lisc.collect_counts¶
- lisc.collect_counts(terms_a, inclusions_a=None, exclusions_a=None, labels_a=None, terms_b=None, inclusions_b=None, exclusions_b=None, labels_b=None, db='pubmed', field='TIAB', api_key=None, collect_coocs=True, logging=None, directory=None, collect_info=True, verbose=False, **eutils_kwargs)[source]¶
Collect count and term co-occurrence data from EUtils.
- Parameters:
- terms_alist of list of str
Search terms.
- inclusions_alist of list of str, optional
Inclusion words for search terms.
- exclusions_alist of list of str, optional
Exclusion words for search terms.
- labels_alist of str, optional
Labels for the search terms.
- terms_blist of list of str, optional
Secondary list of search terms.
- inclusions_blist of list of str, optional
Inclusion words for the second list of search terms.
- exclusions_blist of list of str, optional
Exclusion words for the second list of search terms.
- labels_blist of str
Labels for the second list of search terms.
- dbstr, optional, default: ‘pubmed’
Which database to access from EUtils.
- fieldstr, optional, default: ‘TIAB’
Field to search for term within. Defaults to ‘TIAB’, which is Title/Abstract.
- api_keystr, optional
An API key for a NCBI account.
- collect_coocsbool, optional, default: True
Whether to collect co-occurence data. If False, only collects the counts for first term list.
- logging{None, ‘print’, ‘store’, ‘file’}, optional
What kind of logging, if any, to do for requested URLs.
- directorystr or SCDB, optional
Folder or database object specifying the save location.
- collect_infobool, optional, default: True
Whether to collect database information, to be added to meta data.
- verbosebool, optional, default: False
Whether to print out updates.
- **eutils_kwargs
Additional settings for the EUtils API.
- Returns:
- co_occurences2d array
The numbers of articles found for each combination of terms. Only returned if collect_coocs is True.
- counts1d array or list of 1d array
Number of articles for each term independently.
- meta_datadict
Meta data from the data collection.
Notes
The collection does an exact word search for search terms.
The HTML page returned by the EUtils search includes a ‘count’ field. This field contains the number of articles with both terms. This is extracted.
Examples
Collect counts and co-occurrences for a single set of two search terms:
>>> coocs, counts, meta_data = collect_counts([['frontal lobe'], ['temporal lobe']])
Collect counts and co-occurrences for two sets of search terms:
>>> coocs, counts, meta_data = collect_counts(terms_a=[['frontal lobe'], ['temporal lobe']], ... terms_b=[['attention'], ['perception']])
