Free and open copy of the USGS North American Packrat Midden Database

These data and tools come with no license or warranty. You can use these tools or data for any purposes that are consistent with the original published data found at https://geochange.er.usgs.gov/midden/

Why?

The original database (https://geochange.er.usgs.gov/midden/) is not machine readable and is generally inaccessible for bulk analyses.

The goal of this repository is to provide better access to these data. The entire database can now be read into your favorite coding environment, spreadsheet, or database software from the files in the db folder.

Samples table -- Gives sample level data from the USGS database for all available sites.

Taxa table -- Taxa identified for each sample with taxonomic data.

Ages table -- C14 Ages for each sample with carbon dating data.

How do I use these?

Option 1: read the archived data:

Check on when these files were last updated before proceeding. I plan to update this about every month, but cannot gaurantee that these updates will continue indefinitely. Again USE AT YOUR OWN RISK.

Read directly into your favorite programming language. e.g., in R do:

library(dplyr)

samples = read.csv('https://raw.githubusercontent.com/rsh249/usgs_packrat_midden_db/master/db/samples.csv')
taxa_data = read.csv('https://raw.githubusercontent.com/rsh249/usgs_packrat_midden_db/master/db/taxa.csv')
age_data = read.csv('https://raw.githubusercontent.com/rsh249/usgs_packrat_midden_db/master/db/ages.csv')


taxa_join = inner_join(samples, taxa_data, 'SAMPLE') %>% arrange(-desc(SAMPLE))
head(taxa_join)

ages_join = inner_join(samples, age_data, 'SAMPLE') %>% arrange(-desc(SAMPLE))
head(ages_join)

Option 2: Build a new copy

The R code in html_parser.R will get a new copy of these tables and replace the repository version IF you get your own new copy of the sites2.html file. To do this you will need to go to https://geochange.er.usgs.gov/midden/search.html and press 'Start Search' at the bottom of the page. When the data page loads you will need to view the html source and copy that into sites2.html.

e.g., on a git enabled terminal with R installed (and dplyr, readr, and stringr libraries) run:

git clone https://github.com/rsh249/usgs_packrat_midden_db

# replace sites2.html via manual method above

Rscript 'html_parser.R'

Fin!