Nothing
# node --------------------------------------------------------------------
partynode <- function(id, split = NULL, kids = NULL, surrogates = NULL, info = NULL, centroids = NULL) {
if (!is.integer(id) || length(id) != 1) {
id <- as.integer(id0 <- id)
if (any(is.na(id)) || !isTRUE(all.equal(id0, id)) || length(id) != 1)
stop(sQuote("id"), " ", "must be a single integer")
}
if (is.null(split) != is.null(kids)) {
stop(sQuote("split"), " ", "and", " ", sQuote("kids"), " ",
"must either both be specified or unspecified")
}
if (!is.null(kids)) {
if (!(is.list(kids) && all(sapply(kids, inherits, "partynode")))
|| length(kids) < 2)
stop(sQuote("kids"), " ", "must be an integer vector or a list of",
" ", sQuote("partynode"), " ", "objects")
}
if (!is.null(surrogates)) {
if (!is.list(surrogates) || any(!sapply(surrogates, inherits, "partysplit")))
stop(sQuote("split"), " ", "is not a list of", " ", sQuote("partysplit"),
" ", "objects")
}
node <- list(id = id, split = split, kids = kids, surrogates = surrogates, info = info, centroids = centroids)
class(node) <- "partynode"
return(node)
}
as.partynode.list <- function(x, ...) {
if (!all(sapply(x, inherits, what = "list")))
stop("'x' has to be a list of lists")
if (!all(sapply(x, function(x) "id" %in% names(x))))
stop("each list in 'x' has to define a node 'id'")
ok <- sapply(x, function(x)
all(names(x) %in% c("id", "split", "kids", "surrogates", "info", "centroids")))
if (any(!ok))
sapply(which(!ok), function(i)
warning(paste("list element", i, "defines additional elements:",
paste(names(x[[i]])[!(names(x[[i]]) %in%
c("id", "split", "kids", "surrogates", "info", "centroids"))],
collapse = ", "))))
ids <- as.integer(sapply(x, function(node) node$id))
if(any(duplicated(ids))) stop("nodeids must be unique integers")
x <- x[order(ids)]
ids <- ids[order(ids)]
new_recnode <- function(i) {
x_i <- x[[which(ids == i)]]
if (is.null(x_i$kids))
partynode(id = x_i$id, info = x_i$info)
else
partynode(id = x_i$id, split = x_i$split,
kids = lapply(x_i$kids, new_recnode),
surrogates = x_i$surrogates,
info = x_i$info)
}
ret <- new_recnode(ids[1L])
### <FIXME> duplicates recursion but makes sure
### that the ids are in pre-order notation with
### from defined in as.partynode.partynode
### </FIXME>
as.partynode(ret, ...)
}
kidids_node <- function(node, data, vmatch = 1:length(data), obs = NULL,
perm = NULL) {
primary <- split_node(node)
surrogates <- surrogates_node(node)
### perform primary split
x <- kidids_split(primary, data, vmatch, obs)
### surrogate / random splits if needed
if (any(is.na(x))) {
### surrogate splits
if (length(surrogates) >= 1) {
for (surr in surrogates) {
nax <- is.na(x)
if (!any(nax)) break;
x[nax] <- kidids_split(surr, data, vmatch, obs = obs)[nax]
}
}
nax <- is.na(x)
### random splits
if (any(nax)) {
prob <- prob_split(primary)
x[nax] <- sample(1:length(prob), sum(nax), prob = prob,
replace = TRUE)
}
}
### permute variable `perm' _after_ dealing with surrogates etc.
if (!is.null(perm)) {
if (is.integer(perm)) {
if (varid_split(primary) %in% perm)
x <- .resample(x)
} else {
if (is.null(obs)) obs <- 1:length(data)
strata <- perm[[varid_split(primary)]]
if (!is.null(strata)) {
strata <- strata[obs, drop = TRUE]
for (s in levels(strata))
x[strata == s] <- .resample(x[strata == s])
}
}
}
return(x)
}
kidids_node_predict <- function(node, data, vmatch = 1:length(data), obs = NULL,
perm = NULL) {
primary <- split_node(node)
surrogates <- surrogates_node(node)
### perform primary split
x <- kidids_split_predict(primary, data, vmatch, obs)
### surrogate / random splits if needed
if (any(is.na(x))) {
### surrogate splits
if (length(surrogates) >= 1) {
for (surr in surrogates) {
nax <- is.na(x)
if (!any(nax)) break;
x[nax] <- kidids_split_predict(surr, data, vmatch, obs = obs)[nax]
}
}
nax <- is.na(x)
### random splits
if (any(nax)) {
prob <- prob_split(primary)
x[nax] <- sample(1:length(prob), sum(nax), prob = prob,
replace = TRUE)
}
}
### permute variable `perm' _after_ dealing with surrogates etc.
if (!is.null(perm)) {
if (is.integer(perm)) {
if (varid_split(primary) %in% perm)
x <- .resample(x)
} else {
if (is.null(obs)) obs <- 1:length(data)
strata <- perm[[varid_split(primary)]]
if (!is.null(strata)) {
strata <- strata[obs, drop = TRUE]
for (s in levels(strata))
x[strata == s] <- .resample(x[strata == s])
}
}
}
return(x)
}
fitted_node <- function(node, data, vmatch = 1:length(data),
obs = 1:unique(sapply(data, NROW)), perm = NULL) {
if (is.logical(obs)) obs <- which(obs)
if (is.terminal(node))
return(rep(id_node(node), length(obs)))
retid <- nextid <- kidids_node(node, data, vmatch, obs, perm)
for (i in unique(nextid)) {
indx <- nextid == i
retid[indx] <- fitted_node(kids_node(node)[[i]], data,
vmatch, obs[indx], perm)
}
return(retid)
}
fitted_node_predict <- function(node, data, vmatch = 1:length(data),
obs = 1:unique(sapply(data, NROW)), perm = NULL) {
if (is.logical(obs)) obs <- which(obs)
if (is.terminal(node))
return(rep(id_node(node), length(obs)))
retid <- nextid <- kidids_node_predict(node, data, vmatch, obs, perm)
for (i in unique(nextid)) {
indx <- nextid == i
retid[indx] <- fitted_node_predict(kids_node(node)[[i]], data,
vmatch, obs[indx], perm)
}
return(retid)
}
is.terminal.partynode <- function(x, ...) {
kids <- is.null(kids_node(x))
split <- is.null(split_node(x))
if (kids != split)
stop("x", " ", "is incorrect node")
kids
}
#' @method depth partynode
#' @export
depth.partynode <- function(x, root = FALSE, ...) {
if (is.terminal(x)) return(as.integer(root))
max(sapply(kids_node(x), depth, root = root)) + 1L
}
width.partynode <- function(x, ...) {
if (is.terminal(x)) return(1)
sum(sapply(kids_node(x), width.partynode))
}
# party -------------------------------------------------------------------
party <- function(node, data, fitted = NULL, terms = NULL, names = NULL, info = NULL) {
stopifnot(inherits(node, "partynode"))
stopifnot(inherits(data, "list") | inherits(data, "data.frame"))
#without adding 'data.frame', it throws error for CLS plots
### make sure all split variables are there
ids <- nodeids(node)[!nodeids(node) %in% nodeids(node, terminal = TRUE)]
varids <- unique(unlist(nodeapply(node, ids = ids, FUN = function(x)
varid_split(split_node(x)))))
stopifnot(varids %in% 1:length(data))
if(!is.null(fitted)) {
stopifnot(inherits(fitted, "data.frame"))
stopifnot(all(sapply(data, NROW) == 0L) | all(sapply(data, NROW) == NROW(fitted)))
# try to provide default variable "(fitted)"
if(all(sapply(data, NROW) > 0L)) {
if(!("(fitted)" %in% names(fitted)))
fitted[["(fitted)"]] <- fitted_node(node, data = data)
} else {
stopifnot("(fitted)" == names(fitted)[1L])
}
nt <- nodeids(node, terminal = TRUE)
stopifnot(all(fitted[["(fitted)"]] %in% nt))
node <- as.partynode(node, from = 1L)
nt2 <- nodeids(node, terminal = TRUE)
fitted[["(fitted)"]] <- nt2[match(fitted[["(fitted)"]], nt)]
} else {
node <- as.partynode(node, from = 1L)
# default "(fitted)"
if(all(sapply(data, NROW) > 0L) & missing(fitted))
fitted <- data.frame("(fitted)" = fitted_node(node,
data = data), check.names = FALSE)
}
party <- list(node = node, data = data, fitted = fitted,
terms = NULL, names = NULL, info = info)
class(party) <- "party"
if(!is.null(terms)) {
stopifnot(inherits(terms, "terms"))
party$terms <- terms
}
if (!is.null(names)) {
n <- length(nodeids(party, terminal = FALSE))
if (length(names) != n)
stop("invalid", " ", sQuote("names"), " ", "argument")
party$names <- names
}
party
}
.names_party <- function(party) {
names <- party$names
if (is.null(names))
names <- as.character(nodeids(party, terminal = FALSE))
names
}
predict_party <- function(party, id, newdata = NULL, ...)
