NEWS.md

In ropensci/rplos: Interface to the Search API for 'PLoS' Journals

rplos 1.0

MINOR IMPROVEMENTS

• fix a broken test on cran (#128)

rplos 0.9.0

MINOR IMPROVEMENTS

• functions that use solrium under the hood now have a progress parameter that you can pass htt::progress() to get progress information; especially useful for long running queries (#124)
• move readme images to man/figures (#127)
• replace dplyr::data_frame with dplyr::tibble (#126)

rplos 0.8.6

MINOR IMPROVEMENTS

• use preserve_exact_body_bytes for tests for plosabstract and plosfigtabcaps to avoid non-ascii text problems on debian clang devel (#125)

rplos 0.8.4

MINOR IMPROVEMENTS

• update docs for searchplos() and all wrapper fxns to explain that internal pagination is used, but that users can do their own pagination if they like (#122)

BUG FIXES

• fix to pagination in searchplos() and all wrapper fxns. large numbers were being passed as scientific notation, fixed now (#123)

rplos 0.8.2

NEW FEATURES

• Integration with vcr and webmockr packages for unit test stubbing

BUG FIXES

• for highbrow() open pages with https://doi.org instead of http://dx.doi.org (#117)
• remove message "Looping - printing progress ..." from searchplos() (#120)
• fix internal pagination for searchplos(): were accidentally dropping fq statements if more than 1, woopsy (#121)

rplos 0.8.0

NEW FEATURES

• Now using solrium for under the hood Solr interaction instead of solr package (#106)
• Along with above change, the following: facetplos, searchplos, and highplos lose parameter verbose, and gain parameters error and proxy for changing how verbose error reporting is, and for setting proxy details, respectively.
• Now using crul instead of httr for HTTP requests (#110)

MINOR IMPROVEMENTS

• Fix to placement of images for README requested by CRAN (#114)
• Replaced XML with xml2 (#112)
• citations function for PLOS rich citations is defunct as the service is gone (#113)
• package tm dropped from Enhances (#111)
• added code of conduct, issue and pull request templates

rplos 0.6.4

MINOR IMPROVEMENTS

• URLs to full text XML have been changed - old URLs were working but were going through 2 302 redirects to get there. Updated URLs. (#107)

BUG FIXES

• Fixed content-type check for plos_fulltext() function. XML can be either application/xml or text/xml (#108)

rplos 0.6.0

MINOR IMPROVEMENTS

• Added notes to documentation for relavant functions for how to do phrase searching. (#96) (#97) thanks @poldham
• Removed parameter random parameter from citations() function as it's no longer available in the API (#103)
• Swapped out all uses of dplyr::rbind_all() for dplyr::bind_rows() (#105)
• full_text_urls() now gives back NA when DOIs for annotations are given, which can be easily removed.

BUG FIXES

• Fixed full_text_urls() function to create full text URLs for PLOS Clinical Trials correctly (#104)

rplos 0.5.6

MINOR IMPROVEMENTS

• move ggplot2 from Depends to Imports, and using @importFrom for ggplot2 functions, now all imports are using @importFrom (#99)
• Fixes for httr::content() to parse manually, and use explicit encoding of UTF-8 (#102)

rplos 0.5.4

MINOR IMPROVEMENTS

• Change solr dependency to require version v0.1.6 or less (#94)

rplos 0.5.2

MINOR IMPROVEMENTS

• More tests added (#94)

BUG FIXES

• Fix encoding in parsing of XML data in plos_fulltext() to avoid unicode problems (#93)

rplos 0.5.0

MINOR IMPROVEMENTS

• Now importing non-Base R functions from utils, stats, and methods packages (#90)

BUG FIXES

• Fixes for httr v1 that broke rplos when length 0 list passed to query parameter (#89)

rplos 0.4.7

NEW FEATURES

• New function citations() for querying the PLOS Rich Citations API (http://api.richcitations.org/) (#88)

