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pmmlTreeModel <- function(file, ...) {
stopifnot(requireNamespace("XML"))
as.party(XML::xmlRoot(XML::xmlTreeParse(file)))
}
as.party.XMLNode <- function(obj, ...) {
stopifnot(requireNamespace("XML"))
## check whether XML specifies a TreeModel
stopifnot(c("DataDictionary", "TreeModel") %in% names(obj))
if(any(warnx <- c("MiningBuildTask", "TransformationDictionary", "Extension") %in% names(obj)))
warning(sprintf("%s not yet implemented", paste(names(obj)[warnx], collapse = ", ")))
## process header information
if("Header" %in% names(obj)) {
hdr <- obj[["Header"]]
h_info <- c(Header = paste(as.character(XML::xmlAttrs(hdr)), collapse = ", "))
if(length(hdr) > 0L) {
h_info <- c(h_info,
XML::xmlSApply(hdr, function(x)
paste(c(as.character(XML::xmlAttrs(x)), XML::xmlValue(x)), collapse = ", ")
)
)
}
} else {
h_info <- NULL
}
## parse data dictionary
extract_empty_model_frame <- function(x) {
## extract DataDictionary
dd <- x[["DataDictionary"]]
## currently we can only look at DataField
if(!all(names(dd) == "DataField")) warning("data specifications other than DataField are not yet implemented")
## check columns
nc <- as.numeric(XML::xmlAttrs(dd)["numberOfFields"])
if(!is.na(nc)) stopifnot(nc == length(dd))
## set up data frame (only numeric variables)
mf <- as.data.frame(rep(list(1), nc))[0,]
names(mf) <- XML::xmlSApply(dd, function(x) XML::xmlAttrs(x)["name"])
## modify class if necessary
for(i in 1:nc) {
optype <- XML::xmlAttrs(dd[[i]])["optype"]
switch(optype,
"categorical" = {
mf[[i]] <- factor(integer(0),
levels = XML::xmlSApply(dd[[i]], function(x) gsub("&", "&", XML::xmlAttrs(x)["value"], fixed = TRUE)))
},
"ordinal" = {
mf[[i]] <- factor(integer(0), ordered = TRUE,
levels = XML::xmlSApply(dd[[i]], function(x) gsub("&", "&", XML::xmlAttrs(x)["value"], fixed = TRUE)))
},
"continuous" = {
dataType <- XML::xmlAttrs(dd[[i]])["dataType"]
if(dataType == "integer") mf[[i]] <- integer(0)
}
)
}
return(mf)
}
mf <- extract_empty_model_frame(obj)
mf_names <- names(mf)
mf_levels <- lapply(mf, levels)
## parse MiningSchema
extract_terms <- function(x) {
## extract MiningSchema
ms <- x[["TreeModel"]]
stopifnot("MiningSchema" %in% names(ms))
ms <- ms[["MiningSchema"]]
## currently we can only look at MiningField
if(!all(names(ms) == "MiningField")) warning("MiningField not yet implemented")
## extract variable info
vars <- t(XML::xmlSApply(ms, XML::xmlAttrs))
if(sum(vars[,2] == "predicted") > 1) stop("multivariate responses not yet implemented")
if(!all(vars[,2] %in% c("predicted", "active", "supplementary"))) warning("not yet implemented")
## set up formula
ff <- as.formula(paste(vars[vars[,2] == "predicted",1], "~",
paste(vars[vars[,2] != "predicted",1], collapse = " + ")))
return(terms(ff))
}
trms <- extract_terms(obj)
## parse TreeModel
tm <- obj[["TreeModel"]]
tm_info <- c(XML::xmlAttrs(tm), h_info)
## check response
stopifnot(tm_info["functionName"] %in% c("classification", "regression"))
mf_response <- mf[[deparse(attr(trms, "variables")[[2L]])]]
if(tm_info["functionName"] == "classification") stopifnot(inherits(mf_response, "factor"))
if(tm_info["functionName"] == "regression") stopifnot(is.numeric(mf_response))
## convenience functions for parsing nodes
is_terminal <- function(xnode) !("Node" %in% names(xnode))
is_root <- function(xnode) "True" %in% names(xnode)
n_kids <- function(xnode) sum("Node" == names(xnode))
