Analysis of Plant Disease Epidemics


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Documentation for package ‘epiphy’ version 0.3.4

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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.