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bdvis

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.

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) 

News

bdvis 0.2.22

  • function mapgrid can load a shapefile as basemap
  • function gettaxo has progress param to control progress bar output

bdvis 0.2.17

  • function distrigraph has parameter cumulative for 'efforts' option
  • function distrigraph has 'effortspecis' option in paramater ptype

bdvis 0.2.15

  • Improved documentation
  • function mapgrid has improved map layer arrangement

bdvis 0.2.12

  • function mapgrid has option to map at 0.1 degree grid cells
  • function bdcomplete has option to return 0.1 degree grid cells

bdvis 0.2.9

  • function bdcomplete now returns number of records per grid cell
  • added additional parameter ptsize in chronohorogram
  • bug fix in functions tempolar, distrigraph bdcomplete and bdwebmap.
  • improved documentation

bdvis 0.2.0

  • function bdcomplete bug fixes and visualizatio added in function mapgrid
  • improvements to function mapgrid in legend and color control
  • significant improvement in documentation
  • released to CRAN

bdvis 0.1.35

New Features

  • improved documentation of the package
  • various reported bugs fixed
  • function distrigraph can accept additional plot parameters
  • verbose option added for function gettaxo

bdvis 0.1.25

New Features

  • validations added to functions taxotree and chronohorogram
  • function mapgrid has a Presence map option now
  • seamless support ro package bdsns data frames
  • function gettaxo stores a local database of queried names for future reference and efficiency

bdvis 0.1.15

New Features

  • added function format_bdvis to handle more data formats seamlessly
  • added function datasubset to subset data
  • added function distrigraphs to generate graphs of records distributed across species, time and geography
  • added function bdcalendarheat to generate calendar of data records
  • function bdcomplete has plot showing completeness versus species
  • added function bdwebmap to generate a point map which can be viewed in a browser

bdvis 0.1.5

New Features

  • taxotree has param n, title and legend to control number of rectangles, tatle and legend title
  • taxotree has summerization parameters
  • gettaxo has genus param to improve effeciency
  • avg param in tempolar to display average number of records rather than raw numbers
  • bdsummery has spatial coverage

bdvis 0.1.0

  • released to CRAN

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.
install.packages("bdvis")

0.2.28 by Vijay Barve, 9 months ago

Report a bug at https://github.com/vijaybarve/bdvis/issues

Browse source code at https://github.com/cran/bdvis

Authors: Vijay Barve [aut, cre] , Javier Otegui [aut]

Documentation:   PDF Manual  

GPL-3 license

Imports maps, plotrix, sqldf, plyr, taxize, treemap, ggplot2, lattice, chron, leafletR, rgdal

Suggests rinat

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