BUG FIXES

• Added vignettes/figure to .Rbuildignore as requested by CRAN admin (#87)

rplos 0.4.6

NEW FEATURES

• API key no longer required (#86)

MINOR IMPROVEMENTS

• searchplos() now returns a list of length two, meta and data, and meta is a data.frame of metadata for the search.
• Switched from CC0 to MIT license.
• No longer importing libraries RCurl, data.table, googleVis, assertthat, RJSONIO, and stringr (#79) (#82) (#84)
• Now importing dplyr.
• Moved jsonlite from Suggests to Imports. Replaces use of RJSONIO. (#80)
• crossref() now defunct. See package rcrossref https://github.com/ropensci/rcrossref. (#83)
• highplos() now uses solr::solr_highlight() to do highlight searches.
• searchplos(), plosabstract(), and other functions that wrap searchplos() now use ... to pass in curl options to httr::GET(). You'll now get an error on using callopts parameter.
• Added manual file entry for the dataset isocodes.
• Reworked both plosword() and plot_throughtime() to have far less code, uses httr now instead of RCurl, but to the user, everything should be the same.
• Made documentation more clear on discrepancy between PLOS website behavior and rplos behavior, and how to make them match, or match more closely (#76)
• Added package level man file to allow ?rplos to go to help page.

BUG FIXES

• Removed some examples from searchplos() that are now not working for some unknown reason. (#81)
• Previously when user set limit=0, we still gave back data, this is fixed, and now the meta slot given back, and the data slot gives an NA (#85)

rplos 0.4.1

BUG FIXES

• Fixed some broken tests.

rplos 0.4.0

NEW FEATURES

• Errors from the data provider are reported now. At least we attempt to do so when they are given, for example if you specify asc or desc incorrectly with the sort parameter. See the check_response() function https://github.com/ropensci/rplos/blob/master/tests/testthat/test-check_response.R for examples.
• New functions facetplos() and highplos() using the solr R wrapper to the Solr indexing engine. The PLOS API just exposes the Solr endpoints, so we can use the general Solr wrapper package solr to allow more flexible Solr searching.
• New function highbrow() to visualize highlighting results in a browser.
• New function plos_fulltext() to get full text xml of PLOS articles. Helper function full_text_urls() constructs the URL's for full text xml.

BUG FIXES

• Fixed bug in tests where we forgot to give a key. No key is required per se, but PLOS encourages it so we prevent a call from happening without at least a dumby key.
• Added function check_response() to check responses from the PLOS API, deals with capturing server error messages, and checking for correct content type, etc.

IMPROVEMENTS

• Removed function crossref_r() as we are working on a package for the CrossRef API.
• Parameter arguments in searchplos(), plosauthor(), plosfigtabcaps(), plossubject(), and plostitle() were changed to match closer the Solr parameter names. terms to q. fields to fl. toquery to fq.
• Multiple values passed to fields
• returndf parameter is gone from searchplos(), plosauthor(), plosfigtabcaps(), plossubject(), and plostitle(). You can easily get raw JSON, etc. data using the solr package.
• Now using httr instead of RCurl in plosviews() function.

rplos 0.3.6

NEW FEATURES

• All search functions (searchplos(), plosabstract(), plosauthor(), plosfigtabcaps(), plossubject(), and plostitle()) gain highlighting argument, setting to TRUE (default=FALSE) returns matching sentence fragments that were matched. NOTE that if highlighting=TRUE the output can be a list of data.frame's if returndf=TRUE, with two named elements 'data' and 'highlighting', or a list of lists if returndf=FALSE.
• All search functions (searchplos(), plosabstract(), plosauthor(), plosfigtabcaps(), plossubject(), and plostitle()) gain sort argument. You can pass a field to sort by even if you don't return that field in the output, e.g., sort='counter_total_month desc'.
• A tiny function parsehighlight() added to parse out html code from highlighting output.

