Biodiversity Data Visualizations

Provides a set of functions to create basic visualizations to quickly preview different aspects of biodiversity information such as inventory completeness, extent of coverage (taxonomic, temporal and geographic), gaps and biases.

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)