Nothing
R/metrics.R
In rAltmetric: Retrieves altmerics data for any published paper from altmetric.com
#' Grab altmetric data on any paper
#'
#' This function will retrieve data from Altmetric.com on any paper with an appropriate object identifier. Acceptable identifiers include dois, arXiv ids, pubmed ids and altmetric ids.
#' @param oid \code{oid} Any object ID. Any general object identifier as long as the prefix is "doi","pmid", "arXiv", or "id".
#' @param id The Altmetric \code{id} of a paper. If specifiying directly, the "id" prefix is not necessary.
#' @param doi The \code{doi} of a paper. If specifiying directly, the "doi" prefix is not necessary.
#' @param pmid The \code{pmid} of a paper.If specifiying directly, the "pmid" prefix is not necessary.
#' @param arXiv The \code{arxiv} ID of a paper.If specifiying directly, the "arXiv" prefix is not necessary.
#' @param apikey An API key obtained from altmetric. The key for this application is '37c9ae22b7979124ea650f3412255bf9' and you are free to use it for academic non-commercial research. But if you start seeing rate limits, please contact support at altmetric.com to get your own.
#'
#' The function returns detailed metrics. For more information on all the fields returned by the function, see the API documentation: (\url{http://api.altmetric.com/docs/call_citations.html}). If you get your own key, you can save it in your \code{.rprofile} as \code{options(altmetricKey="YOUR_KEY")}
#' @param curl passes on curl handle in a vectorized operation
#' @param ... additional parameters
#' @export
#' @return \code{list}
#' @examples \dontrun{
#' altmetrics(doi ='10.1890/ES11-00339.1')
#' Or specfiy the doi with the id
#' altmetrics('doi/10.1890/ES11-00339.1')
#' altmetrics(doi ='10.1038/480426a')
#' Or specfiy the doi with the id
#' You can do the same for other providers such as pmid, id, and arxiv
#' altmetrics('doi/10.1038/480426a')
#'}
altmetrics <- function(oid = NULL, id = NULL, doi = NULL, pmid = NULL, arXiv = NULL, apikey = getOption('altmetricKey'), curl = getCurlHandle(), ...) {
if(is.null(apikey))
apikey <- '37c9ae22b7979124ea650f3412255bf9'
acceptable_identifiers <- c("doi", "arXiv", "id", "pmid")
# If you start hitting rate limits, email support@altmetric.com
# to get your own key.
# If no object identifiers were specified, throw an error
if(is.null(oid) && is.null(id) && is.null(doi) && is.null(pmid) && is.null(arXiv))
stop("No valid identfier found. See ?altmetrics for more help", call.=FALSE)
# If an altmetric id is not prefixed by "id", add it in.
if(!is.null(id)) {
prefix <- as.list((strsplit(id,'/'))[[1]])[[1]]
if(prefix != "id")
id <- paste0("id", "/", id)
}
# If an doi id is not prefixed by "id", add it in.
if(!is.null(doi)) {
prefix <- as.list((strsplit(doi,'/'))[[1]])[[1]]
if(prefix != "doi")
doi <- paste0("doi", "/", doi)
}
# If an arXiv id is not prefixed by "arXiv", add it in.
if(!is.null(arXiv)) {
prefix <- as.list((strsplit(arXiv,':|/'))[[1]])[[1]]
arXiv <- paste0("arXiv", "/", as.list((strsplit(arXiv,':|/'))[[1]])[[2]])
}
# If an pubmed id is not prefixed by "pmid", add it in.
if(!is.null(pmid)) {
prefix <- as.list((strsplit(pmid,'/'))[[1]])[[1]]
if(prefix != "pmid")
pmid <- paste0("pmid", "/", pmid)
}
# remove the identifiders that weren't specified
identifiers <- compact(list(oid, id, doi, pmid, arXiv))