UseMethod("predict_party")
### do nothing except returning the fitted ids
predict_party.default <- function(party, id, newdata = NULL, FUN = NULL, ...) {
if (length(list(...)) > 1)
warning("argument(s)", " ", sQuote(names(list(...))), " ", "have been ignored")
## get observation names: either node names or
## observation names from newdata
nam <- if(is.null(newdata)) {
if(is.null(rnam <- rownames(data_party(party)))) names(party)[id] else rnam
} else {
rownames(newdata[[1]])
}
if(length(nam) != length(id)) nam <- NULL
if (!is.null(FUN))
return(.simplify_pred(nodeapply(party,
nodeids(party, terminal = TRUE), FUN, by_node = TRUE), id, nam))
## special case: fitted ids
return(structure(id, .Names = nam))
}
predict_party.constparty <- function(party, id, newdata = NULL,
type = c("response", "prob", "quantile", "density", "node"),
at = if (type == "quantile") c(0.1, 0.5, 0.9),
FUN = NULL, simplify = TRUE, ...)
{
## extract fitted information
response <- party$fitted[["(response)"]]
weights <- party$fitted[["(weights)"]]
fitted <- party$fitted[["(fitted)"]]
if (is.null(weights)) weights <- rep(1, NROW(response))
## get observation names: either node names or
## observation names from newdata
nam <- if(is.null(newdata)) names(party)[id] else rownames(newdata[[1]])
if(length(nam) != length(id)) nam <- NULL
## match type
type <- match.arg(type)
## special case: fitted ids
if(type == "node")
return(structure(id, .Names = nam))
### multivariate response
if (is.data.frame(response)) {
ret <- lapply(response, function(r) {
ret <- .predict_party_constparty(node_party(party), fitted = fitted,
response = r, weights, id = id, type = type, at = at, FUN = FUN, ...)
if (simplify) .simplify_pred(ret, id, nam) else ret
})
if (all(sapply(ret, is.atomic)))
ret <- as.data.frame(ret)
names(ret) <- colnames(response)
return(ret)
}
### univariate response
ret <- .predict_party_constparty(node_party(party), fitted = fitted, response = response,
weights = weights, id = id, type = type, at = at, FUN = FUN, ...)
if (simplify) .simplify_pred(ret, id, nam) else ret[as.character(id)]
}
### functions for node prediction based on fitted / response
.pred_Surv <- function(y, w) {
if (length(y) == 0) return(NA)
survfit(y ~ 1, weights = w, subset = w > 0)
}
.pred_Surv_response <- function(y, w) {
if (length(y) == 0) return(NA)
.median_survival_time(.pred_Surv(y, w))
}
.pred_factor <- function(y, w) {
lev <- levels(y)
sumw <- tapply(w, y, sum)
sumw[is.na(sumw)] <- 0
prob <- sumw / sum(w)
names(prob) <- lev
return(prob)
}
.pred_factor_response <- function(y, w) {
prob <- .pred_factor(y, w)
return(factor(which.max(prob), levels = 1:nlevels(y),
labels = levels(y),
ordered = is.ordered(y)))
return(prob)
}
.pred_numeric_response <- function(y, w)
weighted.mean(y, w, na.rm = TRUE)
.pred_ecdf <- function(y, w) {
if (length(y) == 0) return(NA)
iw <- as.integer(round(w))
if (max(abs(w - iw)) < sqrt(.Machine$double.eps)) {
y <- rep(y, w)
return(ecdf(y))
} else {
stop("cannot compute empirical distribution function with non-integer weights")
}
}
.pred_quantile <- function(y, w) {
y <- rep(y, w)
function(p, ...) quantile(y, probs = p, ...)
}
.pred_density <- function(y, w) {
d <- density(y, weights = w / sum(w))
approxfun(d[1:2], rule = 2)
}
### workhorse: compute predictions based on fitted / response data
.predict_party_constparty <- function(node, fitted, response, weights,
id = id, type = c("response", "prob", "quantile", "density"),
at = if (type == "quantile") c(0.1, 0.5, 0.9), FUN = NULL, ...) {
type <- match.arg(type)
if (is.null(FUN)) {
rtype <- class(response)[1]
if (rtype == "ordered") rtype <- "factor"
if (rtype == "integer") rtype <- "numeric"
if (rtype == "AsIs") rtype <- "numeric"
if (type %in% c("quantile", "density") && rtype != "numeric")
stop("quantile and density estimation currently only implemented for numeric responses")
FUN <- switch(rtype,
"Surv" = if (type == "response") .pred_Surv_response else .pred_Surv,
"factor" = if (type == "response") .pred_factor_response else .pred_factor,
"numeric" = switch(type,
"response" = .pred_numeric_response,
"prob" = .pred_ecdf,
"quantile" = .pred_quantile,
"density" = .pred_density)
)
}
## empirical distribution in each leaf
if (all(id %in% fitted)) {
tab <- tapply(1:NROW(response), fitted,
function(i) FUN(response[i], weights[i]), simplify = FALSE)
} else {
### id may also refer to inner nodes
tab <- as.array(lapply(sort(unique(id)), function(i) {
index <- fitted %in% nodeids(node, i, terminal = TRUE)
ret <- FUN(response[index], weights[index])
### no information about i in fitted
if (all(!index)) ret[1] <- NA
return(ret)
}))
names(tab) <- as.character(sort(unique(id)))
}
if (inherits(tab[[1]], "function") && !is.null(at))
tab <- lapply(tab, function(f) f(at))
tn <- names(tab)
dim(tab) <- NULL
names(tab) <- tn
tab
}
### simplify structure of predictions
.simplify_pred <- function(tab, id, nam) {
if (all(sapply(tab, length) == 1) & all(sapply(tab, is.atomic))) {
ret <- do.call("c", tab)
names(ret) <- names(tab)
#ret <- if (is.factor(tab[[1]]))
# factor(ret[as.character(id)], levels = 1:length(levels(tab[[1]])),
# labels = levels(tab[[1]]), ordered = is.ordered(tab[[1]]))
#else
# ret[as.character(id)]
#names(ret) <- nam
ret <- ret[as.character(id)]
} else if (length(unique(sapply(tab, length))) == 1 &
all(sapply(tab, is.numeric))) {
ret <- matrix(unlist(tab), nrow = length(tab), byrow = TRUE)
colnames(ret) <- names(tab[[1]])
rownames(ret) <- names(tab)
ret <- ret[as.character(id),, drop = FALSE]
rownames(ret) <- nam
} else {
ret <- tab[as.character(id)]
names(ret) <- nam
}
ret
}
data_party <- function(party, id = 1L)
UseMethod("data_party")
data_party.default <- function(party, id = 1L) {
extract <- function(id) {
if(is.null(party$fitted))
if(length(party$data) == 0) return(NULL)
else
stop("cannot subset data without fitted ids")
