#' Produce a summary of the results of fitting a SEIR model
#' @param object a \code{\link{SpatialSEIRModel}} object
#' @param \dots not used
#' @return a summary.SpatialSEIRModel object
#' @export
summary.SpatialSEIRModel = function(object, ...)
{
nLoc = ncol(object$modelComponents$data_model$Y)
nTpt = nrow(object$modelComponents$data_model$Y)
nLags = length(object$modelComponents$distance_model$laggedDistanceList[[1]])
transitionMode = object$modelComponents$transition_priors$mode
hasSpatial = (object$modelComponents$exposure_model$nLoc > 1)
hasReinfection =
(object$modelComponents$reinfection_model$integerMode != 3)
hasReportFraction = object$modelComponents$data_model$type == "fractional"
qtiles = t(apply(object$param.samples, 2, quantile,
probs = c(0.025, 0.975)))
means = apply(object$param.samples, 2, mean)
sds = apply(object$param.samples, 2, sd)
outMatrix = cbind(means, sds, qtiles)
rownames(outMatrix) = colnames(object$param.samples)
colnames(outMatrix) = c("Mean", "SD", "95% LB", "95% UB")
structure(list(modelComponents=object$modelComponents,
parameterEstimates=outMatrix,
nLoc = nLoc,
nTpt = nTpt,
exposureParams = ncol(object$modelComponents$exposure_model$X),
reinfectionParams = Ifelse(hasReinfection,
ncol(object$modelComponents$reinfection_model$X_prs),
0),
spatialParams = Ifelse(hasSpatial,
length(object$modelComponents$distance_model$distanceList) + nLags,
0),
transitionParams = Ifelse(transitionMode == "exponential", 2,
Ifelse(transitionMode == "weibull", 4, 0)),
dataModelParams = Ifelse(hasReportFraction, 1, 0)
), class = "summary.SpatialSEIRModel")
}
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