[R] TreeBUGS - subscript out of bounds

cript out of bounds   Though I've found some information on this general error online, all of it applies to different tests and didn't help me to solve the problem. Has anyone of you encountered this error before, or has a suggestion for me?   Best, Max __

[R] Assessing calibration of Cox model with time-dependent coefficients

I am trying to find methods for testing and visualizing calibration to Cox models with time-depended coefficients. I have read this nice article . In this paper, we can fit three models: fit0 <- coxph(Surv(futime, status) ~ x1 + x2 + x3, da

[R] Time-dependent coefficients in a Cox model with categorical variants

Suppose I have a dataset contain three variants, looks like > head(dta) SextumorsizeHistology time status 01.52 12.1000 0 11.81 38.4000 0 . Sex: 1

[R] failure with merge

0.9815738 0.03881885 Browse[3]> x[, seq_len(l.b), drop = FALSE] select method 2 TRUE GCV.Cp 1 FALSE GCV.Cp and this line executes: Browse[3]> order(x[, seq_len(l.b), drop = FALSE]) [1] 1 2 3 4 although nrow(x) = 2 so this is an issue. Calling it this way stops execu

Re: [R] Installing Caret

The problem is not with `caret. Your output says: > installation of package ‘minqa’ had non-zero exit status `caret` has a dependency that has a dependency on `minqa`. The same is true for `RcppEigen` and the others. What code did you use to do the install? What OS and version or R etc? On Th

Re: [R] Problem while predicting in regression trees

anks and > > > Kind Regards > > > > -- > Muhammad Bilal > Research Fellow and Doctoral Researcher, > Bristol Enterprise, Research, and Innovation Centre (BERIC), > University of the West of England (UWE), > Frenchay Campus, > Bristol, > BS16 1QY > > *muh

Re: [R] Problem while predicting in regression trees

It is extremely difficult to tell what the issue might be without a reproducible example. The only thing that I can suggest is to use the non-formula interface to `train` so that you can avoid creating dummy variables. On Mon, May 9, 2016 at 11:23 AM, Muhammad Bilal < muhammad2.bi...@live.uwe.ac.

Re: [R] Mixture Discriminant Analysis and Penalized LDA

There is a function called `smda` in the sparseLDA package that implements the model described in Clemmensen, L., Hastie, T., Witten, D. and Ersbøll, B. Sparse discriminant analysis, Technometrics, 53(4): 406-413, 2011 Max On Sun, Jan 24, 2016 at 10:45 PM, TJUN KIAT TEO wrote: > Hi &g

Re: [R] Caret - Recursive Feature Elimination Error

Providing a reproducible example and the results of `sessionInfo` will help get your question answered. Also, what is the point of using glmnet with RFE? It already does feature selection. On Wed, Dec 23, 2015 at 1:48 AM, Manish MAHESHWARI wrote: > Hi, > > I am trying to use caret, for feature

Re: [R] Error in 'Contrasts<-' while using GBM.

Providing a reproducible example and the results of `sessionInfo` will help get your question answered. My only guess is that one or more of your predictors are factors and that the in-sample data (used to build the model during resampling) have different levels than the holdout samples. Max On

Re: [R] Ensure distribution of classes is the same as prior distribution in Cross Validation

Right now, using `method = "cv"` or `method = "repeatedcv"` does stratified sampling. Depending on what you mean by "ensure" and the nature of your outcome (categorical?), it probably already does. On Mon, Nov 23, 2015 at 7:04 PM, TJUN KIAT TEO wrote: > In the caret train control function, is it

Re: [R] Caret Internal Data Representation

Providing a reproducible example and the results of `sessionInfo` will help get your question answered. For example, did you use the formula or non-formula interface to `train` and so on On Thu, Nov 5, 2015 at 1:10 PM, Bert Gunter wrote: > I am not familiar with caret/Cubist, but assuming they

Re: [R] Caret and Summary

bjects. Besides this, I do not know of any. Thanks, Max __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and

Re: [R] Imbalanced random forest

This might help: http://bit.ly/1MUP0Lj On Wed, Jul 29, 2015 at 11:00 AM, jpara3 wrote: > ¿How can i set up a study with random forest where the response is highly > imbalanced? > > > > - > > Guided Tours Basque Country > > Guided tours in the three capitals of the Basque Country: Bilbao, >

Re: [R] what constitutes a 'complete sentence'?

