Displaying 20 results from an estimated 4000 matches similar to: "question about boosting(Adaboosting. M1)"
2010 Jun 02
1
how to label the som notes by the majority vote
HI, Dear R community,
I am using the following codes to do the som. I tried to label the notes by
the majority vote. either through mapping or prediction.
I attached my output, the left one dont have any labels in the note, the
right one has more than one label in each note. I need to have only one
label for each note either by majority vote or prediction.
Can anyone give some suggestions or
2010 Apr 26
1
boosting with decision tree
Hi, Dear R community,
Does anyone know how to constructdecision tree with boosting? Is any
tutorial I can read?
--
Sincerely,
Changbin
--
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2010 Apr 26
3
R.GBM package
HI, Dear Greg,
I AM A NEW to GBM package. Can boosting decision tree be implemented in
'gbm' package? Or 'gbm' can only be used for regression?
IF can, DO I need to combine the rpart and gbm command?
Thanks so much!
--
Sincerely,
Changbin
--
[[alternative HTML version deleted]]
2010 Jun 15
1
output from the gbm package
HI, Dear Greg and R community,
I have one question about the output of gbm package. the output of Boosting
should be f(x), from it , how to calculate the probability for each
observations in data set?
SInce it is stochastic, how can guarantee that each observation in training
data are selected at least once? IF SOME obs are not selected, how to
calculate the training error?
Thanks?
--
2010 Apr 29
2
can not print probabilities in svm of e1071
> x <- train[,c( 2:18, 20:21, 24, 27:31)]
> y <- train$out
>
> svm.pr <- svm(x, y, probability = TRUE, method="C-classification",
kernel="radial", cost=bestc, gamma=bestg, cross=10)
>
> pred <- predict(svm.pr, valid[,c( 2:18, 20:21, 24, 27:31)],
decision.values = TRUE, probability = TRUE)
> attr(pred, "decision.values")[1:4,]
2010 Apr 06
2
help output figures in R
somfunc<- function (file) {
aa_som<-scale(file)
final.som<-som(data=aa_som, rlen=10000, grid=somgrid(5,4, "hexagonal"))
pdf(file="/home/cdu/changbin/file.pdf") #output graphic file.
plot(final.som, main="Unsupervised SOM")
dev.off()
}
I have many different files, if I want output pdf file with the same name
as for each dataset I feed to the function
2010 Apr 21
2
?rpart
HI, Dear R community,
Last friday, I used the codes, it works, but today, it does not run?
> fit.dimer <- rpart(outcome ~., method="class", data=p.df)
Error in `[.data.frame`(frame, predictors) : undefined columns selected
DOEs anyone have comments or suggestions? Thanks in advance!
--
Sincerely,
Changbin
--
[[alternative HTML version deleted]]
2010 May 18
2
get the row sums
> head(en.id.pr)
valid.gene_id b.pred rf.pred svm.pred
1521 2500151211 0 0 0
366 639679745 0 0 0
1965 2502081603 1 1 1
1420 644148030 1 1 1
1565 2500626489 1 1 1
1816 2501711016 1 1 1
> p.pred <- data.frame(en.id.pr, sum=apply(en.id.pr[,2:4], 1, sum)) #
2011 Sep 01
3
how to split a data frame by two variables
HI, Dear R community,
I want to split a data frame by using two variables: let and g
> x = data.frame(num =
c(10,11,12,43,23,14,52,52,12,23,21,23,32,31,24,45,56,56,76,45), let =
letters[1:5], g = 1:2)
> x
num let g
1 10 a 1
2 11 b 2
3 12 c 1
4 43 d 2
5 23 e 1
6 14 a 2
7 52 b 1
8 52 c 2
9 12 d 1
10 23 e 2
11 21 a 1
12 23 b 2
13 32 c 1
14
2010 Apr 23
1
help in conditional histogram
Dear Dr. Sarkar,
When I try to run the codes, I found the following problem:
> h<- sample(1:14, 319, rep=T)
> c<- sample(1:14, 608, rep=T)
> n<- sample(1:14, 1140, rep=T)
> vt<-c(h, c, n)
> ta<-rep(c("h", "c", "n"), c(319, 608, 1140))
>
> to<-data.frame(vt,ta)
> library(lattice)
Attaching package: 'lattice'
2010 May 05
2
probabilities in svm output in e1071 package
svm.fit<-svm(as.factor(out) ~ ., data=all_h, method="C-classification",
kernel="radial", cost=bestc, gamma=bestg, cross=10) # model fitting
svm.pred<-predict(svm.fit, hh, decision.values = TRUE, probability = TRUE) #
find the probability, but can not find.
attr(svm.pred, "probabilities")
> attr(svm.pred, "probabilities")
1 0
1 0 0
2 0
2010 Dec 16
1
my function does not work for large data set
Dear R community,
I have one function, it works for small data set, but does not work on large
data set, can anyone help me with this?
