inst/vign/alm_vignette.md
In ropensci/alm: R Client for the Lagotto Altmetrics Platform
alm tutorial
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.
Help
If you are having trouble with this R package, contact the maintainer, Scott. If you are having trouble with the API itself, there is a newish discussion forum for the Lagotto service at http://discuss.lagotto.io/.
Install and load
Stable version from CRAN
install.packages("alm")
Or development version from GitHub
install.packages("devtools")
devtools::install_github("ropensci/alm")
Load alm
library("alm")
Get data
alm_ids(doi="10.1371/journal.pone.0029797")
#> $meta
#> total total_pages page error
#> 1 1 1 1 NA
#>
#> $data
#> .id pdf html readers comments likes total
#> 1 citeulike NA NA 1 NA NA 1
#> 2 crossref NA NA NA NA NA 8
#> 3 nature NA NA NA NA NA 4
#> 4 pubmed NA NA NA NA NA 2
#> 5 scopus NA NA NA NA NA 8
#> 6 counter 2524 30801 NA NA NA 33443
#> 7 researchblogging NA NA NA NA NA 1
#> 8 wos NA NA NA NA NA 7
#> 9 pmc 78 534 NA NA NA 612
#> 10 facebook NA NA 149 22 60 231
#> 11 mendeley NA NA 80 NA NA 80
#> 12 twitter NA NA NA 12 NA 12
#> 13 wikipedia NA NA NA NA NA 50
#> 14 scienceseeker NA NA NA NA NA 0
#> 15 relativemetric NA NA NA NA NA 157436
#> 16 f1000 NA NA NA NA NA 0
#> 17 figshare 0 21 NA NA 0 21
#> 18 pmceurope NA NA NA NA NA 4
#> 19 pmceuropedata NA NA NA NA NA 49
#> 20 openedition NA NA NA NA NA 0
#> 21 wordpress NA NA NA NA NA 0
#> 22 reddit NA NA NA 0 0 0
#> 23 datacite NA NA NA NA NA 0
#> 24 copernicus NA NA NA NA NA 0
#> 25 articlecoverage NA NA NA 0 NA 0
#> 26 articlecoveragecurated NA NA NA 0 NA 0
#> 27 plos_comments NA NA NA 11 NA 16
Details for a single DOI
out <- alm_ids(doi='10.1371/journal.pone.0029797', info='detail')
info
out$data$info
#> doi
#> 1 10.1371/journal.pone.0029797
#> title
#> 1 Ecological Guild Evolution and the Discovery of the World's Smallest Vertebrate
#> canonical_url
#> 1 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0029797
#> pmid pmcid mendeley_uuid
#> 1 22253785 3256195 897fbbd6-5a23-3552-8077-97251b82c1e1
#> update_date issued
#> 1 2014-11-12T21:41:48Z 2012-01-11
sign posts
out$data$signposts
#> doi viewed saved discussed cited
#> 1 10.1371/journal.pone.0029797 34055 81 243 8
totals
out$data$totals
#> .id pdf html readers comments likes total
#> 1 citeulike NA NA 1 NA NA 1
#> 2 crossref NA NA NA NA NA 8
#> 3 nature NA NA NA NA NA 4
#> 4 pubmed NA NA NA NA NA 2
#> 5 scopus NA NA NA NA NA 8
#> 6 counter 2524 30801 NA NA NA 33443
#> 7 researchblogging NA NA NA NA NA 1
#> 8 wos NA NA NA NA NA 7
#> 9 pmc 78 534 NA NA NA 612
#> 10 facebook NA NA 149 22 60 231
#> 11 mendeley NA NA 80 NA NA 80
#> 12 twitter NA NA NA 12 NA 12
#> 13 wikipedia NA NA NA NA NA 50
#> 14 scienceseeker NA NA NA NA NA 0
#> 15 relativemetric NA NA NA NA NA 157436
#> 16 f1000 NA NA NA NA NA 0
#> 17 figshare 0 21 NA NA 0 21
#> 18 pmceurope NA NA NA NA NA 4
#> 19 pmceuropedata NA NA NA NA NA 49
#> 20 openedition NA NA NA NA NA 0
#> 21 wordpress NA NA NA NA NA 0
#> 22 reddit NA NA NA 0 0 0
#> 23 datacite NA NA NA NA NA 0
#> 24 copernicus NA NA NA NA NA 0
