What it is!?
The alm package is a set of functions to access article level metrics via a RESTful API from the Rails app Lagotto created by the Public Library of Science (PLOS). Lagotto is being used by PLOS, and a number of other publishers:
- PLOS (all their journals) at http://alm.plos.org/
- PLOS test server at http://labs.lagotto.io/
- Copernicus (seems to be down for now)
- Public Knowledge Project (PKP) at http://pkp-alm.lib.sfu.ca/
- Crossref at http://det.labs.crossref.org/
- eLife at http://lagotto.svr.elifesciences.org/
- Pensoft at http://alm.pensoft.net:81/
- Making Dat Count at http://dlm.plos.org
A good place to look for the status of various installations of Lagotto is this status page: http://articlemetrics.github.io/status/ (which also includes what version of Lagotto each is running)
Help with Lagotto
Lagotto has a nice support site at http://discuss.lagotto.io/ for any questions about it.
What is an article level metric?
Glad you asked. The canonical URL for this is perhaps altmetrics.org. Basically it is a metric that measures something about an article. This is in stark contrast to journal level metrics, like the Journal Impact Factor.
Are there other altmetrics data providers?
Yes indeedy, but see notes
- ImpactStory - No open data (except for your own data)
- Altmetric.com - Some open data
- PlumAnalytics - No open data
Authentication
You only need an API key for the publishers PKP and Pensoft. You can set the key in your options just for the current session by executing options(PlosApiKey = "YOUalmAPIKEY"), or pass in to each function call with the key parameter, or save in your .Rprofile file.
URLs
The default URL is set for the PLOS data sources: http://alm.plos.org/api/v5/articles
You can change this URL. For example, if you want to get data from the Crossref instance, set the api_url parameter to http://alm.labs.crossref.org/api/v5/articles
Other languages
If R is not your thing, there are Lagotto clients in development for Ruby and Python.
Install
You can get this package from CRAN by:
install.packages("alm")Or the development version by installing with install_github()
install.packages("devtools")
devtools::install_github("ropensci/alm")Load the package
library('alm')The first function we'll look at is alm_ids(), named with ids since we search for data by one of four different choices of identifier.
Get altmetrics data for a single paper
alm_ids(doi = "10.1371/journal.pone.0029797")
#> $meta
#> total total_pages page error
#> 1 1 1 1 NA
#>
#> $data
#> .id pdf html readers comments likes total
#> 1 citeulike NA NA 1 NA NA 1
#> 2 crossref NA NA NA NA NA 8
#> 3 nature NA NA NA NA NA 4
#> 4 pubmed NA NA NA NA NA 2
#> 5 scopus NA NA NA NA NA 9
#> 6 counter 2583 31976 NA NA NA 34683
