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)
#> 
#> Call:
#> bbdml(formula = cbind(W, M - W) ~ DayAmdmt, phi.formula = ~DayAmdmt, 
#>     data = soil_phylum_small_otu1)
#> 
#> 
#> Coefficients associated with abundance:
#>             Estimate Std. Error t value Pr(>|t|)    
#> (Intercept) -0.44595    0.03604 -12.375 7.18e-13 ***
#> DayAmdmt21  -0.16791    0.04067  -4.129 0.000297 ***
#> ---
#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
#> 
#> 
#> Coefficients associated with dispersion:
#>             Estimate Std. Error t value Pr(>|t|)    
#> (Intercept)  -5.3077     0.3537 -15.008 6.44e-15 ***
#> DayAmdmt21   -1.3518     0.5029  -2.688    0.012 *  
#> ---
#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
#> 
#> 
#> Log-likelihood: -286.53

# phyloseq example (only run this if you have phyloseq installed)
if (FALSE) { # \dontrun{
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)
} # }