similar to: 1) variable influence in PCR/PLS models 2) how to cite CRAN packages

Dear list members, I have a statistical question, that doesn't belong to this list, and I apologise for that in advance but I would appreciate your help very much. Is there some convention for selecting the a level for significance testing in scientific (e.g. chemical processes) studies? Most people use the 0.05 level but I could not find a reference to justify this. Why not 0.01 or 0.1?

When I try to run the "sammon" function of the multiv package, I always get this error message: Error in as.vector(dist(a)) : couldn't find function "dist" It happens even with example(sammon). I am running R 1.5.0 on Win98 and I have still installed R 1.4.1 but it doesn't work on the old R version with the older multiv package either. Is there a problem with the

Hello! I need help to use the package pls.pcr in R. I installed R in an IRIX 6.5, using the version of R 0.64.1 from sgifreeware(I didn't get to install the newest version using make). I need to use the package pls.pcr and when I give the command: # R R : Copyright 1999, The R Development Core Team Version 0.64.1 (May 8, 1999) R is free software and comes with ABSOLUTELY NO

Dear R-helpers, Has anybody ever tried to compare pls regression outputs from the pls.pcr R-package developped by Wehrens with outputs from the Unscrambler software developped by CAMO company ? I find very different outputs and wonder if this comes from differences between methods/algorithms SIMPLS (pls.pcr) and PLS1 (Unscrambler). Arnaud ************************* Arnaud DOWKIW Department of

Dear list I am using the mvr function of the package pls.pcr to compute PLS resgression using a X matrix of gene expression variables and a Y matrix of medical varaibles. I would like to obtain the R2 (sum of squares captured by the model) and Q2 (proportion of total sum of squares captured in leave-one-out cross validation) of the model. I am not sure if there are specific slots in the

Dear all, I found pls.pcr package will give different results if the data are centered and scaled using scale(). I am not sure about when I should scale my data, and whether the dependent variable should be scaled. If the dependent variable is scaled, how I give a prediction to the real data? I appreciate for any suggestions and comments. Best regards, Jinsong ===== (Mr.) Jinsong Zhao Ph.D.

How do you install a package from CRAN ? I want to install pls.pcr, so I have downloaded pls.pcr_0.1.1.tar.gz but when I try to install it using the install package(s) from local zip file(s) option it says : > install.packages(choose.files('',filters=Filters[c('zip','All'),]), .libPaths()[1], CRAN = NULL) Error in file(file, "r") : unable to open connection

Dear list, I have a question concerning the above mentioned methods in the pls package with respect to the loadings matrix produced by the call. In some work I am doing I have found that the values produced are nearly of the same magnitude but of opposite sign. When I use the example data (sensory) I find this result reproduced. I am prepared to work this through but I have a feeling that

Hi, Currently I have a dataset of 2400*408. And I would like to apply PCR method to study the any correlation between the tests. My current data is in data.frame and I have formed horizontal(1-407) to be the exact data, and (408) to be my results data(Yes and No) I have also binarized these Yes and No to 1 and -1s. However, when I refer to PCR manual on R, the example of yarn.pcr <-

Hi, I want to calculate PLS package in R. Now I want to calculate R, MSEP, RMSEP and R2 of PLSR and PCR using this. I also add this in library of R. How I can calculate R, MSEP, RMSEP and R2 of PLSR and PCR in R. I s any other method then please also suggest me. Simply I want to calculate these value. Thanking you. -- Nitish Kumar Mishra Junior Research Fellow BIC, IMTECH, Chandigarh, India

Please, forgive my ignorance on statistics, but I have a rather simple question concerning AIC. Small values of AIC mean good fit of the model. How about negative values of AIC? Is a model with AIC=0.5 considered to have better fit than a model with AIC=-500? I couldn't find anything explaining this in the documentation or any elementary statistics textbook that I have at my disposal. Thanks

Hello list members, I am new to this list and don't know very much about what R can do or how to program it, but I am interested in plotting 4 variables as sequential contour plots (or surface plots), something like the conditioning plots for 4 variables (coplot(X1~X2|X3+X4)). To be more specific, I need a tool that will automatically create contour (orsurface) plots of X1 vs X2 vs X3 for

Version 2.0-0 of the pls package is now available on CRAN. The pls package implements partial least squares regression (PLSR) and principal component regression (PCR). Features of the package include - Several plsr algorithms: orthogonal scores, kernel pls and simpls - Flexible cross-validation - A formula interface, with traditional methods like predict, coef, plot and summary - Functions

Version 2.0-0 of the pls package is now available on CRAN. The pls package implements partial least squares regression (PLSR) and principal component regression (PCR). Features of the package include - Several plsr algorithms: orthogonal scores, kernel pls and simpls - Flexible cross-validation - A formula interface, with traditional methods like predict, coef, plot and summary - Functions

I don't know the details of pls (in the pls.pcr package, I assume), but if you use validation="CV", that says you want to use CV to select the best number of components. Then why would you specify ncomp as well? Andy > From: ryszard.czerminski at pharma.novartis.com > > When I try to use ncomp parameter in pls procedure I get > following error: > > >

I'm trying to get the coefficient of partial determination for each of three independent variables. I've tried mvr in package pls.pcr. I'm a little confused by the output. I'm curious how I can order the LV's according to their names rather than their relative contribution to the regression. For instance, using the crabs data from MASS I made a regression of FL~RW+noise

Version 1.0-3 of the pls package is now available on CRAN. The pls package implements partial least squares regression (PLSR) and principal component regression (PCR). Features of the package include - Several plsr algorithms: orthogonal scores, kernel pls and simpls - Flexible cross-validation - A formula interface, with traditional methods like predict, coef, plot and summary - Functions

Version 1.0-3 of the pls package is now available on CRAN. The pls package implements partial least squares regression (PLSR) and principal component regression (PCR). Features of the package include - Several plsr algorithms: orthogonal scores, kernel pls and simpls - Flexible cross-validation - A formula interface, with traditional methods like predict, coef, plot and summary - Functions

Hi - I am using pls package for some pcr computations. There is a data set called gasoline. Would someone be able to tell me what command(s) could be used to produce this graph in R? I am not sure where the log(1/R) - Y-axis - are coming from Thanks much Ravi

Dear R-helpers, I have performed a PLS regression with the mvr function from the pls.pcr package an I have 2 questions : 1- do you know if mvr automatically centers the data ? It seems to me that it does so... 2- why in the situation below does the output say that the optimal number of latent variables is 4 ? In my humble opinion, it is 2 because the RMS increases and the R2 decreases when 3 LVs