R/randeff.R

In ngme2: Linear Latent Non-Gaussian Models with Flexible Distributions

# #' Build random effect structure
# #' @param formula formula
# #' @param data data
# #' @param family distribution of random effect
# #' @return a list of random effect structure
# #' @export
# randeff <- function(
#   map,
#   data,
#   effect_type,
#   name,
#   # replicate,
#   theta_K=NULL,
#   n_repl=NULL, # number of replicates
#   ...
# ) {
#   stopifnot("Please specify random effect type, using effect_type=...,
#     check ngme_randeff_types()" = inherits(effect_type, "ngme_noise") || effect_type %in% ngme_randeff_types())

#   # Design Matrix and Covariance matrix
#   B_reff <- map
#   n_reff <- ncol(B_reff)
#   n_cov_params <- sum(1:n_reff)
#   if (is.null(theta_K)) theta_K <- rep(0, n_cov_params)
#   stopifnot(length(theta_K) == n_cov_params)

#   if (is.character(effect_type)) {
#     mix_var <- if (effect_type=="normal") noise_normal() else noise_nig()
#   } else {
#     mix_var <- effect_type
#   }
#   mix_var <- update_noise(mix_var, n=n_reff)
#   mix_var$single_V = TRUE
#   mix_var$fix_theta_sigma = TRUE
#   mix_var$hessian = FALSE
#   # mix_var$B_mu <- matrix(rep(1, length(B_reff), ncol=n_reff))
#   # mix_var$theta_mu <- rep(0, n_reff)

#   args <- within(list(...), {
#     model        = "re"
#     map          = B_reff
#     A            = ngme_as_sparse(B_reff)
#     n_map        = length_map(map)
#     noise        = mix_var
#     W_size       = n_reff
#     V_size       = n_reff
#     theta_K      = theta_K
#     n_cov_params = n_cov_params
#     n_repl       = n_repl
#     # n_params     = n_cov_params + 1 + 1 #n_reff + 1 #sigma mu nu
#     name         = name
#   })
#   do.call(ngme_model, args)
# }

# #' Print ngme random effect
# #'
# #' @param x random effect object
# #' @param padding number of white space padding in front
# #' @param ... ...
# #'
# #' @return radom effect model
# #' @export
# print.randeff <- function(x, padding = 0, ...) {
#   reff <- x
#   pad_space <- paste(rep(" ", padding), collapse = "")
#   pad_add4_space <- paste(rep(" ", padding + 4), collapse = "")

#   if (is.null(reff)) {
#     cat(pad_space); cat("Effect type - "); cat("NULL"); cat("\n")
#   } else {
#     cat(pad_space); cat("Effect type - "); cat(reff$effect_type); cat("\n")

#     cat(pad_space); cat("Effect formula: ");
#     cat(paste(as.character(reff$formula))); cat("\n")

#     cat(pad_space); cat("Effect covariance: \n")
#     cat(pad_space); print(reff$Sigma)
#   }
#   cat("\n")
#   invisible(reff)
# }