On Tue, Jul 7, 2015 at 8:19 AM, John Fox wrote: > Dear Peter, > > You're correct that these examples aren't verb phrases (though the second > one contains a verb phrase). I don't want to make the discussion even more > pedantic (moving it in this direction was my fault), but "Paragraph" isn't > q

Re: [R] Caret and custom summary function

The version of caret just put on CRAN has a function called mnLogLoss that does this. Max On Mon, May 11, 2015 at 11:17 AM, Lorenzo Isella wrote: > Dear All, > I am trying to implement my own metric (a log loss metric) for a > binary classification problem in Caret. > I must be

Re: [R] Repeated failures to install "caret" package (of Max Kuhn)

gt; > > -Original Message- > > From: wyl...@ischool.utexas.edu > > Sent: Fri, 03 Apr 2015 16:07:57 -0500 > > To: r-help@r-project.org > > Subject: [R] Repeated failures to install "caret" package (of Max Kuhn) > > > > For an edx course,

Re: [R] Prevent line truncation in system2() output

) .OO#. .OO#. rocks...1k > --- > Sent from my phone. Please excuse my brevity. > > On March 15, 2015 11:02:57 AM PDT, Luiz Max Carvalho < > luizepidemiolo...@gmail.com> wrote: > >Hey all, > > > >I'm developing an application that c

[R] Prevent line truncation in system2() output

what messes up what I have set up to read the output. Is there any way of preventing system2() from breaking the lines? I think I can work around this issue, but I'm looking for a cleaner solution for the time being. Cheers, Luiz -- Luiz Max Fagundes de Carvalho PhD student, Institute of Ev

Re: [R] #library("CHAID") - Cross validation for chaid

vote[sample(1:nrow(USvote), 1000),] ## You probably don't want to use `train.formula` as ## it will convert the factors to dummy variables mod <- train(x = USvoteS[,-1], y = USvoteS$vote3, method = modelInfo, trControl = trainControl(method = "cv")) M

Re: [R] Help with caret, please

index = folds, indexOut = folds) tGrid=data.frame(k=1:100) set.seed(3) a_bad_idea <- train(Class ~ ., data=dat, method = "knn", tuneGrid=tGrid, trControl=Control, metric = "ROC") Max On

Re: [R] Training a model using glm

you got to the `training` object (package versions would be nice too). I suspect that Dennis is correct. Try using more normal syntax without the $ indexing in the formula. I wouldn't say it is (absolutely) wrong but it doesn't look right either. Max On Wed, Sep 17, 2014 at 2:04

Re: [R] Use of library(X) in the code of library X.

t explicitly. I don't recall which parallel backend had the issue. The more important lesson is that if you want to "understand some R code written by others" you'll learn more bad habits than good ones if you examine my packages… Max On Fri, Jun 6, 2014 at 2:42 PM, Duncan Murdo

Re: [R] cforest sampling methods

You might look at the 'bag' function in the caret package. It will not do the subsampling of variables at each split but you can bag a tree and down-sample the data at each iteration. The help page has an examples bagging ctree (although you might want to play with the tree depth a lit

Re: [R] how is the model resample performance calculated by caret?

> RSQUARE - is what I am thinking true? It is. Max > > >> plsTune > 524 samples > 615 predictors > > Pre-processing: centered, scaled > Resampling: Cross-Validation (10 fold, repeated 5 times) > > Summary of sample sizes: 472, 472, 471, 471, 471, 471, .