#> 25 articlecoverage NA NA NA 0 NA 0
#> 26 articlecoveragecurated NA NA NA 0 NA 0
#> 27 plos_comments NA NA NA 11 NA 16
history
out$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 NA
Search using various identifiers, including pubmed id, pmc id, and mendeley id
A single PubMed ID (pmid)
alm_ids(pmid=22590526)
#> $meta
#> total total_pages page error
#> 1 1 1 1 NA
#>
#> $data
#> .id pdf html readers comments likes total
#> 1 citeulike NA NA 5 NA NA 5
#> 2 crossref NA NA NA NA NA 5
#> 3 nature NA NA NA NA NA 1
#> 4 pubmed NA NA NA NA NA 5
#> 5 scopus NA NA NA NA NA 9
#> 6 counter 1169 16238 NA NA NA 17455
#> 7 researchblogging NA NA NA NA NA 1
#> 8 wos NA NA NA NA NA 7
#> 9 pmc 65 196 NA NA NA 261
#> 10 facebook NA NA 72 57 56 185
#> 11 mendeley NA NA 70 NA NA 70
#> 12 twitter NA NA NA 161 NA 161
#> 13 wikipedia NA NA NA NA NA 0
#> 14 scienceseeker NA NA NA NA NA 0
#> 15 relativemetric NA NA NA NA NA 43647
#> 16 f1000 NA NA NA NA NA 0
#> 17 figshare 0 0 NA NA 0 0
#> 18 pmceurope NA NA NA NA NA 5
#> 19 pmceuropedata NA NA NA NA NA 0
#> 20 openedition NA NA NA NA NA 0
#> 21 wordpress NA NA NA NA NA 0
#> 22 reddit NA NA NA 0 0 0
#> 23 datacite NA NA NA NA NA 0
#> 24 copernicus NA NA NA NA NA 0
#> 25 articlecoverage NA NA NA 0 NA 0
#> 26 articlecoveragecurated NA NA NA 0 NA 0
#> 27 plos_comments NA NA NA 3 NA 4
A single PubMed Central ID (pmcid)
alm_ids(pmcid=212692)
#> $meta
#> total total_pages page error
#> 1 1 1 1 NA
#>
#> $data
#> .id pdf html readers comments likes total
#> 1 citeulike NA NA 8 NA NA 8
#> 2 crossref NA NA NA NA NA 164
#> 3 nature NA NA NA NA NA 0
#> 4 pubmed NA NA NA NA NA 172
#> 5 scopus NA NA NA NA NA 342
#> 6 counter 2701 21593 NA NA NA 24458
#> 7 researchblogging NA NA NA NA NA 0
#> 8 wos NA NA NA NA NA 323
#> 9 pmc 2387 5119 NA NA NA 7506
#> 10 facebook NA NA 0 0 0 0
#> 11 mendeley NA NA 127 NA NA 127
#> 12 twitter NA NA NA 0 NA 0
#> 13 wikipedia NA NA NA NA NA 0
#> 14 scienceseeker NA NA NA NA NA 0
#> 15 relativemetric NA NA NA NA NA 1570821
#> 16 f1000 NA NA NA NA NA 0
#> 17 figshare 1 10 NA NA 0 11
#> 18 pmceurope NA NA NA NA NA 212
#> 19 pmceuropedata NA NA NA NA NA 56
#> 20 openedition NA NA NA NA NA 0
#> 21 wordpress NA NA NA NA NA 0
#> 22 reddit NA NA NA 0 0 0
#> 23 datacite NA NA NA NA NA 0
#> 24 copernicus NA NA NA NA NA 0
#> 25 articlecoverage NA NA NA 0 NA 0
#> 26 articlecoveragecurated NA NA NA 0 NA 0
#> 27 plos_comments NA NA NA 0 NA 0
Search on many identifiers
dois <- c('10.1371/journal.pone.0001543','10.1371/journal.pone.0040117',
'10.1371/journal.pone.0029797','10.1371/journal.pone.0039395')
out <- alm_ids(doi=dois)
lapply(out$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 6
#> 3 nature NA NA NA NA NA 0
#> 4 pubmed NA NA NA NA NA 5
#> 5 scopus NA NA NA NA NA 12
#> 6 counter 402 2055 NA NA NA 2482
#>
#> $`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 3
#> 6 counter 240 1373 NA NA NA 1642
#>
#> $`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 8
#> 6 counter 2524 30801 NA NA NA 33443
#>
#> $`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 453 2742 NA NA NA 3243
