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feat(code): Add prisma calculation

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Marty Oehme 2024-07-15 20:54:58 +02:00
parent 0d05ed981a
commit 38254d1605
Signed by: Marty
GPG key ID: EDBF2ED917B2EF6A
7 changed files with 99 additions and 62 deletions
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src/model/prisma.py Normal file
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from src.process import add_metadata as meta
from src import globals as g
bib_sample_raw_db = meta.bib_library_from_dir(g.RAW_DATA)
bib_sample = meta.bib_library_from_dir(g.WORKING_DATA)
class PrismaNumbers:
nr_database_query_raw = len(bib_sample_raw_db.entries)
nr_snowballing_raw = 2240
all_keywords = [entry["keywords"] for entry in bib_sample.entries if "keywords" in entry.fields_dict.keys()]
nr_database_deduplicated = len([1 for kw in all_keywords if "sample::database" in kw])
nr_snowballing_deduplicated = len([1 for kw in all_keywords if "sample::snowballing" in kw])
nr_out_superseded = len([1 for kw in all_keywords if "out::superseded" in kw])
FULL_RAW_SAMPLE_NOTHING_REMOVED = nr_database_query_raw + nr_snowballing_raw
FULL_SAMPLE_DUPLICATES_REMOVED = nr_database_deduplicated + nr_snowballing_deduplicated + nr_out_superseded
NON_ZOTERO_CAPTURE_TITLE_REMOVAL = 1150
NON_ZOTERO_CAPTURE_ABSTRACT_REMOVAL = 727
NON_ZOTERO_CAPTURE_FULLTEXT_REMOVAL = 348
nr_out_duplicates = FULL_RAW_SAMPLE_NOTHING_REMOVED - FULL_SAMPLE_DUPLICATES_REMOVED
nr_out_title = len([1 for kw in all_keywords if "out::title" in kw]) + NON_ZOTERO_CAPTURE_TITLE_REMOVAL
nr_out_abstract = len([1 for kw in all_keywords if "out::abstract" in kw]) + NON_ZOTERO_CAPTURE_ABSTRACT_REMOVAL
nr_out_fulltext = len([1 for kw in all_keywords if "out::full-text" in kw]) + NON_ZOTERO_CAPTURE_FULLTEXT_REMOVAL
nr_out_language = len([1 for kw in all_keywords if "out::language" in kw])
nr_extraction_done = len([1 for kw in all_keywords if "done::extracted" in kw])
del bib_sample, bib_sample_raw_db
if __name__ == "__main__":
nr = PrismaNumbers()
# FIXME use 02-data/supplementary undeduplciated counts to get database starting and snowballing counts
outp = f"""
flowchart TD;
search_db["Records identified through database searching (n={nr.nr_database_query_raw})"] --> starting_sample;
search_prev["Records identified through other sources (n={nr.nr_snowballing_raw})"] --> starting_sample["Starting sample (n={nr.FULL_RAW_SAMPLE_NOTHING_REMOVED})"];
starting_sample -- "Duplicate removal ({nr.nr_out_duplicates+nr.nr_out_superseded} removed) "--> dedup["Records after duplicates removed (n={nr.FULL_SAMPLE_DUPLICATES_REMOVED})"];
dedup -- "Title screening ({nr.nr_out_title} excluded)" --> title_screened["Records after titles screened (n={nr.FULL_SAMPLE_DUPLICATES_REMOVED - nr.nr_out_title})"];
title_screened -- "Abstract screening ({nr.nr_out_abstract} excluded)"--> abstract_screened["Records after abstracts screened (n={nr.FULL_SAMPLE_DUPLICATES_REMOVED-nr.nr_out_title-nr.nr_out_abstract})"];
abstract_screened -- " Language screening ({nr.nr_out_language} excluded) "--> language_screened["Records after language screened (n={nr.FULL_SAMPLE_DUPLICATES_REMOVED-nr.nr_out_title-nr.nr_out_abstract-nr.nr_out_language})"];
language_screened -- " Full-text screening ({nr.nr_out_fulltext} excluded) "--> full-text_screened["Full-text articles assessed for eligibility (n={nr.nr_extraction_done})"];
"""
print(outp)