Displaying 20 results from an estimated 7000 matches similar to: "Extract information from S4 object"
2012 Nov 22
2
ROCR package not installing
I have tried installing the package (ROCR) with this command:
Install.packages(ROCR)
And with this command on the command line
R CMD INSTALL ROCR_1.0-4.tar.gz
But both times I get exactly the same error shown below, I don't understand
what is wrong, is this an error in the package code?
Thank you
Philip
probinson@bioinform08:/tmp/RtmpO0rFbx/downloaded_packages$ R CMD
2013 May 27
1
Question about subsetting S4 object in ROCR
Dear list
I'm testing a predictor and I produced nice performance plots with ROCR
package utilizing the 3 standard command
pred <- prediction(predictions, labels)
perf <- performance(pred, measure = "tpr", x.measure = "fpr")
plot(perf, col=rainbow(10))
The pred object and the perfo object are S4
with the following slots
An object of class "performance"
2009 Mar 27
1
ROCR package finding maximum accuracy and optimal cutoff point
If we use the ROCR package to find the accuracy of a classifier
pred <- prediction(svm.pred, testset[,2])
perf.acc <- performance(pred,"acc")
Do we?find the maximum accuracy?as follows?(is there a simplier way?):
> max(perf.acc at x.values[[1]])
Then to find the cutoff point that maximizes the accuracy?do we do the
following?(is there a simpler way):
> cutoff.list <-
2011 Feb 21
3
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 optimizing over SVM cost parameter. Any example ROC for
R-SVM code or guidance can be really useful.
Thanks, Angel.
[[alternative HTML version deleted]]
2009 Sep 24
3
pipe data from plot(). was: ROCR.plot methods, cross validation averaging
All,
I'm trying again with a slightly more generic version of my first question. I can extract the
plotted values from hist(), boxplot(), and even plot.randomForest(). Observe:
# get some data
dat <- rnorm(100)
# grab histogram data
hdat <- hist(dat)
hdat #provides details of the hist output
#grab boxplot data
bdat <- boxplot(dat)
bdat #provides details of the boxplot
2012 Feb 09
2
ROCR crashes for simple recall plot
I'm trying to use ROCR to create a simple cutoff vs recall plot
(recall at p) on the example ROCR.simple dataset:
library(ROCR)
data(ROCR.simple)
pred <- prediction(ROCR.simple$predictions, ROCR.simple$labels)
perf <- performance(pred, "rec")
plot(perf)
But R crashes on me on the last line.
I'm using R 2.14.1, ROCR 1.0-4. ?Any ideas? Thanks in advance.
--
Yang Zhang
2009 Jul 23
1
ROCR - confidence interval for Sens and Spec
Dear List,
I am new to ROC analysis and the package ROCR. I want to compute the confidence intervals of sensitivity and specificity for a given cutoff value. I have used the following to calculate sensitivity and specificity:
data(ROCR.simple)
pred <- prediction(ROCR.simple$predictions, ROCR.simple$labels)
se.sp <- function (cutoff, performance) {
sens <-
2011 Apr 06
3
ROCR - best sensitivity/specificity tradeoff?
Hi,
My questions concerns the ROCR package and I hope somebody here on the list can help - or point me to some better place.
When evaluating a model's performane, like this:
pred1 <- predict(model, ..., type="response")
pred2 <- prediction(pred1, binary_classifier_vector)
perf <- performance(pred, "sens", "spec")
(Where "prediction" and
2010 Aug 17
1
ROCR predictions
Hi everybody,
I am having a problem building a ROC curve with my data using the ROCR
package.
I have 10 lists of proteins such as attached (proteinlist.xls). each of the
lists was calculated with a different p-value.
The goal is to find the optimal p-value for the highest number of true
positives as well as lowaest number of false positives.
As far as I understood the explanations from the
2011 Sep 03
2
ROCR package question for evaluating two regression models
Hello All,
I have used logistic regression glm in R and I am evaluating two models both learned with glm but with different predictors. model1 <- glm (Y ~ x4+ x5+ x6+ x7, data = dat, family = binomial(link=logit))model2 <- glm (Y~ x1 + x2 +x3 , data = dat, family = binomial(link=logit))
and I would like to compare these two models based on the prediction that I get from each model:
pred1 =
2010 Dec 30
2
optim and singularity
Hello,
I was unable to find clues to my problem in ?optim. Using the data and code
below, I get an error ("system is exactly singular") when a particular line
of code is left in, but have found that 'optim' works when I comment it out.
