Analysis of Plant Disease Epidemics

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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.