rxivistr

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:

Installation

To install rxivistr package, run:

devtools::install_github("ikodvanj/rxivistr")

Using rxivistr

Load the package using library() function.

library(rxivistr)

Package contains following functions:

In the following text, examples are provided for each function.

article_details

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  $ abstract    : chr "This paper has been withdrawn by its authors.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] "Indian Institute of Technology Delhi" "Indian Institute of Technology Delhi" "Indian Institute of Technology, New Delhi" "Indian Institute of Technology Delhi" ...
#>   ..$ orcid      : logi [1:9] NA NA NA NA NA NA ...
#>  $ ranks       :List of 4
#>   ..$ alltime  :List of 4
#>   .. ..$ downloads: int 962296
#>   .. ..$ rank     : int 1
#>   .. ..$ out_of   : int 94912
#>   .. ..$ tie      : logi FALSE
#>   ..$ ytd      :List of 4
#>   .. ..$ downloads: int 962296
#>   .. ..$ rank     : int 1
#>   .. ..$ out_of   : int 94912
#>   .. ..$ tie      : logi FALSE
#>   ..$ lastmonth:List of 4
#>   .. ..$ downloads: int 14987
#>   .. ..$ rank     : int 3
#>   .. ..$ out_of   : int 94912
#>   .. ..$ tie      : logi FALSE
#>   ..$ category :List of 4
#>   .. ..$ downloads: int 962296
#>   .. ..$ rank     : int 1
#>   .. ..$ out_of   : int 5736
#>   .. ..$ tie      : logi FALSE
#>  $ publication : Named list()

article_downloads

To investigate the number of downloads, article_downloads function can be used:

authors_rank

To retrieve top 200 authors based on the number of article downloads, authors_rank can be used:

author

With function author, we can retrieve more information about specific author.

author(295517)
#> $id
#> [1] 295517
#> 
#> $name
#> [1] "James Gomes"
#> 
#> $institution
#> [1] "Indian Institute of Technology Delhi"
#> 
#> $orcid
#> NULL
#> 
#> $emails
#> [1] "jgomes@bioschool.iitd.ac.in" "jgomes.bioschool@gmail.com" 
#> 
#> $articles
#>      id                       doi
#> 1 72514 10.1101/2020.01.30.927871
#> 2 83161 10.1101/2020.05.07.082768
#> 3 32598            10.1101/414425
#>                                                   biorxiv_url
#> 1 https://www.biorxiv.org/content/10.1101/2020.01.30.927871v2
#> 2 https://www.biorxiv.org/content/10.1101/2020.05.07.082768v2
#> 3            https://www.biorxiv.org/content/10.1101/414425v1
#>                                       url
#> 1 https://api.rxivist.org/v1/papers/72514
#> 2 https://api.rxivist.org/v1/papers/83161
#> 3 https://api.rxivist.org/v1/papers/32598
#>                                                                                                                               title
#> 1                                        Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag
#> 2 Mutation landscape of SARS-CoV-2 reveals five mutually exclusive clusters of leading and trailing single nucleotide substitutions
#> 3                                                                Immune differentiation regulator p100 tunes NF-κB responses to TNF
#>               category ranks.alltime.downloads ranks.alltime.rank
#> 1 evolutionary-biology                  962296                  1
#> 2             genomics                    1293               8032
#> 3      systems-biology                     318              53888
#>   ranks.alltime.out_of ranks.alltime.tie ranks.ytd.downloads ranks.ytd.rank
#> 1                94912             FALSE              962296              1
#> 2                94912             FALSE                1293           1304
#> 3                94912             FALSE                  55          81139
#>   ranks.ytd.out_of ranks.ytd.tie ranks.lastmonth.downloads ranks.lastmonth.rank
#> 1            94912         FALSE                     14987                    3
#> 2            94912         FALSE                       419                  784
#> 3            94912         FALSE                         8                76347
#>   ranks.lastmonth.out_of ranks.lastmonth.tie ranks.category.downloads
#> 1                  94912               FALSE                   962296
#> 2                  94912               FALSE                     1293
#> 3                  94912               FALSE                      318
#>   ranks.category.rank ranks.category.out_of ranks.category.tie
#> 1                   1                  5736              FALSE
#> 2                1216                  5955              FALSE
#> 3                1569                  2425              FALSE
#> 
#> $ranks
#>   downloads  rank out_of   tie             category
#> 1    963907     1 404161 FALSE              alltime
#> 2    962296     1  20691  TRUE evolutionary-biology
#> 3      1293 14583  42763  TRUE             genomics
#> 4       318  8777  11761  TRUE      systems-biology

category_list

This function returns a list of all categories to which articles are classified:

rxivist_stats

Returns information about the number of articles indexed by the Rxivist.