neotoma

PLEASE NOTE: The most recent change has standardized all function names to singular. This may break functionality.

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

Development

• 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, College of Natural Resources

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.

Currently implemented in neotoma

• 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_dataset - obtain dataset metadata from Neotoma. API
• get_download - obtain full datasets (pollen or mammal) from Neotoma. API
• get_publication - obtain publication information from Neotoma. API
• get_site - obtain information on sites in the Neotoma dataset (which may contain multiple datasets). 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

• Major changes to dataset and site objects, as well as the metadata for downloads. This involved cleaning up the column names.
• Added classes to download, dataset and site objects.

Coming soon

• A broader set of taxonomies for use with datasets, including geography based taxonomies.

Install neotoma

• Development version from GitHub:

install.packages("devtools")
require(devtools)
install_github("neotoma", "ropensci")
require(neotoma)

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(dataset = 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))

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