ananse 1.0.7

A python package to partially automate search term selection and writing search strategies for systematic reviews

Ananse

The Ananse package is a python implementation of the litsearchr R package designed to partially automate search term selection and writing search strategies for systematic reviews. Read the documentation at baasare.github.io/ananse and ananse.readthedocs.io/

Setup

Ananse requires python 3.7 or higher

Using pip

pip install ananse

Directly from the repository

git clone https://github.com/baasare/ananse.git
python ananse/setup.py install

Quick start

Writing your own script

from ananse import Ananse

# Create an object of the package
review = Ananse()

# Import your naive search results from a directory 
imports = review.import_naive_results(path="./")

deduplication_columns =  ['title', 'abstract']

#de-duplicate the imported search results
data = review.deduplicate_dataframe(imports, deduplication_columns)

#extract keywords from article title and abstract as well as author and database tagged keywords
all_terms = review.extract_terms(data)

#create Document-Term Matrix, with columns as terms and rows as articles
dtm, term_columns = review.create_dtm(data.text, all_terms)

#create co-occurrence network using Document-Term Matrix
graph_network = review.create_network(dtm, term_columns)

#plot degree and rank distribution of the network
review.plot_degree_distribution(graph_network)
review.plot_rank_degree_distribution(graph_network)
review.plot_degree_histogram(graph_network)

#Determine cutoff for the relevant keywords
cutoff_strengths = review.find_cutoff(graph_network, "spline", "degree")


#get suggested keywords and save to a csv file
suggested_keywords = review.get_keywords(graph_network, "degree", cutoff_strengths, save_keywords=True)
print("Suggested Keywords")
for word in suggested_keywords:
   print(word)

Using Ananse Test Script

python tests/ananse_test

References

This is a python implementation of the R package as mentioned in paper An automated approach to identifying search terms for systematic reviews using keyword co‐occurrence networks by Eliza M. Grames, Andrew N. Stillman Morgan W. Tingley and Chris S. Elphick