Re: [R] boxcox alternative

'preProcess' that might interest you. See: http://caret.r-forge.r-project.org/preprocess.html#trans Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www

Re: [R] Predictor Importance in Random Forests and bootstrap

/featureSelection.html Max On Tue, Jan 28, 2014 at 5:32 PM, Dimitri Liakhovitski < dimitri.liakhovit...@gmail.com> wrote: > Here is a great response I got from SO: > > There is an important difference between the two importance measures: > MeanDecreaseAccuracy is calculated using out

[R] [R-pkgs] caret version 6.0-21

lan Engelhardt, Tony Cooper, Zachary Mayer and the R Core Team. Please contact me (max.k...@pfizer.com) with any comments, suggestions, questions or ideas for a good wedding toasts. Max ___ R-packages mailing list r-packa...@r-project.org https://

Re: [R] R crashes with memory errors on a 256GB machine (and system shoes only 60GB usage)

Describing the problem would help a lot more. For example, if you were using some of the parallel processing options in R, this can make extra copies of objects and drive memory usage up very quickly. Max On Thu, Jan 2, 2014 at 3:35 PM, Ben Bolker wrote: > Xebar Saram gmail.com>

Re: [R] Variable importance - ANN

t is based on the estimated weights. Max On Wed, Dec 4, 2013 at 6:41 AM, Giulia Di Lauro wrote: > Hi everybody, > I created a neural network for a regression analysis with package ANN, but > now I need to know which is the significance of each predictor variable in > explaining the depen

Re: [R] Inconsistent results between caret+kernlab versions

ption is to use a model where this discrepancy does not exist. > train often crashes with 'memory map' errors!)? I've never seen that. You should describe it more. Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/l

Re: [R] Inconsistent results between caret+kernlab versions

ecause the class designation takes into account the costs but the class probability predictions do not. I alerted both package maintainers to the issue some time ago.) HTH, Max On Fri, Nov 15, 2013 at 1:56 PM, Max Kuhn wrote: > I've looked into this a bit and the issue seems to be with c

Re: [R] C50 Node Assignment

;" conds="1" cover="46" ok="45" lift="2.875" class="virginica" type="2" att="Petal.Width" cut="1.7" result=">" conds="1" cover="46" ok="44" lift="2.8125" clas

Re: [R] Cross validation in R

> How do i make a loop so that the process could be repeated several time, > producing randomly ROC curve and under ROC values? Using the caret package http://caret.r-forge.r-project.org/ -- Max __ R-help@r-project.org mailing list

Re: [R] Error running caret's gbm train function with new version of caret

et", repos="http://R-Forge.R-project.org";) You may also need to ungrade gbm. That package page is: https://code.google.com/p/gradientboostedmodels/downloads/list Let me know if you have any issues. Max On Sat, May 4, 2013 at 5:33 PM, Katrina Bennett wrote: > I am running caret

Re: [R] C50 package in R

ween model trees and Cubist are also substantial and largely undocumented. HTH, Max On Thu, Apr 25, 2013 at 9:40 AM, Indrajit Sen Gupta < indrajit...@rediffmail.com> wrote: > Hi All, > > > > I am trying to use the C50 package to build classification trees in R. > Unfortu

Re: [R] odfWeave: Some questions about potential formatting options

completely buried in the foreseeable future and won't be able to pay much attention to it. To be honest, odfWeave has been fairly neglected by me and lately I've had thoughts of orphaning the package :-/ Thanks, Max On Tue, Apr 16, 2013 at 1:15 PM, Paul Miller wrote: > Hi Milan

Re: [R] Parallelizing GBM

See this: https://code.google.com/p/gradientboostedmodels/issues/detail?id=3 and this: https://code.google.com/p/gradientboostedmodels/source/browse/?name=parallel Max On Sun, Mar 24, 2013 at 7:31 AM, Lorenzo Isella wrote: > Dear All, > I am far from being a guru about pa

Re: [R] CARET and NNET fail to train a model when the input is high dimensional

ue that let's you fit the model. Off the top of my head, you could use something like: MaxNWts = length(levels(trY))*(max(my.grid$.size) * (nCol + 1) + max(my.grid$.size) + 1) Also, this one of the methods for getting help (the other is to just email me). I also try to keep up on stack ex

Re: [R] caret pls model statistics

That the most common formula, but not the only one. See Kvålseth, T. (1985). Cautionary note about $R^2$. *American Statistician*, *39*(4), 279–285. Traditionally, the symbol 'R' is used for the Pearson correlation coefficient and one way to calculate R^2 is... R^2. Max On Sun, M

Re: [R] caret pls model statistics

Charles, You should not be treating the classes as numeric (is virginica really three times setosa?). Q^2 and/or R^2 are not appropriate for classification. Max On Sat, Mar 2, 2013 at 5:21 PM, Charles Determan Jr wrote: > I have discovered on of my errors. The timematrix was unnecessary

Re: [R] odfWeave: Trouble Getting the Package to Work

file". The default value should be sufficient. Max > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDe

Re: [R] CARET: Any way to access other tuning parameters?