Get altmetrics by year
You can also get metrics by day (sum_metrics='day') or month (sum_metrics='month')
alm_ids(doi='10.1371/journal.pone.0036240', sum_metrics='year')
#> $meta
#> total total_pages page error
#> 1 1 1 1 NA
#>
#> $data
#> .id year total pdf html
#> 1 citeulike 2012 5 NA NA
#> 2 crossref 2014 5 NA NA
#> 3 nature 2012 1 NA NA
#> 4 pubmed 2014 5 NA NA
#> 5 scopus 2014 9 NA NA
#> 6 counter 2012 NA 699 10502
#> 7 counter 2013 NA 299 3605
#> 8 counter 2014 NA 171 2131
#> 9 wos 2014 7 NA NA
#> 10 pmc 2012 NA 16 53
#> 11 pmc 2013 NA 13 66
#> 12 pmc 2014 NA 36 77
#> 13 facebook 2014 185 NA NA
#> 14 mendeley 2014 70 NA NA
#> 15 twitter 2012 103 NA NA
#> 16 twitter 2013 33 NA NA
#> 17 twitter 2014 25 NA NA
#> 18 relativemetric 2014 43647 NA NA
#> 19 pmceurope 2014 5 NA NA
#> 20 plos_comments 2012 2 NA NA
#> 21 plos_comments 2014 1 NA NA
Output an-easy-to-combine-with-other-results data.frame
alm_ids(doi='10.1371/journal.pone.0035869', total_details=TRUE)$data[,3:7]
#> citeulike_pdf citeulike_html citeulike_readers citeulike_comments
#> 1 NA NA 27 NA
#> citeulike_likes
#> 1 NA
Get detailed data for altmetrics using almevents
out <- alm_events(doi="10.1371/journal.pone.0029797")
names(out)
#> [1] "citeulike" "crossref" "nature"
#> [4] "pubmed" "scopus" "counter"
#> [7] "researchblogging" "pmc" "facebook"
#> [10] "mendeley" "twitter" "wikipedia"
#> [13] "relativemetric" "figshare" "pmceuropedata"
#> [16] "plos_comments"
Get the results for PubMed Central
# remove those with no data
out <- out[!out %in% c("sorry, no events content yet","parser not written yet")]
out[["pmc"]]
#> $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
#> 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
#>
#> $csl
#> list()
Get the results for twitter
out$twitter$events[1:3,]
#> id
#> 1 237088032224849920
#> 2 237088322290331648
#> 3 263798980054487041
#> text
#> 1 #PLOS: Ecological Guild Evolution and the Discovery of the World's Smallest Vertebrate http://t.co/yEGLyWTf
#> 2 #PLOS: Ecological Guild Evolution and the Discovery of the World's Smallest Vertebrate http://t.co/497NRrMR
#> 3 Happy #Halloween from Maria @PLOSONE, dressed as a tiny frog, complete with dime for scale! http://t.co/YWcdPoGP http://t.co/lAxWAHOG
#> created_at user user_name
#> 1 2012-08-19T07:26:06Z opdebult Jan ten Hoopen
#> 2 2012-08-19T07:27:15Z forestalis forestalis.org
#> 3 2012-11-01T00:25:53Z multidiscipl1ne Lindsay Kelley
#> user_profile_image
#> 1 http://a0.twimg.com/profile_images/1741153180/Tidan_normal.jpg
#> 2 http://a0.twimg.com/profile_images/654250700/ForestalisIco_normal.jpg
#> 3 http://a0.twimg.com/profile_images/1910116023/261235_920680811178_6708085_43508969_7138379_n_normal.jpg
#> event_url
#> 1 http://twitter.com/opdebult/status/237088032224849920
#> 2 http://twitter.com/forestalis/status/237088322290331648
#> 3 http://twitter.com/multidiscipl1ne/status/263798980054487041
#> event_time
#> 1 2012-08-19T07:26:06Z
#> 2 2012-08-19T07:27:15Z
#> 3 2012-11-01T00:25:53Z
Retrieve and plot PLOS article-level metrics signposts.
