similar to: pls -- crossval vs plsr(..., CV=TRUE)

Greetings, I have been exploring the use of the caret package to conduct some plsda modeling. Previously, I have come across methods that result in a R2 and Q2 for the model. Using the 'iris' data set, I wanted to see if I could accomplish this with the caret package. I use the following code: library(caret) data(iris) #needed to convert to numeric in order to do regression #I

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

Hello, I have a data set with 15 variables (first one is the response) and 1200 observations. Now I use pls package to do the plsr as below. trainSet = as.data.frame(scale(trainSet, center = T, scale = T)) trainSet.plsr = mvr(formula, ncomp = 14, data = trainSet, method = "kernelpls", model = TRUE, x = TRUE, y = TRUE) from the model, I wish to know the

Hello, I need help with a partial least square regression in R. I have read both the vignette and the post on R bloggers but it is hard to figure out how to do it. Here is the script I wrote: library(pls) plsrcue<- plsr(cue~fb+cn+n+ph+fung+bact+resp, data = cue, ncomp=7, na.action = NULL, method = "kernelpls", scale=FALSE, validation = "LOO", model = TRUE, x = FALSE, y =

I'm seeing some strange behavior while using the snow package for networked computers. I believe it's caused by name space resolution issues, and would appreciate any suggestions tracking it down. First, is there a way to find out what frame (as in frames in environments, not data frames) a name is being obtained from or put into? Second, how closely does the evaluation environment in

Dear list, I would like to plot points with two types of labels, one at the data point (the name of the point) and another offset a bit with another factor which is either of the two greek characters alpha or beta. I have tried to get the routine to plot a greek character with expression() or with substitute() and have not yet had any success. The following only plots the word in english in

Using R 1.7.0 I get * checking parcv-manual.tex ... ERROR Could not create DVI version. Although there is no apparent error. The dvi file exists. Possibly there is some problem with my TeX setup, but the following messages don't suggest that either. Here's the full log, which does show some documentation issues: sheep:~$R CMD check --library=.R/library/ src/parcv * checking for working

Hi I am attempting to use plsr which is part of the pls package in r. I amconducting analysis on datasets to identify which proteins/peptides are responsible for the variance between sample groups (Biomarker Spoting) in a multivariate fashion. I have a dataset in R called "FullDataListTrans". as you can see below the structure of the data is 40 different rows representing a

Hi I am analysing a dataset of 40 samples each with 90,000 intensity measures for various peptides. I am trying to identify the Biomarkers (i.e. most significant peptides). I beleive that PLS with jack knifing, or alternativeley CMV(cross-model-validation) are multivariateThe 40 samples belong to four different groups. I have managed to conduct the plsr using the commands: BHPLS1 <-

Hi, I need your help, so I send letter to you. I have a problem about plsr in pls package. I want to show how classfied or related each ohter samples, so I tried to use plsr and biplot. But, I failed. Because, I had to change data type of my sample. Unfortunately, I didn't know how change data type. I want you to help me about that. please, help me. I show you my sample data , my scripts

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,

All, I am working with NIR spectral data and it was great to find that the example in ?plsr also used spectral data. Unfortunately, I am having difficulty figuring out how the "yarn" dataset is structured to allow for the plsr model to read: library(pls) data(yard) yarn.oscorespls <- mvr(density ~ NIR, 6, data = yarn, validation = "CV", method = "oscorespls")

Hi, this is my R-Script library(pls) file <- "C:\\TXT\\brix.txt" d <- as.matrix(read.table(file, header=T, sep=",", row.names = NULL)) plsdata <- data.frame(NIR=c(1:nrow(X))) plsdata$NIR <- I(d[,3:603]) plsdata$Brix <- d[,2] results <- plsr(Brix ~ NIR, data=plsdata) after the last string i have this error > results <- plsr(Brix ~ NIR, data=plsdata)

The function crossval (in library bootstrap) works well for the first degree polynomial model, but in the case of the second degree model I got an error message (see below). I would be very greatfull if somebody could give some advices for the following: > library(bootstrap) > > x<-c(22,23.4,24.9,28.5,29.8,31.6,34.2,36.4,37.7,39) >

I am having a similar problem understanding the data structure of the "yarn" dataset described in the "[R] data structure for plsr" posts. I have spectroscopic data I'd like to run through a PLSR and have read the tutorial series, but still do not understand the data format required for the code to process my data. My current data structure consists of a .csv file read into

Dear readers, can anyone give an example how to use cross-validation in the plsr package. I miss to find the number of factors proposed by cross-validation as optimum. Thank you Peter -- View this message in context: http://n4.nabble.com/cross-validation-in-plsr-package-tp1563815p1563815.html Sent from the R help mailing list archive at Nabble.com.

Seems crossval from library(bootstrap) can only be used for leave-one-out and k-fold cross validation? Here is a dumb question, suppose n=80, how to do exactly leave-50-out cross validation? K-fold cross validation is not eligible for this case since n/ngroup is not an integer. Thanks!

I have been working with the pls procedure and have problems getting the procedure to work with matrix or frame data. I suspect the problem lies in my understanding of frames, but can't find anything in the documentation that will help. Here is what I have done: I read in an 10000 x 8 table of data, and assign the first four columns to matrix A and the second four to matrix B pls <-

Hi, I am trying to make a palaeoenvironmental transfer function using the R package rioja that predicts the water-table (measured as depth to the water table) of an area given the testate amoebae that are found there. I've carried out weighted averaging of the data and am trying to produce a graph that shows the observed water-table versues the model's predicted values. Following the

Dear R helpers I'm attempting to create a matrix of scatterplots with X-Y mean lines and regression lines added to each plot in the matrix. I have managed to create the first plot I would like using scatterplot but have run into an odd result when I use par() to set up the page to take multiple plot. Specifically, the mean and regression lines appear to plot in the second plot window, not