R/gamma.R

In ssdtools: Species Sensitivity Distributions

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#' @describeIn ssd_p Cumulative Distribution Function for Gamma Distribution
#' @export
#' @examples
#' 
#' ssd_pgamma(1)
ssd_pgamma <- function(q, shape = 1, scale = 1, lower.tail = TRUE, log.p = FALSE) {
  pdist("gamma", q = q, shape = shape, scale = scale, 
             lower.tail = lower.tail, log.p = log.p)
}

#' @describeIn ssd_q Quantile Function for Gamma Distribution
#' @export
#' @examples
#' 
#' ssd_qgamma(0.5)
ssd_qgamma <- function(p, shape = 1, scale = 1, lower.tail = TRUE, log.p = FALSE) {
  qdist("gamma", p = p, shape = shape, scale = scale, 
        lower.tail = lower.tail, log.p = log.p)
}

#' @describeIn ssd_r Random Generation for Gamma Distribution
#' @export
#' @examples
#' 
#' set.seed(50)
#' hist(ssd_rgamma(10000), breaks = 1000)
ssd_rgamma <- function(n, shape = 1, scale = 1, chk = TRUE) {
  rdist("gamma", n = n, shape = shape, scale = scale, chk = chk)
}

sgamma <- function(data, pars = NULL) {
  if(!is.null(pars)) return(pars)
  x <- mean_weighted_values(data)
  
  var <- var(x, na.rm = TRUE)
  mean <- mean(x, na.rm = TRUE)
  list(
    log_scale = log(var / mean),
    log_shape = log(mean^2 / var)
  )
}

pgamma_ssd <- function(q, shape, scale) {
  if(shape <= 0 || scale <= 0) return(NaN)
  stats::pgamma(q, shape = shape, scale = scale)
}

qgamma_ssd <- function(p, shape, scale) {
  if(shape <= 0 || scale <= 0) return(NaN)
  stats::qgamma(p, shape = shape, scale = scale)
}

rgamma_ssd <- function(n, shape, scale) {
  if(shape <= 0 || scale <= 0) return(rep(NaN, n))
  stats::rgamma(n, shape = shape, scale = scale)
}