Hi Ray,
Have you done any search at all? I did a search on "R package ROC latent
variable" and got several hits.
In particular the package randomLCA seems relevant
https://cran.r-project.org/web/packages/randomLCA/vignettes/randomLCA-package.pdf
I glanced at the documentation which mentions 2 oth
> On Jun 6, 2018, at 10:37 AM, Palmer, Raymond F wrote:
>
> Dear R group.
> Does anyone have an idea how to utilize a latent variable in an ROC (AUC)
> analysis? I want to create a latent variable, then use that latent construct
> as a continuous variable in an ROC.
> I understand both SEM an
Dear R group.
Does anyone have an idea how to utilize a latent variable in an ROC (AUC)
analysis? I want to create a latent variable, then use that latent construct as
a continuous variable in an ROC.
I understand both SEM and ROC analysis can be done in R, but how to use the
latent variable in
List
> 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
Trying to plot an ROC curve to determine effectiveness of a neural network
model in R.
using the neuralnet package I created nn1a:
nn1a<-neuralnet(warstns ~ aigenlz+
p2l+anoclinv2+flinstab+mill+minconl+fllgdppclz+lpoplz+floil+flmtnestz+c_peaceyears,
data=na.omit(dfram1), hidden=4)
then usin
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 Tue, Oct 23, 2012 at 11:52 PM, Luigi wrote:
>
> Any tip on how to proceed?
You may want to do check rocplus package. Its vignette is pretty good.
http://cran.r-project.org/web/packages/rocplus/vignettes/rocplus.pdf
In your case, I think pairwise comparison would be one approach
Best,
Mehmet
Dear all,
I would like to perform a receiver operating characteristics (ROC) curve
analysis on data obtained using molecular assays.
I have here an example: the first column is the sample number, the second is
the response variable and the last three columns are the predictors. I wish
to set the
Wild guess :
You need to have some kind of score for ROC to work (so you can work with a
threshold), so a predict() that only returns classlabels probably won't work.
On 13.07.2012, at 15:25, blerta wrote:
> Hi,
>
> I don't really understand how ROCR works. Here's another example with a
> ran
Hi,
I don't really understand how ROCR works. Here's another example with a
randomforest model: I have the training dataset(bank_training) and testing
dataset(bank_testing) and I ran a randomForest as below:
bankrf<-randomForest(y~., bank_training, mtry=4, ntree=2,
keep.forest=TRUE,im
Hi everybody,
Pascal, your code works, but when I want to do the graph I have an error
message.
here is my code :
x<-rev(unlist(pred@cutoffs))
tpf<-unlist(performance(pred, "tpr")@y.values)
fpf<-unlist(performance(pred,"fpr")@y.values)
ll<-length(x)
p<-(tpf[1:(ll-1)]-tpf[2:ll])/(fpf[1:(ll-1)]-fp
Hi everybody,
Pascal, your script works again but I want to calculate the LR otherwise.
I know the likelihood ratio is linked at the roc curve and so there are
different ways to calculate the LR.
The slope of an ROC curve can be defined in three ways:
(1) as the tangent at a particular point on th
Hi,
I made a mistake, effectively Pascal your method given to the first message
is correct. I didn't use the good data, so it's sure that it could not work
!
But, I have an another question : Can I obtain a same graph except that the
y-axis represents the likelihood ratio ?
All the best,
Camill
Hi,
Pascal, I tried to use your method which functions but the values of the
abscissa are not good. When I talked about “value”, I wanted mean the values
of my starting dataset that I have classified into two classes positive and
negative classes, such as this :
Value Status TPF TN
Hi everybody,
I have a data set with a value and a status (positive or negative case) and
I want make a ROC Analysis. So, with ROCR Package, I have got the ROC curve
(True Positive Fraction [tpf] according 1-True Negative Fraction [1-tnf]).
http://r.789695.n4.nabble.com/file/n4469203/01.png
But
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
Qian Liu gmail.com> writes:
>
> Hi I need some help with ploting the ROC for K-nearest neighbors. Since KNN
> is a non-parametric classification methods, the predicted value will be
> either 0 or 1.
> It will not be able to test for different cutoff to plot ROC. What is the
> package or functio
Hi I need some help with ploting the ROC for K-nearest neighbors. Since KNN
is a non-parametric classification methods, the predicted value will be
either 0 or 1.
It will not be able to test for different cutoff to plot ROC. What is the
package or functions I should use to plot ROC for KNN?
