R/34_DECISION_TREE.R
In andrija-djurovic/PDtoolkit: Collection of Tools for PD Rating Model Development and Validation
Defines functions
predict.cdt
t2p.cat
t2p.num
c_best_split_cat
c_best_split_num
c_best_split
cdt.algo
decision.tree
Documented in
decision.tree
predict.cdt
#' Custom decision tree algorithm
#'
#' \code{decision.tree} runs customized decision tree algorithm. Customization refers to minimum
#' percentage of observations and defaults in each node, maximum tree depth, monotonicity condition
#' at each splitting node and statistical test (test of two proportions) used for node splitting.
#'@seealso \code{\link{predict.cdt}}
#'@param db Data frame of risk factors and target variable supplied for interaction extraction.
#'@param rf Character vector of risk factor names on which decision tree is run.
#'@param target Name of target variable (default indicator 0/1) within db argument.
#'@param min.pct.obs Minimum percentage of observation in each leaf. Default is 0.05 or 30 observations.
#'@param min.avg.rate Minimum percentage of defaults in each leaf. Default is 0.01 or 1 default case.
#'@param p.value Significance level of test of two proportions for splitting criteria. Default is 0.05.
#'@param max.depth Maximum tree depth.
#'@param monotonicity Logical indicator. If \code{TRUE}, observed trend between risk factor and target will be preserved
#' in splitting node.
#'@return The command \code{decision.tree} returns a object of class cdt. For details on output elements see the Examples.
#'@examples
#'suppressMessages(library(PDtoolkit))
#'data(loans)
#'#modify risk factors in order to show how the function works with missing values
#'loans$"Account Balance"[1:10] <- NA
#'loans$"Duration of Credit (month)"[c(13, 15)] <- NA
#'tree.res <- decision.tree(db = loans,
#' rf = c("Account Balance", "Duration of Credit (month)"),
#' target = "Creditability",
#' min.pct.obs = 0.05,
#' min.avg.rate = 0.01,
#' p.value = 0.05,
#' max.depth = NA,
#' monotonicity = TRUE)
#'str(tree.res)
#'@export
decision.tree <- function(db, rf, target, min.pct.obs = 0.05, min.avg.rate = 0.01, p.value = 0.5, max.depth = NA, monotonicity) {
ops <- options(warn = -1)
on.exit(options(ops))
if (!is.data.frame(db)) {
stop("db is not a data frame.")
}
if (any(!c(rf, target)%in%names(db))) {
stop("rf or target variable do not exist in supplied db.")
}
if (!is.numeric(min.pct.obs) | !is.numeric(min.avg.rate) |
min.pct.obs <= 0 | min.pct.obs >= 1 |
min.avg.rate <= 0 | min.avg.rate >= 1) {
stop(" min.pct.obs and min.avg.rate has to be numeric values greater than 0 and less than 1")
}
if (!is.na(max.depth)) {
if (!is.numeric(max.depth) | max.depth < 1) {
stop("max.depth has to be numeric value greater or equal to 1.")
}
}
if (is.na(monotonicity) | !is.logical(monotonicity)) {
stop("monotonicity has to be logical value - TRUE or FALSE")
}
d <- db[, c(target, rf)]
d <- d[!is.na(d[, target]), ]
nr <- nrow(d)
if (nr == 0) {
stop("target contains only missing values.")
}
if (length(unique(d[, target])) == 1) {
stop("target has only 1 class.")
}
if (!sum(d[, target]%in%c(0, 1)) == nr) {
stop("target contains value(s) different than 0 and 1.")
}
nd <- sum(d[, target])
rf.check <- sapply(d[, rf, drop = FALSE], function(x) sum(is.na(x)) == length(x))
if (any(rf.check)) {
msg <- paste0("The following risk factor(s) contain(s) only missing values: ",
paste0(names(rf.check)[rf.check], collapse = ", "), ".")
