R/Beta.R

In spaMM: Mixed-Effect Models, with or without Spatial Random Effects

Beta <- function(link="logit"){
  linktemp <- substitute(link)
  if (!is.character(linktemp)) {
    linktemp <- deparse(linktemp)          
    if (linktemp == "link") {
      warning("use of beta(link=link) is deprecated\n",
              domain = NA)
      linktemp <- eval(link)
      if (!is.character(linktemp) || length(linktemp) != 1)
        stop("'link' is invalid", domain = NA)
    }
  }
  okLinks <- c("logit","probit","cloglog","log", "identity")
  if (linktemp %in% okLinks)
    stats <- make.link(linktemp)
  else if (is.character(link))
    stats <- make.link(link)
  else {
    if (inherits(link, "link-glm")) {
      stats <- link
      if (!is.null(stats$name))
        linktemp <- stats$name
    } else {
      stop(gettextf("link \"%s\" not available for beta family; available links are %s",
                    linktemp, paste(sQuote(okLinks), collapse = ", ")), domain = NA)
    }
  }
  variance <- function(arg1) return(arg1*(1-arg1))
  dev.resids <- function(y, mu, wt) {
    dev <- 2 * wt * (y*log( y/mu) +(1-y)*log((1-y)/(1-mu)))
    return(pmax(dev,0)) ## resids(1/2,1/2,1) might be slightly negative...
  }
  parent.env(environment(variance)) <- environment(stats::Gamma) ## explanations in spaMM_Gamma() source
  structure(list(family = "Beta", link = linktemp, linkfun = stats$linkfun,
                 linkinv = stats$linkinv, variance = variance, dev.resids = dev.resids, mu.eta = stats$mu.eta),
            class = "family")
}