#> 7 researchblogging NA NA NA NA NA 1
#> 8 pmc 81 551 NA NA NA 632
#> 9 facebook NA NA 150 22 60 232
#> 10 mendeley NA NA 86 NA NA 86
#> 11 twitter NA NA NA 12 NA 12
#> 12 wikipedia NA NA NA NA NA 50
#> 13 scienceseeker NA NA NA NA NA 0
#> 14 relativemetric NA NA NA NA NA 243342
#> 15 f1000 NA NA NA NA NA 0
#> 16 figshare 0 31 NA NA 0 31
#> 17 pmceurope NA NA NA NA NA 4
#> 18 pmceuropedata NA NA NA NA NA 49
#> 19 openedition NA NA NA NA NA 0
#> 20 wordpress NA NA NA NA NA 0
#> 21 reddit NA NA NA 0 0 0
#> 22 datacite NA NA NA NA NA 0
#> 23 copernicus NA NA NA NA NA 0
#> 24 articlecoverage NA NA NA 0 NA 0
#> 25 articlecoveragecurated NA NA NA 0 NA 0
#> 26 plos_comments NA NA NA 11 NA 16
#> 27 orcid NA NA 0 NA NA 0Details for a single DOI
alm_ids(doi = "10.1371/journal.pone.0029797", info = "detail")
#> $meta
#> total total_pages page error
#> 1 1 1 1 NA
#>
#> $data
#> $data$info
#> id
#> 1 doi/10.1371/journal.pone.0029797
#> title
#> 1 Ecological Guild Evolution and the Discovery of the World's Smallest Vertebrate
#> publisher_id doi
#> 1 340 10.1371/journal.pone.0029797
#> canonical_url
#> 1 http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029797
#> pmid pmcid scp wos update_date
#> 1 22253785 3256195 84855712734 000301355700052 2015-03-13T09:10:19Z
#> issued
#> 1 2012-01-11
#>
#> $data$signposts
#> id viewed saved discussed cited
#> 1 doi/10.1371/journal.pone.0029797 35315 87 244 9
#>
#> $data$totals
#> .id pdf html readers comments likes total
#> 1 citeulike NA NA 1 NA NA 1
#> 2 crossref NA NA NA NA NA 8
#> 3 nature NA NA NA NA NA 4
#> 4 pubmed NA NA NA NA NA 2
#> 5 scopus NA NA NA NA NA 9
#> 6 counter 2583 31976 NA NA NA 34683
#> 7 researchblogging NA NA NA NA NA 1
#> 8 pmc 81 551 NA NA NA 632
#> 9 facebook NA NA 150 22 60 232
#> 10 mendeley NA NA 86 NA NA 86
#> 11 twitter NA NA NA 12 NA 12
#> 12 wikipedia NA NA NA NA NA 50
#> 13 scienceseeker NA NA NA NA NA 0
#> 14 relativemetric NA NA NA NA NA 243342
#> 15 f1000 NA NA NA NA NA 0
#> 16 figshare 0 31 NA NA 0 31
#> 17 pmceurope NA NA NA NA NA 4
#> 18 pmceuropedata NA NA NA NA NA 49
#> 19 openedition NA NA NA NA NA 0
#> 20 wordpress NA NA NA NA NA 0
#> 21 reddit NA NA NA 0 0 0
#> 22 datacite NA NA NA NA NA 0
#> 23 copernicus NA NA NA NA NA 0
#> 24 articlecoverage NA NA NA 0 NA 0
#> 25 articlecoveragecurated NA NA NA 0 NA 0
#> 26 plos_comments NA NA NA 11 NA 16
#> 27 orcid NA NA 0 NA NA 0
#>
#> $data$sum_metrics
#> .id year month day total X[[1L]]
#> 1 citeulike 2012 1 12 1 NA
#> 2 nature 2012 1 11 1 NA
#> 3 nature 2012 1 12 1 NA
#> 4 nature 2012 2 1 1 NA
#> 5 researchblogging NA NA NA NA NA
#> 6 plos_comments 2012 1 11 1 NA
#> 7 plos_comments 2012 1 12 7 NA
#> 8 plos_comments 2012 1 13 1 NA
#> 9 plos_comments 2012 1 14 1 NASearch on many identifiers
