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# #' Compute functions of matrices from samples of a stanfit object
# #'
# #' @param stanfit object of class stanfit.
# #' @param object name of stan sub object from stanfit to use for calculations.
# #' @param objectindices matrix of indices, with the number of columns matching
# #' the number of dimensions of the object. 'all' computes \code{which( array(1,objdims)==1,arr.ind=TRUE)},
# #' where objdims is what would be returned by dim(object) if the object existed in the R environment.
# #' @param calc string containing R calculation to evaluate, with the string 'object' in place of the actual object name.
# #' @param summary if FALSE, a iterations * parameters matrix is returned, if TRUE,
# #' rstan::monitor is first run on the output.
# #'
# #' @return matrix of values of the specified interactions at each iteration.
# stan_postcalc <-function(stanfit,object,calc='object', objectindices='all', summary=TRUE){
# mc=As.mcmc.list(stanfit)
# m=do.call(rbind,mc)
# outdims = dim(stanfit@inits[[1]][[object]]) #complete
# if(objectindices=='all') objectindices <- which( array(1,outdims)==1,arr.ind=TRUE) else {
# if(ncol(as.matrix(objectindices))!= length(outdims)) stop('Number of columns of object indices must match number of dimensions in object')
# }
# objectindices = objectindices[,outdims!=1] #subset
# outdims = outdims[outdims!=1] #subset
#
# out=array(apply(m,1,function(x) {
# object = array(array(relist(x,skeleton = stanfit@inits[[1]])[[object]],dim=outdims)[objectindices],outdims)
# ret = eval(parse(text=calc))
# } ),dim = c(outdims,nrow(m)) )
#
# if(summary) {
# parnames <- array(1,dim=outdims)
# parnames <- which(parnames==1,arr.ind = TRUE)
# parnames <- apply(parnames,1,function(x) paste0(x, collapse=', '))
# parnames <- paste0(object,'[',parnames,']')
# out <- array(out,dim=c(prod(outdims), nrow(mc[[1]]), length(mc)))
#
# out <- aperm(out,c(2,3,1))
# dimnames(out)[[3]] <- parnames
# out <- monitor(out,warmup=0,digits_summary = 2)
# }
#
# return(out)
# }
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