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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')

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) 

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Version

Install

install.packages('bdvis')

Monthly Downloads

146

Version

0.2.28

License

GPL-3

Maintainer

Vijay Barve

Last Published

January 15th, 2021

Functions in bdvis (0.2.28)

chronohorogram

Draws a chronohorogram of records
bdcomplete

Computes completeness values of the dataset
bdsummary

Provides summary of biodiversity data
taxotree

Treemap based on taxonomic hierarchy of records
mapgrid

Maps the data points on the map in grid format
bdvis

bdvis: Biodiversity Data Visualizations
bdwebmap

Interactive web page based map of records
bdcalendarheat

Calendar heat map of biodiversity data
tempolar

Polar plot of temporal data
distrigraph

Distribution graphs
getcellid

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

Prepare data frame for flagging functions
gettaxo

Get higher taxonomy data