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#' 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)
}
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