@Max - Thanks a lot for your help. I have already been using that website > as a reference, and it's incredibly helpful. I have also been experimenting > with tuneGrid already. My question was specifically if tuneGrid (or caret > in general) supports passing method parameters

Re: [R] CARET: Any way to access other tuning parameters?

James, You really need to read the documentation. Almost every question that you have has been addressed in the existing material. For this one, there is a section on custom models here: http://caret.r-forge.r-project.org/training.html Max On Wed, Feb 13, 2013 at 9:58 AM, James Jong wrote

Re: [R] pROC and ROCR give different values for AUC

A reproducible example sent to the package maintainer(s) might yield results. Max On Wed, Dec 19, 2012 at 7:47 AM, Ivana Cace wrote: > Packages pROC and ROCR both calculate/approximate the Area Under (Receiver > Operator) Curve. However the results are different. > > I am com

Re: [R] Help with this error "kernlab class probability calculations failed; returning NAs"

Your output has: "At least one of the class levels are not valid R variables names; This may cause errors if class probabilities are generated because the variables names will be converted to: X0, X1" Try changing the factor levels to avoid leading numbers and try again. Max On T

Re: [R] Help with this error "kernlab class probability calculations failed; returning NAs"

You didn't provide the results of sessionInfo(). Upgrade to the version just released on cran and see if you still have the issue. Max On Thu, Nov 29, 2012 at 6:55 PM, Brian Feeny wrote: > I have never been able to get class probabilities to work and I am > relatively new to

Re: [R] caret train and trainControl

: k=11 + Fold10: k=17 - Fold10: k=17 + Fold10: k=19 - Fold10: k=19 + Fold10: k=21 - Fold10: k=21 + Fold10: k=23 - Fold10: k=23 Aggregating results Selecting tuning parameters Fitting model on full training set Max On Fri, Nov 23, 2012 at 5:52 PM, Brian Feeny wrote: > > I am used t

[R] Problem with which function

tor" > is(nstu) [1] "matrix""array" "structure" "vector" > nstu[11,1] [1] 84.38 > r[2195,1] [1] 84.38 > which(r==nstu[10,1]) [1] 2225 > which(r==nstu[11,1]) integer(0) why is it like that? Thanks for a answer max ___

Re: [R] column width in .dbf files using write.dbf ... to be continued

Old topic... An answer may be useful for someone else, though... Just do : > environment(write.dbfMODIF)<-environment(foreign::write.dbf ) and it should be good to go. Cheers, -- View this message in context: http://r.789695.n4.nabble.com/column-width-in-dbf-files-using-write-dbf-to-be-con

Re: [R] Decision Tree: Am I Missing Anything?

Vik, On Fri, Sep 21, 2012 at 12:42 PM, Vik Rubenfeld wrote: > Max, I installed C50. I have a question about the syntax. Per the C50 manual: > > ## Default S3 method: > C5.0(x, y, trials = 1, rules= FALSE, > weights = NULL, > control = C5.0Control(), > costs = NULL, ...)

[R] Creating an array from correlation matrices

Hello everyone, a hopefully easy to solve problem from an R novice... I try to calculate a number of correlation matrices that finally should be combined in a three-dimensional array. Here the my code with an R dataset as an example. --- ## Creation an array of

Re: [R] Caret: Use timingSamps leads to error

I can reproduce the errors. I'll take a look. Thanks, Max On Thu, Jul 12, 2012 at 5:24 AM, Dominik Bruhn wrote: > I want to use the caret package and found out about the timingSamps > obtion to obtain the time which is needed to predict results. But, as > soon as I set a value f

Re: [R] caret() train based on cross validation - split dataset to keep sites together?

would fit a model on those site 1 data in the first argument and predict everything else, and so on. I'm not sure if this is what you need, but there you go. Max On Wed, May 30, 2012 at 7:55 AM, Tyrell Deweber wrote: > Hello all, > > I have searched and have not yet identified a s

Re: [R] Using NA as a break point for indicator variable?

