Function reference • epiphy

Data sets

aphids: Counts of aphids.

arthropods: Counts of arthropods.

citrus_ctv: Incidence of citrus tristeza virus (CTV) disease in three fields.

codling_moths: Count of codling moth larvae.

dogwood_anthracnose: Incidence of dogwood anthracnose.

hop_viruses: Incidence of three viruses in an Australian hop garden.

offspring_survival: Offspring survival of rats experiencing different diets.

onion_bacterial_blight: Incidence of bacterial blight of onion.

pyrethrum_ray_blight: Incidence of ray blight disease of pyrethrum.

simulated_epidemics: Examples of simulated epidemic data.

tobacco_viruses: Incidence of tobacco plants infected with viruses.

tomato_tswv: Incidence of tomato spotted wilt virus (TSWV) disease in field trials.

Disease intensity objects

Create and manipulate disease intensity objects (i.e., count, incidence and severity objects).

as.data.frame(<intensity>): Coerce to a data frame.

clump(): Regroup observational data into even clumps of individuals.

count() incidence() severity(): Construct count, incidence and severity objects.

is.intensity() is.count() is.incidence() is.severity(): Test if an object is of class intensity or one of its subclasses.

mapped_var() `mapped_var<-`(): Existing variable mappings.

mapping() mapping_() remap(): Construct data mappings.

split(<intensity>): Divide into groups and reassemble.

Statistical methods

agg_index(): Several aggregation indices.

calpha.test(): C(alpha) test.

chisq.test(): Chi-squared test.

fit_two_distr(): Maximum likelihood fitting of two distributions and goodness-of-fit comparison.

mapcomp(): Map Comparison procedure.

power_law(): Taylor's and binary power laws.

sadie(): Spatial Analysis by Distance IndicEs (SADIE).

spatial_hier(): Spatial hierarchy analysis.

z.test(): Z-test.

Miscellaneous

Mainly helper functions.

a2a(): Easily switch between different power law formulations.

dbetabinom() pbetabinom() qbetabinom() rbetabinom(): The beta-binomial distribution.

logit() probit() cloglog(): Some link functions.

threshold(): To go to higher level in the hierarchy.