dat <- alm_signposts(doi="10.1371/journal.pone.0029797")
plot_signposts(input=dat)
Or plot many identifiers gives a line chart
library("ggplot2")
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) +
theme_grey(base_size = 12)
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('cross_published_journal_key:PLoSONE', 'doc_type:full', 'publication_date:[2010-01-01T00:00:00Z TO 2010-12-31T23:59:59Z]'), limit=75)
Remove non-full article DOIs
dois <- dois$data$id
dois <- dois[!grepl("annotation", dois)]
Collect altmetrics data and combine to a data.frame with ldply
alm <- alm_ids(doi=dois, total_details=TRUE)
alm <- ldply(alm$data)
The default plot
plot_density(alm)
You can change the color of the density plot
plot_density(alm, color="#EFA5A5")
Pass in a title or description subtending the title
plot_density(alm, title="Scopus citations from 2010")
Plot a particular source
plot_density(alm, source="crossref_total")
Plot many sources in different panels in the same plot, and pass in colors just for fun
plot_density(input=alm,
source=c("counter_html","crossref_total","pubmed_total","scopus_total"),
color=c("#83DFB4","#EFA5A5","#CFD470","#B2C9E4")) +
theme_grey(base_size = 12)
#> NULL
CrossRef article level metrics
Notice that we are passing the base url for the Crossref API, whereas the default is for the PLOS url http://alm.plos.org/api/v5/articles.
url <- "http://det.labs.crossref.org/api/v5/articles"
dois <- c("10.1371/journal.pone.0086859", "10.1038/nature12990", "10.5860/choice.51-3037")
alm_ids(doi=dois, api_url = url)
#> $meta
#> total total_pages page error
#> 1 3 1 1 NA
#>
#> $data
#> $data$`10.1038/nature12990`
#> .id pdf html readers comments likes total
#> 1 crossref NA NA NA NA NA 0
#> 2 mendeley NA NA NA NA NA 0
#> 3 facebook NA NA NA NA NA 0
#> 4 pmc NA NA NA NA NA 0
#> 5 citeulike NA NA NA NA NA 0
#> 6 pubmed NA NA NA NA NA 0
#> 7 wordpress NA NA NA NA NA 0
#> 8 reddit NA NA NA NA NA 0
#> 9 wikipedia NA NA NA NA NA 6
#> 10 datacite NA NA NA NA NA 0
#> 11 pmceurope NA NA NA NA NA 0
#> 12 pmceuropedata NA NA NA NA NA 0
#>
#> $data$`10.1371/journal.pone.0086859`
#> .id pdf html readers comments likes total
#> 1 crossref NA NA NA NA NA 0
#> 2 mendeley NA NA NA NA NA 0
#> 3 facebook NA NA NA NA NA 0
#> 4 pmc NA NA NA NA NA 0
#> 5 citeulike NA NA NA NA NA 0
#> 6 pubmed NA NA NA NA NA 0
#> 7 wordpress NA NA NA NA NA 0
#> 8 reddit NA NA NA NA NA 0
#> 9 wikipedia NA NA NA NA NA 2
#> 10 datacite NA NA NA NA NA 0
#> 11 pmceurope NA NA NA NA NA 0
#> 12 pmceuropedata NA NA NA NA NA 0
#>
#> $data$`10.5860/choice.51-3037`
#> .id pdf html readers comments likes total
#> 1 crossref NA NA NA NA NA 0
#> 2 mendeley NA NA NA NA NA 0
#> 3 facebook NA NA NA NA NA 0
#> 4 pmc NA NA NA NA NA 0
#> 5 citeulike NA NA NA NA NA 0
#> 6 pubmed NA NA NA NA NA 0
#> 7 wordpress NA NA NA NA NA 0
#> 8 reddit NA NA NA NA NA 0
#> 9 wikipedia NA NA NA NA NA 0
#> 10 datacite NA NA NA NA NA 0
#> 11 pmceurope NA NA NA NA NA 0
#> 12 pmceuropedata NA NA NA NA NA 0
ropensci/alm documentation built on May 18, 2022, 9:47 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
alm tutorial
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.
