Rxivist indexes articles from bioRxiv, a free preprint server by Cold Spring Harbor Laboratory. This package is a client for the Rxivist API and can be used to access metadata from:
To install rxivistr package from CRAN, run:
install.packages("rxivistr")…or install it from GitHub:
devtools::install_github("ikodvanj/rxivistr")Load the package using library() function.
library(rxivistr)
Package contains following functions:
rxivist_search - retrieves articles with the matching descriptionarticle_details - retrieves data about a single paper and all of its authorsarticle_downloads - retrieves monthly download statistics for articles.authors_rank - retrieves top 200 authors in the specified category.author - provides information about the specified author.category_list - retrieves a list of all categoriesrxivist_stats - retrieves basic statistics about the number of articles indexed by the Rxivist.In the following text, examples are provided for each function.
Following function retrieves articles top 5 most downloaded articles related to COVID-19:
res <- rxivist_search(search_phrase = "COVID-19", from = "alltime", sortby = "downloads", limit = 5) dplyr::glimpse(res) #> Rows: 5 #> Columns: 10 #> $ id <int> 81793, 77469, 76533, 78358, 83296 #> $ metric <int> 219628, 164766, 102134, 98929, 86680 #> $ title <chr> "Spike mutation pipeline reveals the emergence of a more… #> $ url <chr> "https://api.rxivist.org/v1/papers/81793", "https://api.… #> $ biorxiv_url <chr> "https://www.biorxiv.org/content/10.1101/2020.04.29.0690… #> $ doi <chr> "10.1101/2020.04.29.069054", "10.1101/2020.03.22.002386"… #> $ category <chr> "evolutionary-biology", "systems-biology", "microbiology… #> $ first_posted <chr> "2020-04-30", "2020-03-22", "2020-03-12", "2020-03-31", … #> $ abstract <chr> "We have developed an analysis pipeline to facilitate re… #> $ authors <list> [<data.frame[17 x 2]>, <data.frame[100 x 2]>, <data.fra…
At the time of writing this vignette, the most downloaded article had an id 72514. With the following function we will retrieve information about this article:
res <- article_details(72514) dplyr::glimpse(res) #> List of 11 #> $ id : chr "72514" #> $ doi : chr "10.1101/2020.01.30.927871" #> $ first_posted: chr "2020-01-31" #> $ biorxiv_url : chr "https://www.biorxiv.org/content/10.1101/2020.01.30.927871v2" #> $ url : chr "https://api.rxivist.org/v1/papers/72514" #> $ title : chr "Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag" #> $ category : chr "evolutionary-biology" #> $ abstract : chr "This paper has been withdrawn by its authors. They intend to revise it in response to comments received from th"| __truncated__ #> $ authors :'data.frame': 9 obs. of 4 variables: #> ..$ id : int [1:9] 580441 580442 580443 580444 580445 582554 295517 580447 580448 #> ..$ name : chr [1:9] "Prashant Pradhan" "Ashutosh Kumar Pandey" "Akhilesh Mishra" "Parul Gupta" ... #> ..$ institution: chr [1:9] "Acharya Narendra Dev College, University of Delhi" "Kusuma School of biological sciences, Indian institute of technology" "Kusuma School of biological sciences, Indian institute of technology" "Kusuma School of biological sciences, Indian institute of technology" ... #> ..$ orcid : chr [1:9] NA NA NA "http://orcid.org/0000-0002-0190-8753" ... #> $ ranks :List of 4 #> ..$ alltime :List of 4 #> .. ..$ downloads: int 962296 #> .. ..$ rank : int 1 #> .. ..$ out_of : int 99794 #> .. ..$ tie : logi FALSE #> ..$ ytd :List of 4 #> .. ..$ downloads: int 962296 #> .. ..$ rank : int 1 #> .. ..$ out_of : int 99794 #> .. ..$ tie : logi FALSE #> ..$ lastmonth:List of 4 #> .. ..$ downloads: int 14987 #> .. ..$ rank : int 3 #> .. ..$ out_of : int 99794 #> .. ..$ tie : logi FALSE #> ..$ category :List of 4 #> .. ..$ downloads: int 962296 #> .. ..$ rank : int 1 #> .. ..$ out_of : int 5736 #> .. ..$ tie : logi FALSE #> $ publication : Named list()
To investigate the number of downloads, article_downloads function can be used:
article_downloads(72514) #> month year downloads views #> 1 1 2020 564379 93404 #> 2 2 2020 96925 105222 #> 3 3 2020 135194 138613 #> 4 4 2020 101153 144663 #> 5 5 2020 34235 45337 #> 6 6 2020 15423 17637 #> 7 7 2020 10178 17688 #> 8 8 2020 4809 10117
This function returns a list of all categories to which articles are classified:
category_list() #> $results #> [1] "animal-behavior-and-cognition" #> [2] "biochemistry" #> [3] "bioengineering" #> [4] "bioinformatics" #> [5] "biophysics" #> [6] "cancer-biology" #> [7] "cell-biology" #> [8] "clinical-trials" #> [9] "developmental-biology" #> [10] "ecology" #> [11] "epidemiology" #> [12] "evolutionary-biology" #> [13] "genetics" #> [14] "genomics" #> [15] "immunology" #> [16] "microbiology" #> [17] "molecular-biology" #> [18] "neuroscience" #> [19] "paleontology" #> [20] "pathology" #> [21] "pharmacology-and-toxicology" #> [22] "physiology" #> [23] "plant-biology" #> [24] "scientific-communication-and-education" #> [25] "synthetic-biology" #> [26] "systems-biology" #> [27] "zoology"
Returns information about the number of articles indexed by the Rxivist.
res <- rxivist_stats() dplyr::glimpse(res) #> List of 8 #> $ papers_indexed : int 99794 #> $ authors_indexed : int 422246 #> $ missing_abstract : int 1 #> $ missing_date : int 0 #> $ outdated_count :List of 28 #> ..$ animal-behavior-and-cognition : int 1436 #> ..$ biochemistry : int 3132 #> ..$ bioengineering : int 2086 #> ..$ bioinformatics : int 8553 #> ..$ biophysics : int 4021 #> ..$ cancer-biology : int 3287 #> ..$ cell-biology : int 4769 #> ..$ clinical-trials : int 99 #> ..$ developmental-biology : int 2741 #> ..$ ecology : int 4036 #> ..$ epidemiology : int 1554 #> ..$ evolutionary-biology : int 5552 #> ..$ genetics : int 4718 #> ..$ genomics : int 5821 #> ..$ immunology : int 2775 #> ..$ microbiology : int 8102 #> ..$ molecular-biology : int 3172 #> ..$ neuroscience : int 16230 #> ..$ paleontology : int 125 #> ..$ pathology : int 536 #> ..$ pharmacology-and-toxicology : int 879 #> ..$ physiology : int 1287 #> ..$ plant-biology : int 2863 #> ..$ scientific-communication-and-education: int 627 #> ..$ synthetic-biology : int 872 #> ..$ systems-biology : int 2365 #> ..$ zoology : int 486 #> ..$ null : int 49 #> $ missing_authors : int 63 #> $ missing_category : int 4932 #> $ authors_no_papers: int 420