similar to: Help package pls.pcr

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 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

Dear developeRs, I maintain a package 'pls', which has a main fit function mvr(), and functions plsr() and pcr() which are meant to take the same arguments as mvr() and do exactly the same, but have different default values for the 'method' argument. The three functions are all exported from the name space. In the 'pre namespace' era, I took inspiration from lm() and

What version of R, what version of pls.pcr, and on what OS? Have you checked whether your versions of software are up to date? I get: > n <- 1350 > p <- 180 > y <- rnorm(n) > x <- matrix(sample(0:1, n*p, replace=TRUE), n, p) > fit <- mvr(x, y, method="SIMPLS", validat="none", ncomp=2) > xt <- matrix(sample(0:1, 312*p, replace=TRUE), 312,

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

Hello, I am trying to understand how to utilize the "mvr" function in the pls Package of R. I am utilizing the R "pls Package" document dated 18 May 2005 as guidance. My data set consists of a 12 x 12 data frame created from reading in a table of values. I have read the data in via the command: volumes <- read.table("THA_vol.txt", header = TRUE) and then

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

hi R help group, I have installed PLS package in R and use it for princomp & prcomp commands for calculating PCA using its example file(USArrests example). But How I can use PLS for Partial least square, R square, mvrCv one more think how i can import external file in R. When I use plsr, R2, RMSEP it show error could not find function plsr, RMSEP etc. How I can calculate PLS, R2, RMSEP, PCR,

Hi, Newbie question about the pls package. Setup: Mac OS 10.3.9 R: Aqua GUI 1.01, v 2.0.1 I want to get R^2 and Q^2 (LOO and Leave-10-Out) values for each component for my model. I was running into a few problems so I played with the example a little and the results do not match up with the comments in the help pages. $ library(pls) $ data(NIR) $ testing.plsNOCV <- plsr(y ~ X, 6, data =

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 all, I am a newcomer to R. I intend to using R to do stepwise regression and PLS with a data set (a 55x20 matrix, with one dependent and 19 independent variable). Based on the same data set, I have done the same work using SPSS and SAS. However, there is much difference between the results obtained by R and SPSS or SAS. In the case of stepwise, SPSS gave out a model with 4 independent

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.

Hello all, I have generated a principal components regression model using the pcr() function from the PLS package (R version 2.12.0). I am getting a "non-conformable arguments" error when I try to use the predict() function on new data, but only when I try to read in the new data from a separate file. More specifically, when my data looks like this #########training data

dear all, I am a new comer to R and statistic. Now I have a little confuse about the package pls. I have to use 5 components to form a model. There are strong relationship between some of the components, which leads to the changes of the sign of each coeficeince, of course this is unwanted when using the normal regression way. So I choose the way of PLS, which is good at solve this kind of

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

Version 1.1-0 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 1.1-0 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

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

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: > > >