bdvis
About
Biodiversity Data Visualizations using R. This package offers a set of functions to visualize biodiversity occurrence data through R. Please check the paper describing the package Barve, V., and J. Otegui. 2016. bdvis: visualizing biodiversity data in R. Bioinformatics:btw333. https://academic.oup.com/bioinformatics/article/32/19/3049/2196391
The development of the package started as a Google Summer of Code project.
Installation
install.packages("bdvis")
require(bdvis) 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")
distrigraph(inat,ptype="efforts",col="red",cumulative=T,type="l")
distrigraph(inat,ptype="effortspecies",col="red",cumulative=T,type="l")bdcalendarheat
bdcalendarheat(inat)