Package: epiphy 0.5.0.9000

epiphy: 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 Laurence V. Madden, Gareth Hughes, Franck van den Bosch (2007) <doi:10.1094/9780890545058> for further information on these methods. Several data sets that were mainly published in plant disease epidemiology literature are also included in this package.

Authors:Christophe Gigot [aut, cre, cph], Adam H. Sparks [ctb], Katrin Leinweber [ctb]

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epiphy.pdf |epiphy.html✨
epiphy/json (API)
NEWS

# Install 'epiphy' in R:
install.packages('epiphy', repos = c('https://chgigot.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/chgigot/epiphy/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

41 exports 15 stars 2.19 score 37 dependencies 1 mentions 37 scripts 203 downloads

Last updated 10 months agofrom:019e19d9ce. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 28 2024
R-4.5-win-x86_64OKAug 28 2024
R-4.5-linux-x86_64OKAug 28 2024
R-4.4-win-x86_64OKAug 28 2024
R-4.4-mac-x86_64OKAug 28 2024
R-4.4-mac-aarch64OKAug 28 2024
R-4.3-win-x86_64OKAug 28 2024
R-4.3-mac-x86_64OKAug 28 2024
R-4.3-mac-aarch64OKAug 28 2024

Exports:a2aagg_indexcalpha.testchisq.testcloglogclumpcountcount_datadbetabinomfit_two_distrincidenceincidence_dataind2subis.countis.incidenceis.intensityis.severitylogitmapcompmapped_varmapped_var<-mappingmapping_pbetabinompower_lawprobitqbetabinomrbetabinomremapsadieseverityseverity_datasmlesmle_betabinomsmle_binomsmle_nbinomsmle_poisspatial_hiersub2indthresholdz.test

Dependencies:clicolorspacedata.tableexpmfansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmsmmunsellmvtnormnlmepbapplypillarpkgconfigR6RColorBrewerRcppRcppEigenrlangscalessurvivaltibbletransportutf8vctrsviridisLitewithr

Analyzing plant disease epidemics with the R package epiphy

Christophe Gigot

Rendered fromepiphy.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2018-05-20
Started: 2018-05-12

Definitions and relationships between parameters

Christophe Gigot

Rendered fromdefs-and-eqns.Rmdusingknitr::rmarkdownon Aug 28 2024.

Last update: 2018-05-12
Started: 2018-02-08

Readme and manuals

Help Manual

Help pageTopics
Easily switch between different power law formulations.a2a a2a.list a2a.numeric
Several aggregation indices.agg_index
Counts of aphids.aphids
Counts of arthropods.arthropods
Coerce to a data frame.as.data.frame.intensity
The beta-binomial distribution.BetaBinomial dbetabinom pbetabinom qbetabinom rbetabinom
C(alpha) test.calpha.test calpha.test.fisher
Chi-squared test.chisq.test chisq.test.default chisq.test.fisher
Incidence of citrus tristeza virus (CTV) disease in three fields.citrus_ctv
Regroup observational data into even clumps of individuals.clump clump.intensity
Count of codling moth larvae.codling_moths
Incidence of dogwood anthracnose.dogwood_anthracnose
Maximum likelihood fitting of two distributions and goodness-of-fit comparison.fit_two_distr fit_two_distr.count fit_two_distr.default fit_two_distr.incidence
Incidence of three viruses in an Australian hop garden.hop_viruses
Construct count, incidence and severity objects.count count_data incidence incidence_data intensity severity severity_data
Test if an object is of class 'intensity' or one of its subclasses.is.count is.incidence is.intensity is.severity
Some link functions.cloglog link logit probit
Map Comparison procedure.mapcomp mapcomp.count mapcomp.data.frame mapcomp.incidence mapcomp.matrix
Existing variable mappings.mapped_var mapped_var<-
Construct data mappings.mapping mapping_ remap
Offspring survival of rats experiencing different diets.offspring_survival
Incidence of bacterial blight of onion.onion_bacterial_blight
Taylor's and binary power laws.power_law
Incidence of ray blight disease of pyrethrum.pyrethrum_ray_blight
Spatial Analysis by Distance IndicEs (SADIE).sadie sadie.count sadie.data.frame sadie.incidence sadie.matrix
Examples of simulated epidemic data.simulated_epidemics
Spatial hierarchy analysis.spatial_hier
Divide into groups and reassemble.split.intensity
To go to higher level in the hierarchy.threshold
Incidence of tobacco plants infected with viruses.tobacco_viruses
Incidence of tomato spotted wilt virus (TSWV) disease in field trials.tomato_tswv
Z-test.z.test z.test.default z.test.fisher