stop(msg)
}
tree.res <- cdt.algo(d = d,
rf = rf,
target = target,
min.obs = ceiling(ifelse(nr * min.pct.obs < 30, 30, nr * min.pct.obs)),
min.rate = ceiling(ifelse(nd * min.avg.rate < 1, 1, nd * min.avg.rate)),
p.value = p.value,
max.depth = max.depth,
monotonicity = monotonicity)
if (nrow(tree.res) > 1) {
where <- extract.interactions(db = db, tree.info = tree.res)
nodes <- unname(c(where, recursive = TRUE))
} else {
nodes <- rep(1, nrow(db))
}
averages <- cbind.data.frame(where = nodes, target = db[, target]) %>%
group_by(where) %>%
summarise(average = mean(target, na.rm = TRUE))
averages <- averages[!is.na(averages$where), ]
return(structure(list(inputs = data.frame(target, min.pct.obs, min.avg.rate, p.value, max.depth, monotonicity),
tree.info = tree.res,
where = nodes,
average = data.frame(averages),
data = db),
class = "cdt"))
}
#customized decision tree algo
cdt.algo <- function(d, rf, target, min.obs, min.rate, p.value, max.depth, monotonicity) {
rf.num <- sapply(d[, rf, drop = FALSE], is.numeric)
rf.num <- names(rf.num)[rf.num]
rf.cat <- rf[!rf%in%rf.num]
if (monotonicity & length(rf.num) > 0) {
corr.dir <- sapply(rf.num, function(x) sign(cor(d[, x], d[, target],
method = "spearman",
use = "complete.obs")))
} else {
corr.dir <- c()
}
#initialize the process
do.splits <- TRUE
tree.info <- data.frame(node = 1,
rf = NA,
nobs = nrow(d),
filter = NA,
terminal = "split",
stringsAsFactors = FALSE)
#start splitting
while (do.splits) {
to.calculate <- which(tree.info$terminal == "split")
for (i in to.calculate) {
if (!is.na(tree.info$filter[i])) {
tbl.l <- subset(d, eval(parse(text = tree.info$filter[i])))
} else {
tbl.l <- d
}
splitting <- lapply(rf, function(x) {
c_best_split(tbl = tbl.l,
rf.l = x,
target = target,
min.obs = min.obs,
min.rate = min.rate,
p.value = p.value,
monodir = corr.dir[x])})
bs.rf.indx <- which.min(sapply(splitting, "[[", "p.val"))
if (length(bs.rf.indx) == 0) {
tree.info$terminal[i] <- "leaf"
next
}
tmp.sp <- splitting[[bs.rf.indx]]
mn <- max(tree.info$node)
if (tmp.sp$rf.t%in%"numeric") {
tmp.filter <- c(paste(tmp.sp$rf, "<", tmp.sp$split), paste(tmp.sp$rf, ">=", tmp.sp$split))
} else {
tmp.filter <- c(paste0(tmp.sp$rf, "%in%", tmp.sp$split), paste0("!", tmp.sp$rf, "%in%", tmp.sp$split))
}
if (!is.na(tree.info$filter[i])) {
tmp.filter <- paste(tree.info$filter[i], tmp.filter, sep = " & ")
}
tmp.filter.nobs <- paste(paste0("!is.na(", tmp.sp$rf, ")"), tmp.filter, sep = " & ")
tmp.nobs <- sapply(tmp.filter.nobs, FUN = function(i, x) {
nrow(subset(x = x, subset = eval(parse(text = i))))
}, x = tbl.l)
children <- data.frame(node = c(mn + 1, mn + 2),
rf = tmp.sp$rf,
nobs = unname(tmp.nobs),
filter = tmp.filter,
terminal = rep("split", 2),
row.names = NULL)
tree.info$terminal[i] <- "parent"
tree.info <- rbind(tree.info, children)
if (!is.na(max.depth) & sum(tree.info$terminal%in%c("leaf", "split")) > max.depth) {
tree.info$terminal[tree.info$terminal%in%"split"] <- "leaf"
do.splits <- FALSE
break
}
}
do.splits <- !all(tree.info$terminal != "split")
}
tree.info$ind <- as.numeric(ave(tree.info$terminal, tree.info$terminal,
FUN = function(x) if (all(x%in%"leaf")) {1:length(x)} else {NA}))
return(tree.info)
}
#customized node split functions
c_best_split <- function(tbl, rf.l, target, min.obs, min.rate, p.value, monodir) {
rf.c <- is.numeric(tbl[, rf.l])
if (rf.c) {
bs <- c_best_split_num(tbl = tbl,
rf.l = rf.l,
target = target,
min.obs = min.obs,
min.rate = min.rate,
