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> Subject: [R] ROC curve for each fold in one plot
>
> Hi all,
>
> I have tried a 5 fold cross validation using caret package with random forest
> method on iris dataset as example. Then I need ROC curve for each fold:
>
>
> > set.seed(1)
> >
Hi all,
I have tried a 5 fold cross validation using caret package with random forest
method on iris dataset as example. Then I need ROC curve for each fold:
> set.seed(1)
> train_control <- trainControl(method="cv", number=5,savePredictions =
TRUE,classProbs = TRUE)
> output <- train(S
Thanks,
Do you know how to correct it?
Cheers,
Bruno
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On Fri, Nov 23, 2012 at 7:58 AM, brunosm wrote:
> Hi all,
>
> does anyone know why the area under the curve (AUC) is negative?
>
> I'm using ROC function with a logistic regression, package Epi.
>
> First time it happens...
>
>
Have you looked at the ROC curve?
That should tell you whether there
wrong direction for ranking
On Thu, Nov 22, 2012 at 1:58 PM, brunosm wrote:
> the area under the curve (AUC) is negative?
>
> I'm using ROC function with a logistic regression, package Epi.
>
> First time it happens...
>
> Thanks a lot!
>
> Bruno
>
--
==
WenSui Li
Hi all,
does anyone know why the area under the curve (AUC) is negative?
I'm using ROC function with a logistic regression, package Epi.
First time it happens...
Thanks a lot!
Bruno
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Sent fr
On 01/30/2012 08:52 PM, Josiane NJIWA wrote:
Hello all,
I am very new to R and i am facing two problems. First i didn't succeed
changing the konsole language in english even after trying the line command set
language='en'.
I would like to plot ROC curves. I have a serie of 10 threshold tests
On Jan 30, 2012, at 4:52 AM, Josiane NJIWA wrote:
Hello all,
I am very new to R and i am facing two problems. First i didn't
succeed changing the konsole language in english even after trying
the line command set language='en'.
R is a functional language, so it shouldn't surprise you t
Hi Josiane,
Concerning ROC curves, the package ROCR should do what you want to do. Use
install.packages to add it to you library.
Getting you data into a text file format, use read.delim to read into an
data frame. Once you have a data frame, you can use the methods in ROCR to
analyze the data.
Hello all,
I am very new to R and i am facing two problems. First i didn't succeed
changing the konsole language in english even after trying the line command set
language='en'.
I would like to plot ROC curves. I have a serie of 10 threshold tests that i do
for 10 patients. The prediction for
On 07/01/2010 01:33 PM, Changbin Du wrote:
Read the ROCR package, it is very good.
Just be sure you really need an ROC curve. More often than not it gets
in the way of understanding.
Frank
On Thu, Jul 1, 2010 at 9:50 AM, ashu6886 wrote:
Hi,
i have a fairly large amount of genomi
Read the ROCR package, it is very good.
On Thu, Jul 1, 2010 at 9:50 AM, ashu6886 wrote:
>
> Hi,
>
> i have a fairly large amount of genomic data. I have created a dataframe
> which has "Reference" as one column and "Variation" as another. I want to
> plot a ROC curve based on these 2 columns
e posting, please!
