neotoma: Access to the Neotoma Paleoecological Database Through R

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.

Author
Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek [ctb], Karthik Ram [aut], Luke Sosalla [ctb]
Date of publication
2016-09-22 16:51:03
Maintainer
Simon J. Goring <goring@wisc.edu>
License
MIT + file LICENSE
Version
1.6.2
URLs

View on CRAN

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...

Files in this package

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