p.value = p.value,
monodir = monodir)
bs <- cbind.data.frame(rf.t = "numeric", bs)
} else {
bs <- c_best_split_cat(tbl = tbl,
rf.l = rf.l,
target = target,
min.obs = min.obs,
min.rate = min.rate,
p.value = p.value)
bs <- cbind.data.frame(rf.t = "categorical", bs)
}
return(bs)
}
c_best_split_num <- function(tbl, rf.l, target, min.obs, min.rate, p.value, monodir) {
g <- unname(quantile(tbl[, rf.l],seq(1 / 50, 1, length.out = 50), type = 3, na.rm = TRUE))
g <- unique(c(min(tbl[, rf.l], na.rm = TRUE), g))
if (length(g) == 1 | all(is.na(tbl[, rf.l]))) {
res <- data.frame(rf = paste0("`", rf.l, "`"), p.val = NA, split = NA)
return(res)
}
tbl$bin <- cut(tbl[, rf.l], breaks = g, include.lowest = TRUE)
tbl <- tbl[complete.cases(tbl), ]
tbl.s <- tbl %>%
group_by(bin) %>%
summarise(n = n(),
y.sum = sum(!!sym(target)),
y.avg = mean(!!sym(target)),
x.min = min(!!sym(rf.l)),
x.max = max(!!sym(rf.l))) %>%
ungroup() %>%
mutate(n.cs = cumsum(n),
y.cs = cumsum(y.sum),
y.cs.a = y.cs / n.cs,
n.cs.rev = cumsum(rev(n)),
y.cs.rev = cumsum(rev(y.sum)),
y.cs.a.rev = y.cs.rev / n.cs.rev,
dr.c = y.cs / n.cs,
dr.r = (sum(y.sum) - y.cs) / (sum(n) - n.cs))
lt <- min(which(tbl.s$n.cs >= min.obs & tbl.s$y.cs >= min.rate)) + 1
ut <- nrow(tbl.s) - min(which(tbl.s$n.cs.rev >= min.obs & tbl.s$y.cs.rev >= min.rate))
if (lt > ut) {
res <- data.frame(rf = paste0("`", rf.l, "`"), p.val = NA, split = NA)
return(res)
}
if (length(monodir) > 0) {
if (monodir == 1) {
ms <- which(tbl.s$dr.c < tbl.s$dr.r)
} else {
ms <- which(tbl.s$dr.c > tbl.s$dr.r)
}
} else {
ms <- lt:ut
}
sp <- intersect(lt:ut, ms)
if (length(sp) == 0) {
res <- data.frame(rf = paste0("`", rf.l, "`"), p.val = NA, split = NA)
return(res)
}
splits <- tbl.s$x.min[sp]
sl <- length(splits)
p.val <- rep(NA, sl)
for (i in 1:sl) {
split.l <- splits[i]
p.val[i] <- t2p.num(y = tbl[, target],
x = tbl[, rf.l],
sp = split.l,
monodir = monodir)
}
split.at <- splits[which.min(p.val)[1]]
check <- min(p.val) < p.value
split.at <- ifelse(check, split.at, NA)
p.val <- ifelse(check , min(p.val), NA)
res <- data.frame(rf = paste0("`", rf.l, "`"), p.val = p.val, split = split.at)
return(res)
}
c_best_split_cat <- function(tbl, rf.l, target, min.obs, min.rate, p.value) {
if (all(is.na(tbl[, rf.l]))) {
res <- data.frame(rf = paste0("`", rf.l, "`"), p.val = NA, split = NA)
return(res)
}
tbl$bin <- tbl[, rf.l]
tbl <- tbl[complete.cases(tbl), ]
tbl.s <- tbl %>%
group_by(bin) %>%
summarise(n = n(),
y.sum = sum(!!sym(target)),
y.avg = mean(!!sym(target)),
x.min = min(!!sym(rf.l)),
x.max = max(!!sym(rf.l))) %>%
ungroup() %>%
mutate(n.cs = cumsum(n),
y.cs = cumsum(y.sum),
y.cs.a = y.cs / n.cs,
n.cs.rev = cumsum(rev(n)),
y.cs.rev = cumsum(rev(y.sum)),
y.cs.a.rev = y.cs.rev / n.cs.rev,
dr.c = y.cs / n.cs,
dr.r = (sum(y.sum) - y.cs) / (sum(n) - n.cs))
lt <- min(which(tbl.s$n.cs >= min.obs & tbl.s$y.cs >= min.rate))
ut <- nrow(tbl.s) - min(which(tbl.s$n.cs.rev >= min.obs & tbl.s$y.cs.rev >= min.rate))
if (lt > ut) {
res <- data.frame(rf = paste0("`", rf.l, "`"), p.val = NA, split = NA)
return(res)
}
splits <- lt:ut
sl <- length(splits)
p.val <- rep(NA, sl)
monodir <- sign(cor(1:length(tbl.s$bin[!is.infinite(tbl.s$y.avg)]),
tbl.s$y.avg[!is.infinite(tbl.s$y.avg)],
method = "spearman",
use = "complete.obs"))
for (i in 1:sl) {
split.l <- tbl.s$bin[1:splits[i]]
p.val[i] <- t2p.cat(y = tbl[, target],
x = tbl[, rf.l],
sp = split.l,
monodir = monodir)
}
split.at <- splits[which.min(p.val)]