# If user specifies more than one at once, then throw an error
# Users should use lapply(object_list, altmetrics)
# to process multiple objects.
if(length(identifiers) > 1)
stop("Function can only take one object at a time. Use lapply with a list to process multiple objects", call.=FALSE)
if(!is.null(identifiers)) {
ids <- identifiers[[1]]
# Fix arXiv
test <- strsplit(ids, ":")
if(length(test[[1]]) == 2) {
ids <- paste0(as.list(strsplit(ids, ":")[[1]])[[1]], "/", as.list(strsplit(ids, ":")[[1]])[[2]])
}
supplied_id <- as.character(as.list((strsplit(ids,'/'))[[1]])[[1]])
# message(sprintf("%s", supplied_id))
if(!(supplied_id %in% acceptable_identifiers))
stop("Unknown identifier. Please use doi, pmid, arxiv or id (for altmetric id).", call.=F)
}
# message(sprintf("%s", identifiers[[1]]))
url <- "http://api.altmetric.com/v1/"
url <- paste0(url, ids, "?key=", apikey)
metrics <- getURL(url, curl = curl)
if(metrics == "Not Found") {
message(sprintf("No metrics found on %s", identifiers[[1]]))
return(NULL)
} else {
res <- fromJSON(metrics)
class(res) <- "altmetric"
return(res)
}
}
# Make it possible to do either doi or a full list. In case of full list, the first part must be the name of the identifier.
#' Returns a data frame of metrics for a paper
#'
#' @param alt_obj altmetrics object
#' @export
#' @return data.frame
#' @examples \dontrun{
#' altmetric_data(altmetrics(doi='10.1038/489201a'))
#'}
altmetric_data <- function(alt_obj) {
value <- NA
if (is(alt_obj, "altmetric")) {
# Pull our readers and cohorts before squashing the list
reader <- alt_obj$readers
cohort <- alt_obj$cohorts
alt_obj <- alt_obj[-which(names(alt_obj)=="readers")]
alt_obj <- alt_obj[-which(names(alt_obj)=="cohorts")]
# Remove TQ if it exists
if("tq" %in% names(alt_obj)) {
alt_obj <- alt_obj[-which(names(alt_obj)=="tq")]
}
# Basic stats
alt_obj$issns <- paste0(alt_obj$issns, collapse = '', sep = ",")
basic_stuff <- data.frame(matrix(rep(NA, 10), nrow =1))
names(basic_stuff) <- names(alt_obj)[1:10]
basic_data <- data.frame(t(unlist(alt_obj[1:10])))
# basics <- rbind.fill(basic_stuff, basic_data)[-1, ]
basics <- basic_data
# Readers to data.frame
# readers <- unrowname(t(data.frame(reader)))
readers <- t(data.frame(reader))
cohorts <- data.frame("pub" = NA, "sci" = NA, "com" = NA, "doc" = NA)
cohorts2 <- data.frame(unrowname(t(data.frame(cohort))))
cohorts <- rbind.fill(cohorts, cohorts2)[-1,]
# Context (hard to standardize so excluding this for now)
# context <- ldply(alt_obj$context, function(foo) t(data.frame(foo)))
# names(context) <- c("type", "count", "rank", "pct")
# more_metrics <- dcast(melt(context, id.var="type"), 1~variable+type)[, -1]
# # 1, 18
# Counts to data.frame
stats_base <- data.frame("cited_by_gplus_count" =NA, "cited_by_fbwalls_count" =NA,"cited_by_posts_count" =NA, "cited_by_tweeters_count" =NA, "cited_by_accounts_count" =NA, "cited_by_feeds_count" =NA, "cited_by_rdts_count" =NA, "cited_by_msm_count" =NA, "cited_by_delicious_count" =NA, "cited_by_forum_count" = NA, "cited_by_qs_count" = NA, "cited_by_rh_count" = NA)
# stats <- melt(alt_obj[grep("^cited", names(alt_obj))])
stats <- data.frame(alt_obj[grep("^cited", names(alt_obj))])
# stats <- dcast(stats, 1~value+L1)[, -1]
# names(stats) <- gsub("^[0-9]_","", names(stats))
stats <- rbind.fill(stats_base, stats)[-1,]
# 1, 11
alt_obj$subjects <- paste0(alt_obj$subjects, collapse='', sep=",")
alt_obj$scopus_subjects <- paste0(alt_obj$scopus_subjects, collapse='', sep=", ")
if(length(alt_obj$added_on) ==0 || is.null(alt_obj$added_on)) {
alt_obj$added_on <- NA
}
if(length(alt_obj$published_on) ==0 || is.null(alt_obj$published_on)) {
alt_obj$published_on <- NA
}
