RFlocalfdr (version 0.9)

determine_cutoff: evaluate a measure that can be used to determining a significance level for the Mean Decrease in Impurity measure returned by a Random Forest model

Description

evaluate a measure that can be used to determining a significance level for the Mean Decrease in Impurity measure returned by a Random Forest model

Usage

determine_cutoff(
  imp,
  t2,
  cutoff = c(0, 1, 4, 10, 15, 20),
  Q = 0.75,
  plot = NULL,
  verbose = 0,
  try.counter = 3
)

Value

res a matrix if size length(cutoff) by 3. We model the histogram of imp with a kernel density estimate, y. Let t1 be fitted values of the skew normal. Then res contains three columns

• sum((y-t1)^2)

• sum(abs(y-t1)) and

• max(abs(y-t1)), evaluated up to the quantile Q

Arguments

imp

vector of MDI variable importances

t2

number of times each variable is used in the a ranger forest. Returned by count_variables for a ranger RF

cutoff

values to evaluate

Q

-- we examine the fit up to the quartile Q

plot

for 4 selected values of the cutoff. The plot contains

• The data (black) and the fitted density (red)

• The skew-normal fit (blue)

• The quantile Q (vertical red line)

verbose

verbose=0, no output to screen verbose=1, track the cutoff value being used

try.counter

passed to fit.to.data.set.wrapper

Examples

data(imp20000)
imp <- log(imp20000$importances)
t2<- imp20000$counts
length(imp)
hist(imp,col=6,lwd=2,breaks=100,main="histogram of importances")
res.temp <- determine_cutoff(imp, t2 ,cutoff=c(0,1,2,3),plot=c(0,1,2,3),Q=0.75,try.counter=1)

plot(c(0,1,2,3),res.temp[,3])
# the minimum is at 1 so
imp<-imp[t2 > 1]

qq <- plotQ(imp,debug.flag = 0)
ppp<-run.it.importances(qq,imp,debug=0)
aa<-significant.genes(ppp,imp,cutoff=0.2,debug.flag=0,do.plot=2, use_95_q=TRUE)
length(aa$probabilities) #11#
names(aa$probabilities)
#[1] "X101"   "X102"   "X103"   "X104"   "X105"   "X2994"  "X9365"  "X10718"
# [9] "X13371" "X15517" "X16460"
# so the observed FDR is 0.54

# \donttest{
library(ranger)
library(RFlocalfdr.data)
data(smoking)
y<-smoking$y
smoking_data<-smoking$rma
y.numeric <-ifelse((y=="never-smoked"),0,1)
rf1 <- ranger::ranger(y=y.numeric ,x=smoking_data,importance="impurity",seed=123, num.trees = 10000,     
         classification=TRUE)
t2 <-count_variables(rf1)
imp<-log(rf1$variable.importance)
plot(density((imp)))
# Detemine a cutoff to get a unimodal density.
res.temp <- determine_cutoff(imp, t2 ,cutoff=c(1,2,3,4),plot=c(1,2,3,4),Q=0.75)
plot(c(1,2,3,4),res.temp[,3])
# }