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fix(script): Fix screening numbers

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Marty Oehme 2024-02-21 17:24:13 +01:00
parent 5f94649c8f
commit 621da670a8
Signed by: Marty
GPG key ID: EDBF2ED917B2EF6A
1 changed files with 21 additions and 13 deletions
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34
scoping_review.qmd
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@ -417,17 +417,25 @@ and the sources will be added to the sample to undergo the same screening proces
#| echo: false
#| output: asis
FULL_RAW_SAMPLE_NOTHING_REMOVED = 2396
FULL_SAMPLE_DUPLICATES_REMOVED = 2381
nr_database_query_raw = len(bib_sample_raw_db.entries)
nr_out_duplicates = FULL_RAW_SAMPLE_NOTHING_REMOVED - FULL_SAMPLE_DUPLICATES_REMOVED
nr_other_sources = (FULL_SAMPLE_DUPLICATES_REMOVED + nr_out_duplicates) - nr_database_query_raw
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nr_out_superseded = len([1 for kw in all_keywords if "out::superseded" in kw])
nr_out_title = len([1 for kw in all_keywords if "out::title" in kw])
nr_out_abstract = len([1 for kw in all_keywords if "out::abstract" in kw])
nr_out_fulltext = len([1 for kw in all_keywords if "out::full-text" 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])
@ -441,15 +449,15 @@ print(f"""
%%| fig-width: 6
flowchart TD;
search_db["Records identified through database searching (n={nr_database_query_raw})"] --> starting_sample;
search_prev["Records identified through other sources (n={nr_other_sources})"] --> starting_sample["Starting sample (n={FULL_RAW_SAMPLE_NOTHING_REMOVED})"];
search_prev["Records identified through other sources (n={nr_snowballing_raw})"] --> starting_sample["Starting sample (n={FULL_RAW_SAMPLE_NOTHING_REMOVED})"];
starting_sample -- "Duplicate removal ({nr_out_duplicates+nr_out_superseded} removed) "--> dedup["Records after duplicates removed (n={len(bib_sample.entries)})"];
starting_sample -- "Duplicate removal ({nr_out_duplicates+nr_out_superseded} removed) "--> dedup["Records after duplicates removed (n={FULL_SAMPLE_DUPLICATES_REMOVED})"];
dedup -- "Title screening ({nr_out_title} excluded)" --> title_screened["Records after titles screened (n={len(bib_sample.entries) - nr_out_title})"];
dedup -- "Title screening ({nr_out_title} excluded)" --> title_screened["Records after titles screened (n={FULL_SAMPLE_DUPLICATES_REMOVED - nr_out_title})"];
title_screened -- "Abstract screening ({nr_out_abstract} excluded)"--> abstract_screened["Records after abstracts screened (n={len(bib_sample.entries)-nr_out_title-nr_out_abstract})"];
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})"];
abstract_screened -- " Language screening ({nr_out_language} excluded) "--> language_screened["Records after language screened (n={len(bib_sample.entries)-nr_out_title-nr_out_abstract-nr_out_language})"];
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})"];
language_screened -- " Full-text screening ({nr_out_fulltext} excluded) "--> full-text_screened["Full-text articles assessed for eligibility (n={nr_extraction_done})"];
{t3}
@ -478,7 +486,7 @@ For a full list of validity ranks, see @apptbl-validity-external and @apptbl-val
nr_relevant = len([1 for kw in all_keywords if "relevant" in kw])
```
The query execution results in an initial sample of `{python} nr_database_query_raw` potential studies identified from the database search as well as `{python} nr_other_sources` potential studies from other sources, leading to a total initial number of `{python} FULL_RAW_SAMPLE_NOTHING_REMOVED`.
The query execution results in an initial sample of `{python} nr_database_query_raw` potential studies identified from the database search as well as `{python} nr_snowballing_raw` potential studies from other sources, leading to a total initial number of `{python} FULL_RAW_SAMPLE_NOTHING_REMOVED`.
This accounts for all identified studies without duplicate removal, without controlling for literature that has been superseded or applying any other screening criteria.
Of these, `{python} nr_relevant` have been identified as potentially relevant studies for the purposes of this scoping review, from which `{python} nr_extraction_done` have been extracted.