This method worked perfectly! The rle() function was key and I was completely unfamiliar with it. Thanks so much, Max On Thu, May 24, 2012 at 8:52 AM, Rui Barradas wrote: > Hello, > > Assuming that 'd' is your original data.frame and that you've set entire > r

[R] Using NA as a break point for indicator variable?

uot;? The data set is far too large to do this manually, and I must admit I'm completely at a loss. Any help would be much appreciated! Best, Max [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz

Re: [R] caret: Error when using rpart and CV != LOOCV

)^2 [1] 0.3669257 > customSummary(data.frame(obs = simObserved, + pred = simPredicted)) RMSE Rsquared 1.066900 -0.425169 It is somewhat extreme, but it does happen. Max * Kvålseth, T. (1985). Cautionary note about $R^2$. American statistician, 39(4), 279–285. *

Re: [R] caret: Error when using rpart and CV != LOOCV

Dominik, See this line: >   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. >  30.37   30.37   30.37   30.37   30.37   30.37 The variance of the predictions is zero. caret uses the formula for R^2 by calculating the correlation between the observed data and the predictions which uses s

Re: [R] caret: Error when using rpart and CV != LOOCV

failure mode would result in a divide by zero. Try using you own summary function (see ?trainControl) and put a print(summary(data$pred)) in there to verify my claim. Max On Wed, May 16, 2012 at 11:30 AM, Max Kuhn wrote: > More information is needed to be sure, but it is most likely that some &

Re: [R] caret package: custom summary function in trainControl doesn't work with oob?

dle this feature for bagging models, > but if it is already there and I've missed something please let me know. Well, everything is easy for the person not doing it =] If you save the proximity measures, you might gain the sampling indices. WIth these, you would use predict.randomForest(.

[R] nonparametric densities for bounded distributions

zero and one). Thanks, Max [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide co

Re: [R] Custom caret metric based on prob-predictions/rankings

>>> >>> -- >>> Yang Zhang >>> http://yz.mit.edu/ >> >> >> >> -- >> Yang Zhang >> http://yz.mit.edu/ > > > > -- > Yang Zhang > http://yz.mit.edu/ > > __ &g

Re: [R] Choosing glmnet lambda values via caret

/stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Max __ R-help@r-project.org mailing list https://stat.eth

[R] Quality of fit statistics for NLS?

any other means of determining the quality of the curve fit? I have tried applying confidence intervals using confint(dum), but these curves seem unrealistically narrow. Thanks so much for your help! -Max [[alternative HTML version deleted]]

[R] lattice key in blank panel

ad no conditioning bar at the top, only the key. I can find examples of putting the legend outside of the panel locations (e.g to the right of locations 2 and 4 above), but that's not really what I'd like to do. Thanks, Max __ R-help@r-proj

[R] Colorbar too wide in eps

ntour" command - without success. Anybody ran into a similar problem once? Thanks for helping me out, Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/

Re: [R] palettes for the color-blind

Yes, I was aware of the different type and their respective prevalences. The dichromat package helped me find what I needed. Thanks, Max On Wed, Nov 2, 2011 at 6:38 PM, Thomas Lumley wrote: > On Thu, Nov 3, 2011 at 11:04 AM, Carl Witthoft wrote: >> >> Before you pick out a pa

[R] palettes for the color-blind

but to be honest, I'd like to use something a little more vibrant. First, can anyone verify that these the colors in col2 are differentiable to someone who is color blind? Second, are there any other specific palettes that can be recommended? How do the RColorBrewer palettes rate

Re: [R] Contrasts with an interaction. How does one specify the dummy variables for the interaction

This is failing because it is a saturated model and the contrast package tries to do a t-test (instead of a z test). I can add code to do this, but it will take a few days. Max On Fri, Oct 28, 2011 at 2:16 PM, John Sorkin wrote: > Forgive my resending this post. To data I have received only

Re: [R] help with parallel processing code

it is using 2-3 cores it helps). Thanks, Max On Fri, Oct 28, 2011 at 10:49 AM, 1Rnwb wrote: > the part of the question dawned on me now is, should I try to do the parallel > processing of the full code or only the iteration part? if it is full code > then I am at the complete mercy of the R

