Nothing
#' \code{buildScoreCache.mle} and \code{buildScoreCache.bayes} are internal functions called by \code{buildScoreCache}.
#'
#' @describeIn buildScoreCache Fit a given DAG to data with method="bayes".
#' @param force.method "notset", "INLA" or "C". This is specified in \code{\link{buildScoreCache}(control=list(max.mode.error=...))}.
#' @param mylist result returned from \code{\link{check.valid.data}}.
#' @param grouped.vars result returned from \code{\link{check.valid.groups}}.
#' @param group.ids result returned from \code{\link{check.valid.groups}}.
#' @importFrom stats sd
#' @family Bayes
buildScoreCache.bayes <-
function(data.df = NULL,
data.dists = NULL,
group.var = NULL,
cor.vars = NULL,
dag.banned = NULL,
dag.retained = NULL,
max.parents = NULL,
which.nodes = NULL,
defn.res = NULL,
dry.run = FALSE,
centre = TRUE,
force.method = NULL,
mylist = NULL,
grouped.vars = NULL,
group.ids = NULL,
control = build.control(method = "bayes"),
verbose = FALSE,
debugging = FALSE) {
# Multinomial nodes not yet implemented for method "bayes"
if (any(unlist(data.dists, use.names = F) == "multinomial")) {
stop("Multinomial nodes are not yet implemented for method 'bayes'. Try with method='mle'.") # Specifically, in file fit_single_node.c, there is no case for multinomial distribution.
}
set.seed(control[["seed"]])
data.df.original <- data.df
n <- length(data.dists)
## coerce binary factors to become 0/1 integers - the 0 is based on the first entry in levels()
if (!is.null(mylist$bin)) {
## have at least one binary variable
for (i in mylist$bin) {
data.df[, i] <- as.numeric(data.df[, i]) - 1
}
}
## standardize gaussian variables to zero mean and sd=1
if (centre &&
!is.null(mylist$gaus)) {
## have at least one gaussian variable
for (i in mylist$gaus) {
data.df[, i] <- (data.df[, i] - mean(data.df[, i])) / sd(data.df[, i])
}
}
## coerce all data points to doubles
## coerce ALL cols to double equivalents
for (i in 1:dim(data.df)[2]) {
data.df[, i] <- as.double(data.df[, i])
}
## get distributions in terms of a numeric code
var.types <- get.var.types(data.dists)
########################################################################################
## All checking over
## get to here we have suitable data/variables and now generate all the parent combinations
########################################################################################
## down to here we have all the data correct and now call C buildnodecache() to create all the node definitions.
if (is.null(defn.res)) {
## pass to C the number (number_of_nodes,banned_arc_as_vector, retain_arcs_as_vector, max_parents_as_vector
res <- .Call("buildcachematrix",
dim(dag.banned)[1],
as.integer(dag.banned),
as.integer(dag.retained),
as.integer(max.parents),
which.nodes,
PACKAGE = "abn"
)
# extract the results from the list
children <- res[[1]] # this is a vector of node numbers for each node and its parent combinations
node.defn <- matrix(data = res[[2]],
byrow = TRUE,
ncol = dim(data.df)[2],
dimnames = list(NULL, names(data.df))) # this is a matrix of 0/1 for each node and its parent combinations.
rm(res)
} else {
## some check since user has supplied defn.res
if (!is.list(defn.res)) {
stop("'defn.res' must be a list")
}
if (length(defn.res) != 2) {
stop("'defn.res' must have two entries")
}
if (!(is.vector(defn.res[[1]]) &&
is.matrix(defn.res[[2]]))) {
stop("'defn.res' is wrong format")
}
if (!(max(defn.res[[2]]) == 1 &&
min(defn.res[[2]]) == 0)) {
stop("'defn.res' is wrong format - must only be 0,1 in node definitions")
}
# extract the results from the list
children <- defn.res[["children"]]
node.defn <- defn.res[["node.defn"]]
}
# dry run - don't do any computation just return the node definitions
if(dry.run){
if (verbose) cat("No computation - returning only the node combinations\n")
return(list(children=children,node.defn=node.defn))
}
dag.m <- matrix(rep(NA,dim(data.df)[2]^2),ncol=dim(data.df)[2])
colnames(dag.m) <- rownames(dag.m) <- names(data.df)
###########################################################
## Iterate over each node in the DAG separately
### loop through each node and find out what kind of model is to be fitted and then pass to appropriate
### separate call for each individual node-parentcombination
###########################################################
out <- list()
rows <- length(children) # number of child-parent combinations
if (verbose) cat("Start estimation loop.")
