R: Solve the EBNM problem using normal priors

ebnm_normal {ebnm}

R Documentation

Solve the EBNM problem using normal priors

Description

Solves the empirical Bayes normal means (EBNM) problem using the family of normal distributions. Identical to function ebnm with argument prior_family = "normal". For details about the model, see ebnm.

Usage

ebnm_normal(
  x,
  s = 1,
  mode = 0,
  scale = "estimate",
  g_init = NULL,
  fix_g = FALSE,
  output = ebnm_output_default(),
  optmethod = NULL,
  control = NULL
)

Arguments

`x`	A vector of observations. Missing observations (`NA`s) are not allowed.
`s`	A vector of standard errors (or a scalar if all are equal). Standard errors may not be exactly zero, and missing standard errors are not allowed.
`mode`	A scalar specifying the mode of the prior `g` or `"estimate"` if the mode is to be estimated from the data.
`scale`	A scalar specifying the standard deviation of the normal prior or `"estimate"` if the standard deviation is to be estimated from the data.
`g_init`	The prior distribution `g`. Usually this is left unspecified (`NULL`) and estimated from the data. However, it can be used in conjuction with `fix_g = TRUE` to fix the prior (useful, for example, to do computations with the "true" `g` in simulations). If `g_init` is specified but `fix_g = FALSE`, `g_init` specifies the initial value of `g` used during optimization. When supplied, `g_init` should be an object of class `normalmix` or an `ebnm` object in which the fitted prior is an object of class `normalmix`.
`fix_g`	If `TRUE`, fix the prior `g` at `g_init` instead of estimating it.
`output`	A character vector indicating which values are to be returned. Function `ebnm_output_default()` provides the default return values, while `ebnm_output_all()` lists all possible return values. See Value below.
`optmethod`	A string specifying which optimization function is to be used. Options include `"nlm"`, `"lbfgsb"` (which calls `optim` with `method = "L-BFGS-B"`), and `"trust"` (which calls into package `trust`). Other options are `"nohess_nlm"`, `"nograd_nlm"`, and `"nograd_lbfgsb"`, which use numerical approximations rather than exact expressions for the Hessian and (for the latter two) the gradient. The default option is `"nohess_nlm"`.
`control`	A list of control parameters to be passed to the optimization function specified by parameter `optmethod`.

Value

An ebnm object. Depending on the argument to output, the object is a list containing elements:

data: A data frame containing the observations x and standard errors s.
posterior: A data frame of summary results (posterior means, standard deviations, second moments, and local false sign rates).
fitted_g: The fitted prior \hat{g}.
log_likelihood: The optimal log likelihood attained, L(\hat{g}).
posterior_sampler: A function that can be used to produce samples from the posterior. The sampler takes a single parameter nsamp, the number of posterior samples to return per observation.

S3 methods coef, confint, fitted, logLik, nobs, plot, predict, print, quantile, residuals, simulate, summary, and vcov have been implemented for ebnm objects. For details, see the respective help pages, linked below under See Also.