BUG FIXES

• Some examples in docs didn't work - fixed them.
• Fixed bug in searchplos() that was causing elements of a return field to cause failure because they were longer than 1 (e.g., authors). Now concatenating elements of length > 1.
• Fixed bug in searchplos() that was causing elements of length 0 to cause failure. Now removing elements of length 0.
• Fixed parsehighlight function to return NA if highlighting return of length 0.
• Fixed broken test for plosauthor(), plosabstract(), and plot_throughtime().

rplos 0.3.0

NEW FEATURES

• Added httr::stop_for_status() calls to a few functions to give informative http status errors when they happen

BUG FIXES

• Fixed bug in plot_throughtime() that was throwing errors and preventing fxn from working, thanks to Ben Bolker for the fix.
• Simplified code in many functions to have cleaner and simpler code.
• ... parameter in many functions changed to callopts=list(), which passes in curl options to a call to either RCurl::getForm() or httr::GET()
• Fixed bug in function plosviews() that caused errors in some calls. Now forces full document searches, so that you get views data back for full papers only, not sections of papers. See package alm (https://github.com/ropensci/alm) for more in depth PLOS article-level metrics.

rplos 0.2.0

NEW FEATURES

• All functions for interacting with the PLOS ALM (altmetrics) API have been removed, and are now in a separate package called alm (http://github.com/ropensci/alm).
• Convenience functions plosabstract, plosauthor, plosfigtabcaps, plossubject, and plostitle, that search specifically within those sections of papers now wrap searchplos, so they should behave the same way.
• ldfast() fxn added as an attempt to do ldply faster
• performance improvements in searchplos

BUG FIXES

• Dependency on assertthat removed since it's not on CRAN.
• Fixed namespace conflicts by importing only functions needed from some packages.
• searchplos() now removes leading, trailing, and internal whitespace from character strings

rplos 0.1.1

• remove alm*() functions so that this package now only wraps the PLoS search API.

rplos 0.1.0

• The almdateupdated function has been deprecated - use almupdated instead.

• The articlelength function has been deprecated - didn't see the usefulness any longer.

• In general simplified and prettified code.

• Changed from using RCurl to httr in many functions, but not all.

• Added more examples for many functions.

• Added three internal functions: concat_todf, addmissing, and getkey.

• Added Karthik Ram as a package author.

BUG FIXES

• All url arguments in functions put inside functions as they are not likely to change that often.

• Fixed crossref function, and added more examples.

NEW FEATURES

• The alm function (previously almplosallviews) gains many ### new features: now allows up to 50 DOIs per call; you can specify the source you want to get alm data from as an argument; you can specify the year you want to get alm data from as an argument.

• Added the plosfields data file to get all the possible fields to use in function calls.

NEW FUNCTIONS

• almplosallviews changed to alm.

• almplotallviews changed to almplot.

• almevents added to specifically search and get detailed events data for a specific source or N sources.

• crossref_r gets 20 random DOIs from Crossref.org.

• Added package startup message.

• journalnamekey function to get the short name keys for each PLoS Journal.

rplos 0.0-7

IMPROVEMENTS AND ### BUG FIXES

• ALM functions (any functions starting with alm) received updated arguments/parameters according to the ALM API version 3.0 changes.

• Bug fixes in general across library.

• Added tests.

• almplosallviews now outputs different output - two data.frames, one total metrics (summed across time), and history (for metrics for each time period specified in the search)

• crossref function returns R's native bibtype format. See examples in crossref function documentation

rplos 0.0-5

IMPROVEMENTS AND BUG FIXES

• almpub changed to almdatepub

• changed help file rplos to help - use help('rplos') in R

• changed URL from http://ropensci.org/ to https://github.com/ropensci/rplos

• added sleep argument to plosallviews function to allow pauses between API calls when running plosallviews in a loop - this is an attempt to limit hitting the PLoS API too hard

• various other fixed to functions

• more examples added to some functions

NEW FUNCTIONS

• added function journalnamekey to get short keys for journals to use in searching for specific journals

rplos 0.0-1

NEW FEATURES

• released to CRAN

ropensci/rplos documentation built on Sept. 12, 2022, 2:10 p.m.