Help
If you are having trouble with this R package, contact the maintainer, Scott. If you are having trouble with the API itself, there is a newish discussion forum for the Lagotto service at http://discuss.lagotto.io/.
Install and load
Stable version from CRAN
install.packages("alm")
Or development version from GitHub
install.packages("devtools")
devtools::install_github("ropensci/alm")
Load alm
library("alm")
Get data
alm_ids(doi="10.1371/journal.pone.0029797")
#> $meta
#> total total_pages page error
#> 1 1 1 1 NA
#>
#> $data
#> .id pdf html readers comments likes total
#> 1 citeulike NA NA 1 NA NA 1
#> 2 crossref NA NA NA NA NA 8
#> 3 nature NA NA NA NA NA 4
#> 4 pubmed NA NA NA NA NA 2
#> 5 scopus NA NA NA NA NA 8
#> 6 counter 2524 30801 NA NA NA 33443
#> 7 researchblogging NA NA NA NA NA 1
#> 8 wos NA NA NA NA NA 7
#> 9 pmc 78 534 NA NA NA 612
#> 10 facebook NA NA 149 22 60 231
#> 11 mendeley NA NA 80 NA NA 80
#> 12 twitter NA NA NA 12 NA 12
#> 13 wikipedia NA NA NA NA NA 50
#> 14 scienceseeker NA NA NA NA NA 0
#> 15 relativemetric NA NA NA NA NA 157436
#> 16 f1000 NA NA NA NA NA 0
#> 17 figshare 0 21 NA NA 0 21
#> 18 pmceurope NA NA NA NA NA 4
#> 19 pmceuropedata NA NA NA NA NA 49
#> 20 openedition NA NA NA NA NA 0
#> 21 wordpress NA NA NA NA NA 0
#> 22 reddit NA NA NA 0 0 0
#> 23 datacite NA NA NA NA NA 0
#> 24 copernicus NA NA NA NA NA 0
#> 25 articlecoverage NA NA NA 0 NA 0
#> 26 articlecoveragecurated NA NA NA 0 NA 0
#> 27 plos_comments NA NA NA 11 NA 16
Details for a single DOI
out <- alm_ids(doi='10.1371/journal.pone.0029797', info='detail')
info
out$data$info
#> doi
#> 1 10.1371/journal.pone.0029797
#> title
#> 1 Ecological Guild Evolution and the Discovery of the World's Smallest Vertebrate
#> canonical_url
#> 1 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0029797
#> pmid pmcid mendeley_uuid
#> 1 22253785 3256195 897fbbd6-5a23-3552-8077-97251b82c1e1
#> update_date issued
#> 1 2014-11-12T21:41:48Z 2012-01-11
sign posts
out$data$signposts
#> doi viewed saved discussed cited
#> 1 10.1371/journal.pone.0029797 34055 81 243 8
totals
out$data$totals
#> .id pdf html readers comments likes total
#> 1 citeulike NA NA 1 NA NA 1
#> 2 crossref NA NA NA NA NA 8
#> 3 nature NA NA NA NA NA 4
#> 4 pubmed NA NA NA NA NA 2
#> 5 scopus NA NA NA NA NA 8
#> 6 counter 2524 30801 NA NA NA 33443
#> 7 researchblogging NA NA NA NA NA 1
#> 8 wos NA NA NA NA NA 7
#> 9 pmc 78 534 NA NA NA 612
#> 10 facebook NA NA 149 22 60 231
#> 11 mendeley NA NA 80 NA NA 80
#> 12 twitter NA NA NA 12 NA 12
#> 13 wikipedia NA NA NA NA NA 50
#> 14 scienceseeker NA NA NA NA NA 0
#> 15 relativemetric NA NA NA NA NA 157436
#> 16 f1000 NA NA NA NA NA 0
#> 17 figshare 0 21 NA NA 0 21
#> 18 pmceurope NA NA NA NA NA 4
#> 19 pmceuropedata NA NA NA NA NA 49
#> 20 openedition NA NA NA NA NA 0
#> 21 wordpress NA NA NA NA NA 0
#> 22 reddit NA NA NA 0 0 0
#> 23 datacite NA NA NA NA NA 0
#> 24 copernicus NA NA NA NA NA 0
#> 25 articlecoverage NA NA NA 0 NA 0
#> 26 articlecoveragecurated NA NA NA 0 NA 0