# Removing more_metrics for the time being
# return(data.frame(basic_stuff, stats, score = alt_obj$score, readers, url = alt_obj$url, added_on = alt_obj$added_on, published_on = alt_obj$published_on, subjects = alt_obj$subjects, scopus_subjects = alt_obj$scopus_subjects, last_updated = alt_obj$last_updated, readers_count = alt_obj$readers_count, more_metrics, details_url = alt_obj$details_url))
return(data.frame(basics, stats, score = alt_obj$score, readers, url = alt_obj$url,
added_on = alt_obj$added_on, published_on = alt_obj$published_on,
subjects = alt_obj$subjects, scopus_subjects = alt_obj$scopus_subjects,
last_updated = alt_obj$last_updated, readers_count = alt_obj$readers_count,
details_url = alt_obj$details_url))
}
}
#' Returns cleaner metric source names (mostly for internal use)
#'
#' @param provider the data provider
#' @export
#' @keywords internal
#' @examples \dontrun{
#' return_provider('cited_by_gplus_count')
#'}
return_provider <- function(provider) {
services <- data.frame(type = c("cited_by_gplus_count", "cited_by_fbwalls_count", "cited_by_posts_count", "cited_by_tweeters_count", "cited_by_accounts_count", "cited_by_feeds_count", "cited_by_rdts_count", "cited_by_msm_count", "cited_by_delicious_count", "cited_by_forum_count", "cited_by_qs_count"), names = c("Google+", "Facebook", "Cited", "Tweets", "Accounts", "Feeds", "Reddit", "MSM", "Delicious", "Forums", "QS"))
return(services$names[which(services$type == provider)])
}
Try the rAltmetric package in your browser
Any scripts or data that you put into this service are public.
rAltmetric documentation built on May 2, 2019, 4:22 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' Grab altmetric data on any paper
#'
#' This function will retrieve data from Altmetric.com on any paper with an appropriate object identifier. Acceptable identifiers include dois, arXiv ids, pubmed ids and altmetric ids.
#' @param oid \code{oid} Any object ID. Any general object identifier as long as the prefix is "doi","pmid", "arXiv", or "id".
#' @param id The Altmetric \code{id} of a paper. If specifiying directly, the "id" prefix is not necessary.
#' @param doi The \code{doi} of a paper. If specifiying directly, the "doi" prefix is not necessary.
#' @param pmid The \code{pmid} of a paper.If specifiying directly, the "pmid" prefix is not necessary.
#' @param arXiv The \code{arxiv} ID of a paper.If specifiying directly, the "arXiv" prefix is not necessary.
#' @param apikey An API key obtained from altmetric. The key for this application is '37c9ae22b7979124ea650f3412255bf9' and you are free to use it for academic non-commercial research. But if you start seeing rate limits, please contact support at altmetric.com to get your own.
#'
#' The function returns detailed metrics. For more information on all the fields returned by the function, see the API documentation: (\url{http://api.altmetric.com/docs/call_citations.html}). If you get your own key, you can save it in your \code{.rprofile} as \code{options(altmetricKey="YOUR_KEY")}
#' @param curl passes on curl handle in a vectorized operation
#' @param ... additional parameters
#' @export
#' @return \code{list}
#' @examples \dontrun{
#' altmetrics(doi ='10.1890/ES11-00339.1')
#' Or specfiy the doi with the id
#' altmetrics('doi/10.1890/ES11-00339.1')
#' altmetrics(doi ='10.1038/480426a')
#' Or specfiy the doi with the id
#' You can do the same for other providers such as pmid, id, and arxiv
#' altmetrics('doi/10.1038/480426a')
#'}
altmetrics <- function(oid = NULL, id = NULL, doi = NULL, pmid = NULL, arXiv = NULL, apikey = getOption('altmetricKey'), curl = getCurlHandle(), ...) {
if(is.null(apikey))
apikey <- '37c9ae22b7979124ea650f3412255bf9'
acceptable_identifiers <- c("doi", "arXiv", "id", "pmid")