> #creat new variable by dividing each aa dimer by total_length.
> imper<-function(x, file) {
+ round(x/file$length, 5)
+ }
> dim(test)
[1] 999 2402
> test[varname[2:2401]]<-
2010 Oct 25
1
help with adding lines to current plot
HI, Dear R community,
I am using the following codes to plot, however, the lines code works. But
the line was not drawn on the previous plot and did not shown up.
How comes?
# specify the data for missense simulation
x <- seq(0,10, by=1)
y <- c(0.952, 0.947, 0.943, 0.941, 0.933, 0.932, 0.939, 0.932, 0.924, 0.918,
0.920) # missense
z <- c(0.068, 0.082, 0.080, 0.099, 0.108, 0.107,
2010 May 25
4
R eat my data
HI, Dear R community,
My original file has 1932 lines, but when I read into R, it changed to 1068
lines, how comes?
cdu@nuuk:~/operon$ wc -l id_name_gh5.txt
1932 id_name_gh5.txt
> gene_name<-read.table("/home/cdu/operon/id_name_gh5.txt", sep="\t",
skip=0, header=F, fill=T)
> dim(gene_name)
[1] 1068 3
--
Sincerely,
Changbin
--
Changbin Du
DOE Joint Genome
2010 Apr 29
1
variable importance in Random Forest
HI, Dear Andy,
I run the RandomFOrest in R, and get the following resutls in variable
importance:
What is the meaning of MeanDecreaseAccuracy and MeanDecreaseGini?
I found they are raw values, they are not scaled to 1, right?
Which column if most similar to the variable rel.influence in Boosting?
Thanks so much!
> fit$importance
0 1
2011 Sep 22
2
create variables through a loop
HI, Dear R community,
I am trying to created new variables and put into a data frame through a
loop.
My original data set:
head(first)
probe_name chr_id position array1
1 C-7SARK 1 849467 10
2 C-4WYLN 1 854278 10
3 C-3BFNY 1 854471 10
4 C-7ONNE 1 874460 10
5 C-6HYCN 1 874571 10
6 C-7SCGC 1 874609 10
I have
2010 Nov 04
4
how to work with long vectors
HI, Dear R community,
I have one data set like this, What I want to do is to calculate the
cumulative coverage. The following codes works for small data set (#rows =
100), but when feed the whole data set, it still running after 24 hours.
Can someone give some suggestions for long vector?
id reads
Contig79:1 4
Contig79:2 8
Contig79:3 13
Contig79:4 14
Contig79:5 17
2010 Nov 01
2
how to save this result in a vector
HI, Dear R community,
I have the following codes to calculate the commulative coverage. I want to
save the output in a vector, How to do this?
test<-seq(10, 342, by=2)
#cover is a vector
cover_per<-function (cover) {
for (i in min(cover):max(cover)) {print(100*sum(ifelse(cover >= i, 1,
0))/length(cover))}
}
result<-cover_per(test)
> result
NULL
Can anyone help me this this?
2010 May 05
3
sort the data set by one variable
> #sort the data by predicted probability
> b.order<-bo.id.pred[(order(-predict)),]
> b.order[1:20,]
gene_id predict
43 637882902 0.07823997
53 638101634 0.66256490
61 639084581 0.08587504
41 637832824 0.02461066
25 637261662 0.11613879
22 637240022 0.06350477
62 639084582 0.02238538
63 639097718 0.06792841
44 637943079 0.04532625
80 640158389 0.06582658
3 637006517 0.57648451
2011 Jun 27
1
how to replace the following string
HI, Dear R-community,
I have one vector of the following string,
> test<-c("H.1.Y", "N.0.E", "G.1.N", "E.0.P", "W.2.G", "W.4.G", "W.3.W",
"W.0.N", "D.1.H")
> test
[1] "H.1.Y" "N.0.E" "G.1.N" "E.0.P" "W.2.G" "W.4.G" "W.3.W"