dois <- c("10.1371/journal.pone.0001543", "10.1371/journal.pone.0040117", "10.1371/journal.pone.0029797", "10.1371/journal.pone.0039395")
out <- alm_ids(doi = dois)
lapply(out$data, head)
#> $`10.1371/journal.pone.0040117`
#> .id pdf html readers comments likes total
#> 1 citeulike NA NA 0 NA NA 0
#> 2 crossref NA NA NA NA NA 7
#> 3 nature NA NA NA NA NA 0
#> 4 pubmed NA NA NA NA NA 6
#> 5 scopus NA NA NA NA NA 14
#> 6 counter 439 2312 NA NA NA 2780
#>
#> $`10.1371/journal.pone.0039395`
#> .id pdf html readers comments likes total
#> 1 citeulike NA NA 0 NA NA 0
#> 2 crossref NA NA NA NA NA 1
#> 3 nature NA NA NA NA NA 0
#> 4 pubmed NA NA NA NA NA 1
#> 5 scopus NA NA NA NA NA 4
#> 6 counter 384 1678 NA NA NA 2095
#>
#> $`10.1371/journal.pone.0029797`
#> .id pdf html readers comments likes total
#> 1 citeulike NA NA 1 NA NA 1
#> 2 crossref NA NA NA NA NA 8
#> 3 nature NA NA NA NA NA 4
#> 4 pubmed NA NA NA NA NA 2
#> 5 scopus NA NA NA NA NA 9
#> 6 counter 2583 31976 NA NA NA 34683
#>
#> $`10.1371/journal.pone.0001543`
#> .id pdf html readers comments likes total
#> 1 citeulike NA NA 0 NA NA 0
#> 2 crossref NA NA NA NA NA 7
#> 3 nature NA NA NA NA NA 0
#> 4 pubmed NA NA NA NA NA 7
#> 5 scopus NA NA NA NA NA 12
#> 6 counter 472 2809 NA NA NA 3332Output an-easy-to-combine-with-other-results data.frame
res <- alm_ids(doi = "10.1371/journal.pone.0035869", total_details = TRUE)
res$data[, 3:10]
#> citeulike_pdf citeulike_html citeulike_readers citeulike_comments
#> 1 NA NA 27 NA
#> citeulike_likes citeulike_total crossref_pdf crossref_html
#> 1 NA 27 NA NAGet detailed data for altmetrics using almevents
out <- alm_events(doi = "10.1371/journal.pone.0029797")
names(out) # names of sources
#> [1] "citeulike" "crossref" "nature"
#> [4] "pubmed" "scopus" "counter"
#> [7] "researchblogging" "pmc" "facebook"
#> [10] "mendeley" "twitter" "wikipedia"
#> [13] "relativemetric" "figshare" "pmceuropedata"
#> [16] "plos_comments"out <- out[!out %in% c("sorry, no events content yet", "parser not written yet")] # remove those with no data
out[["pmc"]] # get the results for PubMed Central
#> $events_url
#> [1] "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3256195"
#>
#> $events
#> scanned.page.browse month cited.by abstract full.text unique.ip pdf
#> 1 0 1 0 1 51 42 8
#> 2 0 2 0 0 15 11 4
#> 3 0 3 0 0 11 12 4
#> 4 0 4 0 1 6 6 2
#> 5 0 5 0 0 5 5 1
#> 6 0 6 0 0 7 9 2
#> 7 0 7 0 1 6 8 3
#> 8 0 8 0 1 5 4 0
#> 9 0 9 0 0 14 13 5
#> 10 0 10 0 1 20 16 4
#> 11 0 12 0 0 13 12 1
#> 12 0 1 0 0 13 14 7
#> 13 0 3 0 1 22 20 2
#> 14 0 2 0 0 13 10 2
#> 15 0 4 1 1 45 24 4
#> 16 0 11 0 1 10 9 1
#> 17 0 5 0 0 18 21 5
#> 18 0 6 0 0 12 11 1
#> 19 0 7 0 0 27 14 1
#> 20 0 8 0 0 21 13 0
#> 21 0 9 0 0 14 13 0
#> 22 0 10 0 0 14 15 3
#> 23 0 11 0 6 18 16 2
