Learn R Programming

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)

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')
inat <- inat[,c("id","Date_collected", "Latitude", "Longitude", 
                "Scientific_name", "Cell_id", "Centi_cell_id")]

bdsummary

bdsummary(inat) 

mapgrid

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

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) 

Copy Link

Version

Install

install.packages('bdvis')

Monthly Downloads

208

Version

0.2.37

License

GPL-3

Maintainer

Last Published

December 8th, 2023

Functions in bdvis (0.2.37)

bdwebmap

(Deprecated) Interactive web page based map of records
getcellid

Assign GBIF style degree cell ids and generate custom grid cell ids
bdvis

bdvis: Biodiversity Data Visualizations
distrigraph

Distribution graphs
bdcomplete

Computes completeness values of the dataset
bdsummary

Provides summary of biodiversity data
format_bdvis

Prepare data frame for flagging functions
bdcalendarheat

Calendar heat map of biodiversity data
chronohorogram

Draws a chronohorogram of records
gettaxo

Get higher taxonomy data
mapgrid

Maps the data points on the map in grid format
tempolar

Polar plot of temporal data
taxotree

Treemap based on taxonomic hierarchy of records