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###Function to get model fit diagnostics given a spCP object
#'
#' diagnostics
#'
#' Calculates diagnostic metrics using output from the \code{\link{spCP}} model.
#'
#' @param obj A \code{\link{spCP}} model object for which diagnostics
#' are desired from.
#'
#' @param diags A vector of character strings indicating the diagnostics to compute.
#' Options include: Deviance Information Criterion ("dic"), d-infinity ("dinf") and
#' Watanabe-Akaike information criterion ("waic"). At least one option must be included.
#' Note: The probit model cannot compute the DIC or WAIC diagnostics due to computational
#' issues with computing the multivariate normal CDF.
#'
#' @param keepDeviance A logical indicating whether the posterior deviance distribution
#' is returned (default = FALSE).
#'
#' @param keepPPD A logical indicating whether the posterior predictive distribution
#' at each observed location is returned (default = FALSE).
#'
#' @details To assess model fit, DIC, d-infinity and WAIC are used. DIC is based on the
#' deviance statistic and penalizes for the complexity of a model with an effective
#' number of parameters estimate pD (Spiegelhalter et al 2002). The d-infinity posterior
#' predictive measure is an alternative diagnostic tool to DIC, where d-infinity=P+G.
#' The G term decreases as goodness of fit increases, and P, the penalty term, inflates
#' as the model becomes over-fit, so small values of both of these terms and, thus, small
#' values of d-infinity are desirable (Gelfand and Ghosh 1998). WAIC is invariant to
#' parametrization and is asymptotically equal to Bayesian cross-validation
#' (Watanabe 2010). WAIC = -2 * (lppd - p_waic_2). Where lppd is the log pointwise
#' predictive density and p_waic_2 is the estimated effective number of parameters
#' based on the variance estimator from Vehtari et al. 2016. (p_waic_1 is the mean
#' estimator).
#'
#' @return \code{diagnostics} returns a list containing the diagnostics requested and
#' possibly the deviance and/or posterior predictive distribution objects.
#'
#' @author Samuel I. Berchuck
#'
#' @references Gelfand, A. E., & Ghosh, S. K. (1998). Model choice: a minimum posterior predictive loss approach. Biometrika, 1-11.
#' @references Spiegelhalter, D. J., Best, N. G., Carlin, B. P., & Van Der Linde, A. (2002). Bayesian measures of model complexity and fit. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 64(4), 583-639.
#' @references Vehtari, A., Gelman, A., & Gabry, J. (2016). Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC. Statistics and Computing, 1-20.
#' @references Watanabe, S. (2010). Asymptotic equivalence of Bayes cross validation and widely applicable information criterion in singular learning theory. Journal of Machine Learning Research, 11(Dec), 3571-3594.