check <- min(p.val) < p.value
split.at <- ifelse(check, paste0("c(", paste(paste0("'", tbl.s$bin[1:split.at], "'"), collapse = ", "), ")"), NA)
p.val <- ifelse(check , min(p.val), NA)
res <- data.frame(rf = paste0("`", rf.l, "`"), p.val = min(p.val), split = split.at)
return(res)
}
#test of two proportions
t2p.num <- function(y, x, sp, monodir) {
if (length(monodir) > 0) {
alternative <- unname(ifelse(monodir == 1, "less", "greater"))
} else {
alternative <- "two.sided"
}
res <- prop.test(x = c(sum(y[x < sp]), sum(y[x >= sp])),
n = c(sum(x < sp), sum(x >= sp)),
alternative = alternative,
correct = FALSE)$p.value
return(res)
}
t2p.cat <- function(y, x, sp, monodir) {
alternative <- ifelse(monodir == 1, "less", "greater")
res <- prop.test(x = c(sum(y[x%in%sp]), sum(y[!x%in%sp])),
n = c(sum(x%in%sp), sum(!x%in%sp)),
alternative = alternative,
correct = FALSE)$p.value
return(res)
}
#' Predict method for custom decision tree
#'
#'@param object Custom decision tree model (class cdt).
#'@param newdata Optionally, a data frame in which to look for variables with which to predict.
#' If omitted, the fitted predictors are used.
#'@param ... further arguments passed to or from other methods.
#'@return Returns average default rate per leaf.
#'@examples
#' #S3 method for class "cdt"
#'suppressMessages(library(PDtoolkit))
#'data(loans)
#'tree.res <- decision.tree(db = loans,
#' rf = c("Account Balance", "Duration of Credit (month)"),
#' target = "Creditability",
#' min.pct.obs = 0.05,
#' min.avg.rate = 0.01,
#' p.value = 0.05,
#' max.depth = NA,
#' monotonicity = TRUE)
#'str(tree.res)
#' #predict method - development sample
#'pred.1 <- predict(object = tree.res, newdata = NULL)
#'head(pred.1)
#'auc.model(predictions = pred.1$average, observed = loans$Creditability)
#'#predict method - new data
#'set.seed(321)
#'loans.m <- loans[sample(1:nrow(loans), 500, replace = TRUE), ]
#'pred.2 <- predict(object = tree.res, newdata = loans.m)
#'head(pred.2)
#'auc.model(predictions = pred.2$average, observed = loans.m$Creditability)
#'@rdname predict.cdt
#'@export
predict.cdt <- function(object, newdata = NULL, ...) {
if (!class(object)%in%"cdt") {
stop("object has to be of class cdt")
}
avg.pred <- object$average$average
names(avg.pred) <- object$average$where
if (is.null(newdata)) {
res <- data.frame(where = object$where)
res$average <- unname(avg.pred[res$where])
} else {
rfs <- unique(object$tree.info$rf)
rfs <- rfs[!is.na(rfs)]
rfs <- substr(rfs, start = 2, stop = nchar(rfs) - 1)
cond <- !rfs%in%names(newdata)
if (any(cond)) {
msg <- paste(rfs[cond], collapse = ", ")
msg <- paste0("Missing risk factor(s): ", msg, ".")
stop(msg)
}
where <- extract.interactions(db = newdata, tree.info = object$tree.info)
res <- data.frame(where = unname(c(where, recursive = TRUE)))
res$average <- unname(avg.pred[res$where])
}
return(res)
}
andrija-djurovic/PDtoolkit documentation built on Jan. 29, 2024, 9:35 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions predict.cdt t2p.cat t2p.num c_best_split_cat c_best_split_num c_best_split cdt.algo decision.tree
Documented in decision.tree predict.cdt
#' Custom decision tree algorithm
#'
#' \code{decision.tree} runs customized decision tree algorithm. Customization refers to minimum
#' percentage of observations and defaults in each node, maximum tree depth, monotonicity condition
#' at each splitting node and statistical test (test of two proportions) used for node splitting.
