Using biorxivr

Edmund Hart and Silvia Liverani

2020-05-08

Searching

The search functionality comes from the general search form interface, so the search may not be at the granularity you desire without further parsing of results. This is the equivalent of the search box on the main landing page of biorxiv.

library(biorxivr)

## Loading required package: XML

## Loading required package: RCurl

bxEco <- bx_search("Ecology",limit = 10)
summary(bxEco)

##       Length Class  Mode     
## URL   10     -none- character
## ID    10     -none- character
## found  1     -none- numeric  
## query  1     -none- character
## limit  1     -none- numeric

This will return a search results object that has the URL’s for your search results. If you want to get details about all your search results we can extract basic features like DOI, Authors, e-mails, title, abstract text, date as well as metrics on views and downloads.

bxEcoDetails <-  bx_extract(bxEco)

bxEcoDetails[[1]]

## $authors
## $authors$names
## [1] "Dingliang Xing" "Fangliang He"  
## 
## $authors$email
## [1] "dlxing@des.ecnu.edu.cn"
## 
## 
## $paper
## $paper$title
## [1] "Analytical models for β-diversity and the power-law scaling of β-deviation"
## 
## $paper$abstract
## [1] "1.  β -diversity is a primary biodiversity pattern for inferring community assembly. A randomized null model that generates a standardized β -deviation has been widely used for this purpose. However, the null model has been much debated and its application is limited to abundance data.\n\n2.  Here we derive analytical models for β -diversity to address the debate, clarify the interpretation, and extend the application to occurrence data.\n\n3.  The analytical analyses show unambiguously that the standardized β -deviation is a quantification of the effect size of non-random spatial distribution of species on β -diversity for a given species abundance distribution. It robustly scales with sampling effort following a power law with exponent of 0.5. This scaling relationship offers a simple method for comparing β -diversity of communities of different sizes.\n\n4.  Assuming logseries distribution for the metacommunity species abundance distribution, our model allows for calculation of the standardized β -deviation using occurrence data plus a datum on the total abundance.\n\n5.  Our theoretical model justifies and generalizes the use of the β null model for inferring community assembly rules.\n\n### Competing Interest Statement\n\nThe authors have declared no competing interest."
## 
## $paper$date
## [1] "2020-04-20"
## 
## $paper$DOI
## [1] "10.1101/2020.04.19.049163"
## 
## $paper$fulltext_url
## [1] "https://www.biorxiv.org/content/biorxiv/early/2020/04/20/2020.04.19.049163.full.pdf"
## 
## 
## attr(,"class")
## [1] "biorxiv_paper"

#There’s also some basic plotting functionality that will allow you plot views and downloads

#Plot views the number of views an abstract.

#```{r plotting views,fig.align=‘center’,fig.width=4,fig.height=4} #plot(bxEcoDetails[[1]],type=“abs”)

#```

#Plot the number of PDF downloads.

#```{r plotting dl,fig.align=‘center’,fig.width=4,fig.height=4} #plot(bxEcoDetails[[1]],type=“dl”)

#```

Finally, you can easily download PDF’s from all your search results.

bx_download(bxEco,"~/biorxiv_pdfs")