n_obs <- function(xnode) as.numeric(XML::xmlAttrs(xnode)["recordCount"])
has_surrogates <- function(x) {
ns <- sum(c("SimplePredicate", "SimpleSetPredicate", "CompoundPredicate") %in% names(x))
if(ns != 1) stop("invalid PMML")
if("CompoundPredicate" %in% names(x)) {
if(identical(as.vector(XML::xmlAttrs(x[["CompoundPredicate"]])["booleanOperator"]), "surrogate")) return(TRUE)
else return(FALSE)
} else {
return(FALSE)
}
}
has_single_splits <- function(x) {
wi <- which(names(x) %in% c("SimplePredicate", "SimpleSetPredicate", "CompoundPredicate"))
sapply(wi, function(i) {
if(names(x)[i] %in% c("SimplePredicate", "SimpleSetPredicate")) return(TRUE)
if(identical(as.vector(XML::xmlAttrs(x[[i]])["booleanOperator"]), "or")) return(TRUE)
stop("CompoundPredicate not yet implemented")
})
}
n_splits <- function(xnode) {
wi <- which("Node" == names(xnode))
rval <- unique(sapply(wi, function(i) {
xnodei <- if(has_surrogates(xnode[[i]])) xnode[[i]][["CompoundPredicate"]] else xnode[[i]]
rval <- has_single_splits(xnodei)
if(!all(rval)) stop("invalid PMML")
sum(rval)
}))
if(length(rval) > 1) stop("invalid PMML")
return(rval)
}
kid_ids <- function(xnode) {
wi <- which("Node" == names(xnode))
rval <- sapply(wi, function(j) {
as.vector(XML::xmlAttrs(xnode[[j]])["id"])
})
}
get_pred <- function(xnode) {
pred <- as.vector(XML::xmlAttrs(xnode)["score"])
if(is.na(pred)) return(NULL)
if(is.numeric(mf_response)) as.numeric(pred)
else factor(pred, levels = levels(mf_response))
}
get_dist <- function(xnode) {
wi <- which("ScoreDistribution" == names(xnode))
if(length(wi) < 1) return(NULL)
rval <- sapply(wi, function(i) as.numeric(XML::xmlAttrs(xnode[[i]])["recordCount"]))
names(rval) <- sapply(wi, function(i) XML::xmlAttrs(xnode[[i]])["value"])
if(inherits(mf_response, "factor")) rval <- rval[levels(mf_response)]
return(rval)
}
get_error <- function(xnode) {
if(tm_info["functionName"] != "classification") return(NULL)
tab <- get_dist(xnode)
if(is.null(tab)) return(NULL)
c("%" = sum(100 * prop.table(tab)[names(tab) != get_pred(xnode)]))
}
get_extension <- function(xnode) {
if(!("Extension" %in% names(xnode))) return(NULL)
if(length(xnode[["Extension"]]) > 1) warning("currently only one Extension allowed")
rval <- XML::xmlApply(xnode[["Extension"]][[1]], XML::xmlAttrs)
names(rval) <- NULL
rval <- unlist(rval)
to_numeric <- function(x) {
y <- suppressWarnings(as.numeric(x))
if(!is.null(y) && !is.na(y)) y else x
}
sapply(rval, to_numeric)
}
node_info <- function(xnode) list(prediction = get_pred(xnode), n = n_obs(xnode),
error = get_error(xnode), distribution = get_dist(xnode), extension = get_extension(xnode))
get_split_prob <- function(xnode) {
rval <- rep(0, n_kids(xnode))
wi <- XML::xmlAttrs(xnode)["defaultChild"]
if(is.na(wi)) rval <- NULL
else rval[which(kid_ids(xnode) == wi)] <- 1
return(rval)
}
get_split <- function(xnode, i, surrogates) {
wi <- which("Node" == names(xnode))
rval <- sapply(wi, function(j) {
nj <- if(surrogates) xnode[[j]][["CompoundPredicate"]] else xnode[[j]]
if(any(c("SimplePredicate", "SimpleSetPredicate") %in% names(nj))) {
wii <- which(names(nj) %in% c("SimplePredicate", "SimpleSetPredicate"))[i]
c("predicateType" = as.vector(names(nj)[wii]), XML::xmlAttrs(nj[[wii]]))
} else {
wii <- which(names(nj) == "CompoundPredicate")[i]
nj <- nj[[wii]]
if(!identical(as.vector(XML::xmlAttrs(nj)["booleanOperator"]), "or")) stop("not yet implemented")
if(any(names(nj) %in% c("SimpleSetPredicate", "CompoundPredicate"))) stop("not yet implemented")
