Reference

One page for each public function. The text comes from the docstring in the code.

Read PDFs

function	what it does
`harvest()`	Read one PDF, or every PDF in a folder, and return the clean sentences and a drop log.
`extract_dois()`	Find the DOI and the title of each paper in one PDF, or in every PDF in a folder.
`extract_references()`	Find the DOIs that the seed papers cite, in one PDF or in every PDF in a folder.

Download papers

function	what it does
`download_papers()`	Download the open-access PDFs of the DOIs into a folder. Return one status row per DOI.

Find causal claims

function	what it does
`causenet()`	Find the cause -> effect pairs in the sentences.

Group and name constructs

function	what it does
`pairwise_grouping()`	Group the spans that are similar, pair by pair.
`clusterer()`	Group the spans by density, with HDBSCAN.
`label_groups()`	Give each group of spans a name. No thesaurus, no model.
`standardize_constructs()`	Find the closest thesaurus concepts for each span.
`standardize_groups()`	Find the closest thesaurus concepts for each group of spans.

Draw the causal map

function	what it does
`causal_map()`	Build the causal map from the relations and the names of their spans.
`draw_map()`	Draw the causal map as an interactive page.
`save_map()`	Write the causal map to a folder: three CSV tables and one GraphML file.