Summarise output from The Content Mine's AMI plug-in into a format that can be displayed in ami-viz.

Before running this code, run the following Content Mine pipeline (see mine.sh for example commands):

1. getpapers to download articles
2. norma to create scholarly.html for all articles
3. ami2-species or ami2-word to generate the results.xml files

The data directory (stored in the data.dir variable in main.r) should contain one subfolder for each article, named after the article's ID (done automatically by getpapers). After processing with AMI, these subfolders should contain a 'results' folder, which will in turn contain:

• species/binomial/results.xml
• word/frequencies/results.xml

This program will take these files, summarise them across all articles and output JSON files ready to be visualised in an interactive network graph (for example: https://github.com/matthewgthomas/ami-viz).

To use, run the code in main.r.

The program will write three JSON files containing nodes and edge lists:

• words.json -- the top X most frequent words and the articles in which they appear
• words_tdidf.json -- same as above but calculated using term frequency-inverse document frequency (TF-IDF)
• species.json -- occurrences of binomial species names and the articles in which they appear

• Add support for more AMI plugins
• Make faster -- code is slow when running over 100s of articles