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…funct now removed their test files as well also made all text mining fxns deprecated, to notify users of the new package and of future defunctifying #122 bumped patch version
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,93 +1,11 @@ | ||
| #' Search the CrossRef Metatdata API. | ||
| #' | ||
| #' | ||
| #' @export | ||
| #' | ||
| #' @param query Query terms. | ||
| #' @param doi Search by a single DOI or many DOIs. | ||
| #' @param page Page to return from results. | ||
| #' @param rows Number of records to return. | ||
| #' @param sort Sort either by "score" or "year". | ||
| #' @param year Year to search. | ||
| #' @param type Record type, e.g., "Journal Article" or "Journal Issue" | ||
| #' @param ... Named parameters passed on to \code{\link[httr]{GET}} | ||
| #' | ||
| #' @details See \url{http://search.labs.crossref.org/help/api} for more | ||
| #' info on this Crossref API service. | ||
| #' @seealso \code{\link{cr_r}}, \code{\link{cr_citation}}, | ||
| #' \code{\link{cr_search_free}} | ||
| #' @author Scott Chamberlain \email{myrmecocystus@@gmail.com} | ||
| #' @examples \dontrun{ | ||
| #' cr_search(query = c("renear", "palmer")) | ||
| #' | ||
| #' # limit to 4 results | ||
| #' cr_search(query = c("renear", "palmer"), rows = 4) | ||
| #' | ||
| #' # get more results than standard | ||
| #' cr_search(query = c("renear", "palmer"), rows = 40) | ||
| #' | ||
| #' # sort results by score | ||
| #' cr_search(query = c("renear", "palmer"), rows = 10, sort = "score") | ||
| #' | ||
| #' # sort results by year | ||
| #' cr_search(query = c("renear", "palmer"), rows = 10, sort = "year") | ||
| #' | ||
| #' # get results for a certain year | ||
| #' cr_search(query = c("renear", "palmer"), year = 2010) | ||
| #' | ||
| #' # search by a single DOI | ||
| #' cr_search(doi = "10.1890/10-0340.1") | ||
| #' | ||
| #' # search for many DOI's | ||
| #' # find all the records of articles from a journal ISBN | ||
| #' cr_search(query = "1461-0248", type="Journal Article") | ||
| #' | ||
| #' # curl stuff | ||
| #' library('httr') | ||
| #' cr_search(doi = "10.1890/10-0340.1", config=verbose()) | ||
| #' cr_search(query = c("renear", "palmer"), rows = 40, config=progress()) | ||
| #' } | ||
|
|
||
| `cr_search` <- function(query=NULL, doi=NULL, page=NULL, rows=NULL, sort=NULL, | ||
| year=NULL, type=NULL, ...) { | ||
|
|
||
| .Deprecated( | ||
| package = "rcrossref", | ||
| msg = "cr_search is deprecated, and will be removed in next version, see cr_works et al." | ||
| #' @rdname cr_search-defunct | ||
| #' @keywords internal | ||
| `cr_search` <- function(...) { | ||
| .Defunct( | ||
| package = "rcrossref", | ||
| msg = "Removed - see cr_works(), cr_journals(), etc. for similar functionality" | ||
| ) | ||
| url <- "http://search.crossref.org/dois" | ||
| if (!is.null(doi)) { | ||
| doi <- as.character(doi) | ||
| } | ||
| if (is.null(doi)) { | ||
| cr_search_GET(url, query, page, rows, sort, year, type, ...) | ||
| } else { | ||
| ldply(doi, function(z) cr_search_GET(url, x = z, page, rows, sort, | ||
| year, type, ...)) | ||
| } | ||
| } | ||
|
|
||
| cr_search_GET <- function(url, x, page, rows, sort, year, type, ...){ | ||
| if (!is.null(x)) { | ||
| if (length(x) > 1) x <- paste0(x, collapse = " ") | ||
| } | ||
| args <- cr_compact(list(q = x, page = page, rows = rows, | ||
| sort = sort, year = year, type = type)) | ||
| tt <- GET(url, query = args, make_rcrossref_ua(), ...) | ||
| stop_for_status(tt) | ||
| res <- ct_utf8(tt) | ||
| tmp <- jsonlite::fromJSON(res) | ||
| if (NROW(tmp) == 0) { | ||
| NULL | ||
| } else { | ||
| col_classes( | ||
| tmp, | ||
| c("character","numeric","integer","character", | ||
| "character","character","numeric") | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| asnum <- function(x){ | ||
| tmp <- tryCatch(as.numeric(x), warning = function(w) w) | ||
| if (inherits(tmp, "simpleWarning")) x else tmp | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,50 +1,11 @@ | ||
| #' Search the CrossRef Metatdata for DOIs using free form references. | ||
| #' | ||
| #' @export | ||
| #' | ||
| #' @param query Reference query; a character vector of length 1 or greater, | ||
| #' comma-separated of course. | ||
| #' @param url Base url for the Crossref metadata API. | ||
| #' | ||
| #' @details Have to have at least three terms in each search query. | ||
| #' @seealso \code{\link{cr_search}}, \code{\link{cr_r}}, | ||
