<commit_before># FORESTER
_Concept by <NAME>_  
_Scripts by github.com/dellch_  
## Description
FORESTER version 1.0

Trees.rb represents a conventional binary matrix as an array of the Newick trees

Seedlings.rb 
represents a 3TS matrix as an array of the Newick trees

## Requirements
ruby (developed with ruby 2.3)

## trees.rb
### Usage
```
ruby trees.rb NAME_OF_FILE
```

## seedlings.rb
### Usage
```
ruby seedlings.rb NAME_OF_FILE
```
<commit_msg>readme links to paper and includes output filenames<commit_after># FORESTER
_Concept by <NAME>_  
_Scripts by [github.com/dellch](https://github.com/dellch)_  
_Paper available at PeerJ: [A laid-back trip through the Hennigian Forests](https://peerj.com/articles/3578/)_

### Description
FORESTER version 1.0

Trees.rb represents a conventional binary matrix as an array of the Newick trees

Seedlings.rb represents a 3TS matrix as an array of the Newick trees

### Requirements
ruby (developed with ruby 2.3)
## Scripts
### trees.rb
#### Usage
```
ruby trees.rb NAME_OF_FILE
```
#### Outputs
trees.rb outputs three files: 
 * NO_POLY_original-filename.txt
 * WITH_POLY_original-filename.txt
 * ADDITIONAL_FILE_original-filename.txt
### seedlings.rb
#### Usage
```
ruby seedlings.rb NAME_OF_FILE
```
#### Outputs
seedlings.rb outputs one file: 
 * altered_original-filename.txt

{'fraction_non_alphanumeric': 0.1066066066066066, 'fraction_numerical': 0.010510510510510511, 'mean_word_length': 4.745689655172414, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7403206', 'n_tokens_mistral': 476, 'n_tokens_neox': 430, 'n_words': 139}