vignettes/vignette_6_altmetric.md

In kamclean/impactr:

title: "5 - On-line Attention" date: "2020-10-04" always_allow_html: yes output: md_document: variant: gfm vignette: > %\VignetteIndexEntry{Vignette Title} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}

On-line Attention of Research Outputs

On-line attention and engagement for research is now well recognised as important alternative metrics to traditional metrics (although there are well recognised concerns regarding potential for manipulation), and has been repeatedly found to be positively correlated with article citations.

Altmetric is one such system that tracks the attention research outputs receive online, and this package utilises the rAltmetric package developed by the rOpenSci group to incorporate this data.

Note: At present this package only includes Altmetric data. PlumX is the other major source of alternative metrics, however there is no open API available for this product (it requires an authentication token) and so has not been incorporated at present.

impact_altmetric()

Altmetric is a system that tracks the attention that research outputs such as scholarly articles and datasets receive online. It pulls data from:

• Social media like Twitter and Facebook

• Traditional media - both mainstream (The Guardian, New York Times) and field specific (New Scientist, Bird Watching).

• Blogs - both major organisations (Cancer Research UK) and individual researchers.

• Online reference managers like Mendeley and CiteULike

The impact_altmetric() function aims to provide easy access to this source of information in useful format. At present this required articles to a pubmed identification number (pmid), however functionality to use DOI as an alternative is planned.

altmetric <- impactr::impact_altmetric(pmid)

Output

There are 4 outputs from impact_altmetric() as nested dataframes: $df, $temporal, $rank, and $source.

1. Original dataset ($df)

This will return the original dataset with data from altmetric appended as columns. There are 4 broad groups that describes the:

• "alm_score_" prefix: Overall altmetric score over time (see $temporal output below).

• "alm_all " / "alm_journal" prefixes: Context of altmetric score relative to other articles (see $rank output below).

• "n_engage_" prefix: Number of engagements with the article by source (see $source output below).

• "date_" prefix: Dates that the article was published, added to altmetric, and when altmetric data was last updated.

n id id type doi altmetric id title type author list journal journal issn alm score 1w alm score 1m alm score 3m alm score 6m alm score 1y alm score 6d alm score 5d alm score 4d alm score 3d alm score 2d alm score 1d alm score now alm all mean alm all n alm all rank alm all pct alm all higher than alm all prop alm journal all mean alm journal all rank alm journal all n alm journal all pct alm journal all higher than alm journal all prop alm 3m n alm 3m mean alm 3m rank alm 3m pct alm 3m higher than alm 3m prop alm journal 3m mean alm journal 3m rank alm journal 3m n alm journal 3m pct alm journal 3m higher than alm journal 3m prop date publish date update date added n engage fb n engage blogs n engage all n engage twitter posts n engage wikipedia n engage twitter accounts n engage news media n engage policy source n engage peer review sites n engage forum n engage googleplus n engage research highlight n engage linkedin n engage readers n engage other url image 1 30656658 pmid NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NA 2 30579405 pmid 10.1002/bjs.9614 2570470 Impact of postoperative non-steroidal anti-inflammatory drugs on adverse events after gastrointestinal surgery article NA British Journal of Surgery 0007-1323 0 0.5 0.5 0.5 7.55 0 0 0 0 0 0 112.408 9.064135 15958977 187629 98 15771434 0.9882431 12.24805 65 3956 98 3891 0.9838220 196088 8.832371 2431 98 193657 0.9876076 4.626923 1 40 97 39 1.0000000 2014-08-04 2020-09-24 2014-08-05 7 1 393 164 2 174 0 0 0 0 0 0 0 0 0 https://badges.altmetric.com/?size=180&score=113&types=btttttwf 3 30513129 pmid NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 NA 4 29984818 pmid 10.1371/journal.pone.0118899 3798277 Social Media and Internet Driven Study Recruitment: Evaluating a New Model for Promoting Collaborator Engagement and Participation article Chetan Khatri, Stephen J. Chapman, James Glasbey, Michael Kelly, Dmitri Nepogodi... PLoS ONE 1932-6203 0 0.0 0.0 2.0 2.00 0 0 0 0 0 0 41.400 9.007694 15815117 530862 96 15284074 0.9664333 12.97886 8598 156808 94 148206 0.9451750 262834 10.062533 11472 95 251357 0.9563565 13.110770 246 4398 94 4152 0.9442929 2015-03-16 2020-06-11 2015-03-17 0 0 143 72 0 72 0 0 0 0 0 0 0 0 0 https://badges.altmetric.com/?size=180&score=42&types=tttttttt 5 29897171 pmid 10.1186/s12909-015-0326-1 3784521 Promoting research and audit at medical school: evaluating the educational impact of participation in a student-led national collaborative study article Stephen J Chapman, James C D Glasbey, Chetan Khatri, Michael Kelly, Dmitri Nepog... BMC Medical Education 1472-6920 0 0.0 0.0 0.0 2.50 0 0 0 0 0 0 54.050 9.048781 15922255 417371 97 15504714 0.9737870 6.43047 26 2252 98 2226 0.9888988 219704 10.141062 7499 96 212203 0.9658723 0.000000 1 1 1 0 1.0000000 2015-03-13 2020-02-02 2015-03-13 5 0 194 91 0 96 0 0 0 0 0 0 0 0 0 https://badges.altmetric.com/?size=180&score=55&types=tttttfff

2. Focussed Altmetric datasets

The following outputs do not contain additional information beyond what is already provided in $df. However, these provide long format and focussed aspects of data to facilitate easier visualisation and analysis. These exclude any publications not tracked by altmetric.