### which terminal nodes follow node number id?
nt <- nodeids(party, id, terminal = TRUE)
wi <- party$fitted[["(fitted)"]] %in% nt
ret <- if (length(party$data) == 0)
subset(party$fitted, wi)
else
subset(cbind(party$data, party$fitted), wi)
ret
}
if (length(id) > 1)
return(lapply(id, extract))
else
return(extract(id))
}
.list.rules.party <- function(x, i = NULL, ...) {
if (is.null(i)) i <- nodeids(x, terminal = TRUE)
if (length(i) > 1) {
ret <- sapply(i, .list.rules.party, x = x)
names(ret) <- if (is.character(i)) i else names(x)[i]
return(ret)
}
if (is.character(i) && !is.null(names(x)))
i <- which(names(x) %in% i)
stopifnot(length(i) == 1 & is.numeric(i))
stopifnot(i <= length(x) & i >= 1)
i <- as.integer(i)
dat <- data_party(x, i)
if (!is.null(x$fitted)) {
findx <- which("(fitted)" == names(dat))[1]
fit <- dat[,findx:ncol(dat), drop = FALSE]
dat <- dat[,-(findx:ncol(dat)), drop = FALSE]
if (ncol(dat) == 0)
dat <- x$data
} else {
fit <- NULL
dat <- x$data
}
rule <- c()
recFun <- function(node) {
if (id_node(node) == i) return(NULL)
kid <- sapply(kids_node(node), id_node)
whichkid <- max(which(kid <= i))
split <- split_node(node)
ivar <- varid_split(split)
svar <- names(dat)[ivar]
index <- index_split(split)
if (is.factor(dat[, svar])) {
if (is.null(index))
index <- ((1:nlevels(dat[, svar])) > breaks_split(split)) + 1
slevels <- levels(dat[, svar])[index == whichkid]
srule <- paste(svar, " %in% c(\"",
paste(slevels, collapse = "\", \"", sep = ""), "\")",
sep = "")
} else {
if (is.null(index)) index <- 1:length(kid)
breaks <- cbind(c(-Inf, breaks_split(split)),
c(breaks_split(split), Inf))
sbreak <- breaks[index == whichkid,]
right <- right_split(split)
srule <- c()
if (is.finite(sbreak[1]))
srule <- c(srule,
paste(svar, ifelse(right, ">", ">="), sbreak[1]))
if (is.finite(sbreak[2]))
srule <- c(srule,
paste(svar, ifelse(right, "<=", "<"), sbreak[2]))
srule <- paste(srule, collapse = " & ")
}
rule <<- c(rule, srule)
return(recFun(node[[whichkid]]))
}
node <- recFun(node_party(x))
paste(rule, collapse = " & ")
}
# plot --------------------------------------------------------------------
node_inner <- function(obj, id = TRUE, pval = TRUE, abbreviate = FALSE, fill = "white", gp = gpar())
{
meta <- obj$data
nam <- names(obj)
extract_label <- function(node) {
if(is.terminal(node)) return(rep.int("", 2L))
varlab <- character_split(split_node(node), meta)$name
varbas <- character_split(split_node(node), meta)$basid
if(!is.null(varbas)) varlab <- paste0(varlab, '.', varbas)
if(abbreviate > 0L) varlab <- abbreviate(varlab, as.integer(abbreviate))
## FIXME: make more flexible rather than special-casing p-value
if(pval) {
nullna <- function(x) is.null(x) || is.na(x)
pval <- suppressWarnings(try(!nullna(info_node(node)$pvalue), silent = TRUE))
pval <- if(inherits(pval, "try-error")) FALSE else pval
}
if(pval) {
pvalue <- node$info$pvalue
plab <- ifelse(pvalue < 10^(-3L),
paste("p <", 10^(-3L)),
paste("p =", round(pvalue, digits = 3L)))
} else {
plab <- ""
}
return(c(varlab, plab))
}
maxstr <- function(node) {
lab <- extract_label(node)
klab <- if(is.terminal(node)) "" else unlist(lapply(kids_node(node), maxstr))
lab <- c(lab, klab)
lab <- unlist(lapply(lab, function(x) strsplit(x, "\n")))
lab <- lab[which.max(nchar(lab))]
if(length(lab) < 1L) lab <- ""
return(lab)
}
nstr <- maxstr(node_party(obj))
if(nchar(nstr) < 6) nstr <- "aAAAAa"
### panel function for the inner nodes
rval <- function(node) {
pushViewport(viewport(gp = gp, name = paste("node_inner", id_node(node), "_gpar", sep = "")))
node_vp <- viewport(
x = unit(0.5, "npc"),
y = unit(0.5, "npc"),
width = unit(1, "strwidth", nstr) * 1.3,
height = unit(3, "lines"),
name = paste("node_inner", id_node(node), sep = ""),
gp = gp
)
pushViewport(node_vp)
xell <- c(seq(0, 0.2, by = 0.01),
seq(0.2, 0.8, by = 0.05),
seq(0.8, 1, by = 0.01))
yell <- sqrt(xell * (1-xell))
lab <- extract_label(node)
# Fill node box color based on covariates type
cov_type <- attr(meta[[sub("\\..*", "", lab[1])]], 'cov_type')
fill[1] <- if(!is.null(cov_type)){
switch(cov_type,
fdata = 'khaki1',
diagram = 'wheat',
graph = 'darkseagreen1')
} else {
switch(class(meta[[sub("\\..*", "", lab[1])]]),
logical = 'mistyrose',
integer = 'lightsalmon',
numeric = 'lightsalmon',
factor = 'aliceblue')
}
# Fill node id number box with a gray lighter than lightgray
fill[2] <- 'gray96'
grid.polygon(x = unit(c(xell, rev(xell)), "npc"),
y = unit(c(yell, -yell)+0.5, "npc"),
gp = gpar(fill = fill[1]))
## FIXME: something more general instead of pval ?
grid.text(lab[1L], y = unit(1.5 + 0.5 * (lab[2L] != ""), "lines"))
if(lab[2L] != "") grid.text(lab[2L], y = unit(1, "lines"))
if(id) {
nodeIDvp <- viewport(x = unit(0.5, "npc"), y = unit(1, "npc"),
width = max(unit(1, "lines"), unit(1.3, "strwidth", nam[id_node(node)])),
height = max(unit(1, "lines"), unit(1.3, "strheight", nam[id_node(node)])))
pushViewport(nodeIDvp)
grid.rect(gp = gpar(fill = fill[2]))
grid.text(nam[id_node(node)])
popViewport()
}
upViewport(2)
}
return(rval)
}
class(node_inner) <- "grapcon_generator"
.nobs_party <- function(party, id = 1L) {
dat <- data_party(party, id = id)
if("(weights)" %in% names(dat)) sum(dat[["(weights)"]]) else NROW(dat)
}
edge_simple <- function(obj, digits = 3, abbreviate = FALSE, justmin = Inf,
just = c("alternate", "increasing", "decreasing",
"equal"),
fill = "white")
{
meta <- obj$data
justfun <- function(i, split) {
myjust <- if(mean(nchar(split)) > justmin) {
match.arg(just, c("alternate", "increasing", "decreasing", "equal"))
} else {
"equal"
}
k <- length(split)
rval <- switch(myjust,
"equal" = rep.int(0, k),
"alternate" = rep(c(0.5, -0.5), length.out = k),
"increasing" = seq(from = -k/2, to = k/2, by = 1),
"decreasing" = seq(from = k/2, to = -k/2, by = -1)
)
unit(0.5, "npc") + unit(rval[i], "lines")
}
### panel function for simple edge labelling
function(node, i) {
#attempt to retrieve nobs for the kidnodes, instead of using regmatches etc:
#print(nodeapply(obj, ids = id_node(node), FUN = function(n) nrow(n$data), by_node = FALSE))
#would only take to be able to retrieve kidnodes' ids, instead of id_node(node)
curr_split_type <- attr(split_node(node), 'curr_split_type')
split_couple <- character_split(split_node(node), meta, digits = digits)$levels
y <- justfun(i, split_couple)
split <- split_couple[i]
if (any(grep(">", split) > 0) || any(grep("<", split) > 0)) {
# coeff or numeric/integer -> edge: parsed split
#parse to turn '<=' into the symbol 'less than or equal to'
#try() because parse(...) won't work for split = "< 10 Euro", for ex.