if (debugging){
# store each child-parent combination in a separate row
res <- matrix(NA,
nrow = rows,
ncol = 5,
dimnames = list(NULL, c("childParentCombNo", "mlik", "error.code", "hessian.accuracy", "used.INLA")))
for (i in 1:rows) {
res[i, ] <- forLoopContentBayes(row.no = i,
children = children,
node.defn = node.defn,
dag.m = dag.m,
force.method = force.method,
data.df = data.df,
data.dists = data.dists,
var.types = var.types,
control = control,
grouped.vars = grouped.vars,
group.ids = group.ids,
verbose = verbose)
}
} else {
# no debugging
# Prepare multithreading
ncores <- control[["ncores"]]
if (ncores > 1){
if (verbose){
path <- path.expand(paste0(getwd(), "/build_score_cache_bayes.out"))
message(paste("Writing output to", path))
if(file.exists(path)){
file.remove(path)
message(paste("File exists and will be overwritten:", path))
}
cl <- makeCluster(ncores,
type = control[["cluster.type"]],
rscript_args = "--no-environ", # only available for "FORK"
outfile = path)
} else {
# no redirection of output
cl <- makeCluster(ncores,
type = control[["cluster.type"]],
rscript_args = "--no-environ") # only available for "FORK"
}
registerDoParallel(cl)
res <- foreach(i = 1:rows,
.combine = "rbind",
.packages = c("INLA"),
.export = "forLoopContentBayes",
.verbose = verbose) %dopar% {
forLoopContentBayes(row.no = i,
children = children,
node.defn = node.defn,
dag.m = dag.m,
force.method = force.method,
data.df = data.df,
data.dists = data.dists,
var.types = var.types,
control = control,
grouped.vars = grouped.vars,
group.ids = group.ids,
verbose = verbose)
}
# clean up multi-threading
stopCluster(cl)
} else {
res <- foreach(i = 1:rows,
.combine = "rbind",
.packages = c("INLA"),
.export = "forLoopContentBayes",
.verbose = verbose) %do% {
forLoopContentBayes(row.no = i,
children = children,
node.defn = node.defn,
dag.m = dag.m,
force.method = force.method,
data.df = data.df,
data.dists = data.dists,
var.types = var.types,
control = control,
grouped.vars = grouped.vars,
group.ids = group.ids,
verbose = verbose)
}
}
}
if (verbose) cat("################# End of cache building ################### \n")
# sort the results by child-parent combination number
res <- res[order(res[, 1]), ] # important to match later on with the node.defn and children vectors (especially if processed in parallel)
out$children <- children
out$node.defn <- node.defn
# store the results in a list
# out$childParentCombNo <- res[, 1] # no need to store this. Just for reference.
out$mlik <- as.numeric(res[, 2])
out$error.code <- as.numeric(res[, 3])
out$hessian.accuracy <- as.numeric(res[, 4])
out$used.INLA <- as.logical(res[, 5])
# add error code descriptions
out$error.code.desc <- as.character(out$error.code)
out$error.code.desc[out$error.code.desc == 0] <- "success"
out$error.code.desc[out$error.code.desc == 1] <- "warning: mode results may be unreliable (optimiser terminated unusually)"
out$error.code.desc[out$error.code.desc == 2] <- "error - logscore is NA. Model could not be fitted"
# there is no error code 3!
out$error.code.desc[out$error.code.desc == 4] <- "warning: fin.diff hessian estimation terminated unusually"
# Finalise the results
out$data.df <- data.df.original
out$data.dists <- data.dists # used in searchHeuristic() and mostProbable()
out$max.parents <- max.parents
out$dag.retained <- dag.retained
out$dag.banned <- dag.banned
out$group.var <- group.var
out$group.ids <- group.ids
out$group.vars <- grouped.vars
out$cor.vars <- cor.vars
out$mylist <- mylist
out$method <- "bayes"
return(out)
}
#' From each child-parent(s) combination, regress each child on its parents in buildScoreCache.bayes()
#' @describeIn buildScoreCache Internal function called by \code{buildScoreCache.bayes()}.
#' @param row.no The row number of the child-parent combination to be processed.
#' @param children vector of child node integers.
#' @param node.defn child-parent combination table.
