RMedlineFunctions

RMedlineFunctions is intended to be a set of reusable functions for accessing, manipulating, and visualizing data from medline/pubmed via the R library RISmed (https://cran.r-project.org/web/packages/RISmed/index.html).

This project is in early development.

An example using RNotebook can be found here: https://fdsayre.github.io/RMedlineFunctions/ReproExample.nb.html

Future development:

• Compare a set of PMIDs against a search
• Map country publushed to world map
• Map country of affiliation to world map?
• Find common MeSH across a search set (e.g. what MeSH are present in all results?)
• Find minimum MeSH/Keywords to retrieve a set of results
• Recommend additional MeSH and search terms based on existing set
• Find collaborators/co-authors in search set
• Create network graphs based co-athorship
• Compare a set of PMIDs against a search for sensitivity/specificity
• Export results in various formats
  • csv
  • bibtex

Functions

Function: RetrieveArticleData ----

Retrieve a set of article data in medline format (usually not approrpiate for direct analysis) x = 'search query' y = mindate, e.g. 1990 z = maxdate, e.g. 2010 a = maxrecords, e.g. 1000

Function: RetrieveArticleMetadata----

From initial datafile created with RetrieveArticleData function get article level metadata, including Title, Abstract, Year, in a dataframe suitable for analysis x = pubmed_data

Function: RetrieveMostArticleMetadata----

From initial datafile created with RetrieveArticleData function get article level metadata, including Title, Abstract, Year, Pubstatus, and Journal, in a dataframe suitable for analysis Not included: Citation, Pubtype x = pubmed_data

Function: GraphArticlesFreqYears ----

From initial datafile, create a graph of the number of articles published each year x = data frame with 'Year' variable

Function: JournalTitles -----

Get Journal Titles for an initial pubmed dataset

Function: JournalTitlesTop5Graph ----

Get a graph of the top 5 journal titles for a search using a article meta file

Function: PMStatusByYearPlot-------

Create a stacked bar plot of Pubmed Status by year x = pubmed datafile

Function: Top Authors ----

Create a data frame of authors and their frequency from a base data file

Function: MapPubsPerCountry

Maps number of publications published in a journal in a country x = medline data file y = metadata file with PMID as "ID"

Function: GetMeSH ----------

Gets list of all MeSH Descriptors and Qualifiers Very messy, includes redundant ID columns and lots of NAs

Function: CountMeSH

Returns a sorted list of MeSH Descriptors (no qualifiers yet) in decending order x = output df from the GetMeSH function