neotoma: Access to the Neotoma Paleoecological Database Through R
Version 1.6.2

Access paleoecological datasets from the Neotoma Paleoecological Database using the published API (http://api.neotomadb.org/). The functions in this package access various pre-built API functions and attempt to return the results from Neotoma in a usable format for researchers and the public.

Browse man pages Browse package API and functions Browse package files

AuthorSimon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek [ctb], Karthik Ram [aut], Luke Sosalla [ctb]
Date of publication2016-09-22 16:51:03
MaintainerSimon J. Goring <goring@wisc.edu>
LicenseMIT + file LICENSE
Version1.6.2
URL https://github.com/ropensci/neotoma
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("neotoma")

Man pages

ages: Access proxy age data
bind: Function to bind objects together into a longer object.
browse: Open a browser window to display a Neotoma dataset within the...
browse.dataset: Open a browser window to display a Neotoma dataset within the...
browse.dataset_list: Open a browser window to display a Neotoma dataset within the...
browse.default: Open a browser window to display a Neotoma dataset within the...
browse.download: Open a browser window to display a Neotoma dataset within the...
browse.download_list: Open a browser window to display a Neotoma dataset within the...
compile_downloads: Function to convert multiple downloads into a single large...
compile_taxa: Function to convert assemblage taxa to standardized lists.
counts: Access proxy count data
download: A class for download objects.
get_chroncontrol: Function to return chronological control tables used to build...
get_chroncontrol.dataset: Function to return chronological control tables from a...
get_chroncontrol.dataset_list: Function to return chronological control tables from a...
get_chroncontrol.default: Function to return chronological control tables from a...
get_chroncontrol.download: Function to return chronological control tables from a...
get_chroncontrol.download_list: Function to return chronological control tables from a...
get_closest: Find the closest dataset records to a site, dataset or...
get_contact: Get contact information.
get_dataset: Obtain dataset information from the Neotoma Paleoecological...
get_dataset.default: Obtain dataset information from the Neotoma Paleoecological...
get_dataset.download: Obtain dataset information from an existing 'download'...
get_dataset.download_list: Obtain dataset information from a 'download_list'.
get_dataset.geochronologic: Obtain dataset information from an object of class...
get_dataset.geochronologic_list: Obtain dataset information from an object of class...
get_dataset.site: Obtain dataset information from an existing 'site' object.
get_download: Function to return full download records using 'site's,...
get_download.dataset: Function to return full download records using a 'dataset'.
get_download.dataset_list: Function to return full download records using a...
get_download.default: Function to return full download records using 'numeric'...
get_download.site: Function to return full download records using a 'site'.
get_geochron: Function to return geochronological data from records.
get_publication: A function to get publications for sites or datasets in the...
get_publication.dataset: A function to get publications for datasets in the Neotoma...
get_publication.dataset_list: A function to get publications for dataset_lists in the...
get_publication.default: A function to get publications for sites or datasets in the...
get_publication.download: A function to get publications for downloads in the Neotoma...
get_publication.download_list: A function to get publications for datasets in the Neotoma...
get_site: Return Site Information.
get_site.dataset: Return Site Information from a 'dataset'
get_site.dataset_list: Return Site Information from a 'dataset_list'
get_site.default: Return Site Information.
get_site.download: Return Site Information from a 'download'
get_site.download_list: Return Site Information from a 'download_list'
get_site.geochronologic: Return Site Information from a 'geochronologic'
get_site.geochronologic_list: Return Site Information from a 'geochronologic_list'
get_table: Get Neotoma value tables.
get_taxa: Get taxon information from Neotoma.
gp.table: A list of all the geopolitical entities in the Neotoma...
param_check: Internal function to check passed parameters.
pollen.equiv: A table to convert the pollen taxa identified by...
read_bacon: Function to read in defined Bacon outputs.
read.tilia: Read proxy data from Tilia TLX files
Stratiplot.download: Palaeoecological stratigraphic diagrams
Stratiplot.download_list: Palaeoecological stratigraphic diagrams
taxon.list: Neotoma taxon list
translate.table: A table to convert the original taxa to standardized lists.
write_agefile: Write age control file to disk formatted for either Bacon or...

