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.

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
https://github.com/ropensci/neotoma

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...

Functions

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

Files

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

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