# epiphy v0.3.4

Monthly downloads

## 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.

## Readme

# 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")
```

## Functions in epiphy

Name | Description | |

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. | |

No Results! |

## Vignettes of epiphy

Name | ||

biblio.bib | ||

defs-and-eqns.Rmd | ||

epiphy.Rmd | ||

phytopathology_v2.csl | ||

No Results! |

## Last month downloads

## Details

Type | Package |

License | MIT + file LICENSE |

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

BugReports | https://github.com/chgigot/epiphy/issues |

Encoding | UTF-8 |

LazyData | true |

RoxygenNote | 6.0.1 |

LinkingTo | Rcpp |

Collate | 'RcppExports.R' 'betabinom.R' 'data.R' 'utils.R' 'mle-factory.R' 'epiphy.R' 'intensity-classes.R' 'distr-fitting.R' 'indices.R' 'mapcomp.R' 'power-law.R' 'sadie.R' 'spatial-hier.R' |

VignetteBuilder | knitr |

NeedsCompilation | yes |

Packaged | 2018-05-22 19:20:57 UTC; tof |

Repository | CRAN |

Date/Publication | 2018-05-24 13:37:06 UTC |

#### Include our badge in your README

```
[![Rdoc](http://www.rdocumentation.org/badges/version/epiphy)](http://www.rdocumentation.org/packages/epiphy)
```