search for: nipals

I would like to announce the availability of the 'nipals' package on CRAN, https://cran.r-project.org/web/packages/nipals/. The nipals package tries to do just one thing really well...find principal components of a matrix using Nonlinear Partial Least Squares. Missing values are allowed, the principal components are orthogonal, and the code has been...

I would like to announce the availability of the 'nipals' package on CRAN, https://cran.r-project.org/web/packages/nipals/. The nipals package tries to do just one thing really well...find principal components of a matrix using Nonlinear Partial Least Squares. Missing values are allowed, the principal components are orthogonal, and the code has been...

Hello i need some precision about nipals in the chemometrics package in R . When i use nipals in chemometrics i obtain T and P matrix. I really don't understand what to do with these two matrix to obtain the scores for every the component (like in spss fo example) Comp1 Comp2 Comp3 quest1 0,8434 0,54333 0,3...

Dear list members; The code given below corresponds to the PCA-NIPALS (principal component analysis) algorithm adapted from the nipals function in the package chemometrics. The reason for using NIPALS instead of SVD is the ability of this algorithm to handle missing values, but that's a different story. I've been trying to find a way to improve (if possible)...

Hi all, I've been trying to figure out how to superimpose a histogram on a biplot that shows the relative contribution of each axis. I have been using the NIPALS function (http://biomserv.univ-lyon1.fr/~dray/ files/softwares/nipals.R) to run principal component analyses. Here is a toy example. source("http://biomserv.univ-lyon1.fr/~dray/files/softwares/nipals.R") mat=matrix(runif(100,0,1), ncol=10, nrow=10) nipmat=nipals(mat, nf=9) scatter(ni...

Dear all: I am comparing the PLS outputs of R and SAS for the following data set: Y x1 x2 x3 3 6 2 2 3 1 5 5 4 7 4 1 5 6 5 6 2 4 3 2 8 5 0 9 where Y is the dependent variable and x1, x2, x3 are the independent variables. I found several PLS algorithms in R (NIPALS,SIMPLS,KERNEL PLS). SAS has SIMPLS and NIPALS. The following are the NIPALS calculations of the regression coefficients for the above data using 2 principal components: Using R: x1 0.4002324 x2 -0.2679829 x3 0.5684680 Using SAS: x1 0.4671608452 x2 -.1537662492...

I've been using the pcaMethods to develop a scores matrix ======================================= data(iris) pcIr <- pca(iris[,1:4], method="nipals", nPcs=3, cv="q2") test <- scores(pcIr) ======================================== What I'm looking to do is to use lattice's barchart to plot the scores something like below, but expanded to all the scores columns. Can someone give me a clue? I've thought about re...

Friends, Is there a Partial Least Squares package implemented in R? Thanks, Lana [[alternative HTML version deleted]]

...should just compute the nontrivial principal compontents). 2. as an optional behavior, princomp should only calculate (and return) the first A principal components. This is useful, if x is very wide and very short. Some might remark that all this can be done easily by svd or by programming the NIPALS algorithm, but I would prefer to see it in the common version. (by the way, did anyone R-implement Sijmen de Jong's SIMPLS algorithm and predict. plot. summary. print. functions to go with it?) > Kind Regards, > Christian Ritter, Statistical Services > Tel +32 10 477349/ F...

Hi all, I would like to do some QSAR analysis (quantitative structure activity relationship). I need to use some Partial Least Squares (PLS) regression, but I have not seen this option on the R-project. Is it possible to do this kind of regression on R? thank you in advance best regards, olivier [[alternate HTML version deleted]]

Dear R-helpers, I am looking, quite unsuccesfully, for a number of functions/packages. Firstly, I am interested in a package for partial least squares. I have found that there seemed to exist a package called pls, but which seems not to run any more with modern versions of R. I have not been able to find certain "chemometrics package" I found some people discussing about in this

Am I correct to understand from the previous discussions on this topic (a few years back) that if I have a matrix with missing values my PCA options seem dismal if: (1) I don’t want to impute the missing values. (2) I don’t want to completely remove cases with missing values. (3) I do cov() with use=”pairwise.complete.obs”, as this produces negative eigenvalues (which it has in

...> generally unique, especially as to sign. Different PCA applciations may > give you eigenvalues of differing sign. > > Also, eigenvector solutions are not the only way of obtaining > eigenvalues; efficient solutions for a limited number of PC's also > exist, particularly the NIPALS algorithm > > > read your text book to the point where it mentions the eigenvectors of > the ccorrelation (or covariance) matrix > >>> ogbos okike <ogbos.okike@gmail.com> 01/30/10 7:09 PM >>> > Hi, > I am learning how to do principal component analysis i...

Hello, I have a matrix with 267 columns, all rows of which have at least one column missing (NA). All three methods i've tried (pcs, princomp, and prcomp) fail with either "Error in svd(zsmall) : infinite or missing values in 'x'" (latter two) or "Error in cov.wt(z) : 'x' must contain finite values only" The last one happens because of the check if

Hi everybody! Is there any package or functions to make Partial Least Squares analysis with R? Thanks a lot Luis -------------------------------------------- sapo.pt/kitadsl -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html Send "info", "help", or

...extract the first A PCs. If A << min(n, p) there are faster algorithms, but they are not currently implemented in R, and I can think of very few problems where the speed difference would be noticeable. > Some might remark that all this can be done easily by svd or by programming > the NIPALS algorithm, but I would prefer to see it in the common version. It is, in prcomp which uses the svd. -- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1...

...extract the first A PCs. If A << min(n, p) there are faster algorithms, but they are not currently implemented in R, and I can think of very few problems where the speed difference would be noticeable. > Some might remark that all this can be done easily by svd or by programming > the NIPALS algorithm, but I would prefer to see it in the common version. It is, in prcomp which uses the svd. -- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1...

...atter.eig(nipmat$eig, xax=1, yax=2) > > Cheers, > > > > Jennie Lavine wrote: >> Hi all, >> >> I've been trying to figure out how to superimpose a histogram on a >> biplot that shows the relative contribution of each axis. I have >> been using the NIPALS function (http://biomserv.univ-lyon1.fr/~dray/ >> files/softwares/nipals.R) to run principal component analyses. Here >> is a toy example. >> >> source("http://biomserv.univ-lyon1.fr/~dray/files/softwares/nipals.R") >> mat=matrix(runif(100,0,1), ncol=10, nro...