https://github.com/neotomadb/qsr_manuscript
Repository for scripts and figures associated with Neotoma ms. to be submitted to QSR
https://github.com/neotomadb/qsr_manuscript
Last synced: 4 months ago
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Repository for scripts and figures associated with Neotoma ms. to be submitted to QSR
- Host: GitHub
- URL: https://github.com/neotomadb/qsr_manuscript
- Owner: NeotomaDB
- License: mit
- Created: 2017-04-13T15:24:22.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2025-04-05T06:46:31.000Z (about 1 year ago)
- Last Synced: 2025-08-12T17:52:56.995Z (10 months ago)
- Language: R
- Size: 1.36 MB
- Stars: 0
- Watchers: 4
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Code of conduct: code_of_conduct.md
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README
[](https://doi.org/10.1017/qua.2017.105)
# QSR_Manuscript
Repository for scripts and figures associated with Neotoma ms. to be submitted to QSR
## Scraping Data from Neotoma
Outcome: This process will generate a flat csv text file with six columns: datasetID, levels (rows in count matrix), taxa (columns in count matrix), occs (rows * columns in count matrix), date (of submission to NeotomaDB), dataset type.
- Open a terminal/shell with python in the path
- ```cd``` in the ```/scripts``` directory.
- ```python get_neotoma_ds_summaries.py /name/of/file/to/dump/into.csv```. This will run the scraper, dumping contents into the filename specified. Warning: this will erase and overwrite the file if it already exists.
## Summarizing and Cleaning the Data
Outcome: This process will generate a CSV with cumulative sums for each year in the dataset
- Open RStudio
- Open the file ```summarize_records.R```
- Set the working directory
- Set the input file to the file you generated in step 1
- Run the script
## Plotting the data
Outcome: This will produce a stacked line chart of the data in the summaries, generated during step 2.
- Open RStudio
- Open the file ```plot_summaries.R```
- Set the working directory
- Run the script.
- Save the output from the graphics window in RStudio.