#'@seealso \code{\link{predict.cdt}}
#'@param db Data frame of risk factors and target variable supplied for interaction extraction.
#'@param rf Character vector of risk factor names on which decision tree is run.
#'@param target Name of target variable (default indicator 0/1) within db argument.
#'@param min.pct.obs Minimum percentage of observation in each leaf. Default is 0.05 or 30 observations.
#'@param min.avg.rate Minimum percentage of defaults in each leaf. Default is 0.01 or 1 default case.
#'@param p.value Significance level of test of two proportions for splitting criteria. Default is 0.05.
#'@param max.depth Maximum tree depth.
#'@param monotonicity Logical indicator. If \code{TRUE}, observed trend between risk factor and target will be preserved
#' in splitting node.
#'@return The command \code{decision.tree} returns a object of class cdt. For details on output elements see the Examples.
#'@examples
#'suppressMessages(library(PDtoolkit))
#'data(loans)
#'#modify risk factors in order to show how the function works with missing values
#'loans$"Account Balance"[1:10] <- NA
#'loans$"Duration of Credit (month)"[c(13, 15)] <- NA
#'tree.res <- decision.tree(db = loans,
#' rf = c("Account Balance", "Duration of Credit (month)"),
#' target = "Creditability",
#' min.pct.obs = 0.05,
#' min.avg.rate = 0.01,
#' p.value = 0.05,
#' max.depth = NA,
#' monotonicity = TRUE)
#'str(tree.res)
#'@export
decision.tree <- function(db, rf, target, min.pct.obs = 0.05, min.avg.rate = 0.01, p.value = 0.5, max.depth = NA, monotonicity) {
ops <- options(warn = -1)
on.exit(options(ops))
if (!is.data.frame(db)) {
stop("db is not a data frame.")
}
if (any(!c(rf, target)%in%names(db))) {
stop("rf or target variable do not exist in supplied db.")
}
if (!is.numeric(min.pct.obs) | !is.numeric(min.avg.rate) |
min.pct.obs <= 0 | min.pct.obs >= 1 |
min.avg.rate <= 0 | min.avg.rate >= 1) {
stop(" min.pct.obs and min.avg.rate has to be numeric values greater than 0 and less than 1")
}
if (!is.na(max.depth)) {
if (!is.numeric(max.depth) | max.depth < 1) {
stop("max.depth has to be numeric value greater or equal to 1.")
}
}
if (is.na(monotonicity) | !is.logical(monotonicity)) {
stop("monotonicity has to be logical value - TRUE or FALSE")
}
d <- db[, c(target, rf)]
d <- d[!is.na(d[, target]), ]
nr <- nrow(d)
if (nr == 0) {
stop("target contains only missing values.")
}
if (length(unique(d[, target])) == 1) {
stop("target has only 1 class.")
}
if (!sum(d[, target]%in%c(0, 1)) == nr) {
stop("target contains value(s) different than 0 and 1.")
}
nd <- sum(d[, target])
rf.check <- sapply(d[, rf, drop = FALSE], function(x) sum(is.na(x)) == length(x))
if (any(rf.check)) {
msg <- paste0("The following risk factor(s) contain(s) only missing values: ",
paste0(names(rf.check)[rf.check], collapse = ", "), ".")