#' @param dag.m Empty adjacency matrix.
#' @param var.types vector of numeric encoding of distribution types. See \code{get.var.types(data.dists)}
#'
#' @return Named vector of results from one child-parent combination subject to the \code{row.no}.
#' The names are:
#' \describe{
#' \item{childParentCombNo}{The row number of the child-parent combination in the \code{node.defn} table.
#' This must be the same as the row number in \code{node.defn}:
#' careful if \code{buildScoreCache.bayes()} is run in parallel!}
#' \item{mlik}{The marginal log-likelihood of the child-parent combination.}
#' \item{error.code}{The error code returned by \code{inla()}.}
#' \item{hessian.accuracy}{The accuracy of the Hessian matrix returned by \code{inla()}.}
#' \item{used.INLA}{A logical value indicating whether \code{inla()} was used to fit the model.}
#' }
#' @export
#' @keywords internal
forLoopContentBayes <- function(row.no = NULL, # i
children = NULL,
node.defn = NULL,
dag.m = NULL,
force.method = NULL,
data.df = NULL,
data.dists = NULL,
var.types = NULL,
control = NULL,
grouped.vars = NULL,
group.ids = NULL,
verbose = FALSE) {
child <- children[row.no]
FAILED <- FALSE
## to catch any crashes...
###########################################################
if (verbose) cat("###### Processing...",row.no," of ", nrow(node.defn) ,"\n")
dag.m[,] <- 0
## reset to empty
dag.m[child,] <- node.defn[row.no,]
## set parent combination
orig.force.method <- NULL
used.inla <- TRUE
####################################################
### First case is the node a GLM
####################################################
if( !(child%in%grouped.vars)){
## only compute option here is C since fast and INLA slower and less reliable
if(force.method=="notset" || force.method=="C"){
if (verbose) cat("Using internal code (Laplace glm)\n")
r <- try(res.c <- .Call("fit_single_node",
data.df,
as.integer(child), ## childnode
as.integer(dag.m[child,]), ## parent combination
as.integer(dim(dag.m)[1]), ## number of nodes/variables
as.integer(var.types), ## type of densities
as.integer(sum(dag.m[child,])), ## max.parents
as.double(control[["mean"]]),as.double(1/sqrt(control[["prec"]])),as.double(control[["loggam.shape"]]),as.double(1/control[["loggam.inv.scale"]]),
as.integer(control[["max.iters"]]),as.double(control[["epsabs"]]),
as.integer(verbose),as.integer(control[["error.verbose"]]),as.integer(control[["trace"]]),
as.integer(grouped.vars-1), ## int.vector of variables which are mixed model nodes -1 for C
as.integer(group.ids), ## group memberships - note indexed from 1
as.double(control[["epsabs.inner"]]),
as.integer(control[["max.iters.inner"]]),
as.double(control[["finite.step.size"]]),
as.double(control[["hessian.params"]]),
as.integer(control[["max.iters.hessian"]]),
as.integer(0), ## modes only - false here as only applies to glmms
as.double(control[["max.hessian.error"]]), ## Not applicable
as.double(control[["factor.brent"]]), ## Not applicable
as.integer(control[["maxiters.hessian.brent"]]), ## Not applicable
as.double(control[["num.intervals.brent"]]), ## Not applicable
PACKAGE="abn"))
if(length(attr(r,"class")>0) && attr(r,"class")=="try-error"){
if (verbose) cat("## !!! Laplace approximation failed\n")
FAILED <- TRUE
}
used.inla <- FALSE
} else {
## use INLA for glm
if(!requireNamespace("INLA", quietly = TRUE)){stop("library INLA is not available!\nINLA is available from https://www.r-inla.org/download-install.")}
mean.intercept <- control[["mean"]]
## use same as for rest of linear terms
prec.intercept <- control[["prec"]]
## use same as for rest of linear terms
if (verbose) cat("Using INLA (glm)\n")
res.inla <- calc.node.inla.glm(child,
dag.m,
data.df,
data.dists,
rep(1,dim(data.df)[1]),
## ntrials
rep(1,dim(data.df)[1]),
## exposure
TRUE, mean.intercept, prec.intercept, control[["mean"]], control[["prec"]],control[["loggam.shape"]],control[["loggam.inv.scale"]],
verbose.loc = verbose,
nthreads = control[["ncores"]])
if(is.logical(res.inla)){
if (verbose) cat("INLA failed... so reverting to internal code.\n")
r <- try(res.c <- .Call("fit_single_node",