# If you start hitting rate limits, email support@altmetric.com
# to get your own key.
# If no object identifiers were specified, throw an error
if(is.null(oid) && is.null(id) && is.null(doi) && is.null(pmid) && is.null(arXiv))
stop("No valid identfier found. See ?altmetrics for more help", call.=FALSE)
# If an altmetric id is not prefixed by "id", add it in.
if(!is.null(id)) {
prefix <- as.list((strsplit(id,'/'))[[1]])[[1]]
if(prefix != "id")
id <- paste0("id", "/", id)
}
# If an doi id is not prefixed by "id", add it in.
if(!is.null(doi)) {
prefix <- as.list((strsplit(doi,'/'))[[1]])[[1]]
if(prefix != "doi")
doi <- paste0("doi", "/", doi)
}
# If an arXiv id is not prefixed by "arXiv", add it in.
if(!is.null(arXiv)) {
prefix <- as.list((strsplit(arXiv,':|/'))[[1]])[[1]]
arXiv <- paste0("arXiv", "/", as.list((strsplit(arXiv,':|/'))[[1]])[[2]])
}
# If an pubmed id is not prefixed by "pmid", add it in.
if(!is.null(pmid)) {
prefix <- as.list((strsplit(pmid,'/'))[[1]])[[1]]
if(prefix != "pmid")
pmid <- paste0("pmid", "/", pmid)
}
# remove the identifiders that weren't specified
identifiers <- compact(list(oid, id, doi, pmid, arXiv))
# If user specifies more than one at once, then throw an error
# Users should use lapply(object_list, altmetrics)
# to process multiple objects.
if(length(identifiers) > 1)
stop("Function can only take one object at a time. Use lapply with a list to process multiple objects", call.=FALSE)
if(!is.null(identifiers)) {
ids <- identifiers[[1]]
# Fix arXiv
test <- strsplit(ids, ":")
if(length(test[[1]]) == 2) {
ids <- paste0(as.list(strsplit(ids, ":")[[1]])[[1]], "/", as.list(strsplit(ids, ":")[[1]])[[2]])
}
supplied_id <- as.character(as.list((strsplit(ids,'/'))[[1]])[[1]])
# message(sprintf("%s", supplied_id))
if(!(supplied_id %in% acceptable_identifiers))
stop("Unknown identifier. Please use doi, pmid, arxiv or id (for altmetric id).", call.=F)
}
# message(sprintf("%s", identifiers[[1]]))
url <- "http://api.altmetric.com/v1/"
url <- paste0(url, ids, "?key=", apikey)
metrics <- getURL(url, curl = curl)
if(metrics == "Not Found") {
message(sprintf("No metrics found on %s", identifiers[[1]]))
return(NULL)
} else {
res <- fromJSON(metrics)
class(res) <- "altmetric"
return(res)
}
}
# Make it possible to do either doi or a full list. In case of full list, the first part must be the name of the identifier.