Functions

Stratiplot.download Man page Source code
Stratiplot.download_list Man page Source code
ages Man page
ages.download Man page
ages.download_list Man page
bind Man page Source code
bind.default Source code
browse Man page Source code
browse.dataset Man page Source code
browse.dataset_list Man page Source code
browse.default Man page Source code
browse.download Man page Source code
browse.download_list Man page Source code
compile_downloads Man page Source code
compile_taxa Man page Source code
counts Man page
counts.download Man page
counts.download_list Man page
download Man page
get_chroncontrol Man page Source code
get_chroncontrol.dataset Man page Source code
get_chroncontrol.dataset_list Man page Source code
get_chroncontrol.default Man page Source code
get_chroncontrol.download Man page Source code
get_chroncontrol.download_list Man page Source code
get_closest Man page Source code
get_closest.dataset Source code
get_closest.default Source code
get_closest.download Source code
get_closest.site Source code
get_contact Man page Source code
get_dataset Man page Source code
get_dataset.default Man page Source code
get_dataset.download Man page Source code
get_dataset.download_list Man page Source code
get_dataset.geochronologic Man page Source code
get_dataset.geochronologic_list Man page Source code
get_dataset.site Man page Source code
get_download Man page Source code
get_download.dataset Man page Source code
get_download.dataset_list Man page Source code
get_download.default Man page Source code
get_download.site Man page Source code
get_geochron Man page Source code
get_geochron.dataset Source code
get_geochron.dataset_list Source code
get_geochron.default Source code
get_geochron.site Source code
get_publication Man page Source code
get_publication.dataset Man page Source code
get_publication.dataset_list Man page Source code
get_publication.default Man page Source code
get_publication.download Man page Source code
get_publication.download_list Man page Source code
get_site Man page Source code
get_site.dataset Man page Source code
get_site.dataset_list Man page Source code
get_site.default Man page Source code
get_site.download Man page Source code
get_site.download_list Man page Source code
get_site.geochronologic Man page Source code
get_site.geochronologic_list Man page Source code
get_table Man page Source code
get_taxa Man page Source code
gp.table Man page
param_check Man page Source code
plot.dataset Source code
plot.dataset_list Source code
plot.download Source code
plot.download_list Source code
plot.site Source code
pollen.equiv Man page
print.chroncontrol Source code
print.dataset Source code
print.dataset_list Source code
print.download Source code
print.download_list Source code
print.geochronologic Source code
print.geochronologic_list Source code
print.site Source code
read.tilia Man page
read_bacon Man page Source code
taxon.list Man page
translate.table Man page
write_agefile Man page Source code

Files

inst
inst/CITATION
inst/img
inst/img/mammothsites.png
inst/img/histogramplot.png
inst/img/Thumbs.db
inst/img/inkspot_neotoma.gif
inst/crystal.tlx
tests
tests/testthat
tests/testthat/test_neotoma.R
tests/testthat/test_examples.R
tests/testthat/test_simple_paper.R
tests/test-all.R
NAMESPACE
NEWS
R
R/get_download.R
R/read_methods.R
R/get_chroncontrol.R
R/print.dataset.R
R/Stratiplot.download.R
R/print.geochronologic_list.R
R/param_check.R
R/compile_downloads.R
R/taxon.table.R
R/gp.table.R
R/print.download.R
R/print.chroncontrol.R
R/browse.R
R/pollen.equiv.R
R/write_agefile.R
R/clamodel.R
R/get_site.R
R/get_dataset.R
R/sysdata.rda
R/print.geochronologic.R
R/plot-methods.R
R/print.dataset_list.R
R/get_table.R
R/counts.R
R/print.download_list.R
R/bind.R
R/compile_taxa.R
R/download.R
R/get_publication.R
R/ages.R
R/get_taxa.R
R/print.site.R
R/read_bacon.R
R/get_closest.R
R/translate.table.R
R/get_contact.R
R/get_geochron.R
README.md
MD5
DESCRIPTION
man
man/gp.table.Rd
man/download.Rd
man/get_publication.download_list.Rd
man/get_chroncontrol.download.Rd
man/compile_taxa.Rd
man/compile_downloads.Rd
man/get_site.geochronologic_list.Rd
man/write_agefile.Rd
man/get_publication.dataset.Rd
man/browse.download.Rd
man/taxon.list.Rd
man/get_chroncontrol.dataset.Rd
man/get_dataset.geochronologic.Rd
man/get_taxa.Rd
man/get_chroncontrol.Rd
man/get_publication.download.Rd
man/get_chroncontrol.dataset_list.Rd
man/bind.Rd
man/get_chroncontrol.download_list.Rd
man/get_site.dataset_list.Rd
man/get_site.dataset.Rd
man/get_site.download.Rd
man/counts.Rd
man/get_download.Rd
man/get_publication.Rd
man/get_chroncontrol.default.Rd
man/browse.download_list.Rd
man/browse.dataset_list.Rd
man/get_site.Rd
man/get_publication.dataset_list.Rd
man/get_closest.Rd
man/browse.default.Rd
man/Stratiplot.download_list.Rd
man/read_bacon.Rd
man/get_download.dataset.Rd
man/Stratiplot.download.Rd
man/get_site.download_list.Rd
man/get_dataset.site.Rd
man/get_table.Rd
man/get_contact.Rd
man/ages.Rd
man/get_geochron.Rd
man/get_dataset.download.Rd
man/translate.table.Rd
man/get_site.geochronologic.Rd
man/get_site.default.Rd
man/param_check.Rd
man/get_download.site.Rd
man/browse.dataset.Rd
man/get_download.dataset_list.Rd
man/read.tilia.Rd
man/browse.Rd
man/get_dataset.download_list.Rd
man/get_dataset.Rd
man/get_dataset.geochronologic_list.Rd
man/get_publication.default.Rd
man/get_download.default.Rd
man/pollen.equiv.Rd
man/get_dataset.default.Rd
LICENSE
neotoma documentation built on May 20, 2017, 2:05 a.m.