Programmatic R interface to the Neotoma Paleoecological Database.
Latest commit bbdb643 Oct 25, 2016 @SimonGoring SimonGoring One more try. Dumb mistakes late at night. Test examples are in the c…
…hecks, but the checks fail because they time out in appveyor. Yerg.
Failed to load latest commit information.
R One more try. Dumb mistakes late at night. Test examples are in the c… Oct 25, 2016
inst Had to fix the plotting methods for records that might not have defin… Sep 7, 2016
man Hadn't pushed the change to `depths.Rd`. A flurry of annoying changes… Oct 25, 2016
revdep Added a gitignore to the profiling. May 6, 2016
tests Commented out the simple paper tests. They fail on AppVeyor. Sep 22, 2016
.Rbuildignore Had to fix the plotting methods for records that might not have defin… Sep 7, 2016
.Rprofile Changed the license year, modified the `DESCRIPTION` file and edited … May 2, 2015
.gitignore Had to fix the plotting methods for records that might not have defin… Sep 7, 2016
.travis.yml Is it this slack integration that's screwing things up? editing `.tra… Jul 24, 2015
DESCRIPTION Updated the Description, NEWS & README files. Sep 21, 2016
LICENSE Updated LICENSE year & NEWS information. May 4, 2016
NAMESPACE A block of code in `get_download` to fix checks for empty sample unit… Oct 24, 2016
NEWS Added some new examples. Oct 21, 2016
appveyor.yml changed slack room to builds in appveyor file Sep 10, 2014 Reformatted the code_of_conduct May 6, 2016 Updating the `cran-comments`. Sep 22, 2016
download.out Adding local_don't run and the download.out May 4, 2016
package_check.R Cleaned up `get_table` in response to `devtools::check` note. Jun 28, 2016


Build Status Build status rstudio mirror downloads cran version

The neotoma package is a programmatic R interface to the Neotoma Paleoecological Database. The package is intended to both allow users to search for sites and to download data for use in analyical workflows of paleoecological research.

neotoma is part of the rOpenSci project and is also hosted on Figshare. The neotoma package is also available on CRAN as of May 3, 2015.

For more information on the package please refer to:

Goring, S., Dawson, A., Simpson, G. L., Ram, K., Graham, R. W., Grimm, E. C., & Williams, J. W.. (2015). neotoma: A Programmatic Interface to the Neotoma Paleoecological Database. Open Quaternary, 1(1), Art. 2. DOI: 10.5334/oq.ab


We welcome contributions from any individual, whether code, documentation, or issue tracking. All participants are expected to follow the code of conduct for this project.

  • Simon Goring - University of Wisconsin-Madison, Department of Geography


  • Gavin Simpson - University of Regina, Department of Biology
  • Jeremiah Marsicek - University of Wyoming, Department of Geology and Geophysics
  • Karthik Ram - University of California - Berkely, Berkeley Institue for Data Science.
  • Luke Sosalla - University of Wisconsin, Department of Geography

Package functions resolve various Neotoma APIs and re-form the data returned by the Neotoma database into R data objects. The format of the Neotoma data, and the actual API functions can be accessed on the Neotoma API website.

If you have used the package please consider providing us feedback through a short survey.

Install neotoma

  • CRAN:
  • Development version from GitHub:

Currently implemented in neotoma

More functions are available through the package help. These represent the core functions:

  • get_site - obtain information on sites in the Neotoma dataset (which may contain multiple datasets). API
  • get_dataset - obtain dataset metadata from Neotoma. API
  • get_download - obtain full datasets (pollen or mammal) from Neotoma. API
  • compile_list - using established pollen-related taxonomies from the literature, take the published taxon list and standardize it to allow cross site analysis.
  • get_contact - find contact information for data contributors to Neotoma. API
  • get_publication - obtain publication information from Neotoma. API
  • get_table - return matrices corresponding to one of the Neotoma database tables. tables
  • get_taxa - Get taxon information from Neotoma. API
  • get_chroncontrol - Get chronological information used to build the age-depth model for the record. API

Recent Changes

  • 1.6.2: Improved the basic plot method based on tests against Tilia files in the Neotoma Holding Tank & built more robust interpolation in read_bacon so that age models without interpolated dates can still be imported. browse now opens multiple datastes in the Neotoma Explorer at once.
  • 1.6.1: New Stratiplot method, using the analogue package to plot dataset diagrams from download and download_list objects, bug fixes for write_agefile and a new function, read_bacon, to read in and integrate Bacon chronologies into download objects.
  • 1.6.0: Support for vector inputs in the gpid selection. Added a get_closest function to find the closest sample site. Mostly clean-up of reported bugs by users. Revised examples for faster check speed.
  • 1.5.1: Minor fix to the get_dataset for site level data to account for some datasets with empty submission data. Some style changes to code (non-functional changes)
  • 1.5.0: More extensive testing to support multiple dataset types. Water chemistry datasets still unsupported. Function read.tilia added to read Tilia ( style XML files. Moved to using xml2, httr and jsonlite to support parsing.
  • 1.4.1: Small changes to get_geochron to address bug reports and improve object printing methods.
  • 1.4.0: Added plot method for datasets, sites & downloads. Fixed a bug with records missing chronologies.

A few examples:

Find the distribution of sites with Mammoth fossils in Neotoma

#  Example requires the mapdata package:

#  You may use either '%' or '*' as wildcards for search terms:
test <- get_dataset(taxonname='Mammuthus*')

The API call was successful, you have returned  3273 records.

site.locs <- get_site(test)

# A crude way of making the oceans blue.
plot(1, type = 'n',
     xlim=range(site.locs$long)+c(-10, 10),
     ylim=range(site.locs$lat)+c(-10, 10),
     xlab='Longitude', ylab = 'Latitude')
rect(par("usr")[1],par("usr")[3],par("usr")[2],par("usr")[4],col = "lightblue")
    xlim=range(site.locs$long)+c(-10, 10),
    ylim=range(site.locs$lat)+c(-10, 10),

points(site.locs$long, site.locs$lat, pch=19, cex=0.5, col='red')


Plot the proportion of publications per year for datasets in Neotoma

# Requires ggplot2
pubs <- get_publication()

pub.years <- ldply(pubs, "[[", "meta")

ggplot(data=pub.years, aes(x = year)) +
     stat_bin(aes(y=..density..*100, position='dodge'), binwidth=1) +
     theme_bw() +
     ylab('Percent of Publications') +
     xlab('Year of Publication') +
     scale_y_continuous(expand = c(0, 0.1)) +
     scale_x_continuous(breaks = seq(min(pub.years$year, na.rm=TRUE), 2014, by=20))


Cumulative plot of record uploads to Neotoma since 1998.

Found at this gist


Obtain records & Rebuild Chronologies with Bacon

Found at this gist. Prepared in part for a Bacon (Blaauw & Christen, 2011) workshop at the 2015 International Limnogeology Conference in Reno-Tahoe, Nevada led by Amy Myrbo (University of Minnesota).

Simple paleo-data visualization

Simple paleo-data visualization in R, linking the rioja, neotoma and dplyr packages. Found at this gist.


Find all site elevations in California:

Found at Simon Goring's gist..

Match all Neotoma taxa to external databases using taxize:

Found at Simon Goring's gist..

neotoma Workshops

We have provided a set of educational tools through the NeotomaDB GitHub repository in the Workshops repository. These are free to share, and can be modified as needed.