similar to: caret package

All, For my understanding, I wanted to see if I can get glmnet predictions using both the predict function and also by multiplying coefficients by the variable matrix. This is not worked out. Could anyone suggest where I am going wrong? I understand that I may not have the mean/intercept correct, but the scaling is also off, which suggests a bigger mistake. Thanks for your help. Juliet Hannah

Dear list, I have a problem on persp() x <- u1data #first coloum in attached data y <- u2data #second coloum in attached data f <- function(x,y){qgev(pnorm(rhoF*qnorm(pnorm((qnorm(y)-rho2*qnorm(x)/sqrt(1-rho2^2)))) +sqrt(1-rhoF^2)*qnorm(0.95)),-0.3935119, 0.4227890, 0.2701648)} z <- outer(x,y,f) persp(x,y,z) The R will display: "Error in persp.default(x, y,

thanks for your attention. temporarily with the following script I'm looking at myself. #!/bin/bash INTERVAL=180 LOG=true function log { if $LOG; then echo $1 fi } while true; do testx=`ps -auxw | grep "smbd" | wc -l` testy=`netstat -ap | grep samba | grep sock | wc -l` if test "$testx" -gt "50" -a "$testy" -gt "50" ;then echo "samba

Readers, How to solve this unicode input error please? > postscript("~/tmp/test.eps",width=100/25.4,height=100/25.4,horizontal=FALSE,onefile=TRUE,paper="special") > testx<-seq(1:5) > testy<-seq(1:5) > plot(testy~testx) > mtext('text (O?)\n more text',side=3,line=1) Warning messages: 1: In mtext("text (O?)\n more text", side = 3, line =

Hi all, I am trying to create a function that will open connections to all files of one type within the working directory. I've got the function to open the connections, but I am having a bugger of a time trying to get these connections named as objects in the workspace. I am at the point where I can do it outside of the function, but not inside, using assign. I'm sure I'm

Hi list, I´m working on a predictive modeling task using the caret package. I found the best model parameters using the train() and trainControl() command. Now I want to evaluate my model and make predictions on a test dataset. I tried to follow the instructions in the manual and the vignettes but unfortunately I´m getting an error message I can`t figure out. Here is my code: rfControl <-

I reported the problem two months ago . I knew this would happen . :(( 2016-09-17 22:42 GMT+03:00 Edson Tadeu Almeida da Silveira via samba < samba at lists.samba.org>: > Sorry, the problem came back, after 3 hours. > > att, > > 2016-09-17 13:11 GMT-03:00 Edson Tadeu Almeida da Silveira < > edson.tadeu at gmail.com>: > > > I don't know if it is a

Dear R-helper, How could I count only some variable was exist after running sample (random) function. For example, > testx <- factor(c("Game","Paper","Internet","Time","Money")) > for(i in 1:2) { + x <- sample(testx,replace=TRUE) + print(x) + } [1] Money Money Time Internet Time Levels: Game Internet

Hello Please see the example below > class(testX) [1] "matrix" > class(testX[1,]) [1] "numeric" Why not matrix? What am I missing here? Is there a way to keep the same class? The reason for the question is that I want to implement a k-step ahead prediction for my own routines and R wrecks does not seem to like [1,] as shown below. >

I want to use the caret package to train linear models. I want to compare these models when using different degrees (aka degrees of interaction). This is possible for the 'earth' method (using the '.degree' parameter) but I found no possibility of customizing the degree for the 'lm' method. This might be due to the fact that the basic 'lm' function does not support

Hi, I have a question about using lm on matrix, have to admit it is very trivial but I just couldn't find the answer after searched the mailing list and other online tutorial. It would be great if you could help. I have a matrix "trainx" of 492(rows) by 220(columns) that is my x, and trainy is 492 by 1. Also, I have the newdata testx which is 240 (rows) by 220 (columns). Here is

Using str() in a function. I am in the early phase of learning R, and I find I spend a lot of time trying to figure out what is actually in objects I have created or read in from a file. I'm trying to make a simple little function to display a couple of things about a object, let's say the summary() and the str(), sequentially, preferably without a bunch of surplus lines between them. I

Dear all, I am confused with the behaviour of survfit with newdata option. I am using the latest version R-2-15-0. In the simple example below I am building a coxph model on 90 patients and trying to predict 10 patients. Unfortunately the survival curve at the end is for 90 patients. Could somebody please from the survival package confirm that this behaviour is as expected or not - because I

Dear folks: Let?s suppose I want a function to print return the name of the object passed to it. > myname <- function(object) {out<-deparse(substitute(object)); out} This works fine on a single object: > O1 <-c(1:4) > myname(O1) [1] "O1" However it does not work if you use lapply to pass it the same object from a list: > O2 <-c(1:4) > object.list <-

Having some problems with using hclust.identify on my data, I revert to trying it out on the example in the help manual. My result is still the same (as with my own data): data(iris) hci <- hclust(dist(iris[,1:4])) plot(hci) testx<-identify.hclust(hci) Error in rect.hclust(x, k = k, x = x$x, cluster = cluster[, k - 1], border = "red") : k must be between 2 and 0

Hi, I run R on a server via SSH, over a terminal. After loading a specific package, how do I know what functions are in that package? Is there any way to list or display them? tia. -- View this message in context: http://www.nabble.com/Check-functions-in-package-tp24707084p24707084.html Sent from the R help mailing list archive at Nabble.com.

Hi all, I am using the glmnet R package to run LASSO with binary logistic regression. I have over 290 samples with outcome data (0 for alive, 1 for dead) and over 230 predictor variables. I currently using LASSO to reduce the number of predictor variables. I am using the cv.glmnet function to do 10-fold cross validation on a sequence of lambda values which I let glmnet determine. I then take

Hi, is there any chance to install glmnet with gcc-4.5.2? For me it fails on all systems with: trying URL 'http://mirrors.softliste.de/cran/src/contrib/glmnet_1.7.tar.gz' Content type 'application/x-gzip' length 522888 bytes (510 Kb) opened URL ================================================== downloaded 510 Kb * installing *source* package ?glmnet? ... This package has only

Dear All, I want to generate survival curve with cox model but I want to estimate the coefficients using glmnet. However, I also want to include a strata() term in the model. Could anyone please tell me how to have this strata() effect in the model in glmnet? I tried converting a formula with strata() to a design matrix and feeding to glmnet, but glmnet just treats the strata() term with one

Hi, I am attempting to evaluate the prediction error of a coxph model that was built after feature selection with glmnet. In the preprocessing stage I used na.omit (dataset) to remove NAs. I reconstructed all my factor variables into binary variables with dummies (using model.matrix) I then used glmnet lasso to fit a cox model and select the best performing features. Then I fit a coxph model