#> 24 0 12 0 0 14 9 1
#> 25 0 1 0 0 22 16 1
#> 26 0 2 0 0 13 12 1
#> 27 0 3 0 0 11 10 1
#> 28 0 5 0 0 15 12 0
#> 29 0 6 0 0 12 12 2
#> 30 0 4 0 0 8 9 1
#> 31 0 8 0 0 18 14 3
#> 32 0 9 0 0 18 20 2
#> 33 0 10 0 0 23 18 4
#> 34 0 11 0 0 17 16 3
#> year figure scanned.summary supp.data
#> 1 2012 9 0 0
#> 2 2012 11 0 2
#> 3 2012 0 0 0
#> 4 2012 0 0 0
#> 5 2012 0 0 0
#> 6 2012 2 0 0
#> 7 2012 3 0 0
#> 8 2012 0 0 0
#> 9 2012 3 0 0
#> 10 2012 1 0 0
#> 11 2012 1 0 0
#> 12 2013 0 0 0
#> 13 2013 0 0 0
#> 14 2013 0 0 0
#> 15 2013 3 0 1
#> 16 2012 0 0 0
#> 17 2013 0 0 1
#> 18 2013 0 0 1
#> 19 2013 0 0 0
#> 20 2013 0 0 0
#> 21 2013 0 0 1
#> 22 2013 2 0 0
#> 23 2013 0 0 0
#> 24 2013 0 0 0
#> 25 2014 0 0 0
#> 26 2014 0 0 0
#> 27 2014 2 0 0
#> 28 2014 0 0 1
#> 29 2014 0 0 0
#> 30 2014 0 0 1
#> 31 2014 0 0 0
#> 32 2014 0 0 0
#> 33 2014 0 0 0
#> 34 2014 2 0 0
#>
#> $csl
#> list()Retrieve and plot PLOS article-level metrics signposts.
dat <- alm_signposts(doi = "10.1371/journal.pone.0029797")
plot_signposts(dat)Or plot many identifiers get a faceted bar chart, note the tick labels have just the last part of the DOI in this case to help you identify each DOI - printing the entire DOI would make lables overlap one another.
dois <- c("10.1371/journal.pone.0001543", "10.1371/journal.pone.0040117", "10.1371/journal.pone.0029797", "10.1371/journal.pone.0039395")
dat <- alm_signposts(doi = dois)
plot_signposts(input = dat)Or make an interactive chart by doing plot_signposts(input=dat, type="multiBarChart"). Try it out! It should open in your browser and you can interact with it.
Density and histogram plots from PLOS Article Level Metrics data
Note: Do you the key below in the searchplos call in this example, but if you plan to use rplos more, get your own API key here.
library('rplos')
library('plyr')
dois <- searchplos(q = "science", fl = "id", fq = list("-article_type:correction", "cross_published_journal_key:PLoSONE", "doc_type:full", "publication_date:[2010-01-01T00:00:00Z TO 2010-12-31T23:59:59Z]"), limit = 50)
dois <- dois$data$idCollect altmetrics data and combine to a data.frame with ldply
alm <- alm_ids(doi = dois, total_details = TRUE)
alm <- ldply(alm$data)The default plot
plot_density(alm)Plot many sources in different panels in the same plot, and pass in colors just for fun
plot_density(alm,
source = c("counter_total", "crossref_total", "twitter_total"),
color = c("#83DFB4", "#EFA5A5", "#CFD470"))Work with data from non-PLOS publishers
Crossref
crurl <- "http://det.labs.crossref.org/api/v5/articles"
crkey <- getOption("crossrefalmkey")
alm_ids(doi='10.1371/journal.pone.0086859', api_url = crurl, key = crkey)eLife
elifeurl <- "http://alm.svr.elifesciences.org/api/v5/articles"
elifekey <- getOption("elifealmkey")
