Analysis of Plant Disease Epidemics

A toolbox to make it easy to analyze plant disease epidemics. It provides a common framework for plant disease intensity data recorded over time and/or space. Implemented statistical methods are currently mainly focused on spatial pattern analysis (e.g., aggregation indices, Taylor and binary power laws, distribution fitting, SADIE and mapcomp methods). See Madden LV, Hughes G, van den Bosch F (2007, ISBN: 978-089054-354-2) for further information on these methods. Several data sets that were mainly published in plant disease epidemiology literature are also included in this package.


Travis-CI Build Status

Overview

epiphy makes it easy to analyze plant disease epidemics. It provides a common framework for plant disease intensity data recorded over time and/or space. Implemented statistical methods are currently mainly focused on spatial pattern analysis (e.g., aggregation indices, Taylor and binary power laws, distribution fitting, SADIE and mapcomp methods). Several data sets that were mainly published in plant disease epidemiology literature are also included in this package. The online documentation is available at epiphy.org.

Installation

Install the latest released version from CRAN:

install.packages("epiphy")

Install the latest development version from GitHub:

# install.packages("devtools")
devtools::install_github("chgigot/epiphy")

News

epiphy 0.3.4

  • Minor bug fixes.
  • Improve documentation.
  • Add Travis CI and a website.

epiphy 0.3.3

  • Add a grayscale feature in plot for intensity objects.
  • Improve documentation and examples (sadie, intensity objects).

epiphy 0.3.2

Major new features

  • Fixed bugs in the SADIE algorithm.
  • Mapcomp procedure proposed by Lavigne et al. (2010).

epiphy 0.3.0

Major new features

  • Computation of aggregation indices (Fisher's, Lloyd's, etc.).
  • Distribution fitting, with two distributions, for count and incidence data. It is thus an R alternative to the BBD software from Madden & Hughes (1994) for incidence data.
  • Spatial hierarchy analysis.
  • Power law analysis (Taylor's and binary forms).
  • A first working version of the SADIE procedure.
  • Twelve historical data sets.
  • Many other features!

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("epiphy")

0.3.4 by Christophe Gigot, 7 months ago


http://epiphy.org, https://github.com/chgigot/epiphy


Report a bug at https://github.com/chgigot/epiphy/issues


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


Authors: Christophe Gigot [aut, cre]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports stats, methods, utils, grDevices, ggplot2, transport, msm, pbapply, Rcpp

Suggests magrittr, dplyr, tidyr, spdep, emdist, vegan, MASS, emdbook, knitr, rmarkdown

Linking to Rcpp


See at CRAN