similar to: Running random forest using different training and testing schemes

Displaying 20 results from an estimated 1000 matches similar to: "Running random forest using different training and testing schemes"

2009 Apr 08
2
help with random forest package
Hello, I am a phd student in Bioinformatics and I am using the Random Forest package in order to classify my data, but I have some questions. Is there a function in order to visualize the trees, so as to get the rules? Also, could you please provide me with the code of "randomForest" function, as I would like to see how it works. I was wondering if I can get the classification having
2009 Jul 08
1
heatmap.2: question regarding the "raw z-score"
Hi, I am analysing gene expression data using the heatmap.2 function in R and I was wondering what is the formula of the "raw z-score" bar which shows the colors for each pixel. According to that post: https://mailman.stat.ethz.ch/pipermail/r-help/2006-September/113598.html, it is the (actual value - mean of the group) / standard deviation. But, mean of which group? Mean of the gene
2009 Sep 28
1
how to visualize gini coefficient in each node in RF?
Dear all, I am working with randomForest package and I am interested in examining the "Gini importance" measures that are used as a general indicator of feature relevance. Is there a possibility of getting the Gini measure that is being estimated in each tree by the output of the getTree() function? Thanks a lot, Chrysanthi [[alternative HTML version deleted]]
2010 Jan 11
1
Help me! using random Forest package, how to calculate Error Rates in the training set ?
now I am learining random forest and using random forest package, I can get the OOB error rates, and test set rate, now I want to get the training set error rate, how can I do? pgp.rf<-randomForest(x.tr,y.tr,x.ts,y.ts,ntree=1e3,keep.forest=FALSE,do.trace=1e2) using the code can get oob and test set error rate, if I replace x.ts and y.ts with x.tr and y.tr,respectively, is the error rate
2011 Jul 29
1
Cplex solver and optimization in R
Dear all, I want to work with R in an optimization problem and I was wondering if there are any available solvers. I found RCplex package but downloading it, I get problems. Why? Is it not free? are there any other solvers available? many thanks! -- View this message in context: http://r.789695.n4.nabble.com/Cplex-solver-and-optimization-in-R-tp3703385p3703385.html Sent from the R help
2011 Jul 25
1
Problem with random number simulation
Hi this is my first post. I am trying to run a simulation for a computer playing Von Neumann poker and adjusting it's expectation of an opponent's behavior according to how the opponent plays. This program involves random generation of "hands" and shifting of parameters. However, when I run the code, no errors come up, but the program doesn't do anything. Could someone
2012 Apr 23
1
change color scheme in mvpart
Hello everyone, I am currently using the mvpart package and would like to change the color scheme it uses, and was hoping someone could help me out. All of the papers I have found have used a grayscale but I can't seem to figure out how they did that! Currently, mvpart plots barplots in a repeating sequence of 3 shades of blue. So if you have 6 response variables the same shade of blue is used
2010 Mar 12
1
using xval in mvpart to specify cross validation groups
Dear R's I'm trying to use specific rather than random cross-validation groups in mvpart. The man page says: xval Number of cross-validations or vector defining cross-validation groups. And I found this reply to the list by Terry Therneau from 2006 The rpart function allows one to give the cross-validation groups explicitly. So if the number of observations was 10, you could use
2009 Jun 09
3
rpart - the xval argument in rpart.control and in xpred.rpart
Dear R users, I'm working with the rpart package and want to evaluate the performance of user defined split functions. I have some problems in understanding the meaning of the xval argument in the two functions rpart.control and xpred.rpart. In the former it is defined as the number of cross-validations while in the latter it is defined as the number of cross-validation groups. If I am
2013 Mar 22
1
Trouble embedding functions (e.g., deltaMethod) in other functions
Dear R community, I've been writing simple functions for the past year and half and have come across a similar problem several times. The execution of a function within my own function produces NaN's or fails to execute as intended. My conundrum is that I can execute the function outside of my function without error, so it's difficult for me, as a novice functioneer, to figure out
2004 Sep 24
5
AW: How to improve the quality of curve/line plots?
