README.md

In neotoma: A Package to access the Neotoma Paleoecological Database using an API.

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

Development by

Simon Goring - University of Wisconsin-Madison, 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.

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_contacts - find contact information for data contributors to Neotoma. API
• get_datasets - 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_sites - 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

Coming soon

• A broader set of taxonomies for use with datasets, including geography based taxonomies.
• Functions to turn single-site datasets into multi-site datasets.
• Age-modelling capabilities.

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 plyr package and the mapdata package:
> require(plyr)
> test <- get_datasets(taxonname='Mammuthus*')
The API call was successful, you have returned  3273 records.
> site.locs <- ldply(test, function(x)x$Site)
> map('world', xlim=range(site.locs$LongitudeWest)+c(-10, 10), ylim=range(site.locs$LatitudeNorth)+c(-10, 10))
> points(site.locs$LongitudeWest, site.locs$LatitudeNorth, pch=19, cex=0.5)

Plot the proportion of publications per year for datasets in Neotoma

> # Requires ggplot2
> library(ggplot2)
> pubs <- get_publication()
The API call was successful, you have returned  3693 records.
Warning message:
In getForm(base.uri, .params = cl) : No inputs passed to form
> pub.years <- as.numeric(as.character(pubs$Year))
Warning message:
NAs introduced by coercion
> ggplot(data=data.frame(x = pub.years), aes(x)) +
+     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, na.rm=TRUE), 2013, by=20))

neotoma documentation built on May 2, 2019, 5:55 p.m.