Re: [R] help with parallel processing code

Devices utils datasets methods base other attached packages: [1] doMPI_0.1-5 Rmpi_0.5-9 doMC_1.2.3 multicore_0.1-7 foreach_1.3.2 codetools_0.2-8 iterators_1.0.5 Max On Thu, Oct 27, 2011 at 4:30 PM, 1Rnwb wrote: > If i understand correctly you mean to write the line as be

Re: [R] difference between createPartition and createfold functions

Mon, Oct 3, 2011 at 11:10 AM, wrote: > Hi Max, > > Thanks for the note. In your last paragraph, did you mean "in > createDataPartition"? I'm a little vague about what returnTrain option does. > > Bonnie > > Quoting Max Kuhn : > >> Basically, create

Re: [R] difference between createPartition and createfold functions

Monte Carlos CV aka repeated training test splits). createFolds is exclusively for k-fold CV. Their usage is simular when you use the returnTrain = TRUE option in createFolds. Max On Sun, Oct 2, 2011 at 4:00 PM, Steve Lianoglou wrote: > Hi, > > On Sun, Oct 2, 2011 at 3:54 PM,   wro

Re: [R] Multivariate spline regression and predicted values

Thank you for the reply, it looks like the second option (te) will work perfectly! Max On Tue, Sep 20, 2011 at 2:39 PM, Max Farrell wrote: > One possibility is > > library(mgcv) > > ## isotropic thin plate spline smoother > b <- gam(Y~s(X[,1],X[,2])) > pr

[R] Multivariate spline regression and predicted values

ine version of the smooth.lf command above, or the multivariate version of smooth.spline. Any ideas/help? Thanks, Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: [R] odfWeave: Combining multiple output statements in a function

formatting.odf, page 7. The results are in formattingOut.odt On Thu, Sep 15, 2011 at 2:44 PM, Jan van der Laan wrote: > Max, > > Thank you for your answer. I have had another look at the examples (I > already had before mailing the list), but could find the example you > men

Re: [R] odfWeave: Combining multiple output statements in a function

ist > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Max __ R-help@r-project.org mailing

Re: [R] Trying to extract probabilities in CARET (caret) package with a glmStepAIC model

s://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Max __ R-help@r-project.org mailing list h

[R] Competing risk regression with CRR slow on large datasets?

better? Is it the 64-bit version that improves the performance? - Can I do something to speed things up? - Is the simulation similarly slow on your computer? (see simulation code at the end) Thanks Max To see the output and the simulation code see the original question at http://stats.stackex

[R] aggregating data

this using "cast" or "melt"? Ideally, I would also like to see the unique probes corresponding to each gene in the wide format. Thanks in advance Max Maxy Mariasegaram| Reserach Fellow | Australian Prostate Cancer Research Centre| Level 1, Building 33 | Princess Alexandra Ho

[R] plotnetwork {spaa} : how to get an absolute interval (i.e. not based on the range of input data) ?

I'm using plotnetwork {spaa} in order to get a correlation network plot of my data (e.g.: http://www.oga-lab.net/RGM2/func.php?rd_id=spaa:plotnetwork). By default, 'interval' argument indicate the number of intervals by which the range of input data is partitioned (the number of partitions betw

Re: [R] aucRoc in caret package [SEC=UNCLASSIFIED]

ch doesn't really make sense. Try getting the class probabilities for predicted1 and predicted2 and use those instead. Thanks, Max On Wed, Jun 1, 2011 at 9:24 PM, wrote: > > Please note that predicted1 and predicted2 are two sets of predictions > instead of predictors. As you can

Re: [R] issue with odfWeave running on Windows XP; question about installing packages under Linux

ike, I can send you the eventual fixes if you would like to test them. Thanks, Max On Tue, May 17, 2011 at 3:35 PM, wrote: > I also have a problem using odfWeave on Windows XP with R > R2.11.1. odfWeave > fails, giving mysterious error messages. (Not quite the same as yours, but &g

Re: [R] Can ROC be used as a metric for optimal model selection for randomForest?

that statistical inference is not the goal. Ref: Friedman. Greedy function approximation: a gradient boosting machine. Annals of Statistics (2001) pp. 1189-1232 Thanks, Max On Fri, May 13, 2011 at 8:11 AM, Frank Harrell wrote: > Using anything other than deviance (or likelihood) as the o

Re: [R] Can ROC be used as a metric for optimal model selection for randomForest?

