For display in findings summaries we can now allow arbitrary strength
of evidence binning. We simply pass in a dict with the strength (as
float) as the key and the string-representation that should appear
in the table as value.
Since we add the studies that bring findings for the finding tables manually,
this ensures that we spot any mistakes when entering them, or similar
discrepancies on the other side of the raw data.
Instead of it lying in the src directory (where, reasonably, only python
data extraction, processing and modelling code should lie), I turned
the retorque filter into a simple quarto extension.
Could reasonably be repackaged separately from this repo since I believe
other people could profit off it.
Validity calculation belongs to the modelling, so we put it into the
validity module.
Extracting our matrix is a processing step so we made its own matrix
module and put it in their.
Should hopefully provide better separation of concerns going forward.
From strength of findings to the more general validity module, which can then
in turn contain the 'add_to_findings' function which unsurprisingly adds
validities to findings. Makes more sense to me.
All findings tables can use the validities functionality to add strength of
evidence (internal/external) to themselves. Generalized the function to
work for any main findings csv (to dataframe) table not just institional
findings.
Quarto 1.4 does not like a bare 'zotero' metadata frontmatter key with
sub keys for the filter options. This commit updates the zotero-live
citations filter plugin by retorque and changes its configuration so
it takes settings either through the 'zotero' key or, if that one is
not found, through the 'zoterolive' key. Same options.
When running data python script (`src/data.py`) directly through the command line,
we now use pandas to output the collected data directly as a csv to stdout.
Can then be redirected to e.g. a file to save the data in csv format.
For the first time we use the actual final extracted data from relevant studies
to do analysis on instead of just the intermediate Zotero-provided metadata.
We still inject the intermediate metadata where it may be useful (things like
citation counts and keywords) but otherwise switch to the new data.