#'
#' @export
diagnostics <- function(obj, diags = c("dic", "dinf", "waic"), keepDeviance = FALSE, keepPPD = FALSE) {
###Check Inputs
if (!is.spCP(obj)) stop('"obj" must be of class "spCP"')
if (missing(obj)) stop('"obj" is missing')
if (sum((!diags %in% c("dic", "dinf", "waic"))) > 0) stop('"diags" must contain at least one of "dic", "dinf" or "waic"')
if (!is.logical(keepDeviance)) stop('"keepDeviance" must be a logical')
if (!is.logical(keepPPD)) stop('"keepPPD" must be a logical')
###Unload STBDwDM objects
DatObj <- obj$datobj
DatAug <- obj$dataug
###Set seed for reproducibility
set.seed(54)
###Set data objects
OneM <- DatObj$OneM
tNu <- DatObj$tNu
t1 <- DatObj$t1
XThetaInd <- DatObj$XThetaInd
TimeVec <- DatObj$TimeVec
OneNu <- DatObj$OneNu
OneN <- DatObj$OneN
N <- DatObj$N
M <- DatObj$M
YObserved <- DatObj$YObserved
###Construct parameter object
Para <- list()
Para$Beta0 <- obj$beta0
Para$Beta1 <- obj$beta1
Para$Lambda0 <- obj$lambda0
Para$Lambda1 <- obj$lambda1
Para$Eta <- obj$eta
Beta0Mean <- apply(Para$Beta0, 2, median)
Beta1Mean <- apply(Para$Beta1, 2, median)
BetaMean <- matrix(rbind(Beta0Mean, Beta1Mean), ncol = 1)
Lambda0Mean <- apply(Para$Lambda0, 2, median)
Lambda1Mean <- apply(Para$Lambda1, 2, median)
LambdaMean <- matrix(rbind(Lambda0Mean, Lambda1Mean), ncol = 1)
EtaMean <- apply(Para$Eta, 2, median)
ThetaMean <- pmax(pmin(tNu * OneM, EtaMean), t1 * OneM)
XThetaMean = GetXTheta(ThetaMean, XThetaInd, TimeVec, OneNu, OneN, tNu, N, M)
MuMean = XThetaMean %*% BetaMean;
Sigma2Mean = exp(2 * (XThetaMean %*% LambdaMean));
Para$MuMean <- MuMean
Para$Sigma2Mean <- Sigma2Mean
###Set mcmc object
NKeep <- dim(obj$delta)[1]
###Compute Log-likelihood using Rcpp function GetLogLik
LogLik <- NULL
if (("dic" %in% diags) | ("waic" %in% diags)) {
###Compute log-likelihood
requireNamespace("mvtnorm", quietly = TRUE) #Requred for pmvnorm in Rcpp function
LogLik <- GetLogLik(DatObj, Para, NKeep)
}
###Compute DIC diagnostics
dic <- NULL
if ("dic" %in% diags) {
###Compute mean log-likelihood
LogLikMean <- GetLogLikMean(DatObj, Para)
###Calculate DIC objects
DBar <- -2 * mean(LogLik)
DHat <- -2 * LogLikMean
pD <- DBar - DHat
DIC <- DBar + pD
dic <- list(dic = DIC, pd = pD)
}
###Compute PPD diagnostics
ppd <- PPD <- NULL
if ("dinf" %in% diags) {
###Get PPD
PPD <- SamplePPD(DatObj, Para, NKeep)
###Compute PPD Diagnostics
PPDMean <- apply(PPD, 1, mean)
PPDVar <- apply(PPD, 1, var)
P <- sum(PPDVar)
G <- sum( (PPDMean - YObserved) ^ 2)
DInf <- G + P
ppd <- list(p = P, g = G, dinf = DInf)
}
###Compute WAIC diagnostics
waic <- NULL
if ("waic" %in% diags) {
###Get WAIC
# The calculation of Waic! Returns lppd, p_waic_1, p_waic_2, and waic, which we define
# as 2*(lppd - p_waic_2), as recommmended in BDA
lppd <- log( apply(exp(LogLik), 2, mean) )
p_waic_1 <- 2 * (lppd - apply(LogLik, 2, mean) )
p_waic_2 <- apply(LogLik, 2, var)
waic <- -2 * lppd + 2 * p_waic_2
waic <- list(waic = waic, p_waic = p_waic_2, lppd = lppd, p_waic_1 = p_waic_1)
}
###Output diagnostics
if (!keepDeviance & !keepPPD) diags <- list(dic = dic, dinf = ppd, waic = waic)
if (!keepDeviance & keepPPD) diags <- list(dic = dic, dinf = ppd, waic = waic, PPD = t(PPD))
if (keepDeviance & !keepPPD) diags <- list(dic = dic, dinf = ppd, waic = waic, deviance = -2 * LogLik)
if (keepDeviance & keepPPD) diags <- list(dic = dic, dinf = ppd, waic = waic, deviance = -2 * LogLik, PPD = t(PPD))
return(diags)
}
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