https://github.com/benmarwick/kwakmarwickaas2015
https://github.com/benmarwick/kwakmarwickaas2015
compendium reproducible-paper
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/benmarwick/kwakmarwickaas2015
- Owner: benmarwick
- License: mit
- Created: 2015-06-12T21:55:55.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2017-03-27T23:46:37.000Z (about 9 years ago)
- Last Synced: 2025-03-06T05:47:51.911Z (about 1 year ago)
- Topics: compendium, reproducible-paper
- Language: HTML
- Size: 3.81 MB
- Stars: 1
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: readme.md
- License: LICENSE
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README
## Supplementary Materials for "Food processing and pottery use in the Early Bronze Age, Central part of the Korean Peninsula"
### Compendium DOI: http://dx.doi.org/10.6084/m9.figshare.1444025
### Authors of this repository:
Seungki Kwak and Ben Marwick (skkwak@uw.edu, bmarwick@uw.edu)
### How to use:
First, ensure that you have installed R, RStudio, and the `ggplot2` package. We also recommend installing the dependencies listed below to recreate our computational environment.
Second, download and unzip our compendium from [http://dx.doi.org/10.6084/m9.figshare.1444025](http://dx.doi.org/10.6084/m9.figshare.1444025) or clone it from github.
Third, once you have a local copy of the compendium, open and run the `kwak_marwick_jas.Rproj` file in RStudio. This will set the working directory to the location of the files.
Fourth, run `devtools::install("kwakmarwick2015")` to install the functions used by this compendium.
Fifth, look in the `analysis/` directory and open the `analysis.Rmd` file in RStudio. Then run `rmarkdown::render()` or click the 'knit' button in RStudio. This will generate a HTML document that includes the plots from the manuscript.
### Contents
The `analysis/` folder contains an R markdown file that, when executed, will generate the figures found in the manuscript.
Also within the `analysis/` folder is the `data/` folder which contains CSV files.
"sampling_Kimpo.CSV" and "sampling_Sosa.CSV" are the data files of the entire collected samples in this paper.
"CSIA_KM.CSV" and "CSIA_SS.CSV" are the data files of GC-MS and compound specific isotope analysis. CSIA_KM.CSV contains data from the Kimpo-Yangchon site. CSIA_SS.CSV contains data from the Sosa-Dong site.
"GC-MS_exported_data_Figure5a/b.CSV" is the data file that includes retention time and peak area data of the GC-MS chromatogram in the paper (Figure 5).
The `R/` folder contains an a R script file with our two custom plotting functions. These functions are for general use with GC-MS and CSIA data relating to archaeological foodways. The other items in our compendium are typical components of a simple R package.
Licenses:
Text: CC-BY-4.0 http://creativecommons.org/licenses/by/4.0/
Code: MIT http://opensource.org/licenses/MIT 2015 Kwak & Marwick
Data: CC0 http://creativecommons.org/publicdomain/zero/1.0/ attribution requested in reuse
Dependencies:
The pacakges required to run this code are listed in the `DESCRIPTION` file. The `analsyis.html` file also has details of the specific computational environment that we used to generate thr figures.
Contact:
Seungki Kwak, Doctoral candidate, Department of Anthropology, Denny Hall 117, Box 353100, University of Washington Seattle, WA 98195-3100 USA
t. (+1) 206.543.5240 e. skkwak@uw.edu f. (+1) 206.543.3285 w. http://depts.washington.edu/anthweb/users/skkwak
Ben Marwick, Assistant Professor, Department of Anthropology, Denny Hall 117, Box 353100, University of Washington Seattle, WA 98195-3100 USA
t. (+1) 206. 543.5240 e. bmarwick@uw.edu f. (+1) 206.543.3285 w. http://faculty.washington.edu/bmarwick/