https://github.com/ropensci/neotoma
Programmatic R interface to the Neotoma Paleoecological Database.
https://github.com/ropensci/neotoma
cran neotoma neotoma-apis neotoma-database nsf paleoecology r r-package rstats
Last synced: 9 months ago
JSON representation
Programmatic R interface to the Neotoma Paleoecological Database.
- Host: GitHub
- URL: https://github.com/ropensci/neotoma
- Owner: ropensci
- License: other
- Created: 2013-01-29T20:41:23.000Z (over 13 years ago)
- Default Branch: master
- Last Pushed: 2022-11-30T19:07:47.000Z (over 3 years ago)
- Last Synced: 2025-09-08T12:56:35.202Z (11 months ago)
- Topics: cran, neotoma, neotoma-apis, neotoma-database, nsf, paleoecology, r, r-package, rstats
- Language: R
- Homepage: https://docs.ropensci.org/neotoma
- Size: 9.96 MB
- Stars: 31
- Watchers: 8
- Forks: 16
- Open Issues: 32
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: code_of_conduct.md
Awesome Lists containing this project
README
neotoma
========
[](https://travis-ci.org/ropensci/neotoma)
[](https://ci.appveyor.com/project/sckott/neotoma/branch/master)
[](https://codecov.io/github/ropensci/neotoma?branch=master)
[](https://github.com/metacran/cranlogs.app)
[](https://cran.r-project.org/package=neotoma)
[](https://nsf.gov/awardsearch/showAward?AWD_ID=1550707)
[](https://nsf.gov/awardsearch/showAward?AWD_ID=1948926)
**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 The package has been replaced by [neotoma2](https://github.com/NeotomaDB/neotoma2).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 (goring@wisc.edu) 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](http://www.neotomadb.org/). 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](http://ropensci.org) project and is also hosted on [Figshare](http://dx.doi.org/10.6084/m9.figshare.677131). The `neotoma` package has been available on [CRAN](https://cran.r-project.org/package=neotoma) 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](http://doi.org/10.5334/oq.ab)
For ongoing news, issues or information please join the [Neotoma Slack server](https://bit.ly/2FrZyYD) (and add the #r channel). [Slack](http://www.slack.com/) 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](https://github.com/ROpensci/neotoma/blob/master/code_of_conduct.md) for this project.*
+ [Simon Goring](http://goring.org) - University of Wisconsin-Madison, Department of Geography
### Contributors
+ [Gavin Simpson](http://www.fromthebottomoftheheap.net/) - University of Regina, Department of Biology
+ [Jeremiah Marsicek](http://geoweb.uwyo.edu/ggstudent/jmarsice/Site/Home.html) - University of Wyoming, Department of Geology and Geophysics
+ [Karthik Ram](http://nature.berkeley.edu/~kram/) - University of California - Berkely, Berkeley Institue for Data Science.
+ [Luke Sosalla](https://github.com/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](http://api.neotomadb.org/doc/resources/home).
If you have used the package please consider providing us feedback through a [short survey](https://docs.google.com/forms/d/e/1FAIpQLSdRNat6L9grRF0xU5gibkr26xq9jD9wyHgw_AWxhrgn0lWv7w/viewform).
### Install `neotoma`
+ CRAN:
```r
install.packages('neotoma')
```
+ Development version from GitHub:
```r
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](http://api.neotomadb.org/doc/resources/sites)
+ `get_dataset` - obtain dataset metadata from Neotoma. [API](http://api.neotomadb.org/doc/resources/datasets)
+ `get_download` - obtain full datasets (pollen or mammal) from Neotoma. [API](http://api.neotomadb.org/doc/resources/downloads)
+ `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](http://api.neotomadb.org/doc/resources/contacts)
+ `get_publication` - obtain publication information from Neotoma. [API](http://api.neotomadb.org/doc/resources/publications)
+ `get_table` - return matrices corresponding to one of the Neotoma database tables. [tables](http://api.neotomadb.org/doc/resources/dbtables)
+ `get_taxa` - Get taxon information from Neotoma. [API](http://api.neotomadb.org/doc/resources/taxa)
+ `get_chroncontrol` - Get chronological information used to build the age-depth model for the record. [API](http://api.neotomadb.org/doc/resources/chroncontrol)
### 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
```r
# 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
```R
# 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](https://gist.github.com/SimonGoring/718a654f304f2d16ce4b)
#### Obtain records & Rebuild Chronologies with Bacon
Found at [this gist](https://gist.github.com/SimonGoring/877dd71cc3ad6bf8531e). 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](https://gist.github.com/SimonGoring/dbb4c8e0087882dc143baa89fa041d2b).
#### Find all site elevations in California:
Found at [Simon Goring's gist.](https://gist.github.com/SimonGoring/6a2ba1d55a3a7f78723b37e896b55b70).
#### Match all Neotoma taxa to external databases using `taxize`:
Found at [Simon Goring's gist.](https://gist.github.com/SimonGoring/24fb1228204f768f3f0020f37060db18).
#### Other Resources Using `neotoma`
* [A simple `neotoma` workshop](http://www.goring.org/resources/Neotoma_Lesson.html)
* [Data exploration and chronologies with `neotoma`](http://www.goring.org/resources/neotoma_lab_meeting.html)
### `neotoma` Workshops
We have provided a set of educational tools through the [NeotomaDB](http://github.com/neotomaDB) GitHub repository in the [Workshops](http://github.com/NeotomaDB/Workshops) repository. These are free to share, and can be modified as needed.