tr <- suppressWarnings(try(parse(text = paste("phantom(0)", split)), silent = TRUE))
#FIXME: parse adds unnecessary space to the left
if(!inherits(tr, "try-error")) split <- tr
grid.rect(y = y, gp = gpar(fill = fill, col = 0), width = unit(1.5, "strwidth", split))
grid.text(split, y = y, just = "center")
} else if (!is.null(curr_split_type) && curr_split_type == 'cluster'){
#cluster -> edge: nobs in the kidnode
#the number of obs in each kid node is calculated as the number of
#commas appearing in split (which is a string where the levels are
#separated by commas), plus one
n_kid <- as.character(lengths(regmatches(split, gregexpr(",", split))) + 1)
n_kid <- paste('n =', n_kid)
grid.rect(y = y, gp = gpar(fill = fill, col = 0), width = unit(1, "strwidth", n_kid))
grid.text(n_kid, y = y, just = "center")
} else {
#all the others -> edge: split
grid.rect(y = y, gp = gpar(fill = fill, col = 0), width = unit(1, "strwidth", split))
grid.text(split, y = y, just = "center")
}
}
}
class(edge_simple) <- "grapcon_generator"
.plot_node <- function(node, xlim, ylim, nx, ny,
terminal_panel, inner_panel, edge_panel,
tnex = 2, drop_terminal = TRUE, debug = FALSE) {
### the workhorse for plotting trees
### set up viewport for terminal node
if (is.terminal(node)) {
x <- xlim[1] + diff(xlim)/2
y <- ylim[1] + 0.5
tn_vp <- viewport(x = unit(x, "native"),
y = unit(y, "native") - unit(0.5, "lines"),
width = unit(1, "native"),
height = unit(tnex, "native") - unit(1, "lines"),
just = c("center", "top"),
name = paste("Node", id_node(node), sep = ""))
pushViewport(tn_vp)
if (debug)
grid.rect(gp = gpar(lty = "dotted", col = 4))
terminal_panel(node)
upViewport()
return(NULL)
}
## convenience function for computing relative position of splitting node
pos_frac <- function(node) {
if(is.terminal(node)) 0.5 else {
width_kids <- sapply(kids_node(node), width)
nk <- length(width_kids)
rval <- if(nk %% 2 == 0) sum(width_kids[1:(nk/2)]) else
mean(cumsum(width_kids)[nk/2 + c(-0.5, 0.5)])
rval/sum(width_kids)
}
}
## extract information
split <- split_node(node)
kids <- kids_node(node)
width_kids <- sapply(kids, width)
nk <- length(width_kids)
### position of inner node
x0 <- xlim[1] + pos_frac(node) * diff(xlim)
y0 <- max(ylim)
### relative positions of kids
xfrac <- sapply(kids, pos_frac)
x1lim <- xlim[1] + cumsum(c(0, width_kids))/sum(width_kids) * diff(xlim)
x1 <- x1lim[1:nk] + xfrac * diff(x1lim)
if (!drop_terminal) {
y1 <- rep(y0 - 1, nk)
} else {
y1 <- ifelse(sapply(kids, is.terminal), tnex - 0.5, y0 - 1)
}
### draw edges
for(i in 1:nk) grid.lines(x = unit(c(x0, x1[i]), "native"), y = unit(c(y0, y1[i]), "native"))
### create viewport for inner node
in_vp <- viewport(x = unit(x0, "native"),
y = unit(y0, "native"),
width = unit(1, "native"),
height = unit(1, "native") - unit(1, "lines"),
name = paste("Node", id_node(node), sep = ""))
pushViewport(in_vp)
if(debug) grid.rect(gp = gpar(lty = "dotted"))
inner_panel(node)
upViewport()
### position of labels
y1max <- max(y1)
ypos <- y0 - (y0 - y1max) * 0.5
xpos <- x0 - (x0 - x1) * 0.5 * (y0 - y1max)/(y0 - y1)
### setup labels
for(i in 1:nk) {
sp_vp <- viewport(x = unit(xpos[i], "native"),
y = unit(ypos, "native"),
width = unit(diff(x1lim)[i], "native"),
height = unit(1, "lines"),
name = paste("edge", id_node(node), "-", i, sep = ""))
pushViewport(sp_vp)
if(debug) grid.rect(gp = gpar(lty = "dotted", col = 2))
edge_panel(node, i)
upViewport()
}
## call workhorse for kids
for(i in 1:nk) .plot_node(kids[[i]],
c(x1lim[i], x1lim[i+1]), c(y1[i], 1), nx, ny,
terminal_panel, inner_panel, edge_panel,
tnex = tnex, drop_terminal = drop_terminal, debug = debug)
}
node_barplot <- function(obj,
col = "black",
fill = NULL,
bg = "white",
beside = NULL,
ymax = NULL,
ylines = NULL,
widths = 1,
gap = NULL,
reverse = NULL,
rot = 0,
just = c("center", "top"),
id = TRUE,
mainlab = NULL,
text = c("none", "horizontal", "vertical"),
gp = gpar())
{
## extract response
y <- obj$fitted[["(response)"]]
stopifnot(is.factor(y) || isTRUE(all.equal(round(y), y)) || is.data.frame(y))
## FIXME: This could be avoided by
## predict_party(obj, nodeids(obj, terminal = TRUE), type = "prob")
## but only for terminal nodes ^^^^
probs_and_n <- function(x) {
y1 <- x$fitted[["(response)"]]
if(!is.factor(y1)) {
if(is.data.frame(y1)) {
y1 <- t(as.matrix(y1))
} else {
y1 <- factor(y1, levels = min(y):max(y))
}
}
w <- x$fitted[["(weights)"]]
if(is.null(w)) w <- rep.int(1L, length(y1))
sumw <- if(is.factor(y1)) tapply(w, y1, sum) else drop(y1 %*% w)
sumw[is.na(sumw)] <- 0
prob <- c(sumw/sum(w), sum(w))
names(prob) <- c(if(is.factor(y1)) levels(y1) else rownames(y1), "nobs")
prob
}
probs <- do.call("rbind", nodeapply(obj, nodeids(obj), probs_and_n, by_node = FALSE))
nobs <- probs[, "nobs"]
probs <- probs[, -ncol(probs), drop = FALSE]
if(is.factor(y)) {
ylevels <- levels(y)
if(is.null(beside)) beside <- if(length(ylevels) < 3L) FALSE else TRUE
if(is.null(ymax)) ymax <- if(beside) 1.1 else 1
if(is.null(gap)) gap <- if(beside) 0.1 else 0
} else {
if(is.null(beside)) beside <- TRUE
if(is.null(ymax)) ymax <- if(beside) max(probs) * 1.1 else max(probs)
ylevels <- colnames(probs)
if(length(ylevels) < 2) ylevels <- ""
if(is.null(gap)) gap <- if(beside) 0.1 else 0
}
if(is.null(reverse)) reverse <- !beside
if(is.null(fill)) fill <- gray.colors(length(ylevels))
if(is.null(ylines)) ylines <- if(beside) c(3, 2) else c(1.5, 2.5)