XiaoLiu, I can't see the options in bootControl you used here. Your error is consistent with leaving classProbs and summaryFunction unspecified. Please double check that you set them with classProbs = TRUE and summaryFunction = twoClassSummary before you ran. Max On Thu, May 12, 2011 at 7:

Re: [R] Bigining with a Program of SVR

As far as caret goes, you should read http://cran.r-project.org/web/packages/caret/vignettes/caretVarImp.pdf and look at rfe() and sbf(). On Fri, May 6, 2011 at 2:53 PM, ypriverol wrote: > Thanks Max. I'm using now the library caret with my data. But the models > showed a correl

Re: [R] Bigining with a Program of SVR

/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Max __ R-help@r-project.org mailing list https://stat.ethz.ch/ma

Re: [R] Bigining with a Program of SVR

.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained

Re: [R] caret - prevent resampling when no parameters to find

Yeah, that didn't work. Use fitControl<-trainControl(index = list(seq(along = mdrrClass))) See ?trainControl to understand what this does in detail. Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help P

Re: [R] caret - prevent resampling when no parameters to find

od='glm') If y is a factor, it automatically adds the 'family = binomial' option when the model is fit (so you don't have to). Max On Sun, May 1, 2011 at 7:18 PM, pdb wrote: > glm.fit - answered my own question by reading the manual!-- > View this message in c

Re: [R] caret - prevent resampling when no parameters to find

sets (i.e. they are not the same data set). In the end, the original training set is used to fit the final model that is used for prediction. Max On Sun, May 1, 2011 at 6:41 PM, pdb wrote: > Hi Max, > > But in this example, it says the sample size is the same as the total number > of

Re: [R] Bigining with a Program of SVR

When you say "variable" do you mean predictors or responses? In either case, they do. You can generally tell by reading the help files and looking at the examples. Max On Fri, Apr 29, 2011 at 3:47 PM, ypriverol wrote: > Hi: >  I'm starting a research of Support Vector

Re: [R] caret - prevent resampling when no parameters to find

, the performance it gives is the apparent error rate. Max On Sun, May 1, 2011 at 5:57 PM, pdb wrote: > I want to use caret to build a model with an algorithm that actually has no > parameters to find. > > How do I stop it from repeatedly building the same model 25 times? > > >

Re: [R] odfWeave Error unzipping file in Win 7

hough > > cheers > psycho-ld > > -- > View this message in context: > http://r.789695.n4.nabble.com/odfWeave-Error-unzipping-file-in-Win-7-tp3232359p3232359.html > Sent from the R help mailing list archive at Nabble.com. > > _____

Re: [R] Specify feature weights in model prediction (CARET)

> Using the 'CARET' package, is it possible to specify weights for features > used in model prediction? For what model? > And for the 'knn' implementation, is there a way > to choose a distance metric (i.e. Mahalanob

Re: [R] use "caret" to rank predictors by random forest model

t not plot.varImp). Max On Mon, Mar 7, 2011 at 3:27 PM, Xiaoqi Cui wrote: > Hi, > > I'm using package "caret" to rank predictors using random forest model and > draw predictors importance plot. I used below commands: > > rf.fit<-randomForest(x,y,ntree=500,importan

[R] Course: R for Predictive Modeling: A Hands-On Introduction

R for Predictive Modeling: A Hands-On Introduction Predictive Analytics World in San Francisco Sunday March 13, 9am to 4:30pm This one-day session provides a hands-on introduction to R, the well-known open-source platform for data analysis. Real examples are employed in order to methodically expo

Re: [R] ROC from R-SVM?

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: >

Re: [R] Random Forest & Cross Validation

RF is like any other method. -- Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: [R] caret::train() and ctree()

Andrew, ctree only tunes over mincriterion and ctree2 tunes over maxdepth (while fixing mincriterion = 0). Seeing both listed as the function is being executed is a bug. I'll setup checks to make sure that the columns specified in tuneGrid are actually the tuning parameters that are used.

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