bdvis v0.2.20

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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.

Readme

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)

Functions in bdvis

Name Description
bdsummary Provides summary of biodiversity data
bdcalendarheat Calendar heat map of biodiversity data
bdcomplete Computes completeness values of the dataset
format_bdvis Prepare data frame for flagging functions
getcellid Assign GBIF style degree cell ids
taxotree Treemap based on taxonomic hierarchy of records
tempolar Polar plot of temporal data
bdwebmap Interactive web page based map of records
chronohorogram Draws a chronohorogram of records
distrigraph Distribution graphs
fixstr Change structure of the data frame according to the package's needs
gettaxo Get higher taxonomy data
mapgrid Maps the data points on the map in grid format
bdvis bdvis: Biodiversity Data Visualizations
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Details

Type Package
Date 2018-01-29
License GPL-3
RoxygenNote 6.0.1
NeedsCompilation no
Packaged 2018-02-13 04:08:13 UTC; Narayani
Repository CRAN
Date/Publication 2018-02-13 04:30:15 UTC

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