neotoma

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

Development

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

• 1.7.2: 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 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:
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')

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))

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.