## text labels?
if(isTRUE(text)) text <- "horizontal"
if(!is.character(text)) text <- "none"
text <- match.arg(text, c("none", "horizontal", "vertical"))
### panel function for barplots in nodes
rval <- function(node) {
## id
nid <- id_node(node)
## parameter setup
pred <- probs[nid,]
if(reverse) {
pred <- rev(pred)
ylevels <- rev(ylevels)
}
np <- length(pred)
nc <- if(beside) np else 1
fill <- rep(fill, length.out = np)
widths <- rep(widths, length.out = nc)
col <- rep(col, length.out = nc)
ylines <- rep(ylines, length.out = 2)
gap <- gap * sum(widths)
yscale <- c(0, ymax)
xscale <- c(0, sum(widths) + (nc+1)*gap)
top_vp <- viewport(layout = grid.layout(nrow = 2, ncol = 3,
widths = unit(c(ylines[1], 1, ylines[2]), c("lines", "null", "lines")),
heights = unit(c(1, 1), c("lines", "null"))),
width = unit(1, "npc"),
height = unit(1, "npc") - unit(2, "lines"),
name = paste0("node_barplot", nid),
gp = gp)
pushViewport(top_vp)
grid.rect(gp = gpar(fill = bg, col = 0))
## main title
top <- viewport(layout.pos.col=2, layout.pos.row=1)
pushViewport(top)
if (is.null(mainlab)) {
mainlab <- if(id) {
function(id, nobs) sprintf("Node %s (n = %s)", id, nobs)
} else {
function(id, nobs) sprintf("n = %s", nobs)
}
}
if (is.function(mainlab)) {
mainlab <- mainlab(names(obj)[nid], nobs[nid])
}
grid.text(mainlab)
popViewport()
plot <- viewport(layout.pos.col=2, layout.pos.row=2,
xscale=xscale, yscale=yscale,
name = paste0("node_barplot", node$nodeID, "plot"),
clip = FALSE)
pushViewport(plot)
if(beside) {
xcenter <- cumsum(widths+gap) - widths/2
if(length(xcenter) > 1) grid.xaxis(at = xcenter, label = FALSE)
grid.text(ylevels, x = xcenter, y = unit(-1, "lines"),
just = just, rot = rot,
default.units = "native", check.overlap = TRUE)
grid.yaxis()
grid.rect(gp = gpar(fill = "transparent"))
grid.clip()
for (i in 1:np) {
grid.rect(x = xcenter[i], y = 0, height = pred[i],
width = widths[i],
just = c("center", "bottom"), default.units = "native",
gp = gpar(col = col[i], fill = fill[i]))
if(text != "none") {
grid.text(x = xcenter[i], y = pred[i] + 0.025,
label = paste(format(round(100 * pred[i], 1), nsmall = 1), "%", sep = ""),
just = if(text == "horizontal") c("center", "bottom") else c("left", "center"),
rot = if(text == "horizontal") 0 else 90,
default.units = "native")
}
}
} else {
ycenter <- cumsum(pred) - pred
if(np > 1) {
grid.text(ylevels[1], x = unit(-1, "lines"), y = 0,
just = c("left", "center"), rot = 90,
default.units = "native", check.overlap = TRUE)
grid.text(ylevels[np], x = unit(-1, "lines"), y = ymax,
just = c("right", "center"), rot = 90,
default.units = "native", check.overlap = TRUE)
}
if(np > 2) {
grid.text(ylevels[-c(1,np)], x = unit(-1, "lines"), y = ycenter[-c(1,np)],
just = "center", rot = 90,
default.units = "native", check.overlap = TRUE)
}
grid.yaxis(main = FALSE)
grid.clip()
grid.rect(gp = gpar(fill = "transparent"))
for (i in 1:np) {
grid.rect(x = xscale[2]/2, y = ycenter[i], height = min(pred[i], ymax - ycenter[i]),
width = widths[1],
just = c("center", "bottom"), default.units = "native",
gp = gpar(col = col[i], fill = fill[i]))
}
}
grid.rect(gp = gpar(fill = "transparent"))
upViewport(2)
}
return(rval)
}
class(node_barplot) <- "grapcon_generator"
node_boxplot <- function(obj,
col = "black",
fill = "lightgray",
bg = "white",
width = 0.5,
yscale = NULL,
ylines = 3,
cex = 0.5,
id = TRUE,
mainlab = NULL,
gp = gpar())
{
y <- obj$fitted[["(response)"]]
stopifnot(is.numeric(y))
if (is.null(yscale))
yscale <- range(y) + c(-0.1, 0.1) * diff(range(y))
### panel function for boxplots in nodes
rval <- function(node) {
## extract data
nid <- id_node(node)
dat <- data_party(obj, nid)
yn <- dat[["(response)"]]
wn <- dat[["(weights)"]]
if(is.null(wn)) wn <- rep(1, length(yn))
## parameter setup
x <- boxplot(rep.int(yn, wn), plot = FALSE)
top_vp <- viewport(layout = grid.layout(nrow = 2, ncol = 3,
widths = unit(c(ylines, 1, 1),
c("lines", "null", "lines")),
heights = unit(c(1, 1), c("lines", "null"))),
width = unit(1, "npc"),
height = unit(1, "npc") - unit(2, "lines"),
name = paste("node_boxplot", nid, sep = ""),
gp = gp)
pushViewport(top_vp)
grid.rect(gp = gpar(fill = bg, col = 0))
## main title
top <- viewport(layout.pos.col=2, layout.pos.row=1)
pushViewport(top)
if (is.null(mainlab)) {
mainlab <- if(id) {
function(id, nobs) sprintf("Node %s (n = %s)", id, nobs)
} else {
function(id, nobs) sprintf("n = %s", nobs)
}
}
if (is.function(mainlab)) {
mainlab <- mainlab(names(obj)[nid], sum(wn))
}
grid.text(mainlab)
popViewport()
plot <- viewport(layout.pos.col = 2, layout.pos.row = 2,
xscale = c(0, 1), yscale = yscale,
name = paste0("node_boxplot", nid, "plot"),
clip = FALSE)
pushViewport(plot)
grid.yaxis()
grid.rect(gp = gpar(fill = "transparent"))
grid.clip()
xl <- 0.5 - width/4
xr <- 0.5 + width/4
## box & whiskers
grid.lines(unit(c(xl, xr), "npc"),
unit(x$stats[1], "native"), gp = gpar(col = col))
grid.lines(unit(0.5, "npc"),
unit(x$stats[1:2], "native"), gp = gpar(col = col, lty = 2))
grid.rect(unit(0.5, "npc"), unit(x$stats[2], "native"),
width = unit(width, "npc"), height = unit(diff(x$stats[c(2, 4)]), "native"),
just = c("center", "bottom"),
gp = gpar(col = col, fill = fill))
grid.lines(unit(c(0.5 - width/2, 0.5+width/2), "npc"),
unit(x$stats[3], "native"), gp = gpar(col = col, lwd = 2))
grid.lines(unit(0.5, "npc"), unit(x$stats[4:5], "native"),
gp = gpar(col = col, lty = 2))
grid.lines(unit(c(xl, xr), "npc"), unit(x$stats[5], "native"),
gp = gpar(col = col))
## outlier
n <- length(x$out)
if (n > 0) {
index <- 1:n ## which(x$out > yscale[1] & x$out < yscale[2])
if (length(index) > 0)
grid.points(unit(rep.int(0.5, length(index)), "npc"),
unit(x$out[index], "native"),
size = unit(cex, "char"), gp = gpar(col = col))
}
upViewport(2)
}
return(rval)
}
class(node_boxplot) <- "grapcon_generator"
node_surv <- function(obj, col = "black", bg = "white", yscale = c(0, 1), ylines = 2,
id = TRUE, mainlab = NULL, gp = gpar(), ...)
