import_xml_pubmed: Import an XML file from Pubmed/Medline

In jomuller/rigaps: R Interface to Generate Analysis like the Program SIGAPS

Description

Import an XML file from Pubmed/Medline

Usage

import_xml_pubmed(xml_path, lastname, firstname, ...)

Arguments

xml_path	A file path or an URL to the xml file
lastname	Lastname of the targeted author
firstname	Firstname of hte targeted author
...	Arguments passed on to xml2::read_xml x A string, a connection, or a raw vector. A string can be either a path, a url or literal xml. Urls will be converted into connections either using base::url or, if installed, curl::curl. Local paths ending in .gz, .bz2, .xz, .zip will be automatically uncompressed. If a connection, the complete connection is read into a raw vector before being parsed. encoding Specify a default encoding for the document. Unless otherwise specified XML documents are assumed to be in UTF-8 or UTF-16. If the document is not UTF-8/16, and lacks an explicit encoding directive, this allows you to supply a default. as_html Optionally parse an xml file as if it's html. options Set parsing options for the libxml2 parser. Zero of more of RECOVER recover on errors NOENT substitute entities DTDLOAD load the external subset DTDATTR default DTD attributes DTDVALID validate with the DTD NOERROR suppress error reports NOWARNING suppress warning reports PEDANTIC pedantic error reporting NOBLANKS remove blank nodes SAX1 use the SAX1 interface internally XINCLUDE Implement XInclude substitition NONET Forbid network access NODICT Do not reuse the context dictionary NSCLEAN remove redundant namespaces declarations NOCDATA merge CDATA as text nodes NOXINCNODE do not generate XINCLUDE START/END nodes COMPACT compact small text nodes; no modification of the tree allowed afterwards (will possibly crash if you try to modify the tree) OLD10 parse using XML-1.0 before update 5 NOBASEFIX do not fixup XINCLUDE xml:base uris HUGE relax any hardcoded limit from the parser OLDSAX parse using SAX2 interface before 2.7.0 IGNORE_ENC ignore internal document encoding hint BIG_LINES Store big lines numbers in text PSVI field

Details

The xml file imported must be produced by Pubmed and have to focus on the particular author or list of publication the user wants to compute the sigaps score.

jomuller/rigaps documentation built on May 29, 2019, 12:39 p.m.