoma Paleoecology Database.

Value

object of class sites

S4 class for specimens information

Description

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

Value

object of class specimens

Obtain speleothems and samples from a record or multiple records.

Description

Obtain speleothems and samples from a record or multiple records.

Usage

speleothemdetails(x)

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

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

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

Arguments

x

sites object

Value

data.frame with record information at speleothem level

speleothemdetails

Description

Obtain elements on the speleothems level Experimental function: API and behavior may change.

Usage

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

Arguments

x

site object

Value

data.frame with speleothem records

Author(s)

Socorro Dominguez [email protected]

Examples

## Not run: 
kesang <- get_sites(sitename = "Kesang cave") %>%
  get_datasets() %>%
  filter(datasettype == "pollen") %>%
  get_speleothems()
sp <- speleothemdetails(kesang)

## End(Not run)

Obtain speleothems from a record or multiple records.

Description

Obtain speleothems from a record or multiple records.

Usage

speleothems(x)

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

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

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

Arguments

x

sites object

Value

data.frame with record information at speleothem level

S4 class for speleothem information

Description

The S4 class for speleothem data.

Value

object of class speleothems

speleothems

Description

Obtain all speleothems within a sites object Experimental function: API and behavior may change.

Usage

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

Arguments

x

sites object

Value

data.frame with sample records

Author(s)

Socorro Dominguez [email protected]

Examples

## Not run: 
ds <- get_datasets(37302)
sp <- speleothems(ds)

## End(Not run)

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

object

sites object
...

additional properties passed to summary

Value

data.frame object with site summary information

taxa

Description

Show the samples table

Usage

taxa(object)

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

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

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

Arguments

object

Sites object to extract taxa table from

Value

data.frame with taxa records

S4 class for taxa information

Description

Taxa details from the Neotoma Paleoecology Database.

Value

object of class taxon

Extract taxonomic data from a set of sites.

Description

Extract taxonomic data from a set of sites.

Usage

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

Arguments

object

A sites object.

Value

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

Author(s)

Socorro Dominguez [email protected]

Examples

## Not run: 
somesites <- get_sites(datasettype = "diatom") %>%
  get_downloads()
diatomtaxa <- taxa(somesites)

## End(Not run)

toWide

Description

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

Usage

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

Arguments

x

dataframe object with samples
variablenames

Optional vector to filter by specific variable names.
ecologicalgroups

Vector stating the ecological groups to be filtered by, e.g "DIAT", "TRSH"
elementtypes

Label of element type to filter by, e.g. "pollen", "valve"
unit

Label stating which units to filter by, e.g. "NISP"
groupby

Group by 'age' or 'depth'
operation

label or vector of operations to be chosen from: 'prop', 'sum', 'presence'.

Value

wide data.frame obtained from long samples data.frame

Author(s)

Socorro Dominguez [email protected]

Examples

## Not run: 
fc_sites <- neotoma2::get_datasets(limit=5, datasettype = "vertebrate fauna")
fc_ds <- fc_sites %>%
   neotoma2::get_downloads()
fc_dl1 <- fc_dl[[1]]
fc_smp <- samples(fc_dl1)
toWide(fc_smp, ecologicalgroups=c('AVES', 'RODE'),
       elementtypes='bone/tooth', unit='present/absent')

## End(Not run)