`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")) 
mapgrid(inat,ptype="records",bbox=c(60,100,5,40),region=c("India"),gridscale=0.1)

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)

bdvis