| #' \code{\link{cr_citation}} | ||
| #' @author Scott Chamberlain \email{myrmecocystus@@gmail.com} | ||
| #' @examples \dontrun{ | ||
| #' # search with title, author, year, and journal | ||
| #' cr_search_free(query = "Piwowar Sharing Detailed Research Data Is | ||
| #' Associated with Increased Citation Rate PLOS one 2007") | ||
| #' | ||
| #' cr_search_free(query="Renear 2012") # too few words, need at least 3 | ||
| #' | ||
| #' # multiple queries | ||
| #' cr_search_free(query=c("Renear 2012","Piwowar sharing data PLOS one")) | ||
| #' | ||
| #' # Get a DOI and get the citation using cr_search | ||
| #' doi <- cr_search_free(query="Piwowar sharing data PLOS one")$doi | ||
| #' cr_search(doi = doi) | ||
| #' | ||
| #' # Queries can be quite complex too | ||
| #' cr_search_free("M. Henrion, D. J. Mortlock, D. J. Hand, and A. Gandy, | ||
| #' \"A Bayesian approach to star-galaxy classification,\" Monthly Notices of | ||
| #' the Royal Astronomical Society, vol. 412, no. 4, pp. 2286-2302, Apr. 2011.") | ||
| #' | ||
| #' # Lots of queries | ||
| #' queries <- c( | ||
| #' "Piwowar sharing data PLOS one", "Priem Scientometrics 2.0 social web", | ||
| #' "William Gunn A Crosstalk Between Myeloma Cells", | ||
| #' "karthik ram Metapopulation dynamics override local limits") | ||
| #' cr_search_free(queries) | ||
| #' } | ||
|
|
||
| `cr_search_free` <- function(query, url = "http://search.crossref.org/links") { | ||
| .Deprecated(package = "rcrossref", | ||
| msg = "cr_search_free is deprecated, and will be removed in next version, see cr_works et al.") | ||
| tt <- POST( | ||
| url, | ||
| config = c(content_type_json(), accept_json()), | ||
| body = jsonlite::toJSON(query)) | ||
| stop_for_status(tt) | ||
| res <- ct_utf8(tt) | ||
| fromJSON(res)$results | ||
| #' @rdname cr_search_free-defunct | ||
| #' @keywords internal | ||
| `cr_search_free` <- function(...) { | ||
| .Defunct( | ||
| package = "rcrossref", | ||
| msg = "Removed - see cr_works(), cr_journals(), etc. for similar functionality" | ||
| ) | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,54 +1,11 @@ | ||
| #' Crosscite - citation formatter | ||
| #' | ||
| #' @export | ||
| #' @param dois Search by a single DOI or many DOIs. | ||
| #' @param style a CSL style (for text format only). See | ||
| #' \code{\link{get_styles}} for options. Default: apa. If there's a style that | ||
| #' CrossRef doesn't support you'll get a \code{(500) Internal Server Error} | ||
| #' @param locale Language locale. See \code{?Sys.getlocale} | ||
| #' @template moreargs | ||
| #' @details See \url{http://www.crosscite.org/cn/} for more info on the | ||
| #' Crossref Content Negotiation API service. | ||
| #' | ||
| #' This function is now deprecated. It will be removed in the next version | ||
| #' of this package. Use \code{\link{cr_cn}} instead. | ||
| #' | ||
| #' @examples \dontrun{ | ||
| #' crosscite("10.5284/1011335") | ||
| #' crosscite(c('10.5169/SEALS-52668','10.2314/GBV:493109919', | ||
| #' '10.2314/GBV:493105263', '10.2314/GBV:487077911', | ||
| #' '10.2314/GBV:607866403')) | ||
| #' } | ||
|
|
||
| `crosscite` <- function(dois, style = 'apa', locale = "en-US", | ||
| .progress = "none", ...) { | ||
|
|
||
| .Deprecated( | ||
| new = "cr_cn", | ||
| package = "rcrossref", | ||
| msg = "crosscite is deprecated - will be removed in next version, use cr_cn" | ||
| #' @rdname crosscite-defunct | ||
| #' @keywords internal | ||
| `crosscite` <- function(...) { | ||
| .Defunct( | ||
| package = "rcrossref", | ||
| msg = "Removed - see cr_works(), cr_journals(), etc. for similar functionality" | ||
| ) | ||
| if (length(dois) > 1) { | ||
| llply(dois, function(z, ...) { | ||
| out <- try(ccite(z, style, locale, ...), silent=TRUE) | ||
| if ("try-error" %in% class(out)) { | ||
| warning( | ||
| paste0("Failure in resolving '", z, "'. See error detail in results.") | ||
| ) | ||
| out <- list(doi=z, error=out[[1]]) | ||
| } | ||
| return(out) | ||
| }, .progress=.progress) | ||
| } else { | ||
| ccite(dois, style, locale, ...) | ||
| } | ||
| } | ||
|
|
||
| ccite <- function(doi, style, locale, ...) { | ||
| args <- cr_compact(list(doi = doi, style = style, locale = locale)) | ||
| res <- GET(ccurl(), query = args, make_rcrossref_ua(), ...) | ||
| stop_for_status(res) | ||
| gsub("\n", "", ct_utf8(res)) | ||
| } | ||
|
|
||
| ccurl <- function() "http://crosscite.org/citeproc/format" |
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