{
## extract response
y <- obj$fitted[["(response)"]]
stopifnot(inherits(y, "Surv"))
## helper functions
mysurvfit <- function(y, weights, ...)
survfit(y ~ 1, weights = weights)
### structure(
### survival:::survfitKM(x = gl(1, NROW(y)), y = y, casewt = weights, ...),
### class = "survfit")
dostep <- function(x, y) {
### create a step function based on x, y coordinates
### modified from `survival:print.survfit'
if (is.na(x[1] + y[1])) {
x <- x[-1]
y <- y[-1]
}
n <- length(x)
if (n > 2) {
# replace verbose horizonal sequences like
# (1, .2), (1.4, .2), (1.8, .2), (2.3, .2), (2.9, .2), (3, .1)
# with (1, .2), (3, .1). They are slow, and can smear the looks
# of the line type.
dupy <- c(TRUE, diff(y[-n]) !=0, TRUE)
n2 <- sum(dupy)
#create a step function
xrep <- rep(x[dupy], c(1, rep(2, n2-1)))
yrep <- rep(y[dupy], c(rep(2, n2-1), 1))
RET <- list(x = xrep, y = yrep)
} else {
if (n == 1) {
RET <- list(x = x, y = y)
} else {
RET <- list(x = x[c(1,2,2)], y = y[c(1,1,2)])
}
}
return(RET)
}
### panel function for Kaplan-Meier curves in nodes
rval <- function(node) {
## extract data
nid <- id_node(node)
dat <- data_party(obj, nid)
yn <- dat[["(response)"]]
wn <- dat[["(weights)"]]
if(is.null(wn)) wn <- rep(1, NROW(yn))
## get Kaplan-Meier curver in node
km <- mysurvfit(yn, weights = wn, ...)
a <- dostep(km$time, km$surv)
## set up plot
yscale <- yscale
xscale <- c(0, max(y[,1]))
top_vp <- viewport(layout = grid.layout(nrow = 2, ncol = 3,
widths = unit(c(ylines, 1, 1),
c("lines", "null", "lines")),
heights = unit(c(1, 1), c("lines", "null"))),
width = unit(1, "npc"),
height = unit(1, "npc") - unit(2, "lines"),
name = paste("node_surv", nid, sep = ""), gp = gp)
pushViewport(top_vp)
grid.rect(gp = gpar(fill = bg, col = 0))
## main title
top <- viewport(layout.pos.col=2, layout.pos.row=1)
pushViewport(top)
if (is.null(mainlab)) {
mainlab <- if(id) {
function(id, nobs) sprintf("Node %s (n = %s)", id, nobs)
} else {
function(id, nobs) sprintf("n = %s", nobs)
}
}
if (is.function(mainlab)) {
mainlab <- mainlab(nid, sum(wn))
}
grid.text(mainlab)
popViewport()
plot <- viewport(layout.pos.col=2, layout.pos.row=2,
xscale=xscale, yscale = yscale,
name = paste0("node_surv", nid, "plot"),
clip = FALSE)
pushViewport(plot)
grid.xaxis()
grid.yaxis()
grid.rect(gp = gpar(fill = "transparent"))
grid.clip()
grid.lines(unit(a$x, "native"), unit(a$y, "native"), gp = gpar(col = col))
upViewport(2)
}
return(rval)
}
class(node_surv) <- "grapcon_generator"
node_ecdf <- function(obj, col = "black", bg = "white", ylines = 2,
id = TRUE, mainlab = NULL, gp = gpar(), ...)
{
## extract response
y <- obj$fitted[["(response)"]]
stopifnot(inherits(y, "numeric") || inherits(y, "integer"))
dostep <- function(f) {
x <- knots(f)
y <- f(x)
### create a step function based on x, y coordinates
### modified from `survival:print.survfit'
if (is.na(x[1] + y[1])) {
x <- x[-1]
y <- y[-1]
}
n <- length(x)
if (n > 2) {
# replace verbose horizonal sequences like
# (1, .2), (1.4, .2), (1.8, .2), (2.3, .2), (2.9, .2), (3, .1)
# with (1, .2), (3, .1). They are slow, and can smear the looks
# of the line type.
dupy <- c(TRUE, diff(y[-n]) !=0, TRUE)
n2 <- sum(dupy)
#create a step function
xrep <- rep(x[dupy], c(1, rep(2, n2-1)))
yrep <- rep(y[dupy], c(rep(2, n2-1), 1))
RET <- list(x = xrep, y = yrep)
} else {
if (n == 1) {
RET <- list(x = x, y = y)
} else {
RET <- list(x = x[c(1,2,2)], y = y[c(1,1,2)])
}
}
return(RET)
}
### panel function for ecdf in nodes
rval <- function(node) {
## extract data
nid <- id_node(node)
dat <- data_party(obj, nid)
yn <- dat[["(response)"]]
wn <- dat[["(weights)"]]
if(is.null(wn)) wn <- rep(1, NROW(yn))
## get ecdf in node
f <- .pred_ecdf(yn, wn)
a <- dostep(f)
## set up plot
yscale <- c(0, 1)
xscale <- range(y)
a$x <- c(xscale[1], a$x[1], a$x, xscale[2])
a$x <- a$x - min(a$x)
a$x <- a$x / max(a$x)
a$y <- c(0, 0, a$y, 1)
top_vp <- viewport(layout = grid.layout(nrow = 2, ncol = 3,
widths = unit(c(ylines, 1, 1),
c("lines", "null", "lines")),
heights = unit(c(1, 1), c("lines", "null"))),
width = unit(1, "npc"),
height = unit(1, "npc") - unit(2, "lines"),
name = paste("node_ecdf", nid, sep = ""), gp = gp)
pushViewport(top_vp)
grid.rect(gp = gpar(fill = bg, col = 0))
## main title
top <- viewport(layout.pos.col=2, layout.pos.row=1)
pushViewport(top)
if (is.null(mainlab)) {
mainlab <- if(id) {
function(id, nobs) sprintf("Node %s (n = %s)", id, nobs)
} else {
function(id, nobs) sprintf("n = %s", nobs)
}
}
if (is.function(mainlab)) {
mainlab <- mainlab(nid, sum(wn))
}
grid.text(mainlab)
popViewport()
plot <- viewport(layout.pos.col=2, layout.pos.row=2,
xscale=xscale, yscale=yscale,
name = paste0("node_surv", nid, "plot"),
clip = FALSE)
pushViewport(plot)
grid.xaxis()
grid.yaxis()
grid.rect(gp = gpar(fill = "transparent"))
grid.clip()
grid.lines(a$x, a$y, gp = gpar(col = col))
upViewport(2)
}
return(rval)
}
class(node_ecdf) <- "grapcon_generator"
node_mvar <- function(obj, which = NULL, id = TRUE, pop = TRUE, ylines = NULL, mainlab = NULL, varlab = TRUE, bg = "white", ...)
{
## obtain dependent variables
y <- obj$fitted[["(response)"]]
## fitted node ids
fitted <- obj$fitted[["(fitted)"]]
## number of panels needed
if(is.null(which)) which <- 1L:NCOL(y)
k <- length(which)
rval <- function(node) {
tid <- id_node(node)
nobs <- .nobs_party(obj, id = tid)
## set up top viewport
top_vp <- viewport(layout = grid.layout(nrow = k, ncol = 2,
widths = unit(c(ylines, 1), c("lines", "null")), heights = unit(k, "null")),
width = unit(1, "npc"), height = unit(1, "npc") - unit(2, "lines"),
name = paste("node_mvar", tid, sep = ""))
pushViewport(top_vp)
grid.rect(gp = gpar(fill = bg, col = 0))
## main title
if (is.null(mainlab)) {
mainlab <- if(id) {
function(id, nobs) sprintf("Node %s (n = %s)", id, nobs)
} else {
function(id, nobs) sprintf("n = %s", nobs)
}
}
if (is.function(mainlab)) {
mainlab <- mainlab(tid, nobs)
}
for(i in 1L:k) {
tmp <- obj
tmp$fitted[["(response)"]] <- y[,which[i]]
if(varlab) {
nm <- names(y)[which[i]]
if(i == 1L) nm <- paste(mainlab, nm, sep = ": ")
} else {
nm <- if(i == 1L) mainlab else ""
}
pfun <- switch(sapply(y, class)[which[i]],
"Surv" = node_surv(tmp, id = id, mainlab = nm, ...),
"factor" = node_barplot(tmp, id = id, mainlab = nm, ...),
"ordered" = node_barplot(tmp, id = id, mainlab = nm, ...),
node_boxplot(tmp, id = id, mainlab = nm, ...))
