removed richtations, makred defunct

bumpd dev version
removed a donttest to just commenting out the eg

DESCRIPTION

@@ -7,7 +7,7 @@ Description: A programmatic interface to the 'SOLR' based
     articles, making plots, doing 'faceted' searches,
     'highlight' searches, and viewing results of 'highlighted'
     searches in a browser.
-Version: 0.6.7.9200
+Version: 0.6.7.9910
 License: MIT + file LICENSE
 Authors@R: c(
     person("Scott", "Chamberlain", role = c("aut", "cre"), email = "[email protected]"),

NEWS.md

@@ -77,7 +77,7 @@ rplos 0.4.7
 
 ### NEW FEATURES
 
-* New function `citations()` for querying the [PLOS Rich Citations API](http://api.richcitations.org/) (#88)
+* New function `citations()` for querying the PLOS Rich Citations API (http://api.richcitations.org/) (#88)
 
 ### BUG FIXES
 

R/citations.R

@@ -1,51 +1,7 @@
-#' Search PLOS Rich Citations API
-#'
+#' This function is defunct.
 #' @export
-#' @param uri (character) A URI, of the form \code{http://dx.doi.org/<DOI>}
-#' @param doi (character) A PLOS journals DOI
-#' @param parse (logical) Passed to \code{\link[jsonlite]{fromJSON}}, toggles
-#' whether we return json parsed to data.frame's where possible, or not.
-#' Default: FALSE
-#' @param ... Curl options passed to \code{\link[httr]{GET}}
-#' @return A list
-#' @references \url{http://api.richcitations.org/}
-#' @details To get an API key, email \email{ploslabs@@plos.org} and request a key
-#' @examples \dontrun{
-#' # get citations for an article (via its DOI)
-#' # uri <- "http://dx.doi.org/10.1371%2Fjournal.pone.0000000"
-#' # citations(uri)
-#' # citations(uri, parse = TRUE)
-#'
-#' # pass in a DOI, url encoded or not
-#' # citations(doi = "10.1371%2Fjournal.pone.0000000")
-#' # citations(doi = "10.1371/journal.pone.0000000")
-#' # ids <- searchplos(q='ecology', fl='id', limit = 20)$data$id
-#' # citations(doi = ids[1])
-#' }
-
-citations <- function(uri = NULL, doi = NULL, parse = FALSE, ...) {
-  calls <- names(sapply(match.call(), deparse))[-1]
-  if ("random" %in% calls) stop("The parameter 'random' has been removed", call. = FALSE)
-
-  # one has to be non-NULL
-  stopifnot(length(ploscompact(list(uri, doi))) == 1)
-  uri <- uriparse(uri, doi)
-  args <- ploscompact(list(uri = uri))
-  if (length(args) == 0) args <- NULL
-  res <- GET(richbase(), query = args, ...)
-  stop_for_status(res)
-  jsonlite::fromJSON(utf8cont(res), parse)
-}
-
-richbase <- function() "http://api.richcitations.org/papers"
-
-uriparse <- function(x, y) {
-  # both can't be null
-  stopifnot(xor(!is.null(x), !is.null(y)))
-  # check for url encoding
-  if (!is.null(y)) {
-    paste0("http://dx.doi.org/", sub("/", "%2F", y))
-  } else {
-    x
-  }
+#' @rdname citations-defunct
+#' @keywords internal
+citations <- function(...) {
+  .Defunct(msg = "the data provider behind citations() is gone")
 }

R/highplos.r

@@ -12,10 +12,8 @@
 #' highplos(q='alcohol', hl.fl='abstract', hl.snippets=5, hl.mergeContiguous='true', rows=5)
 #' highplos(q='alcohol', hl.fl='abstract', hl.useFastVectorHighlighter='true', rows=5)
 #' highplos(q='everything:"experiment"', fq='doc_type:full', rows=100, hl.fl = 'title')
-#' }
-#'
-#' @examples \donttest{
-#' highplos(q='alcohol', hl.fl = 'abstract', rows=1200)
+#' 
+#' # highplos(q='alcohol', hl.fl = 'abstract', rows=1200)
 #' }
 
 highplos <- function(q, fl=NULL, fq=NULL, hl.fl = NULL, hl.snippets = NULL, hl.fragsize = NULL,

R/plosabstract.R

@@ -8,7 +8,6 @@
 #' plosabstract(q = 'drosophila', fl=c('id','author'), limit = 5)
 #' plosabstract(q = 'drosophila', fl='author', limit = 5)
 #' plosabstract(q = 'drosophila', fl=c('id','author','title'), limit = 5)
-#' plosabstract(q = 'drosophila', fl=c('id','author','title'), limit = 5, config=verbose())
 #' }
 
 plosabstract <- function(q = NULL, fl = 'id', fq = NULL, sort = NULL, start = 0,

R/rplos-package.R

@@ -56,6 +56,7 @@ NULL
 #' \itemize{
 #'  \item \code{\link{crossref}}: service no longer provided - 
 #'  see the package \code{rcrossref}
+#'  \item \code{\link{citations}}: service no longer available
 #' }
 #'
 #' @name rplos-defunct

README.Rmd

@@ -49,7 +49,7 @@ rplos tutorial at rOpenSci website [here](http://ropensci.org/tutorials/rplos_tu
 
 PLoS API documentation [here](http://api.plos.org/)
 
-Crossref API documentation [here](https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md), [here](http://crosstech.crossref.org/2014/04/%E2%99%AB-researchers-just-wanna-have-funds-%E2%99%AB.html), and [here](http://help.crossref.org/#home). Note that we are working on a new package [rcrossref](https://github.com/ropensci/rcrossref) ([on CRAN](https://cran.r-project.org/package=rcrossref)) with a much fuller implementation of R functions for all Crossref endpoints.
+Crossref API documentation [here](https://github.com/CrossRef/rest-api-doc/blob/master/rest_api.md), and [here](http://help.crossref.org/#home). Note that we are working on a new package [rcrossref](https://github.com/ropensci/rcrossref) ([on CRAN](https://cran.r-project.org/package=rcrossref)) with a much fuller implementation of R functions for all Crossref endpoints.
 
 ## Quick start