similar to: Possibly more coefficients?

Hi There, I am trying to fit a logit model to some data in a CSV file in R. Here is my code: Prepared_Data = read.csv("Prepared_Data.csv", header=TRUE) Prepared_Data attach(Prepared_Data) lrfit<-glm(C3~A1*B2*D4*E5,family = binomial) anova(lrfit, test="Chisq") write.csv(anova(lrfit, test="Chisq"), file="CWModelA.csv") shell.exec("CWModelA.csv")

Dear R users: Recently, I learn to use penalized logistic regression. Two packages (penalized and glmnet) have the function of lasso. So I write these code. However, I got different results of coef. Can someone kindly explain. # lasso using penalized library(penalized) pena.fit2<-penalized(HRLNM,penalized=~CN+NoSus,lambda1=1,model="logistic",standardize=TRUE) pena.fit2

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

?s 13:27 de 07/04/2024, javad bayat escreveu: > Dear all; > I have a question about the water level of a reservoir, when the volume > changed or doubled. > There is a DEM file with the highest elevation 1267 m. The lowest elevation > is 1230 m. The current volume of the reservoir is 7,000,000 m3 at 1240 m. > Now I want to know what would be the water level if the volume rises to

I spent a lot of time searching and came up empty handed on the following query. Is there an equivalent to rowSums that does product or cumulative product and avoids use of apply or looping? I found a rowProd in a package but it was a convenience function for apply. As part of a likelihood calculation called from optim, I?m computing products and cumulative products of rows of matrices with

Aside from the fact that the original question might well be a class exercise (or homework), the question is unanswerable given the data given by the original poster. One needs to know the dimensions of the reservoir, above and below the current waterline. Are the sides, above and below the waterline smooth? Is the region currently above the waterline that can store water a mirror image of the

Dear R-help, I have been trying really hard to generate the following vector given the data (x) and parameter (alpha) efficiently. Let y be the output list, the aim is to produce the the following vector(y) with at least half the time used by the loop example below. y[1] = alpha * x[1] y[2] = alpha^2 * x[1] + alpha * x[2] y[3] = alpha^3 * x[1] + alpha^2 * x[2] + alpha * x[3] ..... below are

Full_Name: J. Sisk Version: 1.6.1 OS: Linux (RedHat 8) Submission from: (NULL) (67.119.41.66) Suppose you make a data-frame like so: xxx <- data.frame(a=10,b=20,c=30,d=40) Then cumprod(xxx[1,]) returns > cumprod(xxx[1,]) a b c d 1 10 20 30 40 The documentation for cumprod says that it should work on "numerical objects", and this is a data-frame, but it

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

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

Hello fellow R users, I have been getting a strange error message when using the cv.glmnet function in the glmnet package. I am attempting to fit a multinomial regression using the lasso. covars is a matrix with 80 rows and roughly 4000 columns, all the covariates are binary. resp is an eight level factor. I can fit the model with no errors but when I try to cross-validate after about 30 seconds

Dear All, ? I have found differences between glmnet versions 1.7 and 1.7.1 which, in my opinion, are not cosmetic and do not appear in the ChangeLog. If I am not mistaken, glmnet appears to return different number of selected input variables, i.e. nonzeroCoef(fit$beta[[1]]) differes between versions. The code below is the same for 1.7.1 and 1.7, but you can see that outputs differ. I would

Hi, I am trying to do multinomial regression using the glmnet package, but the following gives me an error (for no reason apparent to me): library(glmnet) cv.glmnet(x=matrix(c(1,2,3,4,5,6,1,2,3,4,5,6), nrow=6),y=as.factor(c(1,2,1,2,3,3)),family='multinomial',alpha=0.5, nfolds=2) The error i get is: Error in if (outlist$msg != "Unknown error") return(outlist) : argument is of

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

Hello all, I am having trouble with the glmnet package. I used it for the first time last week, after updating R to the current version (2.10.1, running in Windows XP). It seemed to be working fine as I explored what it could do with one of my datasets. A day or two later, using the exact same dataset, it suddenly stopped working. I get the following error every time I try to use glmnet with

Hi, I was trying to install package glmnet in R, but failed and it show such messages: * Installing *source* package glmnet ... This package has only been tested with gfortran. So some checks are needed. R_HOME is /home/username/R/R-2.9.0 Attempting to determine R_ARCH... R_ARCH is Attempting to detect how R was configured for Fortran 90.... Unsupported Fortran 90 compiler or Fortran 90

Hello, I got an error message saying Error in lognet(x, is.sparse, ix, jx, y, weights, offset, alpha, nobs, : NA/NaN/Inf in foreign function call (arg 5) when I try to analysis a binary trait using glmnet(R) by running the following code library(glmnet) Xori <- read.table("c:\\SNP.txt", sep='\t'); Yori <- read.table("c:\\Trait.txt", sep=',');

Dear List, I'm running simulations using the glmnet package. I need to use an 'automated' method for model selection at each iteration of the simulation. The cv.glmnet function in the same package is handy for that purpose. However, in my simulation I have p >> N, and in some cases the selected model from cv.glmet is essentially shrinking all coefficients to zero. In this case,

John, Your reaction was what my original reaction was until I realized I had to find out what a DEM file was and that contains enough of the kind of depth-dimension data you describe albeit what may be a very irregular cross section to calculate for areas and thence volumes. If I read it correctly, this can be a very real-world problem worthy of a solution, such as in places like California

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