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
>
>
>
> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
> On
> Behalf Of ashu6886
> Sent: Thursday, July 01, 2010 9:51 AM
> To: r-help@r-
Try the ROCR package. http://rocr.bioinf.mpi-sb.mpg.de/ROCR.pdf
Saeed
On Thu, Jul 1, 2010 at 9:50 AM, ashu6886 wrote:
>
> Hi,
>
> i have a fairly large amount of genomic data. I have created a dataframe
> which has "Reference" as one column and "Variation" as another. I want to
> plot a ROC curve
atistics
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of ashu6886
Sent: Thursday, July 01, 2010 9:51 AM
To: r-help@r-project.org
Subject: [R] ROC curve in R
Hi,
i have a fairly large amount of genomic data. I have created a dat
On Jul 1, 2010, at 12:50 PM, ashu6886 wrote:
Hi,
i have a fairly large amount of genomic data. I have created a
dataframe
which has "Reference" as one column and "Variation" as another. I
want to
plot a ROC curve based on these 2 columns. I have serached the R
manual but
I could not und
Hi,
i have a fairly large amount of genomic data. I have created a dataframe
which has "Reference" as one column and "Variation" as another. I want to
plot a ROC curve based on these 2 columns. I have serached the R manual but
I could not understand. Can anybody help me with the R code for plotti
On 05/24/2010 02:14 AM, Claudia Beleites wrote:
Dear Changbin,
I want to know how to select the optimal decision threshold from the ROC
curve?
Depends on what optimal means. I think there are a bunch of different
criteria used:
- point closest to the ideal model
- point furthest from the "gue
Dear Changbin,
I want to know how to select the optimal decision threshold from the ROC
curve?
Depends on what optimal means. I think there are a bunch of different criteria
used:
- point closest to the ideal model
- point furthest from the "guessing" model
- these criteria may include costs
HI, Dear R community,
I want to know how to select the optimal decision threshold from the ROC
curve? At what threshold will give the highest accuracy?
Thanks!
--
Sincerely,
Changbin
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require(randomForest)
rf.pred<-predict(fit, valid, type="prob")
> rf.pred[1:20, ]
0 1
16 0. 1.
23 0.3158 0.6842
43 0.3030 0.6970
52 0.0886 0.9114
55 0.1216 0.8784
75 0.0920 0.9080
82 0.4332 0.5668
120 0.2302 0.7698
128 0.1336 0.8664
147 0.4272 0.5728
148 0.0490 0.9510
I'm using randomSurvivalForest to predict survival from a rather small
sample. As it's not enough data to have training and validation set, I
rely on the "Estimate of error rate" computed by the randomForest. If I
understand the method correctly, it repeatedly partitions the data into
varying t
Have look in the ROCR package and Example's.
HTH Christian
What is the difference between ROC curve and gains/lift chart?
how to do them in R?
Thanks.
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PLEASE do rea
What is the difference between ROC curve and gains/lift chart?
how to do them in R?
Thanks.
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Dear R-help,
I am resending as I believe I screwed up the e-mail address to R-help
earlier. Sorry for my lack of attention to detail, and for any
inconvenience.
I have also sent the question to the package maintainer, as suggested
in the posting guide.
Regards,
Cliff
-- Forwarded me
Dear R-help list,
I'm attempting to use the ROC routine from the epicalc package after
performing a logistic regression analysis. My code is included after
the sessionInfo() result. The datafile (GasketMelt1.csv) is attached.
I updated both R and the epicalc packages and tried again before
send
Hi there,
See ?lroc in the epicalc package.
HTH,
Jorge
On Mon, Sep 8, 2008 at 4:02 AM, gallon li <[EMAIL PROTECTED]> wrote:
> I know how to compute the ROC curve and the empirical AUC from the logistic
> regression after fitting the model.
>
> But here is my question, how can I compute the s
;- resta
oper <- 0
}
vpj <- vpj/(pos*(pos-1))
vqk <- vqk/(neg*(neg-1))
var <- sum(vpj)+sum(vqk)
s <- sqrt(var)
return(list(AUC=area, std=s))
}
-Original Message-
From: [EMAIL PROTECTED] [ma
gallon li wrote:
I know how to compute the ROC curve and the empirical AUC from the logistic
regression after fitting the model.
But here is my question, how can I compute the standard error for the AUC
estimator resulting form logistic regression? The variance should be more
complicated than AU
I know how to compute the ROC curve and the empirical AUC from the logistic
regression after fitting the model.
But here is my question, how can I compute the standard error for the AUC
estimator resulting form logistic regression? The variance should be more
complicated than AUC based on known te
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