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epiphy

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 https://chgigot.github.io/epiphy/.

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")

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Version

Install

install.packages('epiphy')

Monthly Downloads

284

Version

0.5.0

License

MIT + file LICENSE

Issues

Pull Requests

Stars

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Repository

https://github.com/chgigot/epiphy

Homepage

https://chgigot.github.io/epiphy/

Maintainer

Christophe Gigot

Last Published

November 16th, 2023

Functions in epiphy (0.5.0)

dogwood_anthracnose

Incidence of dogwood anthracnose.

Chi-squared test.

Incidence of tomato spotted wilt virus (TSWV) disease in field trials.

split.intensity

Divide into groups and reassemble.

Spatial hierarchy analysis.

Calculate Variance-Covariance Matrix for a Fitted Model Object

Some link functions.

Test if an object is of class intensity or one of its subclasses.

Taylor's and binary power laws.

as.data.frame.intensity

Coerce to a data frame.

To go to higher level in the hierarchy.

Counts of arthropods.

pyrethrum_ray_blight

Incidence of ray blight disease of pyrethrum.

Construct count, incidence and severity objects.

tobacco_viruses

Incidence of tobacco plants infected with viruses.

onion_bacterial_blight

Incidence of bacterial blight of onion.

offspring_survival

Offspring survival of rats experiencing different diets.

Wrappers using maximum likelihood estimation for some distributions

Retrieve vector or array indices

Simple maximum likelihood estimation

Regroup observational data into even clumps of individuals.

The beta-binomial distribution.

Easily switch between different power law formulations.

Several aggregation indices.

Incidence of citrus tristeza virus (CTV) disease in three fields.

Maximum likelihood fitting of two distributions and goodness-of-fit comparison.

Existing variable mappings.

Extract Model Coefficients

Incidence of three viruses in an Australian hop garden.

Counts of aphids.

epiphy: An R package to analyze plant disease epidemics.

Count of codling moth larvae.

Spatial Analysis by Distance IndicEs (SADIE).

simulated_epidemics

Examples of simulated epidemic data.

Map Comparison procedure.

Extract log-likelihood

Construct data mappings.