Title:	Working with the Neotoma Paleoecology Database
Date:	2025-11-15
Version:	1.0.8
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:	7.3.3
Suggests:	testthat, knitr, pkgdown, rmarkdown, ggplot2, Bchron, covr,
Imports:	rlang, magrittr, sf, digest, geojsonsf, purrr, httr, jsonlite, methods, dplyr, leaflet, assertthat, stringr, progress, uuid, utils, tidyr
VignetteBuilder:	knitr
NeedsCompilation:	no
Packaged:	2025-11-16 01:20:28 UTC; sedv8808
Author:	Dominguez Vidana Socorro [aut, cre], Simon Goring [aut]
Maintainer:	Dominguez Vidana Socorro <dominguezvid@wisc.edu>
Repository:	CRAN
Date/Publication:	2025-11-18 08:50:02 UTC

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

Value

neotoma2 object with reassigned 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

Value

value at chosen slot in the site object

Pipe operator See magrittr::%>% for details.

Description

Pipe operator See magrittr::%>% for details.

Usage

lhs %>% rhs

Value

NULL; allows using tidyverse pipe operator.

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

Value

site object with reassigned character values

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

Value

sliced site object

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

Value

sites object with reassigned values

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

Value

sliced site object

Examples

tryCatch({
  some_site <- get_sites(sitename = "Site%", limit=3)
  some_site[[2]]
}, error = function(e) {
  message("Neotoma server not responding. Try again later.")
})

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

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 dominguezvid@wisc.edu

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

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

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

Value

contacts object

Author(s)

Simon Goring goring@wisc.edu

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

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

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

Value

chronologies object with all chronologies used.

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

Value

chronologies from a collunit object

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

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

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

Value

data.frame object with citation information.

Examples

{
tryCatch({
ds <- get_datasets(1)
cite_data(ds)
}, error = function(e) {
message("Neotoma server not responding. Try again later.")
})
}

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

Value

clean neotoma objects without duplicates after concatenation

Author(s)

Simon Goring goring@wisc.edu

Examples

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.")
})

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

Value

collunits detail from a sites 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

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

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

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 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

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

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

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

Value

data.frame object with DOIs information.

Examples

{
tryCatch({
ds <- get_datasets(1)
doi(ds)
}, error = function(e) {
message("Neotoma server not responding. Try again later.")
})
}

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

Value

filtered sites object

Author(s)

Simon Goring goring@wisc.edu

Socorro Dominguez dominguezvid@wisc.edu

Examples

# 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.") 
})

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

Value

contacts object

Author(s)

Simon Goring goring@wisc.edu

Socorro Dominguez dominguezvid@wisc.edu

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, ...)

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

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.")
})

get_documentation

Description

Open up the Neotoma R homepage.

Usage

get_documentation()

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

Examples

if (interactive()) {
 get_documentation()
}

get_downloads

Description

Download sites objects up to datum and chronology detail level.

Usage

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

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

## S3 method for class 'sites'
get_downloads(x, 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:
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.")
})

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_params

Description

get_params

Usage

get_params(obj)

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

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, ...)

## 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, ...)

Arguments

Value

publications object

Examples

# 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.")
})

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(...)

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
tryCatch({
  sites_12to25 <- get_sites(altmin=12, altmax=25)
}, error = function(e) {
  message("Neotoma server not responding. Try again later.")
})
## Return all sites, using a minimum altitude of 2500m (returns >500 sites):
tryCatch({
  sites_2500 <- get_sites(altmin=2500, all_data = TRUE)
}, error = function(e) {
  message("Neotoma server not responding. Try again later.")
})
  ## 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]]]}'
tryCatch({
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))
}
}, error = function(e) {
  message("Neotoma server not responding. Try again later.")
})

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

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 dominguezvid@wisc.edu

Examples

{
## Find speleothems by numeric datasetid:
tryCatch({
  speleo <- get_speleothems(c(2,5))
}, error = function(e) {
  message("Neotoma server not responding. Try again later.")
})
}

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

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

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

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.
tryCatch({
someSpec <- get_table('specimens')
}, error = function(e) {
 message("Neotoma server not responding. Try again later.")
})
}

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

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 dominguezvid@wisc.edu

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

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 dominguezvid@wisc.edu

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

Value

data.frame containing siteid, datasetid, and collunitid

Author(s)

Simon Goring goring@wisc.edu

Examples

tryCatch({
marion <- get_sites(sitename = "Marion Lake")
collunitids <- getids(collunits(marion))
}, error = function(e) {
 message("Neotoma server not responding. Try again later.")
})

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

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

Value

NULL.

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, ...)

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

Arguments

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

Value

leaflet map with site markers

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

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:
tryCatch({
modernSites <- get_sites(keyword = "Modern")
plotLeaflet(modernSites)
}, error = function(e) {
 message("Neotoma server not responding. Try again later.")
})

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

Value

data.frame with record information at sample level

samples

Description

Obtain all samples within a sites object

Usage

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

Arguments

Value

data.frame with sample records

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

Simon Goring goring@wisc.edu

Examples

{
tryCatch({
dw <- get_downloads(1)
pollen <- samples(dw)
}, error = function(e) {
 message("Neotoma server not responding. Try again later.")
})
}

S4 class for samples information

Description

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

Value

object of class sample

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

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

Simon Goring goring@wisc.edu

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

Value

collunit object

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

Simon Goring goring@wisc.edu

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

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

Value

dataset object

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

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_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

Value

publication object

Author(s)

Simon Goring goring@wisc.edu

Socorro Dominguez dominguezvid@wisc.edu

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

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

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)

Author(s)

Simon Goring goring@wisc.edu

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

Arguments

Value

site object

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

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

Value

speleothem object

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

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

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

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

Value

data.frame with speleothem records

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

Examples

tryCatch({
kesang <- get_sites(sitename = "Kesang cave") %>%
  get_datasets() %>%
  filter(datasettype == "pollen") %>%
  get_speleothems()
sp <- speleothemdetails(kesang)
}, error = function(e) {
message("Neotoma server not responding. Try again later.")
})

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

Value

data.frame with record information at speleothem level

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

Value

data.frame with sample records

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

Examples

{
tryCatch({
ds <- get_datasets(37302)
sp <- speleothems(ds)
}, error = function(e) {
message("Neotoma server not responding. Try again later.")
})
}

S4 class for speleothem information

Description

The S4 class for speleothem data.

Value

object of class speleothems

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)

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

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

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

Arguments

Value

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

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

Examples

tryCatch({
somesites <- get_sites(datasettype = "diatom") %>%
  get_downloads()
diatomtaxa <- taxa(somesites)
}, error = function(e) {
message("Neotoma server not responding. Try again later.")
})
  

S4 class for taxa information

Description

Taxa details 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 = NA,
  ecologicalgroups = NA,
  elementtypes = NA,
  unit = NA,
  groupby = "age",
  operation = "prop"
)

Arguments

Value

wide data.frame obtained from long samples data.frame

Author(s)

Socorro Dominguez dominguezvid@wisc.edu

Examples

tryCatch({
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')
}, error = function(e) {
message("Neotoma server not responding. Try again later.")
})