stop(msg)
}
tree.res <- cdt.algo(d = d,
rf = rf,
target = target,
min.obs = ceiling(ifelse(nr * min.pct.obs < 30, 30, nr * min.pct.obs)),
min.rate = ceiling(ifelse(nd * min.avg.rate < 1, 1, nd * min.avg.rate)),
p.value = p.value,
max.depth = max.depth,
monotonicity = monotonicity)
if (nrow(tree.res) > 1) {
where <- extract.interactions(db = db, tree.info = tree.res)
nodes <- unname(c(where, recursive = TRUE))
} else {
nodes <- rep(1, nrow(db))
}
averages <- cbind.data.frame(where = nodes, target = db[, target]) %>%
group_by(where) %>%
summarise(average = mean(target, na.rm = TRUE))
averages <- averages[!is.na(averages$where), ]
return(structure(list(inputs = data.frame(target, min.pct.obs, min.avg.rate, p.value, max.depth, monotonicity),
tree.info = tree.res,
where = nodes,
average = data.frame(averages),
data = db),
class = "cdt"))
}
#customized decision tree algo
cdt.algo <- function(d, rf, target, min.obs, min.rate, p.value, max.depth, monotonicity) {
rf.num <- sapply(d[, rf, drop = FALSE], is.numeric)
rf.num <- names(rf.num)[rf.num]
rf.cat <- rf[!rf%in%rf.num]
if (monotonicity & length(rf.num) > 0) {
corr.dir <- sapply(rf.num, function(x) sign(cor(d[, x], d[, target],
method = "spearman",
use = "complete.obs")))
} else {
corr.dir <- c()
}
#initialize the process
do.splits <- TRUE
tree.info <- data.frame(node = 1,
rf = NA,
nobs = nrow(d),
filter = NA,
terminal = "split",
stringsAsFactors = FALSE)
#start splitting
while (do.splits) {
to.calculate <- which(tree.info$terminal == "split")
for (i in to.calculate) {
if (!is.na(tree.info$filter[i])) {
tbl.l <- subset(d, eval(parse(text = tree.info$filter[i])))
} else {
tbl.l <- d
}
splitting <- lapply(rf, function(x) {
c_best_split(tbl = tbl.l,
rf.l = x,
target = target,
min.obs = min.obs,
min.rate = min.rate,
p.value = p.value,
monodir = corr.dir[x])})
bs.rf.indx <- which.min(sapply(splitting, "[[", "p.val"))
if (length(bs.rf.indx) == 0) {
tree.info$terminal[i] <- "leaf"
next
}
tmp.sp <- splitting[[bs.rf.indx]]
mn <- max(tree.info$node)
if (tmp.sp$rf.t%in%"numeric") {
tmp.filter <- c(paste(tmp.sp$rf, "<", tmp.sp$split), paste(tmp.sp$rf, ">=", tmp.sp$split))
} else {
tmp.filter <- c(paste0(tmp.sp$rf, "%in%", tmp.sp$split), paste0("!", tmp.sp$rf, "%in%", tmp.sp$split))
}
if (!is.na(tree.info$filter[i])) {
tmp.filter <- paste(tree.info$filter[i], tmp.filter, sep = " & ")
}
tmp.filter.nobs <- paste(paste0("!is.na(", tmp.sp$rf, ")"), tmp.filter, sep = " & ")
tmp.nobs <- sapply(tmp.filter.nobs, FUN = function(i, x) {
nrow(subset(x = x, subset = eval(parse(text = i))))
}, x = tbl.l)
children <- data.frame(node = c(mn + 1, mn + 2),
rf = tmp.sp$rf,
nobs = unname(tmp.nobs),
filter = tmp.filter,
terminal = rep("split", 2),
row.names = NULL)
tree.info$terminal[i] <- "parent"
tree.info <- rbind(tree.info, children)
if (!is.na(max.depth) & sum(tree.info$terminal%in%c("leaf", "split")) > max.depth) {
tree.info$terminal[tree.info$terminal%in%"split"] <- "leaf"
do.splits <- FALSE
break
}
}
do.splits <- !all(tree.info$terminal != "split")
}
tree.info$ind <- as.numeric(ave(tree.info$terminal, tree.info$terminal,
FUN = function(x) if (all(x%in%"leaf")) {1:length(x)} else {NA}))
return(tree.info)
}
#customized node split functions
c_best_split <- function(tbl, rf.l, target, min.obs, min.rate, p.value, monodir) {