#' Returns a data frame of metrics for a paper
#'
#' @param alt_obj altmetrics object
#' @export
#' @return data.frame
#' @examples \dontrun{
#' altmetric_data(altmetrics(doi='10.1038/489201a'))
#'}
altmetric_data <- function(alt_obj) {
value <- NA
if (is(alt_obj, "altmetric")) {
# Pull our readers and cohorts before squashing the list
reader <- alt_obj$readers
cohort <- alt_obj$cohorts
alt_obj <- alt_obj[-which(names(alt_obj)=="readers")]
alt_obj <- alt_obj[-which(names(alt_obj)=="cohorts")]
# Remove TQ if it exists
if("tq" %in% names(alt_obj)) {
alt_obj <- alt_obj[-which(names(alt_obj)=="tq")]
}
# Basic stats
alt_obj$issns <- paste0(alt_obj$issns, collapse = '', sep = ",")
basic_stuff <- data.frame(matrix(rep(NA, 10), nrow =1))
names(basic_stuff) <- names(alt_obj)[1:10]
basic_data <- data.frame(t(unlist(alt_obj[1:10])))
# basics <- rbind.fill(basic_stuff, basic_data)[-1, ]
basics <- basic_data
# Readers to data.frame
# readers <- unrowname(t(data.frame(reader)))
readers <- t(data.frame(reader))
cohorts <- data.frame("pub" = NA, "sci" = NA, "com" = NA, "doc" = NA)
cohorts2 <- data.frame(unrowname(t(data.frame(cohort))))
cohorts <- rbind.fill(cohorts, cohorts2)[-1,]
# Context (hard to standardize so excluding this for now)
# context <- ldply(alt_obj$context, function(foo) t(data.frame(foo)))
# names(context) <- c("type", "count", "rank", "pct")
# more_metrics <- dcast(melt(context, id.var="type"), 1~variable+type)[, -1]
# # 1, 18
# Counts to data.frame
stats_base <- data.frame("cited_by_gplus_count" =NA, "cited_by_fbwalls_count" =NA,"cited_by_posts_count" =NA, "cited_by_tweeters_count" =NA, "cited_by_accounts_count" =NA, "cited_by_feeds_count" =NA, "cited_by_rdts_count" =NA, "cited_by_msm_count" =NA, "cited_by_delicious_count" =NA, "cited_by_forum_count" = NA, "cited_by_qs_count" = NA, "cited_by_rh_count" = NA)
# stats <- melt(alt_obj[grep("^cited", names(alt_obj))])
stats <- data.frame(alt_obj[grep("^cited", names(alt_obj))])
# stats <- dcast(stats, 1~value+L1)[, -1]
# names(stats) <- gsub("^[0-9]_","", names(stats))
stats <- rbind.fill(stats_base, stats)[-1,]
# 1, 11
alt_obj$subjects <- paste0(alt_obj$subjects, collapse='', sep=",")
alt_obj$scopus_subjects <- paste0(alt_obj$scopus_subjects, collapse='', sep=", ")
if(length(alt_obj$added_on) ==0 || is.null(alt_obj$added_on)) {
alt_obj$added_on <- NA
}
if(length(alt_obj$published_on) ==0 || is.null(alt_obj$published_on)) {
alt_obj$published_on <- NA
}
# Removing more_metrics for the time being
# return(data.frame(basic_stuff, stats, score = alt_obj$score, readers, url = alt_obj$url, added_on = alt_obj$added_on, published_on = alt_obj$published_on, subjects = alt_obj$subjects, scopus_subjects = alt_obj$scopus_subjects, last_updated = alt_obj$last_updated, readers_count = alt_obj$readers_count, more_metrics, details_url = alt_obj$details_url))
return(data.frame(basics, stats, score = alt_obj$score, readers, url = alt_obj$url,
added_on = alt_obj$added_on, published_on = alt_obj$published_on,
subjects = alt_obj$subjects, scopus_subjects = alt_obj$scopus_subjects,
last_updated = alt_obj$last_updated, readers_count = alt_obj$readers_count,
details_url = alt_obj$details_url))
}
}
#' Returns cleaner metric source names (mostly for internal use)
#'
#' @param provider the data provider
#' @export
#' @keywords internal
#' @examples \dontrun{
#' return_provider('cited_by_gplus_count')
#'}
return_provider <- function(provider) {
services <- data.frame(type = c("cited_by_gplus_count", "cited_by_fbwalls_count", "cited_by_posts_count", "cited_by_tweeters_count", "cited_by_accounts_count", "cited_by_feeds_count", "cited_by_rdts_count", "cited_by_msm_count", "cited_by_delicious_count", "cited_by_forum_count", "cited_by_qs_count"), names = c("Google+", "Facebook", "Cited", "Tweets", "Accounts", "Feeds", "Reddit", "MSM", "Delicious", "Forums", "QS"))
return(services$names[which(services$type == provider)])
}
Try the rAltmetric package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.