Thanks for the tip using a smoothing technique before plotiing in order to get a curve instead of a line connecting the observations. But that's not the solution for my main problem with the "unclean" line plot. In order to show my problem let's take this simple example: > xval <- c(1, 2, 3, 4, 5, 6, 7, 8) > yval <- c(10, 30, 40, 50, 70, 90, 100, 110) > plot
2000 Jan 10
1
'at' parameter in mtext(.., adj=0, outer=T) (PR#396)
Depending on the setting of par()$usr, the 'at' setting in mtext(.., adj=0, outer=T) may cause the text to appear in an anomalous position (e. g. in the first instance below, at the left of the plot region rather than at 'at=0' in the figure region), or the text may not appear at all. If one does not set the 'at' parameter the text appears (with 'adj=0') on the
2009 Sep 24
3
pipe data from plot(). was: ROCR.plot methods, cross validation averaging
All, I'm trying again with a slightly more generic version of my first question. I can extract the plotted values from hist(), boxplot(), and even plot.randomForest(). Observe: # get some data dat <- rnorm(100) # grab histogram data hdat <- hist(dat) hdat #provides details of the hist output #grab boxplot data bdat <- boxplot(dat) bdat #provides details of the boxplot
2009 Jul 25
4
ROCR package question
I use ROCR to plot multiple runs' performance. Using the sample code as example: # plot ROC curves for several cross-validation runs (dotted # in grey), overlaid by the vertical average curve and boxplots # showing the vertical spread around the average. data(ROCR.xval) pred <- prediction(ROCR.xval$predictions, ROCR.xval$labels) perf <- performance(pred,"tpr","fpr")
1999 Aug 26
1
error bars on barplots
Hello again I'm trying to put error bars onto a barplot. I've tried something that Bill Simpson suggested a while ago, ie: x<-c(1,2,3,4,5) y<-c(1.1, 2.3, 3.0, 3.9, 5.1) ucl<-c(1.3, 2.4, 3.5, 4.1, 5.3) lcl<-c(.9, 1.8, 2.7, 3.8, 5.0) plot(x,y, ylim=range(c(lcl,ucl))) arrows(x,ucl,x,lcl,length=.05,angle=90,code=3) #or segments(x,ucl,x,lcl) but I can't get it to work on a
2007 Mar 01
1
Generating R plots through Perl
Hello, I am in the process of writing a Perl program to carry out and analyze large numbers of regressions using R as the regression engine, and I am using Statistics::R to create the communication bridge between the two programs. Statistics::R creates a pipe between R and Perl and uses Rterm.exe (hidden during run-time) to carry out the R commands. This communication bridge works well for
2010 Oct 12
2
repeating an analysis
Hi All, I have to say upfront that I am a complete neophyte when it comes to programming. Nevertheless I enjoy the challenge of using R because of its incredible statistical resources. My problem is this .........I am running a regression tree analysis using "rpart" and I need to run the calculation repeatedly (say n=50 times) to obtain a distribution of results from which I will pick
2009 Apr 02
2
Scatter plot
Hi. How do I plot the straight line and r? in a scatter plot using a simple file x~y? Sueli Rodrigues Eng. Agr?noma - UNESP Mestranda - USP/ESALQ PPG-Solos e Nutri??o de Plantas Fones (19)93442981 (19)33719762
2011 Mar 19
2
cross-validation in rpart
I am trying to find out what type of sampling scheme is used to select the 10 subsets in 10-fold cross-validation process used in rpart to choose the best tree. Is it simple random sampling? Is there any documentation available on this? Thanks, Penny. -- View this message in context: http://r.789695.n4.nabble.com/cross-validation-in-rpart-tp3389329p3389329.html Sent from the R help mailing list
2004 Jun 21
2
visualizing a list of probabilities
Hi, I'm using nnet to work on a 2 class classification problem. The result of my code is data.frame of true class, predicted class and associated probability. One way of summarizing the data is by a confusion matrix. However are there any graphical ways I could represent the data - specifically, I'd like to show the probabilities associated with each member of my prediction set? (I