bdvis v0.2.18

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by Vijay Barve

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. 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

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

Type Package
Date 2017-07-20
License GPL-3
RoxygenNote 6.0.1
NeedsCompilation no
Packaged 2017-07-21 03:19:05 UTC; Narayani
Repository CRAN
Date/Publication 2017-07-21 03:31:08 UTC

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