#> 27 plos_comments NA NA NA 11 NA 16
history
out$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 NA
Search using various identifiers, including pubmed id, pmc id, and mendeley id
A single PubMed ID (pmid)
alm_ids(pmid=22590526)
#> $meta
#> total total_pages page error
#> 1 1 1 1 NA
#>
#> $data
#> .id pdf html readers comments likes total
#> 1 citeulike NA NA 5 NA NA 5
#> 2 crossref NA NA NA NA NA 5
#> 3 nature NA NA NA NA NA 1
#> 4 pubmed NA NA NA NA NA 5
#> 5 scopus NA NA NA NA NA 9
#> 6 counter 1169 16238 NA NA NA 17455
#> 7 researchblogging NA NA NA NA NA 1
#> 8 wos NA NA NA NA NA 7
#> 9 pmc 65 196 NA NA NA 261
#> 10 facebook NA NA 72 57 56 185
#> 11 mendeley NA NA 70 NA NA 70
#> 12 twitter NA NA NA 161 NA 161
#> 13 wikipedia NA NA NA NA NA 0
#> 14 scienceseeker NA NA NA NA NA 0
#> 15 relativemetric NA NA NA NA NA 43647
#> 16 f1000 NA NA NA NA NA 0
#> 17 figshare 0 0 NA NA 0 0
#> 18 pmceurope NA NA NA NA NA 5
#> 19 pmceuropedata NA NA NA NA NA 0
#> 20 openedition NA NA NA NA NA 0
#> 21 wordpress NA NA NA NA NA 0
#> 22 reddit NA NA NA 0 0 0
#> 23 datacite NA NA NA NA NA 0
#> 24 copernicus NA NA NA NA NA 0
#> 25 articlecoverage NA NA NA 0 NA 0
#> 26 articlecoveragecurated NA NA NA 0 NA 0
#> 27 plos_comments NA NA NA 3 NA 4
A single PubMed Central ID (pmcid)
alm_ids(pmcid=212692)
#> $meta
#> total total_pages page error
#> 1 1 1 1 NA
#>
#> $data
#> .id pdf html readers comments likes total
#> 1 citeulike NA NA 8 NA NA 8
#> 2 crossref NA NA NA NA NA 164
#> 3 nature NA NA NA NA NA 0
#> 4 pubmed NA NA NA NA NA 172
#> 5 scopus NA NA NA NA NA 342
#> 6 counter 2701 21593 NA NA NA 24458
#> 7 researchblogging NA NA NA NA NA 0
#> 8 wos NA NA NA NA NA 323
#> 9 pmc 2387 5119 NA NA NA 7506
#> 10 facebook NA NA 0 0 0 0
#> 11 mendeley NA NA 127 NA NA 127
#> 12 twitter NA NA NA 0 NA 0
#> 13 wikipedia NA NA NA NA NA 0
#> 14 scienceseeker NA NA NA NA NA 0
#> 15 relativemetric NA NA NA NA NA 1570821
#> 16 f1000 NA NA NA NA NA 0
#> 17 figshare 1 10 NA NA 0 11
#> 18 pmceurope NA NA NA NA NA 212
#> 19 pmceuropedata NA NA NA NA NA 56
#> 20 openedition NA NA NA NA NA 0
#> 21 wordpress NA NA NA NA NA 0
#> 22 reddit NA NA NA 0 0 0
#> 23 datacite NA NA NA NA NA 0
#> 24 copernicus NA NA NA NA NA 0
#> 25 articlecoverage NA NA NA 0 NA 0
#> 26 articlecoveragecurated NA NA NA 0 NA 0
#> 27 plos_comments NA NA NA 0 NA 0
Search on many identifiers
dois <- c('10.1371/journal.pone.0001543','10.1371/journal.pone.0040117',
'10.1371/journal.pone.0029797','10.1371/journal.pone.0039395')
out <- alm_ids(doi=dois)
lapply(out$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 6
#> 3 nature NA NA NA NA NA 0
#> 4 pubmed NA NA NA NA NA 5
#> 5 scopus NA NA NA NA NA 12
#> 6 counter 402 2055 NA NA NA 2482
#>
#> $`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 3
#> 6 counter 240 1373 NA NA NA 1642
#>
#> $`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 8
#> 6 counter 2524 30801 NA NA NA 33443
#>
#> $`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 453 2742 NA NA NA 3243
Get altmetrics by year
