Here, we explore the history of scientific publishing delays. The findings from the analysis are discussed in a blog post by Daniel Himmelstein and feature in Nature News.

Delays are calculated from publisher-deposited PubMed history dates. Only journal articles published between 1960 and 2015 are included. Specifically, two delay types are calculated:

• acceptance delay — the number of days from receival to acceptance
• publication delay — the number of days from acceptance to online publication

To re-execute the analysis, run the following notebooks in the following order:

1. eutilities.ipynb (python): Use PubMed's EUtility API to retrieve the list of relevant IDs using ESearch and article summaries using ESummary.
2. process-esummary.ipynb (python): Extract history dates from the ESummary XML output.
3. extract-delays.ipynb (R): Calculate acceptance and publications delays from the PubMed history dates.
4. process-nlm-catalog.ipynb (python): Download and process the NLM Catalog which contains the journals indexed by PubMed.
5. visualize-history.ipynb (R): Plot historical delays and export several TSV summaries of the dataset.
6. webapp.ipynb (python): Create JSON files used to initialize the select2 journal selection for the blog post.

The following data files are generated during execution:

1. pubmed-journals.tsv: a dataframe of the NLM Catalog (journals in PubMed)
2. history-dates.tsv.bz2: a dataframe with all history dates extracted from the PubMed XML
3. delays.tsv.gz: a dataframe of all acceptance and publication delays
4. journal-summaries.tsv: a dataframe of summarizing delays for each journal
5. yearly-summaries.tsv: a dataframe of summarizing delays for each year
6. yearly-percentiles.tsv: a dataframe of delay percentiles for each year
7. slopes.tsv: a dataframe journal-specific delay slopes (Δ days of delay per year)

The following data files, generated by eutilities.ipynb, are ignored due to large file size:

1. download/esearch_journal-articles_1960-2015.tsv.gz with the list of relevant PubMed IDs
2. download/esummary_journal-articles_1960-2015.xml.bz2 with combined XML output from the ESummary API queries

These files, along with several of the other files listed above, are available via figshare.