rf.c <- is.numeric(tbl[, rf.l])
if (rf.c) {
bs <- c_best_split_num(tbl = tbl,
rf.l = rf.l,
target = target,
min.obs = min.obs,
min.rate = min.rate,
p.value = p.value,
monodir = monodir)
bs <- cbind.data.frame(rf.t = "numeric", bs)
} else {
bs <- c_best_split_cat(tbl = tbl,
rf.l = rf.l,
target = target,
min.obs = min.obs,
min.rate = min.rate,
p.value = p.value)
bs <- cbind.data.frame(rf.t = "categorical", bs)
}
return(bs)
}
c_best_split_num <- function(tbl, rf.l, target, min.obs, min.rate, p.value, monodir) {
g <- unname(quantile(tbl[, rf.l],seq(1 / 50, 1, length.out = 50), type = 3, na.rm = TRUE))
g <- unique(c(min(tbl[, rf.l], na.rm = TRUE), g))
if (length(g) == 1 | all(is.na(tbl[, rf.l]))) {
res <- data.frame(rf = paste0("`", rf.l, "`"), p.val = NA, split = NA)
return(res)
}
tbl$bin <- cut(tbl[, rf.l], breaks = g, include.lowest = TRUE)
tbl <- tbl[complete.cases(tbl), ]
tbl.s <- tbl %>%
group_by(bin) %>%
summarise(n = n(),
y.sum = sum(!!sym(target)),
y.avg = mean(!!sym(target)),
x.min = min(!!sym(rf.l)),
x.max = max(!!sym(rf.l))) %>%
ungroup() %>%
mutate(n.cs = cumsum(n),
y.cs = cumsum(y.sum),
y.cs.a = y.cs / n.cs,
n.cs.rev = cumsum(rev(n)),
y.cs.rev = cumsum(rev(y.sum)),
y.cs.a.rev = y.cs.rev / n.cs.rev,
dr.c = y.cs / n.cs,
dr.r = (sum(y.sum) - y.cs) / (sum(n) - n.cs))
lt <- min(which(tbl.s$n.cs >= min.obs & tbl.s$y.cs >= min.rate)) + 1
ut <- nrow(tbl.s) - min(which(tbl.s$n.cs.rev >= min.obs & tbl.s$y.cs.rev >= min.rate))
if (lt > ut) {
res <- data.frame(rf = paste0("`", rf.l, "`"), p.val = NA, split = NA)
return(res)
}
if (length(monodir) > 0) {
if (monodir == 1) {
ms <- which(tbl.s$dr.c < tbl.s$dr.r)
} else {
ms <- which(tbl.s$dr.c > tbl.s$dr.r)
}
} else {
ms <- lt:ut
}
sp <- intersect(lt:ut, ms)
if (length(sp) == 0) {
res <- data.frame(rf = paste0("`", rf.l, "`"), p.val = NA, split = NA)
return(res)
}
splits <- tbl.s$x.min[sp]
sl <- length(splits)
p.val <- rep(NA, sl)
for (i in 1:sl) {
split.l <- splits[i]
p.val[i] <- t2p.num(y = tbl[, target],
x = tbl[, rf.l],
sp = split.l,
monodir = monodir)
}
split.at <- splits[which.min(p.val)[1]]
check <- min(p.val) < p.value
split.at <- ifelse(check, split.at, NA)
p.val <- ifelse(check , min(p.val), NA)
res <- data.frame(rf = paste0("`", rf.l, "`"), p.val = p.val, split = split.at)
return(res)
}
c_best_split_cat <- function(tbl, rf.l, target, min.obs, min.rate, p.value) {
if (all(is.na(tbl[, rf.l]))) {
res <- data.frame(rf = paste0("`", rf.l, "`"), p.val = NA, split = NA)
return(res)
}
tbl$bin <- tbl[, rf.l]
tbl <- tbl[complete.cases(tbl), ]
tbl.s <- tbl %>%
group_by(bin) %>%
summarise(n = n(),
y.sum = sum(!!sym(target)),
y.avg = mean(!!sym(target)),
x.min = min(!!sym(rf.l)),
x.max = max(!!sym(rf.l))) %>%
ungroup() %>%
mutate(n.cs = cumsum(n),
y.cs = cumsum(y.sum),
y.cs.a = y.cs / n.cs,
n.cs.rev = cumsum(rev(n)),
y.cs.rev = cumsum(rev(y.sum)),
y.cs.a.rev = y.cs.rev / n.cs.rev,
dr.c = y.cs / n.cs,
dr.r = (sum(y.sum) - y.cs) / (sum(n) - n.cs))
lt <- min(which(tbl.s$n.cs >= min.obs & tbl.s$y.cs >= min.rate))
ut <- nrow(tbl.s) - min(which(tbl.s$n.cs.rev >= min.obs & tbl.s$y.cs.rev >= min.rate))
if (lt > ut) {
res <- data.frame(rf = paste0("`", rf.l, "`"), p.val = NA, split = NA)
return(res)
}
splits <- lt:ut
sl <- length(splits)