## select panel
plot_vpi <- viewport(layout.pos.col = 2L, layout.pos.row = i)
pushViewport(plot_vpi)
## call panel function
pfun(node)
if(pop) popViewport() else upViewport()
}
if(pop) popViewport() else upViewport()
}
return(rval)
}
class(node_mvar) <- "grapcon_generator"
# split -------------------------------------------------------------------
partysplit <- function(varid, breaks = NULL, index = NULL, right = TRUE,
prob = NULL, info = NULL, centroids = NULL, basid = NULL) {
### informal class for splits
split <- vector(mode = "list", length = 8)
names(split) <- c("varid", "breaks", "index", "right", "prob", "info", "centroids", "basid")
### split is an id referring to a variable
if (!is.integer(varid))
stop(sQuote("varid"), " ", "is not integer")
split$varid <- varid
if (is.null(breaks) && is.null(index))
stop("either", " ", sQuote("breaks"), " ", "or", " ",
sQuote("index"), " ", "must be given")
### vec
if (!is.null(breaks)) {
if (is.numeric(breaks) && (length(breaks) >= 1)) {
### FIXME: I think we need to make sure breaks are double in C
split$breaks <- as.double(breaks)
} else {
stop(sQuote("break"), " ",
"should be a numeric vector containing at least one element")
}
}
if (!is.null(index)) {
if (is.integer(index)) {
if (!(length(index) >= 2))
stop(sQuote("index"), " ", "has less than two elements")
if (!(min(index, na.rm = TRUE) == 1))
stop("minimum of", " ", sQuote("index"), " ", "is not equal to 1")
if (!all.equal(diff(sort(unique(index))), rep(1, max(index, na.rm = TRUE) - 1)))
stop(sQuote("index"), " ", "is not a contiguous sequence")
split$index <- index
} else {
stop(sQuote("index"), " ", "is not a class", " ", sQuote("integer"))
}
if (!is.null(breaks)) {
if (length(breaks) != (length(index) - 1))
stop("length of", " ", sQuote("breaks"), " ",
"does not match length of", " ", sQuote("index"))
}
}
if (is.logical(right) & !is.na(right))
split$right <- right
else
stop(sQuote("right"), " ", "is not a logical")
if (!is.null(prob)) {
if (!is.double(prob) ||
(any(prob < 0) | any(prob > 1) | !isTRUE(all.equal(sum(prob), 1))))
stop(sQuote("prob"), " ", "is not a vector of probabilities")
if (!is.null(index)) {
if (!(max(index, na.rm = TRUE) == length(prob)))
stop("incorrect", " ", sQuote("index"))
}
if (!is.null(breaks) && is.null(index)) {
if (!(length(breaks) == (length(prob) - 1)))
stop("incorrect", " ", sQuote("breaks"))
}
split$prob <- prob
}
if (!is.null(info))
split$info <- info
if (!is.null(centroids))
split$centroids <- centroids
if (!is.null(basid))
if (!is.integer(varid)){
stop(sQuote("varid"), " ", "is not integer")
} else {
split$basid <- basid
}
class(split) <- "partysplit"
return(split)
}
centroids_split <- function(split) {
if (!(inherits(split, "partysplit")))
stop(sQuote("split"), " ", "is not an object of class",
" ", sQuote("partysplit"))
split$centroids
}
basid_split <- function(split) {
if (!(inherits(split, "partysplit")))
stop(sQuote("split"), " ", "is not an object of class",
" ", sQuote("partysplit"))
split$basid
}
kidids_split <- function(split, data, vmatch = 1:length(data), obs = NULL) {
varid <- varid_split(split)
basid <- basid_split(split)
class(data) <- "list" ### speed up
if(!is.null(basid)){ #coeff
x <- data[[vmatch[varid]]][[as.character(basid)]]
} else {
x <- data[[vmatch[varid]]]
}
if (!is.null(obs)) x <- x[obs]
if (is.null(breaks_split(split))) {
if (storage.mode(x) != "integer")
stop("variable", " ", vmatch[varid], " ", "is not integer")
} else {
### labels = FALSE returns integers and is faster
### <FIXME> use findInterval instead of cut?
# x <- cut.default(as.numeric(x), labels = FALSE,
# breaks = unique(c(-Inf, breaks_split(split), Inf)), ### breaks_split(split) = Inf possible (MIA)
# right = right_split(split))
x <- .bincode(as.numeric(x), # labels = FALSE,
breaks = unique(c(-Inf, breaks_split(split), Inf)), ### breaks_split(split) = Inf possible (MIA)
right = right_split(split))
### </FIXME>
}
index <- index_split(split)
### empty factor levels correspond to NA and return NA here
### and thus the corresponding observations will be treated
### as missing values (surrogate or random splits):
if (!is.null(index))
x <- index[x]
return(x)
}
kidids_split_predict <- function(split, data, vmatch = 1:length(data), obs = NULL) {
varid <- varid_split(split)
basid <- basid_split(split)
class(data) <- "list" ### speed up
if(!is.null(basid)){ #coeff
x <- data[[vmatch[varid]]][[as.character(basid)]]
} else {
x <- data[[vmatch[varid]]]
}
if (!is.null(obs)) x <- x[obs]
if (is.null(breaks_split(split))) {
if(!is.null(centroids_split(split))){
centroids <- centroids_split(split)
centroids_dist <- sapply(centroids, dist_comp_cl, x = x, lp = 2)
x <- if(!is.null(dim(centroids_dist))) apply(centroids_dist, 1, which.min)
else which.min(centroids_dist)
}
if (storage.mode(x) != "integer")
stop("variable", " ", vmatch[varid], " ", "is not integer")