You can also get metrics by day (sum_metrics='day') or month (sum_metrics='month')
alm_ids(doi='10.1371/journal.pone.0036240', sum_metrics='year')
#> $meta
#> total total_pages page error
#> 1 1 1 1 NA
#>
#> $data
#> .id year total pdf html
#> 1 citeulike 2012 5 NA NA
#> 2 crossref 2014 5 NA NA
#> 3 nature 2012 1 NA NA
#> 4 pubmed 2014 5 NA NA
#> 5 scopus 2014 9 NA NA
#> 6 counter 2012 NA 699 10502
#> 7 counter 2013 NA 299 3605
#> 8 counter 2014 NA 171 2131
#> 9 wos 2014 7 NA NA
#> 10 pmc 2012 NA 16 53
#> 11 pmc 2013 NA 13 66
#> 12 pmc 2014 NA 36 77
#> 13 facebook 2014 185 NA NA
#> 14 mendeley 2014 70 NA NA
#> 15 twitter 2012 103 NA NA
#> 16 twitter 2013 33 NA NA
#> 17 twitter 2014 25 NA NA
#> 18 relativemetric 2014 43647 NA NA
#> 19 pmceurope 2014 5 NA NA
#> 20 plos_comments 2012 2 NA NA
#> 21 plos_comments 2014 1 NA NA
Output an-easy-to-combine-with-other-results data.frame
alm_ids(doi='10.1371/journal.pone.0035869', total_details=TRUE)$data[,3:7]
#> citeulike_pdf citeulike_html citeulike_readers citeulike_comments
#> 1 NA NA 27 NA
#> citeulike_likes
#> 1 NA
Get detailed data for altmetrics using almevents
out <- alm_events(doi="10.1371/journal.pone.0029797")
names(out)
#> [1] "citeulike" "crossref" "nature"
#> [4] "pubmed" "scopus" "counter"
#> [7] "researchblogging" "pmc" "facebook"
#> [10] "mendeley" "twitter" "wikipedia"
#> [13] "relativemetric" "figshare" "pmceuropedata"
#> [16] "plos_comments"
Get the results for PubMed Central
# remove those with no data
out <- out[!out %in% c("sorry, no events content yet","parser not written yet")]
out[["pmc"]]
#> $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
#> 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
#>
#> $csl
#> list()
Get the results for twitter
out$twitter$events[1:3,]
#> id
#> 1 237088032224849920
#> 2 237088322290331648
#> 3 263798980054487041
#> text
#> 1 #PLOS: Ecological Guild Evolution and the Discovery of the World's Smallest Vertebrate http://t.co/yEGLyWTf
#> 2 #PLOS: Ecological Guild Evolution and the Discovery of the World's Smallest Vertebrate http://t.co/497NRrMR
#> 3 Happy #Halloween from Maria @PLOSONE, dressed as a tiny frog, complete with dime for scale! http://t.co/YWcdPoGP http://t.co/lAxWAHOG
#> created_at user user_name
#> 1 2012-08-19T07:26:06Z opdebult Jan ten Hoopen
#> 2 2012-08-19T07:27:15Z forestalis forestalis.org
#> 3 2012-11-01T00:25:53Z multidiscipl1ne Lindsay Kelley
#> user_profile_image
#> 1 http://a0.twimg.com/profile_images/1741153180/Tidan_normal.jpg
#> 2 http://a0.twimg.com/profile_images/654250700/ForestalisIco_normal.jpg
#> 3 http://a0.twimg.com/profile_images/1910116023/261235_920680811178_6708085_43508969_7138379_n_normal.jpg
#> event_url
#> 1 http://twitter.com/opdebult/status/237088032224849920
#> 2 http://twitter.com/forestalis/status/237088322290331648
#> 3 http://twitter.com/multidiscipl1ne/status/263798980054487041
#> event_time
#> 1 2012-08-19T07:26:06Z
#> 2 2012-08-19T07:27:15Z
#> 3 2012-11-01T00:25:53Z
Retrieve and plot PLOS article-level metrics signposts.