p.val <- rep(NA, sl)
monodir <- sign(cor(1:length(tbl.s$bin[!is.infinite(tbl.s$y.avg)]),
tbl.s$y.avg[!is.infinite(tbl.s$y.avg)],
method = "spearman",
use = "complete.obs"))
for (i in 1:sl) {
split.l <- tbl.s$bin[1:splits[i]]
p.val[i] <- t2p.cat(y = tbl[, target],
x = tbl[, rf.l],
sp = split.l,
monodir = monodir)
}
split.at <- splits[which.min(p.val)]
check <- min(p.val) < p.value
split.at <- ifelse(check, paste0("c(", paste(paste0("'", tbl.s$bin[1:split.at], "'"), collapse = ", "), ")"), NA)
p.val <- ifelse(check , min(p.val), NA)
res <- data.frame(rf = paste0("`", rf.l, "`"), p.val = min(p.val), split = split.at)
return(res)
}
#test of two proportions
t2p.num <- function(y, x, sp, monodir) {
if (length(monodir) > 0) {
alternative <- unname(ifelse(monodir == 1, "less", "greater"))
} else {
alternative <- "two.sided"
}
res <- prop.test(x = c(sum(y[x < sp]), sum(y[x >= sp])),
n = c(sum(x < sp), sum(x >= sp)),
alternative = alternative,
correct = FALSE)$p.value
return(res)
}
t2p.cat <- function(y, x, sp, monodir) {
alternative <- ifelse(monodir == 1, "less", "greater")
res <- prop.test(x = c(sum(y[x%in%sp]), sum(y[!x%in%sp])),
n = c(sum(x%in%sp), sum(!x%in%sp)),
alternative = alternative,
correct = FALSE)$p.value
return(res)
}
#' Predict method for custom decision tree
#'
#'@param object Custom decision tree model (class cdt).
#'@param newdata Optionally, a data frame in which to look for variables with which to predict.
#' If omitted, the fitted predictors are used.
#'@param ... further arguments passed to or from other methods.
#'@return Returns average default rate per leaf.
#'@examples
#' #S3 method for class "cdt"
#'suppressMessages(library(PDtoolkit))
#'data(loans)
#'tree.res <- decision.tree(db = loans,
#' rf = c("Account Balance", "Duration of Credit (month)"),
#' target = "Creditability",
#' min.pct.obs = 0.05,
#' min.avg.rate = 0.01,
#' p.value = 0.05,
#' max.depth = NA,
#' monotonicity = TRUE)
#'str(tree.res)
#' #predict method - development sample
#'pred.1 <- predict(object = tree.res, newdata = NULL)
#'head(pred.1)
#'auc.model(predictions = pred.1$average, observed = loans$Creditability)
#'#predict method - new data
#'set.seed(321)
#'loans.m <- loans[sample(1:nrow(loans), 500, replace = TRUE), ]
#'pred.2 <- predict(object = tree.res, newdata = loans.m)
#'head(pred.2)
#'auc.model(predictions = pred.2$average, observed = loans.m$Creditability)
#'@rdname predict.cdt
#'@export
predict.cdt <- function(object, newdata = NULL, ...) {
if (!class(object)%in%"cdt") {
stop("object has to be of class cdt")
}
avg.pred <- object$average$average
names(avg.pred) <- object$average$where
if (is.null(newdata)) {
res <- data.frame(where = object$where)
res$average <- unname(avg.pred[res$where])
} else {
rfs <- unique(object$tree.info$rf)
rfs <- rfs[!is.na(rfs)]
rfs <- substr(rfs, start = 2, stop = nchar(rfs) - 1)
cond <- !rfs%in%names(newdata)
if (any(cond)) {
msg <- paste(rfs[cond], collapse = ", ")
msg <- paste0("Missing risk factor(s): ", msg, ".")
stop(msg)
}
where <- extract.interactions(db = newdata, tree.info = object$tree.info)
res <- data.frame(where = unname(c(where, recursive = TRUE)))
res$average <- unname(avg.pred[res$where])
}
return(res)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.