Thanks
Hi,
I am working on a ROC plot problem. Thanks in advance for any help.
We run 20 cross validation (CV) on our data for each customized threshold,
i.e. from 0.1 to 0.9.
Then for these 9 threshold values, we get the overall performance, that is
we are able to get overall sensitivity and specifi
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Angel Russo
Sent: Monday, February 21, 2011 3:34 PM
To: r-help@r-project.org
Subject: [R] ROC from R-SVM?
*Hi,
*Does anyone know how can I show an *ROC curve for R-SVM*? I understand in
R-SVM we are not
-learning-classifiers-r/
>
>
>
> -Original Message-----
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
> On Behalf Of Angel Russo
> Sent: Monday, February 21, 2011 3:34 PM
> To: r-help@r-project.org
> Subject: [R] ROC from R-SVM?
>
> *Hi,
&g
The objects functions for kernel methods are unrelated to the area
under the ROC curve. However, you can try to choose the cost and
kernel parameters to maximize the ROC AUC.
See the caret package, specifically the train function.
Max
On Mon, Feb 21, 2011 at 5:34 PM, Angel Russo wrote:
> *Hi,
>
*Hi,
*Does anyone know how can I show an *ROC curve for R-SVM*? I understand in
R-SVM we are not optimizing over SVM cost parameter. Any example ROC for
R-SVM code or guidance can be really useful.
Thanks, Angel.
[[alternative HTML version deleted]]
_
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
ert Gunter wrote:
> Did you try googling on "R ROC function" (or something similar) or using
> the
> RSiteSearch() function?
>
> ?RSiteSearch
>
> RSiteSearch("ROC",restr="func")
>
> Learn to use R's various search capabilities befor
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
Did you try googling on "R ROC function" (or something similar) or using the
RSiteSearch() function?
?RSiteSearch
RSiteSearch("ROC",restr="func")
Learn to use R's various search capabilities before posting, please!
Bert Gunter
Genentech Nonclinical Biost
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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R-help@r-projec
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
[Going through some old and from what I see unanswered messages
Hard to tell what is going on without telling us the data. Works with
the examples, so may be related to one of the objects scicomp5.model1,
pred, T, or auc.
> PLEASE do read the posting guide
http://www.R-project.org/posting-g
My question would be related more to time-dependent ROC (survivalROC package):
I would like to know how true positives (TP) and false positives (FP) are
related to the order of survival times and diagnostic markers. That is, having
the a set of TP and FP, each of them is calculated from which di
I am trying to create the roc plot bootstrap method from library(verification),
and when I set the plot =both or emp then I get the following error. The
roc.plot works fine when the plot is set to binorm. This is my first time using
this function in R and am not sure what this error means or how
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
Would you be interested in the cross-validation that's on pp 3 and 4 of the
ROCR package PDF?
plot(perf,lwd=3,avg="vertical",spread.estimate="boxplot",add=TRUE)
there are various options for the 'spread.estimate'
David Freedman
marc bernard-2 wrote:
>
>
> Dear all, I am looking for an R pack
Dear all, I am looking for an R package that allows me to calculate and plot
the confidence intervals for the roc curve using for example some
bootstrapping. I tried "ROCR" who seems doing such work but i couldn't find the
right option in it. Many thanks Bests Marc
_
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
Eleni Christodoulou wrote:
> Richard, thanks, I think it will work. I will calculate the cutoff value
> and then, from the prediction object, find the fpr that is related to it and
> put it as argument to performance. I will keep you informed.
>
> Eleni
You will probably need to bootstrap the en
Richard, thanks, I think it will work. I will calculate the cutoff value
and then, from the prediction object, find the fpr that is related to it and
put it as argument to performance. I will keep you informed.
Eleni
On Wed, Mar 19, 2008 at 11:51 AM, Richard Pearson <
[EMAIL PROTECTED]> wrote:
Eleni
Does the fpr.stop argument do what you want? This is described in
?performance under the details of the "auc" measure. Try, e.g.
perform=performance(pred,measure="auc",fpr.stop=0.5)
Richard.
Eleni Christodoulou wrote:
> Hello list,
>
> I am trying to perform ROC analysis and count the
Hello list,
I am trying to perform ROC analysis and count the AUC in order to validate
my results. I use package ROCR. I would like to count the AUC not under the
cutoff found by "performance" but to use another cutoff that I calculate.
How could I change the following command in order to get wha
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