} else {
### labels = FALSE returns integers and is faster
### <FIXME> use findInterval instead of cut?
# x <- cut.default(as.numeric(x), labels = FALSE,
# breaks = unique(c(-Inf, breaks_split(split), Inf)), ### breaks_split(split) = Inf possible (MIA)
# right = right_split(split))
x <- .bincode(as.numeric(x), # labels = FALSE,
breaks = unique(c(-Inf, breaks_split(split), Inf)), ### breaks_split(split) = Inf possible (MIA)
right = right_split(split))
### </FIXME>
}
index <- index_split(split)
### empty factor levels correspond to NA and return NA here
### and thus the corresponding observations will be treated
### as missing values (surrogate or random splits):
if (!is.null(index) & is.null(centroids_split(split)))
x <- index[x]
return(x)
}
character_split <- function(split, data = NULL, digits = getOption("digits") - 2) {
varid <- varid_split(split)
basid <- basid_split(split)
if (!is.null(data)) {
## names and labels
lev <- lapply(data, levels)[[varid]]
mlab <- names(data)[varid]
## determine split type
type <- sapply(data, function(x) class(x)[1])[varid_split(split)]
type[!(type %in% c("factor", "ordered"))] <- "numeric"
} else {
## (bad) default names and labels
lev <- NULL
mlab <- paste("V", varid, sep = "")
type <- "numeric"
}
## process defaults for breaks and index
breaks <- breaks_split(split)
index <- index_split(split)
right <- right_split(split)
if (is.null(breaks)) breaks <- 1:(length(index) - 1)
if (is.null(index)) index <- 1:(length(breaks) + 1)
## check whether ordered are really ordered
if (type == "ordered") {
if (length(breaks) > 1)
type <- "factor"
}
### <FIXME> format ordered multiway splits? </FIXME>
switch(type,
"factor" = {
nindex <- index[cut(seq_along(lev), c(-Inf, breaks, Inf), right = right)]
dlab <- as.vector(tapply(lev, nindex, paste, collapse = ", "))
},
"ordered" = {
if (length(breaks) == 1) {
if (right)
dlab <- paste(c("<=", ">"), lev[breaks], sep = " ")
else
dlab <- paste(c("<", ">="), lev[breaks], sep = " ")
} else {
stop("") ### see above
}
dlab <- dlab[index]
},
"numeric" = {
breaks <- round(breaks, digits)
if (length(breaks) == 1) {
if (right)
dlab <- paste(c("<=", ">"), breaks, sep = " ")
else
dlab <- paste(c("<", ">="), breaks, sep = " ")
} else {
dlab <- levels(cut(0, breaks = c(-Inf, breaks, Inf),
right = right))
}
dlab <- as.vector(tapply(dlab, index, paste, collapse = " | "))
}
)
return(list(name = mlab, basid = basid, levels = dlab))
}
# print -------------------------------------------------------------------
print.partynode <- function(x, data = NULL, names = NULL,
inner_panel = function(node) "", terminal_panel = function(node) " *",
prefix = "", first = TRUE, digits = getOption("digits") - 2, ...)
{
ids <- nodeids(x)
if(first) {
if(is.null(names)) names <- as.character(ids)
cat(paste(prefix, "[", names[which(ids == id_node(x))], "] root", sep = ""))
if(is.terminal(x)) {
char <- terminal_panel(x)
if(length(char) > 1L) {
cat(paste(char[1L], "\n",
paste(prefix, " ", char[-1L], sep = "", collapse = "\n"),
sep = ""), "\n")
} else {
cat(char, "\n")
}
} else {
cat("\n")
}
}
if (length(x) > 0) {
## add indentation
nextprefix <- paste(prefix, "| ", sep = "")
## split labels
slabs <- character_split(split_node(x), data = data, digits = digits, ...)
slabs <- ifelse(substr(slabs$levels, 1, 1) %in% c("<", ">"),
paste(if(!is.null(slabs$basid))
paste0(slabs$name, '.', slabs$basid) else slabs$name,
slabs$levels),
paste(if(!is.null(slabs$basid))
paste0(slabs$name, '.', slabs$basid) else slabs$name,
"in", slabs$levels))
## kid labels
knodes <- kids_node(x)
knam <- sapply(knodes, function(z) names[which(ids == id_node(z))])
klabs <- sapply(knodes, function(z)
if(is.terminal(z)) {
char <- terminal_panel(z)
if(length(char) > 1L) {
paste(char[1L], "\n",
paste(nextprefix, " ", char[-1L], sep = "", collapse = "\n"),
sep = "")
} else {
char
}
} else {
paste(inner_panel(z), collapse = "\n")
})
## merge, cat, and call recursively
labs <- paste("| ", prefix, "[", knam, "] ", slabs, klabs, "\n", sep = "")
for (i in 1:length(x)) {
cat(labs[i])
print.partynode(x[i], data = data, names = names[match(nodeids(x[i]), ids)],
inner_panel = inner_panel, terminal_panel = terminal_panel,
prefix = nextprefix, first = FALSE, digits = digits, ...)
}
}
}
print.party <- function(x,
terminal_panel = function(node) formatinfo_node(node, default = "*", prefix = ": "), tp_args = list(),
inner_panel = function(node) "", ip_args = list(),
header_panel = function(party) "",
footer_panel = function(party) "",
digits = getOption("digits") - 2, ...)
{
## header
cat(paste(header_panel(x), collapse = "\n"))
## nodes
if(inherits(terminal_panel, "grapcon_generator"))
terminal_panel <- do.call("terminal_panel", c(list(x), as.list(tp_args)))
if(inherits(inner_panel, "grapcon_generator"))
inner_panel <- do.call("inner_panel", c(list(x), as.list(ip_args)))
print(node_party(x), x$data, names = names(x),
terminal_panel = terminal_panel, inner_panel = inner_panel,
digits = digits, ...)
## footer
cat(paste(footer_panel(x), collapse = "\n"))
}
print.simpleparty <- function(x, digits = getOption("digits") - 4,
header = NULL, footer = TRUE, ...)
{
## header panel
if(is.null(header)) header <- !is.null(terms(x))
header_panel <- if(header) function(party) {
c("", "Model formula:", deparse(formula(terms(party))), "", "Fitted party:", "")
} else function(party) ""
## footer panel
footer_panel <- if(footer) function(party) {
n <- width(party)
n <- format(c(length(party) - n, n))
c("", paste("Number of inner nodes: ", n[1]),
paste("Number of terminal nodes:", n[2]), "")
} else function (party) ""
## terminal panel
terminal_panel <- function(node) formatinfo_node(node,
FUN = .make_formatinfo_simpleparty(x, digits = digits),
default = "*", prefix = ": ")
print.party(x, terminal_panel = terminal_panel,
header_panel = header_panel, footer_panel = footer_panel, ...)
}
# other -------------------------------------------------------------------
.make_formatinfo_simpleparty <- function(x, digits = getOption("digits") - 4, sep = "")
{
## digit processing
digits <- max(c(0, digits))
digits2 <- max(c(0, digits - 2))
## type of predictions
y <- node_party(x)$info$prediction
yclass <- class(y)[1]
if(yclass == "ordered") yclass <- "factor"
if(!(yclass %in% c("survfit", "factor"))) yclass <- "numeric"
## type of weights
n <- node_party(x)$info$n
if(is.null(names(n))) {
wdigits <- 0
wsym <- "n"
} else {
if(names(n) == "w") {
wdigits <- max(c(0, digits - 2))
wsym <- "w"
} else {
wdigits <- 0
wsym <- "n"
}
}
## compute terminal node labels
FUN <- function(info) {
yhat <- info$prediction
if (yclass == "survfit") {
yhat <- .median_survival_time(yhat)
yclass <- "numeric"
}
if(yclass == "numeric") yhat <- format(round(yhat, digits = digits), nsmall = digits)
w <- info$n
yerr <- if(is.null(info$error)) "" else paste(", err = ",
format(round(info$error, digits = digits2), nsmall = digits2),
names(info$error), sep = "")
rval <- paste(yhat, sep,
" (", wsym, " = ", format(round(w, digits = wdigits), nsmall = wdigits),
yerr, ")", sep = "")
unlist(strsplit(rval, "\n"))
}
return(FUN)
}
.resample <- function(x, ...) x[sample.int(length(x), ...)]
.median_survival_time <- function(x) {
minmin <- function(y, xx) {
if (any(!is.na(y) & y==.5)) {
if (any(!is.na(y) & y <.5))
.5*(min(xx[!is.na(y) & y==.5]) + min(xx[!is.na(y) & y<.5]))
else
.5*(min(xx[!is.na(y) & y==.5]) + max(xx[!is.na(y) & y==.5]))
} else min(xx[!is.na(y) & y<=.5])
}
med <- suppressWarnings(minmin(x$surv, x$time))
return(med)
}
### get the recursive index
### obj is of class "partynode"
.get_path <- function(obj, i) {
idx <- c()
recFun <- function(node, i) {
if (id_node(node) == i) return(NULL)
idx <<- c(idx, which(names(unclass(node)) == "kids"))
kid <- sapply(kids_node(node), id_node)
nextid <- max(which(kid <= i))
idx <<- c(idx, nextid)
return(recFun(node[[nextid]], i))
}
out <- recFun(obj, i)
return(idx)
}
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