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neotoma

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NOTE The package neotoma has now been deprecated. Unfortunately our wnapi.neotomadb.org server reached end of life and was no longer operable. The package has been replaced by neotoma2. As much as possible we have kept many of the same patterns, but there are new data structures. The wnapi server was only passing along data submitted before June 2020. The new package accesses all data up until the present. Please contact us directly either by email () or on our slack workspace (there is an it_r channel) and we can help assist you in migrating to neotoma2.

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 has been available on CRAN since 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

For ongoing news, issues or information please join the Neotoma Slack server (and add the #r channel). Slack is a real time chat application and collaboration hub with mobile and desktop applications.

Development

We expect no further development of this package, however, 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

Contributors

  • 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:
install.packages('neotoma')
  • Development version from GitHub:
install.packages("devtools")
library(devtools)
install_github("ropensci/neotoma")
library(neotoma)

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

  • 1.7.6: Updated the API endpoints to correctly point to the new windows API endpoint, in preparation for migration; Fixed the help for get_closest(); Changed character encoding for two data tables, pollen.equiv and taxon.list, made them available in the main package using data().
  • 1.7.4: Bug fix: get_dataset(gpid=123) was returning an error, fix corrects the error to allow unassigned x variables. Updated the allowable dataset types for searching to reflect the larger set of dataset types within Neotoma.
  • 1.7.3: Added numeric/integer methods to the get_site() and get_dataset() functions so that a vector of dataset or siteids can be passed to improve more general workflow methods.
  • 1.7.2: Bugfixes, added the taxa() function to easily extract taxa from one or multiple download objects.
  • 1.7.1: Bugfix for compile_download(), single sample downloads were failing to compile properly, added the taxa() function to extract taxa lists from large download objects.
  • 1.7.0: Added plot_leaflet() to allow interactive exploration of downloaded Neotoma data. Integrates with the Neotoma Explorer. Minor bugfix for get_download() to allow records to be sent to Neotoma and to be filtered.
  • 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 (http://tiliait.com) 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 print 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:
library('mapdata')

#  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")
map('world',
    interior=TRUE,
    fill=TRUE,
    col='gray',
    xlim=range(site.locs$long)+c(-10, 10),
    ylim=range(site.locs$lat)+c(-10, 10),
    add=TRUE)

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

Plot the proportion of publications per year for datasets in Neotoma 

# Requires ggplot2
library('ggplot2')
library('plyr')
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))
thing
thing

Cumulative plot of record uploads to Neotoma since 1998.

Found at this gist

cumulativerecords
cumulativerecords

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.

gif
gif

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..

Other Resources Using neotoma

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.