diff --git a/scoping_review.qmd b/scoping_review.qmd index 64e5330..8f27091 100644 --- a/scoping_review.qmd +++ b/scoping_review.qmd @@ -46,13 +46,13 @@ bib_string="" for partial_bib in RAW_DATA.glob("**/*.bib"): with open(partial_bib) as f: bib_string+="\n".join(f.readlines()) -sample_raw = bibtexparser.parse_string(bib_string) +bib_sample_raw_db = bibtexparser.parse_string(bib_string) bib_string="" for partial_bib in WORKING_DATA.glob("**/*.bib"): with open(partial_bib) as f: bib_string+="\n".join(f.readlines()) -sample = bibtexparser.parse_string(bib_string) +bib_sample = bibtexparser.parse_string(bib_string) ``` # Introduction @@ -388,22 +388,17 @@ and the sources will be added to the sample to undergo the same screening proces #| echo: false #| output: asis -sample_out_title = [] -sample_out_abstract = [] -sample_out_fulltext = [] -sample_out_language = [] -sample_relvant_done = [] +FULL_RAW_SAMPLE_NOTHING_REMOVED = 2396 +nr_database_query_raw = len(bib_sample_raw_db.entries) +nr_out_duplicates = FULL_RAW_SAMPLE_NOTHING_REMOVED - len(bib_sample.entries) +nr_other_sources = (len(bib_sample.entries) + nr_out_duplicates) - nr_database_query_raw -for e in sample.entries: - if "keywords" in e.fields_dict.keys(): - if "out::title" in e["keywords"]: - sample_out_title.append(e) - elif "out::abstract" in e["keywords"]: - sample_out_abstract.append(e) - elif "out::full-text" in e["keywords"]: - sample_out_fulltext.append(e) - elif "done::extracted" in e["keywords"] and "relevant" in e["keywords"]: - sample_relvant_done.append(e) +all_keywords = [entry["keywords"] for entry in bib_sample.entries if "keywords" in entry.fields_dict.keys()] +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]) +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]) t3 = "`" * 3 # FIXME use 02-data/supplementary undeduplciated counts to get database starting and snowballing counts @@ -414,18 +409,18 @@ print(f""" %%| fig-cap: "Sample sorting process through identification and screening" %%| fig-width: 6 flowchart TD; - search_db["Records identified through database searching (n=1643)"] --> starting_sample; - search_prev["Records identified through other sources (n=753)"] --> starting_sample["Starting sample (n=2396)"]; + 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})"]; - starting_sample -- "Duplicate removal ({2396 - len(sample.entries)} removed) "--> dedup["Records after duplicates removed (n={len(sample.entries)})"]; + starting_sample -- "Duplicate removal ({nr_out_duplicates} removed) "--> dedup["Records after duplicates removed (n={len(bib_sample.entries)})"]; - dedup -- "Title screening ({len(sample_out_title)} excluded)" --> title_screened["Records after titles screened (n={len(sample.entries)-len(sample_out_title)})"]; + dedup -- "Title screening ({nr_out_title} excluded)" --> title_screened["Records after titles screened (n={len(bib_sample.entries) - nr_out_title})"]; - title_screened -- "Abstract screening ({len(sample_out_abstract)} excluded)"--> abstract_screened["Records after abstracts screened (n={len(sample.entries)-len(sample_out_title)-len(sample_out_abstract)}"]; + 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}"]; - abstract_screened -- " Language screening ({len(sample_out_language)} excluded) "--> language_screened["Records after language screened (n={len(sample.entries)-len(sample_out_title)-len(sample_out_abstract)-len(sample_out_language)})"]; + 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})"]; - language_screened -- " Full-text screening ({len(sample_out_fulltext)} excluded) "--> full-text_screened["Full-text articles assessed for eligibility (n={len(sample_relvant_done)})"]; + language_screened -- " Full-text screening ({nr_out_fulltext} excluded) "--> full-text_screened["Full-text articles assessed for eligibility (n={nr_extraction_done})"]; {t3} """) ``` @@ -437,18 +432,13 @@ The results to be identified in the matrix include a study’s: i) key outcome m ```{python} #| echo: false - -sample_size_all = len(sample_raw.entries) - -sample_relevant = [] -for e in sample.entries: - if "keywords" in e.fields_dict.keys() and "relevant" in e["keywords"]: - sample_relevant.append(e) +# TODO Remove redundant 'relevant' studies observation below once all studies are extracted. +nr_relevant = len([1 for kw in all_keywords if "relevant" in kw]) md(f""" -The query execution results in an initial sample of {sample_size_all} potential studies after the identification process. +The query execution results in an initial sample of {nr_database_query_raw} potential studies identified from the database search as well as {nr_other_sources} potential studies from other sources, leading to a total initial number of {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, {len(sample_relevant)} have been identified as relevant studies for the purposes of this scoping review. +Of these, {nr_relevant} have been identified as potentially relevant studies for the purposes of this scoping review, from which {nr_extraction_done} have been extracted. """) ```