rvali <- sapply(which(names(nj) == "SimplePredicate"), function(j)
c("predicateType" = as.vector(names(nj)[j]), XML::xmlAttrs(nj[[j]])))
if(is.null(dim(rvali))) rvali <- matrix(rvali, ncol = 1)
stopifnot(length(unique(rvali["predicateType",])) == 1)
stopifnot(length(unique(rvali["field",])) == 1)
stopifnot(all(rvali["operator",] == "equal"))
c("predicateType" = "simpleSetPredicate",
"field" = rvali["field", 1],
"booleanOperator" = "isIn")
}
})
stopifnot(length(unique(rval["predicateType",])) == 1)
stopifnot(length(unique(rval["field",])) == 1)
if(rval["predicateType", 1] == "SimplePredicate") {
stopifnot(length(unique(rval["value",])) == 1)
if(ncol(rval) != 2) stop("not yet implemented")
if(!(identical(as.vector(sort(rval["operator",])), c("greaterThan", "lessOrEqual")) |
identical(as.vector(sort(rval["operator",])), c("greaterOrEqual", "lessThan")))
) stop("not yet implemented")
partysplit(
varid = which(rval["field", 1] == mf_names),
breaks = as.numeric(rval["value", 1]),
index = if(substr(rval["operator", 1], 1, 1) != "l") 2:1 else NULL,
right = "lessOrEqual" %in% rval["operator",],
prob = if(i == 1) get_split_prob(xnode) else NULL
)
} else {
varid <- which(rval["field", 1] == mf_names)
lev <- mf_levels[[varid]]
stopifnot(length(lev) > 1)
idx <- rep(NA, length(lev))
lab <- lapply(wi, function(j) {
nj <- if(surrogates) xnode[[j]][["CompoundPredicate"]] else xnode[[j]]
if(any(names(nj) %in% c("SimplePredicate", "SimpleSetPredicate"))) {
wii <- which(names(nj) %in% c("SimplePredicate", "SimpleSetPredicate"))[i]
ar <- nj[[wii]][["Array"]]
stopifnot(XML::xmlAttrs(ar)["type"] == "string")
rv <- XML::xmlValue(ar)
rv <- gsub(""", "\"", rv, fixed = TRUE)
rv <- if(substr(rv, 1, 1) == "\"" & substr(rv, nchar(rv), nchar(rv)) == "\"") {
strsplit(substr(rv, 2, nchar(rv) - 1), "\" \"")[[1]]
} else {
strsplit(rv, " ")[[1]]
}
stopifnot(length(rv) == as.numeric(XML::xmlAttrs(ar)["n"]))
return(rv)
} else {
wii <- which(names(nj) == "CompoundPredicate")[i]
as.vector(XML::xmlSApply(nj[[wii]], function(z) XML::xmlAttrs(z)["value"]))
}
})
for(j in 1:ncol(rval)) {
if(rval["booleanOperator",j] == "isIn") idx[which(lev %in% lab[[j]])] <- j
else idx[which(!(lev %in% lab[[j]]))] <- j
}
stopifnot(all(na.omit(idx) > 0))
if(min(idx, na.rm = TRUE) != 1) stop(sprintf("variable levels (%s) and split labels (%s)",
paste(lev, collapse = ", "), paste(sapply(lab, paste, collapse = ", "), collapse = " | ")))
partysplit(
varid = varid,
breaks = NULL,
index = as.integer(idx),
prob = if(i == 1) get_split_prob(xnode) else NULL
)
}
}
## function for setting up nodes
## (using global index ii)
pmml_node <- function(xnode) {
ii <<- ii + 1
if(is_terminal(xnode)) return(partynode(as.integer(ii),
info = node_info(xnode)
))
wi <- which("Node" == names(xnode))
ns <- n_splits(xnode)
nd <- partynode(as.integer(ii),
split = get_split(xnode, 1, has_surrogates(xnode[[wi[1]]])),
kids = lapply(wi, function(j) pmml_node(xnode[[j]])),
surrogates = if(ns < 2) NULL else lapply(2:ns, function(j) get_split(xnode, j, TRUE)),
info = node_info(xnode)
)
nd
}
## set up node
ii <- 0
if(is_root(tm[["Node"]])) nd <- pmml_node(tm[["Node"]]) else stop("root node not declared, invalid PMML?")
## set up party
## FIXME: extend info slot?
pt <- party(node = nd, data = mf, fitted = NULL, terms = trms, names = NULL, info = tm_info)
class(pt) <- c("simpleparty", class(pt))
return(pt)
}
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