2. a). altmetric score over time ($temporal)

altmetric records the altmetric score contemporaneous, and at set intervals following publication (1 week, 1 month, 3 months, 6 months, 1 year). It also records date of publication which allows calculation of a standardised time since publication (alm_time).

id doi date_update date_added alm_time alm_score 29292217 10.1001/jamasurg.2015.0806 2015-07-28 2015-05-09 0 0 29292217 10.1001/jamasurg.2015.0806 2015-07-28 2015-05-09 1 0 29292217 10.1001/jamasurg.2015.0806 2015-07-28 2015-05-09 2 0 29292217 10.1001/jamasurg.2015.0806 2015-07-28 2015-05-09 3 0 29292217 10.1001/jamasurg.2015.0806 2015-07-28 2015-05-09 4 0 29292217 10.1001/jamasurg.2015.0806 2015-07-28 2015-05-09 5 0 29292217 10.1001/jamasurg.2015.0806 2015-07-28 2015-05-09 6 0 29292217 10.1001/jamasurg.2015.0806 2015-07-28 2015-05-09 7 0 29292217 10.1001/jamasurg.2015.0806 2015-07-28 2015-05-09 30 0

Figure 1: Plot of altmetric score over time for each paper

altmetric$temporal %>% 
  ggplot() +
  aes(x = alm_time, y = alm_score, group = pmid, colour = pmid) +
  geom_line() + geom_point() + theme_bw()

## Error: Aesthetics must be either length 1 or the same as the data (247): group and colour

2 b). altmetric ranking ($rank)

The altmetric score is not normalised, and so it is meaningless without context. As such, altmetric allows you to see the score relative to other articles (whether from all indexed by altmetric or those from the same journal at the same time). Within $rank these categories (alm_category) include:

• all: All papers recorded by altmetric.

• journal_all: All papers recorded by altmetric for that journal

• journal_3m: All papers recorded by altmetric for that journal within a 3 month period

For each category, altmetric records the following measures:

• The mean altmetric score (mean).

• The number (n) of all papers, and the rank of the specific paper within those (rank).

• The proportion of papers (prop) that the paper outranks (rank / n).

id doi journal alm_score comparator_journal comparator_time mean n rank prop 30579405 10.1002/bjs.9614 British Journal of Surgery 112.408 all ever 9.064135 15958977 187629 0.9882431 30579405 10.1002/bjs.9614 British Journal of Surgery 112.408 British Journal of Surgery ever 12.248053 3956 65 0.9838220 30579405 10.1002/bjs.9614 British Journal of Surgery 112.408 all 3 months 8.832371 196088 2431 0.9876076 30579405 10.1002/bjs.9614 British Journal of Surgery 112.408 British Journal of Surgery 3 months 4.626923 40 1 1.0000000 29984818 10.1371/journal.pone.0118899 PLoS ONE 41.400 all ever 9.007694 15815117 530862 0.9664333 29984818 10.1371/journal.pone.0118899 PLoS ONE 41.400 PLoS ONE ever 12.978864 156808 8598 0.9451750 29984818 10.1371/journal.pone.0118899 PLoS ONE 41.400 all 3 months 10.062533 262834 11472 0.9563565 29984818 10.1371/journal.pone.0118899 PLoS ONE 41.400 PLoS ONE 3 months 13.110770 4398 246 0.9442929 29897171 10.1186/s12909-015-0326-1 BMC Medical Education 54.050 all ever 9.048781 15922255 417371 0.9737870

Figure 2: Plot of the percentage rank of each publication within each altmetric category.

altmetric$rank %>%
  dplyr::mutate(journal = gsub(": The British Journal of Anaesthesia", "", journal),
                pmid = as.character(pmid)) %>%
  dplyr::mutate("Altmetric Ranking (%)" = round(prop*100, 1),
                "Altmetric Category" = factor(as.character(alm_category), levels=c("all", "journal_all", "journal_3m"))) %>%
  ggplot() +
  aes(x = `Altmetric Category`, y = `Altmetric Ranking (%)`) +
  geom_point() + geom_boxplot() +
  theme_bw()

## Error: Invalid index: out of bounds

## Error in grid.draw(plot): object 'plot_alm_rank' not found

2 c). altmetric sources ($source)

The Altmetric score for a research output provides an indicator of the amount of attention that it has received from, and as such records both the type and amount of attention recieved. This data excludes any sources not recorded for any of the papers.

id doi n_engage_all source n total prop 30579405 10.1002/bjs.9614 393 fb 7 174 0.0402299 30579405 10.1002/bjs.9614 393 blogs 1 174 0.0057471 30579405 10.1002/bjs.9614 393 twitter 164 174 0.9425287 30579405 10.1002/bjs.9614 393 wikipedia 2 174 0.0114943 30579405 10.1002/bjs.9614 393 news_media 0 174 0.0000000 29984818 10.1371/journal.pone.0118899 143 fb 0 72 0.0000000 29984818 10.1371/journal.pone.0118899 143 blogs 0 72 0.0000000 29984818 10.1371/journal.pone.0118899 143 twitter 72 72 1.0000000 29984818 10.1371/journal.pone.0118899 143 wikipedia 0 72 0.0000000 29984818 10.1371/journal.pone.0118899 143 news_media 0 72 0.0000000 29897171 10.1186/s12909-015-0326-1 194 fb 5 96 0.0520833 29897171 10.1186/s12909-015-0326-1 194 blogs 0 96 0.0000000

Figure 3: Plot of the proportion of altmetric sources for each paper

altmetric$source %>% 
  ggplot() +
  aes(x = pmid, y = prop, colour = source, fill = source) +
  geom_col() + coord_flip()+ theme_bw()

## Error: Aesthetics must be either length 1 or the same as the data (100): x

kamclean/impactr documentation built on Jan. 11, 2023, 2:51 p.m.