alm_ids(doi='10.7554/eLife.00471', api_url = elifeurl, key = elifekey)
#> $meta
#> total total_pages page error
#> 1 1 1 1 NA
#>
#> $data
#> .id pdf html shares groups comments likes citations total
#> 1 pmc 667 1520 NA NA NA NA NA 2187
#> 2 crossref NA NA NA NA NA NA 154 154
#> 3 scopus NA NA NA NA NA NA 154 154
#> 4 facebook NA NA 3 NA 0 0 NA 3
#> 5 mendeley NA NA 0 0 NA NA NA 0
#> 6 twitter_search NA NA NA NA 0 NA NA 0
#> 7 citeulike NA NA 1 NA NA NA NA 1
#> 8 pubmed NA NA NA NA NA NA 111 111
#> 9 wordpress NA NA NA NA NA NA 0 0
#> 10 reddit NA NA NA NA 0 0 NA 0
#> 11 wikipedia NA NA NA NA NA NA 1 1
#> 12 datacite NA NA NA NA NA NA 0 0
#> 13 pmceurope NA NA NA NA NA NA 151 151
#> 14 pmceuropedata NA NA NA NA NA NA 1 1
#> 15 scienceseeker NA NA NA NA NA NA 0 0
#> 16 nature NA NA NA NA NA NA 0 0
#> 17 openedition NA NA NA NA NA NA 0 0
#> 18 f1000 NA NA NA NA NA NA 4 4
#> 19 figshare NA NA NA NA NA NA 0 0
#> 20 plos_comments NA NA NA NA NA NA 0 0
#> 21 connotea NA NA NA NA NA NA 0 0
#> 22 postgenomic NA NA NA NA NA NA 0 0
#> 23 bloglines NA NA NA NA NA NA 0 0
#> 24 biod NA NA NA NA NA NA NA 0Pensoft
psurl <- 'http://alm.pensoft.net:81/api/v5/articles'
pskey <- getOption("pensoftalmkey")
alm_ids(doi='10.3897/zookeys.88.807', api_url = psurl, key = pskey)
#> $meta
#> total total_pages page error
#> 1 1 1 1 NA
#>
#> $data
#> .id pdf html readers comments likes total
#> 1 facebook NA NA NA NA NA 0
#> 2 citeulike NA NA 1 NA NA 1
#> 3 mendeley NA NA 123 NA NA 123
#> 4 wordpress NA NA NA NA NA 0
#> 5 datacite NA NA NA NA NA 0
#> 6 wikipedia NA NA NA NA NA 137
#> 7 copernicus 0 0 NA NA NA 0
#> 8 nature NA NA NA NA NA 0
#> 9 f1000 NA NA NA NA NA 0
#> 10 scopus NA NA NA NA NA 192
#> 11 pmceuropedata NA NA NA NA NA 0
#> 12 figshare NA NA NA NA NA 0
#> 13 counter NA NA NA NA NA 0
#> 14 crossref NA NA NA NA NA 81
#> 15 reddit NA NA NA 0 0 0
#> 16 twitter_search NA NA NA 0 NA 0
#> 17 pmceurope NA NA NA NA NA 52
#> 18 pubmed NA NA NA NA NA 51Making Data Count - Dataset altmetrics
dlmurl <- 'http://dlm.plos.org/api/v5/articles'
alm_ids('10.5061/dryad.7fj1k', api_url = dlmurl)
#> $meta
#> total total_pages page error
#> 1 1 1 1 NA
#>
#> $data
#> .id pdf html readers comments likes total
#> 1 citeulike NA NA 0 NA NA 0
#> 2 wordpress NA NA NA NA NA 0
#> 3 wikipedia NA NA NA NA NA 0
#> 4 datacite NA NA NA NA NA 96
#> 5 pmceuropedata NA NA NA NA NA 0
#> 6 mendeley NA NA 0 NA NA 0
#> 7 facebook NA NA 0 0 0 0
#> 8 twitter_search NA NA NA NA NA 0
#> 9 europe_pmc_fulltext NA NA NA NA NA 1
#> 10 plos_fulltext NA NA NA NA NA 1
#> 11 orcid NA NA 0 NA NA 0
#> 12 bmc_fulltext NA NA NA NA NA 0
#> 13 nature_opensearch NA NA NA NA NA 0Meta
- Please report any issues or bugs.
- License: MIT
- Get citation information for
almin R doingcitation(package = 'alm')