bbdml: Maximum Likelihood for the Beta-binomial Distribution

In corncob: Count Regression for Correlated Observations with the Beta-Binomial

Maximum Likelihood for the Beta-binomial Distribution

Description

Maximum Likelihood for the Beta-binomial Distribution

Usage

bbdml(
  formula,
  phi.formula,
  data,
  link = "logit",
  phi.link = "logit",
  method = "trust",
  control = list(maxit = 1000, reltol = 1e-14),
  numerical = FALSE,
  nstart = 1,
  inits = NULL,
  allow_noninteger = FALSE,
  robust = FALSE,
  ...
)

Arguments

formula	an object of class formula: a symbolic description of the model to be fitted to the abundance
phi.formula	an object of class formula without the response: a symbolic description of the model to be fitted to the dispersion
data	a data frame or phyloseq object containing the variables in the models
link	link function for abundance covariates, defaults to "logit"
phi.link	link function for dispersion covariates, defaults to "logit"
method	optimization method, defaults to "trust", or see optimr for other options
control	optimization control parameters (see optimr)
numerical	Boolean. Defaults to FALSE. Indicator of whether to use the numeric Hessian (not recommended).
nstart	Integer. Defaults to 1. Number of starts for optimization.
inits	Optional initializations as rows of a matrix. Defaults to NULL.
allow_noninteger	Boolean. Defaults to FALSE. Should noninteger W's and M's be allowed? This behavior was not permitted prior to v4.1, needs to be explicitly allowed.
robust	Should robust standard errors be returned? If not, model-based standard arras are used. Logical, defaults to FALSE.
...	Optional additional arguments for optimr or trust

Value

An object of class bbdml.

Examples

# data frame example
data(soil_phylum_small_otu1)
bbdml(formula = cbind(W, M - W) ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = soil_phylum_small_otu1)

# phyloseq example (only run this if you have phyloseq installed)
## Not run: 
data(soil_phylum_small_sample)
data(soil_phylum_small_otu)
data_phylo <- phyloseq::phyloseq(phyloseq::sample_data(soil_phylum_small_sample),
phyloseq::otu_table(soil_phylum_small_otu, taxa_are_rows = TRUE))
bbdml(formula = Proteobacteria ~ DayAmdmt,
phi.formula = ~ DayAmdmt,
data = data_phylo)

## End(Not run)

corncob documentation built on May 29, 2024, 7:15 a.m.