bdvis

About

Biodiversity Data Visualizations using R. This package offers a set of functions to visualize biodiversity occurrence data through R. The development of the package started as a Google Summer of Code project. The detailed proposal is available on this blog entry.

Installation

Install the latest version using install_github within Hadley's devtools package.

install.packages("devtools") 
require(devtools)
install_github("vijaybarve/bdvis") 
require(bdvis) 

Note:

Windows users have to first install Rtools.

Packages bdvis depends on

• [maps] (http://cran.r-project.org/web/packages/maps/index.html)
• [sqldf] (http://cran.r-project.org/web/packages/sqldf/index.html)
• [plotrix] (http://cran.r-project.org/web/packages/plotrix/index.html)
• [treemap] (http://cran.r-project.org/web/packages/treemap/index.html)
• [plyr] (http://cran.r-project.org/web/packages/plyr/index.html)
• [taxize] (http://cran.r-project.org/web/packages/taxize/index.html)
• [ggplot2] (http://cran.r-project.org/web/packages/ggplot2/index.html)
• [grid] (http://cran.r-project.org/web/packages/grid/)
• [lattice] (http://cran.r-project.org/web/packages/lattice/)
• [chron] (http://cran.r-project.org/web/packages/chron/)

Packages bdvis suggests

(for the purpose of building examples)

• [rinat] (https://github.com/ropensci/rinat)

Functions currently available

For the sake of examples, we will work with some data obtained using the package rinat

install.packages("rinat") 
require(rinat)  # Data download might take some time
inat=get_inat_obs_project("reptileindia") 
inat=format_bdvis(inat,source='rinat')

bdsummary

bdsummary(inat) 

mapgrid

mapgrid(inat,ptype="records",bbox=c(60,100,5,40),region=c("India")) 

tempolar

tempolar(inat, color="green", title="iNaturalist daily", plottype="r", timescale="d") 
tempolar(inat, color="blue", title="iNaturalist weekly", plottype="p", timescale="w") 
tempolar(inat, color="red", title="iNaturalist monthly", plottype="r", timescale="m") 

taxotree

inat=gettaxo(inat) 
taxotree(inat) 

chronohorogram

chronohorogram(inat) 

bdcomplete

comp=bdcomplete(inat,recs=5)
mapgrid(comp,ptype="complete",bbox=c(60,100,5,40),region=c("India"))

distrigraph

distrigraph(inat,ptype="cell",col="tomato") 
distrigraph(inat,ptype="species",ylab="Species") 
distrigraph(inat,ptype="efforts",col="red") 
distrigraph(inat,ptype="efforts",col="red",type="s") 

bdcalendarheat

bdcalendarheat(inat)