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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 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")

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Version

Install

install.packages('epiphy')

Monthly Downloads

284

Version

0.3.4

License

MIT + file LICENSE

Issues

2

Pull Requests

1

Stars

14

Forks

6

Maintainer

Christophe Gigot

Last Published

May 24th, 2018

Functions in epiphy (0.3.4)

aphids

Counts of aphids.
sadie

Spatial Analysis by Distance IndicEs (SADIE).
fit_two_distr

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

Z-test.
simulated_epidemics

Examples of simulated epidemic data.
mapping

Construct data mappings.
mapped_var

Existing variable mappings.
offspring_survival

Offspring survival of rats experiencing different diets.
vcov.smle

Calculate Variance-Covariance Matrix for a Fitted Model Object
smle

Simple maximum likelihood estimation
onion_bacterial_blight

Incidence of bacterial blight of onion.
pyrethrum_ray_blight

Incidence of ray blight disease of pyrethrum.
power_law

Taylor's and binary power laws.
smle_wrappers

Wrappers using maximum likelihood estimation for some distributions
tomato_tswv

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

Incidence of tobacco plants infected with viruses.
logLik.smle

Extract log-likelihood
threshold

To go to higher level in the hierarchy.
mapcomp

Map Comparison procedure.
spatial_hier

Spatial hierarchy analysis.
split.intensity

Divide into groups and reassemble.
agg_index

Several aggregation indices.
chisq.test

Chi-squared test.
clump

Regroup observational data into even clumps of individuals.
BetaBinomial

The beta-binomial distribution.
as.data.frame.intensity

Coerce to a data frame.
calpha.test

C(alpha) test.
a2a

Easily switch between different power law formulations.
is.intensity

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

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

Count of codling moth larvae.
arthropods

Counts of arthropods.
link

Some link functions.
indAndSub

Retrieve vector or array indices
epiphy

epiphy: An R package to analyze plant disease epidemics.
dogwood_anthracnose

Incidence of dogwood anthracnose.
coef.smle

Extract Model Coefficients
intensity

Construct count, incidence and severity objects.
hop_viruses

Incidence of three viruses in an Australian hop garden.