data.df,
as.integer(child), ## childnode
as.integer(dag.m[child,]), ## parent combination
as.integer(dim(dag.m)[1]), ## number of nodes/variables
as.integer(var.types), ## type of densities
as.integer(sum(dag.m[child,])), ## max.parents
as.double(control[["mean"]]),as.double(1/sqrt(control[["prec"]])),as.double(control[["loggam.shape"]]),as.double(1/control[["loggam.inv.scale"]]),
as.integer(control[["max.iters"]]),as.double(control[["epsabs"]]),
as.integer(verbose),as.integer(control[["error.verbose"]]),as.integer(control[["trace"]]),
as.integer(grouped.vars-1), ## int.vector of variables which are mixed model nodes -1 for C
as.integer(group.ids), ## group memberships - note indexed from 1
as.double(control[["epsabs.inner"]]),
as.integer(control[["max.iters.inner"]]),
as.double(control[["finite.step.size"]]),
as.double(control[["hessian.params"]]),
as.integer(control[["max.iters.hessian"]]),
as.integer(0), ## modes only - false here as only applies to glmms
as.double(control[["max.hessian.error"]]), ## Not applicable
as.double(control[["factor.brent"]]), ## Not applicable
as.integer(control[["maxiters.hessian.brent"]]), ## Not applicable
as.double(control[["num.intervals.brent"]]), ## Not applicable
PACKAGE="abn"))
if(length(attr(r,"class")>0) && attr(r,"class")=="try-error"){
if (verbose) cat("## !!! Laplace approximation failed\n")
FAILED <- TRUE
}
used.inla <- FALSE
## flip
}
## INLA failed
}
## use INLA
## End of GLM node
###########################################################
} else {
###########################################################
## Have a GLMM node
###########################################################
## have a glmm, so two options, INLA or C
if(force.method=="notset" || force.method=="INLA"){##
if(!requireNamespace("INLA", quietly = TRUE)){
stop("library INLA is not available!\nINLA is available from https://www.r-inla.org/download-install.");
}
mean.intercept <- control[["mean"]]
## use same as for rest of linear terms
prec.intercept <- control[["prec"]]
## use same as for rest of linear terms
res.inla <- calc.node.inla.glmm(child,
dag.m,
data.frame(data.df,group=group.ids),
data.dists,
rep(1,dim(data.df)[1]), ## ntrials
rep(1,dim(data.df)[1]), ## exposure
TRUE, ## always compute marginals - since only way to check results
mean.intercept, prec.intercept, control[["mean"]], control[["prec"]],control[["loggam.shape"]],control[["loggam.inv.scale"]],
verbose.loc = verbose,
nthreads = control[["ncores"]])
## CHECK FOR INLA CRASH
if(is.logical(res.inla)){
if (verbose) cat("INLA failed... so reverting to internal code\n");
orig.force.method <- force.method;## save original
force.method="C"; ## Easiest way is just to force C for this node
} else {
res.inla.modes <- getModeVector(list.fixed=res.inla$marginals.fixed,list.hyper=res.inla$marginals.hyperpar);
}
}
if (verbose) cat("fit a glmm at node ",rownames(dag.m)[child],"using C\n");
if(force.method=="notset"){
r <- try(res.c <- .Call("fit_single_node",
data.df,
as.integer(child), ## childnode
as.integer(dag.m[child,]),## parent combination
as.integer(dim(dag.m)[1]),## number of nodes/variables
as.integer(var.types),## type of densities
as.integer(sum(dag.m[child,])),## max.parents
as.double(control[["mean"]]),as.double(1/sqrt(control[["prec"]])),as.double(control[["loggam.shape"]]),as.double(1/control[["loggam.inv.scale"]]),
as.integer(control[["max.iters"]]),as.double(control[["epsabs"]]),
as.integer(verbose),as.integer(control[["error.verbose"]]),as.integer(control[["trace"]]),
as.integer(grouped.vars-1),## int.vector of variables which are mixed model nodes -1 for C
as.integer(group.ids),## group memberships - note indexed from 1
as.double(control[["epsabs.inner"]]),
as.integer(control[["max.iters.inner"]]),
as.double(control[["finite.step.size"]]),
as.double(control[["hessian.params"]]),
as.integer(control[["max.iters.hessian"]]),
as.integer(1), ## turn on ModesONLY
as.double(control[["max.hessian.error"]]),## Not applicable
as.double(control[["factor.brent"]]), ## Not applicable
as.integer(control[["maxiters.hessian.brent"]]),## Not applicable
