R/lopodSummary.R

In bayesLopod: Bayesian Inference of Landscape Occupancy from Presence-Only Data

#' Summary statistics for a LopodModel
#'
#' @param LopodModel A LopodModel object
#' @param params Parameters to be plotted. Default is NULL, which plots all global parameters
#' @param probs Quantiles to be estimated
#' @return  Returns a dataframe which contain summaries for  all chains merged for the Global Parameters of a LopodModel. Included in the summary are quantiles, means, standard deviations (sd), effective sample sizes (n_eff), Monte Carlo standard errors (se_mean) and Rhats.
#' @export
#' @examples
#'
#'  \dontrun{
#' data("simSpRecords", package = "bayesLopod")
#' data("simSpSamplingEffort", package = "bayesLopod")
#' simSpRasters = xyToRaster(xyRecords = simSpRecords,xySamplingEffort = simSpSamplingEffort,
#' basemap = NULL, nrows = 50, extentExpansion = 0)
#' ld_Raster_adMatrix = rasterLopodData(rasterN = simSpRasters[["samplingEffort"]],
#' rasterY = simSpRasters[["spDetections"]], Adjacency = TRUE )
#' mLopodRaster = modelLopod(LopodData = ld_Raster_adMatrix, varP = TRUE, q = NULL,
#' pmin = 0.1, CAR = FALSE, nChains = 4,warmup = 500,sampling = 100,nCores = 4)
#' lopodSummary(mLopodRaster, params = c("psi","p","q"))
#'
#' data("Andropogon_shape", package = "bayesLopod")
#' ld_Shape = shapeLopodData(Shapefile = Andropogon_shape, fieldN = "sampEffort",
#' fieldY = "detections",  Adjacency = TRUE, keepFields = FALSE)
#' mLopodShape = modelLopod(LopodData = ld_Shape, varP = TRUE, q = NULL,
#' pmin = 0, CAR = TRUE, nChains = 4,warmup = 500,sampling = 100,nCores =4)
#' lopodSummary(mLopodRaster)
#' }



lopodSummary =  function(LopodModel, params=NULL,  probs = c(0.05, 0.50, 0.95)){

  #Summary for all global parameters is return if params is NULL

  if(class(LopodModel) != "LopodModel") stop("Object needs to be a LopdModel")

  modelPar = modelParams(LopodModel)
  sumPars = modelPar$globalPars

  if(is.null(params)==F){
    if(sum(params %in% sumPars)!=length(params)){
      stop(paste("For this model only the summary of the following global parameters can be returned:",toString(sumPars)))
    }else{
      sumPars = params
    }

  }


  return(rstan::summary(LopodModel@StanFit, pars=sumPars, probs=probs, use_cache=FALSE)$summary)

}