# Analysis of Plant Disease Epidemics

## Documentation for package ‘epiphy’ version 0.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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