as.double(control[["num.intervals.brent"]])## Not applicable
,PACKAGE="abn" ## uncomment to load as package not shlib
));
if(length(attr(r,"class")>0) && attr(r,"class")=="try-error"){ if (verbose) cat(" Laplace approximation failed\n");
FAILED <- TRUE;}
if(!FAILED){
res.c.modes <- res.c[[1]][-c(1:3)];## remove mlik - this is first entry, and error code and hessian accuracy
res.c.modes <- res.c.modes[which(res.c.modes!=.Machine$double.xmax)];## this discards all "empty" parameters
## get difference in modes proportion relative to C
diff.in.modes <- (res.inla.modes-res.c.modes)/res.c.modes;
error.modes <- max(abs(diff.in.modes));
}
} ## end of notset
if( !FAILED && force.method=="C" || (force.method=="notset" && error.modes>(control[["max.mode.error"]]/100))){ ## INLA might be unreliable so use C (slower)
if(force.method=="notset"){
if (verbose) cat("Using internal code (Laplace glmm)\n=>max. abs. difference (in %) with INLA is ");
if (verbose) cat(formatC(100*error.modes,format="f",digits=1)," and exceeds tolerance\n");
} else {
if (verbose) cat("Using internal code (Laplace glmm)\n");}
r <- try(res.c <- .Call("fit_single_node",
data.df,
as.integer(child), ## childnode
as.integer(dag.m[child,]),## parent combination
as.integer(dim(dag.m)[1]),## number of nodes/variables
as.integer(var.types),## type of densities
as.integer(sum(dag.m[child,])),## max.parents
as.double(control[["mean"]]),as.double(1/sqrt(control[["prec"]])),as.double(control[["loggam.shape"]]),as.double(1/control[["loggam.inv.scale"]]),
as.integer(control[["max.iters"]]),as.double(control[["epsabs"]]),
as.integer(verbose),as.integer(control[["error.verbose"]]),as.integer(control[["trace"]]),
as.integer(grouped.vars-1),## int.vector of variables which are mixed model nodes -1 for C
as.integer(group.ids),## group memberships - note indexed from 1
as.double(control[["epsabs.inner"]]),
as.integer(control[["max.iters.inner"]]),
as.double(control[["finite.step.size"]]),
as.double(control[["hessian.params"]]),
as.integer(control[["max.iters.hessian"]]),
as.integer(0), ## turn on ModesONLY
as.double(control[["max.hessian.error"]]),## Not applicable
as.double(control[["factor.brent"]]),## Not applicable
as.integer(control[["maxiters.hessian.brent"]]),## Not applicable
as.double(control[["num.intervals.brent"]])## Not applicable
,PACKAGE="abn" ## uncomment to load as package not shlib
));
if(length(attr(r,"class")>0) && attr(r,"class")=="try-error"){
if (verbose) cat("## !!! Laplace approximation failed\n");
FAILED <- TRUE;
}
used.inla <- FALSE;## flip
} else {
if (verbose) cat("Using INLA (glmm)\n");
}## end of if inla bad
} ## end of if GLMM
###########################################################
## End of GLMM node
###########################################################
###########################################################
## End of all external computations
###########################################################
## computation for current node is all done so sort out the
## output into nicer form and give labels
###########################################################
if(!FAILED){
if(used.inla==FALSE){## organize output from C
mlik <- res.c[[1]][1]
error.code <- res.c[[1]][2]
hessian.accuracy <- res.c[[1]][3]
used.INLA <- FALSE
} else {
## organize output from INLA
mlik <- res.inla$mlik[2]## [2] is for Gaussian rather than Integrated estimate
error.code <- NA## not available from INLA
hessian.accuracy <- NA## not available from INLA
used.INLA <- TRUE
}
} else {## FAILED
mlik <- NA
error.code <- 2## model could not be fitted
hessian.accuracy <- NA
used.INLA <- FALSE
}
if(!is.null(orig.force.method)){
force.method <- orig.force.method;
} ## reset force.method after INLA crash
############################################################
## Finished with current node
############################################################
return(c(childParentCombNo=row.no, mlik=mlik,error.code=error.code,hessian.accuracy=hessian.accuracy,used.INLA=used.INLA))
} ## end of nodes loop
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