The line of code in question is after the closeAllConnections() line of code
and contains a call to "na.approx" from the zoo package.
2010 Feb 17
2
extract the data that match
Hi r-users,
I would like to extract the data that match. Attached is my data:
I'm interested in matchind the value in column 'intg' with value in column 'rand_no'
> cbind(z=z,intg=dd,rand_no = rr)
z intg rand_no
[1,] 0.00 0.000 0.001
[2,] 0.01 0.000 0.002
[3,] 0.02 0.000 0.002
[4,] 0.03 0.000 0.003
[5,] 0.04 0.000 0.003
[6,]
2009 Feb 25
3
Using package ROCR
I am trying to use package ROCR to analyze classification accuracy,
unfortunately there are some problems right at the beginning.
Question 1)
When I try to run demo I am getting the following error message
> library(ROCR)
> demo(ROCR)
> if(dev.cur() <= 1) .... [TRUNCATED]
Error in get(getOption("device")) : wrong first argument
When I issue the command
> dev.cur()
it
2007 Jun 16
1
selecting cut-off in Logistic regression using ROCR package
Hi,
I am using logistic regression to classify a binary psychometric data. using
glm() and then predict.glm() i got the predicted odds ratio of the testing
data. Next i am going to plot ROC curve for the analysis of my study.
Now what i will do:
1. first select a cut-off (say 0.4) and classify the output of predict.glm()
into {0,1} segment and then use it to draw ROC curve using ROCR package
2008 May 22
1
Extracting slots from ROCR prediction objects
Hi,
I have an object from the prediction function from the ROCR package and I would like to extract one of the slots from the object, for example the cutoffs slot. However the usual techniques ($, [["name"]]) of subsetting don't work. How can I assess the lists in the slots?
Here is an example of what I am working with:
library(ROCR)
data(ROCR.simple)
pred <-
2009 Jul 25
4
ROCR package question
I use ROCR to plot multiple runs' performance. Using the sample code
as example:
# plot ROC curves for several cross-validation runs (dotted
# in grey), overlaid by the vertical average curve and boxplots
# showing the vertical spread around the average.
data(ROCR.xval)
pred <- prediction(ROCR.xval$predictions, ROCR.xval$labels)
perf <- performance(pred,"tpr","fpr")
2014 Jun 20
2
Como construir una curva ROC
Hola!
Tengo que hacer una curva ROC com unos datos que obtuve de hacer una macro
de excel y aplicar unas reglas, y basicamente tengo que a partir de la
variacion del tiempo y la velocidad del barco obtengo diferentes
porcentajes de true positives (TP) y false positives (FP) y con eso deberia
de construir una curva ROC.
Dada mi ignorância en este tema, no se muy bien por donde empezar , estuve
2012 Dec 19
2
pROC and ROCR give different values for AUC
Packages pROC and ROCR both calculate/approximate the Area Under (Receiver Operator) Curve. However the results are different.
I am computing a new variable as a predictor for a label. The new variable is a (non-linear) function of a set of input values, and I'm checking how different parameter settings contribute to prediction. All my settings are predictive, but some are better.
The AUC i
2010 Aug 25
1
Documenting S4 Methods
I'm in the process of converting some S3 methods to S4 methods.
I have this function :
setGeneric("enrichmentCalc", function(rs, organism, seqLen, ...){standardGeneric("enrichmentCalc")})
setMethod("enrichmentCalc", c("GenomeDataList", "BSgenome"), function(rs, organism, seqLen, ...) {
... ... ...
})
2014 Jun 23
2
Resumen de R-help-es, Vol 64, Envío 33
Hola, Marta,
Por lo que he podido ver tus datos ya tienen calculados las tasas de verdaderos y falsos positivos (TPR y FPR). También parece que los tienes ordenados por la variable FishSpeed y supongo que también por las que parecen marcas de tiempo. No necesitas ROCR porque con un simple plot te sale algo parecido a una curva. Eso sí, veo que son medidas repetidas en el tiempo para cada valor de