46 lines
2.8 KiB
Python
46 lines
2.8 KiB
Python
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nr_database_query_raw = len(bib_sample_raw_db.entries)
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nr_snowballing_raw = 2240
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all_keywords = [entry["keywords"] for entry in bib_sample.entries if "keywords" in entry.fields_dict.keys()]
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nr_database_deduplicated = len([1 for kw in all_keywords if "sample::database" in kw])
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nr_snowballing_deduplicated = len([1 for kw in all_keywords if "sample::snowballing" in kw])
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nr_out_superseded = len([1 for kw in all_keywords if "out::superseded" in kw])
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FULL_RAW_SAMPLE_NOTHING_REMOVED = nr_database_query_raw + nr_snowballing_raw
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FULL_SAMPLE_DUPLICATES_REMOVED = nr_database_deduplicated + nr_snowballing_deduplicated + nr_out_superseded
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NON_ZOTERO_CAPTURE_TITLE_REMOVAL = 1150
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NON_ZOTERO_CAPTURE_ABSTRACT_REMOVAL = 727
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NON_ZOTERO_CAPTURE_FULLTEXT_REMOVAL = 348
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nr_out_duplicates = FULL_RAW_SAMPLE_NOTHING_REMOVED - FULL_SAMPLE_DUPLICATES_REMOVED
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nr_out_title = len([1 for kw in all_keywords if "out::title" in kw]) + NON_ZOTERO_CAPTURE_TITLE_REMOVAL
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nr_out_abstract = len([1 for kw in all_keywords if "out::abstract" in kw]) + NON_ZOTERO_CAPTURE_ABSTRACT_REMOVAL
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nr_out_fulltext = len([1 for kw in all_keywords if "out::full-text" in kw]) + NON_ZOTERO_CAPTURE_FULLTEXT_REMOVAL
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nr_out_language = len([1 for kw in all_keywords if "out::language" in kw])
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nr_extraction_done = len([1 for kw in all_keywords if "done::extracted" in kw])
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t3 = "`" * 3
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# FIXME use 02-data/supplementary undeduplciated counts to get database starting and snowballing counts
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# from: https://github.com/quarto-dev/quarto-cli/discussions/6508
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print(f"""
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```{{mermaid}}
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%%| label: fig-prisma
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%%| fig-cap: "Sample sorting process through identification and screening"
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%%| fig-width: 6
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flowchart TD;
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search_db["Records identified through database searching (n={nr_database_query_raw})"] --> starting_sample;
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search_prev["Records identified through other sources (n={nr_snowballing_raw})"] --> starting_sample["Starting sample (n={FULL_RAW_SAMPLE_NOTHING_REMOVED})"];
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starting_sample -- "Duplicate removal ({nr_out_duplicates+nr_out_superseded} removed) "--> dedup["Records after duplicates removed (n={FULL_SAMPLE_DUPLICATES_REMOVED})"];
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dedup -- "Title screening ({nr_out_title} excluded)" --> title_screened["Records after titles screened (n={FULL_SAMPLE_DUPLICATES_REMOVED - nr_out_title})"];
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title_screened -- "Abstract screening ({nr_out_abstract} excluded)"--> abstract_screened["Records after abstracts screened (n={FULL_SAMPLE_DUPLICATES_REMOVED-nr_out_title-nr_out_abstract})"];
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abstract_screened -- " Language screening ({nr_out_language} excluded) "--> language_screened["Records after language screened (n={FULL_SAMPLE_DUPLICATES_REMOVED-nr_out_title-nr_out_abstract-nr_out_language})"];
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language_screened -- " Full-text screening ({nr_out_fulltext} excluded) "--> full-text_screened["Full-text articles assessed for eligibility (n={nr_extraction_done})"];
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{t3}
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""")
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