search for: plsda

Hello, I would like to perform a Partial least square discriminate analysis (PLSDA) in R. To do this I use the package mixOmics. I could perform the PLSDA in R. however I would also like to perform a leave-one-out cross validation in order to assess the performance of my model. My supervisor told me that I should focus on the R2/Q2 ratios. However when I read the instruction f...

Hi. I was used to draw 2D plot to show distribution of my samples. It was very powerful in small samples. Recently , I handle a lot of type of samples as more 15. so, I want to use more dimention. I was used that I conduct plsda function and draw biplot, such as, p1=plsda(mw, sp) biplot(p1) How can I draw 3D graph with my data?? I don't know exactly numerical value each spot. please, help me. [[alternative HTML version deleted]]

Hello, I would like to do a partial least square discriminant analysis (PLSDA) in R using the package "ropls" Which is in R available via the R command : source("https://bioconductor.org/biocLite.R") I try to do a PLSDA to illustrate the impact of two genders (AP,C) on 5 compounds measured in persons (samples) should be illustrated. When I try to do a...

Hello, I would like to do a partial least square discriminant analysis (PLSDA) in R using the package "ropls" Which is in R available via the R command : source("https://bioconductor.org/biocLite.R") When I try to do a PLSDA using my own data. The impact of two genders (AP,C) on 5 compounds measured in persons (samples) should be illustrated. When I tr...

Hi, Is there any R package doing permutation/randomization test for PLS/PLSDA? I found some codes for MatLab, but I want to use R program. Thank you very much in advance. Kohkichi Hosoda

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 regr...

...on are much more efficient. Wherever possible, caret tries to avoid re-fitting models if it can get predictions from sub-models. For example, an object for a boosted tree with 500 trees can often be used to get predictions for any boosted tree with less than 500 trees. The affected models are: pls, plsda, earth, rpart, gbm, gamboost, glmboost, blackboost, ctree, pam, enet and lasso. The caretLSF package is a parallel processing version of caret. The other caret package, caretNWS, will be updated to work with the new version of caret shortly. Please email me at max dot kuhn at pfizer dot com with...

...boost, glmboost, gamboost, logitboost), bagged models (trees, earth, fda), randomforests (randomforest and cforest), rule-based models (Ripper and M5 prime), discriminant models (lda, fda, rda, ssda, slda), kernel methods (lssvm, ksvm, rvm, gausspr), nnet, nnet with initial pca step, multinom, pls, plsda, gpls, nearest shrunken centroids, the lasso, the elastic net, supervised pca, knn, lvq and NaiveBayes. Recent changes include: - Estimation of class probabilities from PLS discriminant analysis using Bayes rule (in addition to softmax) - Added predict.train and predit.list - More lattice plots t...

...re fit in train(). Now, the function used to compute the models is passed in as a parameter (defaulting to lapply). In this way, users can use their own parallel processing software without new versions of caret. Examples using MPI and NWS are given in ?train. The package now contains a function (splsda) that extends the spls function to classification (in the same manner than caret's plsda function extends plsr). Also, fixed a bug where the MSE (instead of RMSE) was reported for random forest OOB resampling There are more examples in ?train. Changes to confusionMatrix, sensitivity, specifi...

...on are much more efficient. Wherever possible, caret tries to avoid re-fitting models if it can get predictions from sub-models. For example, an object for a boosted tree with 500 trees can often be used to get predictions for any boosted tree with less than 500 trees. The affected models are: pls, plsda, earth, rpart, gbm, gamboost, glmboost, blackboost, ctree, pam, enet and lasso. The caretLSF package is a parallel processing version of caret. The other caret package, caretNWS, will be updated to work with the new version of caret shortly. Please email me at max dot kuhn at pfizer dot com with...

...boost, glmboost, gamboost, logitboost), bagged models (trees, earth, fda), randomforests (randomforest and cforest), rule-based models (Ripper and M5 prime), discriminant models (lda, fda, rda, ssda, slda), kernel methods (lssvm, ksvm, rvm, gausspr), nnet, nnet with initial pca step, multinom, pls, plsda, gpls, nearest shrunken centroids, the lasso, the elastic net, supervised pca, knn, lvq and NaiveBayes. Recent changes include: - Estimation of class probabilities from PLS discriminant analysis using Bayes rule (in addition to softmax) - Added predict.train and predit.list - More lattice plots t...

Hi, List The elastic net package (by Hastie and Zou at Stanford) is used to do regularization and variable selection, it can also do regression. I am wondering if it can perform binary classification (discrete outcome). Anybody having similar experience? Many thanks, -Jack [[alternative HTML version deleted]]

...re fit in train(). Now, the function used to compute the models is passed in as a parameter (defaulting to lapply). In this way, users can use their own parallel processing software without new versions of caret. Examples using MPI and NWS are given in ?train. The package now contains a function (splsda) that extends the spls function to classification (in the same manner than caret's plsda function extends plsr). Also, fixed a bug where the MSE (instead of RMSE) was reported for random forest OOB resampling There are more examples in ?train. Changes to confusionMatrix, sensitivity, specifi...

Hi. I want to show easily classified samples in the one biplot. My samples have 14 types and each type have 21 samples So, I cannot understand distribution of samples after plsda. I want to give a color each types text in the graph. How can I do that? [[alternative HTML version deleted]]

Greetings R users, I have been working on running plsda and I would like to have the R2 and Q2 values. I know the function R2 from the 'pls' package will generate both R2 and Q2 but they are for each separate class. Is there a way to get the cumulative R2 and Q2 for the whole model? R2(pls.new, estimate="all") Response: B (I...

...the good graces of those who wish to help. Thanks to those who have helped in multiple circumstances. However, I wanted to post this question once more. I hope someone will read it and perhaps have some additional insight into what I may be able to do. Thank you, I have been working on running plsda and I would like to have the R2 and Q2 values. I know the function R2 from the 'pls' package will generate both R2 and Q2 but they are for each separate class. Is there a way to get the cumulative R2 and Q2 for the whole model? R2(pls.new, estimate="all") Response: B (I...

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