dat <- alm_signposts(doi="10.1371/journal.pone.0029797")
plot_signposts(input=dat)
Or plot many identifiers gives a line chart
library("ggplot2")
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) +
theme_grey(base_size = 12)
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('cross_published_journal_key:PLoSONE', 'doc_type:full', 'publication_date:[2010-01-01T00:00:00Z TO 2010-12-31T23:59:59Z]'), limit=75)
Remove non-full article DOIs
dois <- dois$data$id
dois <- dois[!grepl("annotation", dois)]
Collect altmetrics data and combine to a data.frame with ldply
alm <- alm_ids(doi=dois, total_details=TRUE)
alm <- ldply(alm$data)
The default plot
plot_density(alm)
You can change the color of the density plot
plot_density(alm, color="#EFA5A5")
Pass in a title or description subtending the title
plot_density(alm, title="Scopus citations from 2010")
Plot a particular source
plot_density(alm, source="crossref_total")
Plot many sources in different panels in the same plot, and pass in colors just for fun
plot_density(input=alm,
source=c("counter_html","crossref_total","pubmed_total","scopus_total"),
color=c("#83DFB4","#EFA5A5","#CFD470","#B2C9E4")) +
theme_grey(base_size = 12)
#> NULL
CrossRef article level metrics
Notice that we are passing the base url for the Crossref API, whereas the default is for the PLOS url http://alm.plos.org/api/v5/articles.
url <- "http://det.labs.crossref.org/api/v5/articles"
dois <- c("10.1371/journal.pone.0086859", "10.1038/nature12990", "10.5860/choice.51-3037")
alm_ids(doi=dois, api_url = url)
#> $meta
#> total total_pages page error
#> 1 3 1 1 NA
#>
#> $data
#> $data$`10.1038/nature12990`
#> .id pdf html readers comments likes total
#> 1 crossref NA NA NA NA NA 0
#> 2 mendeley NA NA NA NA NA 0
#> 3 facebook NA NA NA NA NA 0
#> 4 pmc NA NA NA NA NA 0
#> 5 citeulike NA NA NA NA NA 0
#> 6 pubmed NA NA NA NA NA 0
#> 7 wordpress NA NA NA NA NA 0
#> 8 reddit NA NA NA NA NA 0
#> 9 wikipedia NA NA NA NA NA 6
#> 10 datacite NA NA NA NA NA 0
#> 11 pmceurope NA NA NA NA NA 0
#> 12 pmceuropedata NA NA NA NA NA 0
#>
#> $data$`10.1371/journal.pone.0086859`
#> .id pdf html readers comments likes total
#> 1 crossref NA NA NA NA NA 0
#> 2 mendeley NA NA NA NA NA 0
#> 3 facebook NA NA NA NA NA 0
#> 4 pmc NA NA NA NA NA 0
#> 5 citeulike NA NA NA NA NA 0
#> 6 pubmed NA NA NA NA NA 0
#> 7 wordpress NA NA NA NA NA 0
#> 8 reddit NA NA NA NA NA 0
#> 9 wikipedia NA NA NA NA NA 2
#> 10 datacite NA NA NA NA NA 0
#> 11 pmceurope NA NA NA NA NA 0
#> 12 pmceuropedata NA NA NA NA NA 0
#>
#> $data$`10.5860/choice.51-3037`
#> .id pdf html readers comments likes total
#> 1 crossref NA NA NA NA NA 0
#> 2 mendeley NA NA NA NA NA 0
#> 3 facebook NA NA NA NA NA 0
#> 4 pmc NA NA NA NA NA 0
#> 5 citeulike NA NA NA NA NA 0
#> 6 pubmed NA NA NA NA NA 0
#> 7 wordpress NA NA NA NA NA 0
#> 8 reddit NA NA NA NA NA 0
#> 9 wikipedia NA NA NA NA NA 0
#> 10 datacite NA NA NA NA NA 0
#> 11 pmceurope NA NA NA NA NA 0
#> 12 pmceuropedata NA NA NA NA NA 0
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