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PLS toolbox Tips and Tricks: How to Perform PCA, MCR, XGBoost and More with MATLAB


PLS toolbox for matlab free download




If you are looking for a powerful and versatile software for multivariate analysis and machine learning, you might be interested in PLS toolbox. This software is designed to work within the MATLAB computational environment and provides over 300 tools for data exploration, pattern recognition, classification, regression, design of experiments, curve resolution and more. In this article, we will explain what PLS toolbox is, why you should use it, how to get it and how to use it with a simple example.




Pls toolbox for matlab free download



What is PLS toolbox?




PLS toolbox is a software developed by Eigenvector Research, Inc., a company that specializes in chemometrics and data science. Chemometrics is the application of mathematical and statistical methods to analyze chemical data. PLS toolbox is based on the partial least squares (PLS) regression method, which is a popular technique for building predictive models from complex data sets. However, PLS toolbox offers much more than just PLS regression. It also includes other methods such as principal components analysis (PCA), support vector machines (SVM), artificial neural networks (ANN), boosted regression and classification trees (XGBoost), multivariate curve resolution (MCR) and many others. PLS toolbox has a unified graphical interface that allows users to perform various tasks with ease. It also has an object-oriented code that can be accessed via the command line for more advanced users who want to customize or automate their analyses.


Why use PLS toolbox?




PLS toolbox is a software that can help you to fully utilize your data and build predictive models for various purposes. Here are some of the benefits and applications of using PLS toolbox:


  • Data exploration and visualization: You can use PLS toolbox to explore your data and find patterns, outliers, trends and relationships. You can also create different plots and graphs to display your data in a visually appealing way.



  • Data preprocessing: You can use PLS toolbox to apply various preprocessing methods to your data such as centering, scaling, smoothing, derivatizing, transforming, baselining and more. These methods can help you to improve the quality and accuracy of your data analysis.



  • Data analysis and modeling: You can use PLS toolbox to perform various types of data analysis and modeling such as PCA, PLS, SVM, ANN, XGBoost, MCR and more. These methods can help you to reduce the dimensionality of your data, extract relevant features, identify latent variables, classify or cluster your data into groups, predict outcomes or responses, resolve mixtures or spectra and more.



  • Data interpretation: You can use PLS toolbox to interpret your data analysis and modeling results such as scores, loadings, explained variance, coefficients, residuals, predictions and more. These results can help you to understand the underlying structure and meaning of your data.



  • Data standardization: You can use PLS toolbox to standardize your data across different instruments or platforms using methods such as piece-wise direct standardization (PDS), spectral subspace transformation (SST) or orthogonal signal correction (OSC). These methods can help you to eliminate unwanted variations or interferences in your data.



  • Data integration: You can use PLS toolbox to integrate your data from different sources or formats using methods such as multiblock analysis or multiway analysis. These methods can help you to combine or compare multiple data sets or modalities.



How to get PLS toolbox?




If you are interested in getting PLS toolbox for matlab free download , you have three options:


Option 1: Buy from Eigenvector Research




The first option is to buy the software directly from Eigenvector Research. This option gives you access to the latest version of the software with all the features and updates. You also get a license that allows you to use the software on multiple computers or devices. You also get technical support from Eigenvector Research via email or phone. The price of this option depends on the type of license you choose (single user, academic user, site license or enterprise license). You can check the price list on their website https://eigenvector.com/software/pls-toolbox/ . To buy this option , you need to fill out an order form on their website https://eigenvector.com/order/ .


Option 2: Download a trial version




The second option is to download a trial version of the software from Eigenvector Research. This option gives you access to a limited version of the software for a limited time (usually 30 days). You can use this option to test the software before buying it or if you only need it for a short-term project. The trial version has some limitations such as reduced functionality , reduced number of tools , reduced number of samples , reduced number of variables , reduced number of components , reduced number of clusters , etc. To download this option , you need to register on their website https://eigenvector.com/register/ .


Option 3: Use Solo




The third option is to use Solo , which is an alternative standalone product that does not require MATLAB . Solo has the same functionality as PLS toolbox but it runs on its own platform without depending on MATLAB . This option is suitable for users who do not have MATLAB or who prefer a simpler interface . Solo also has a lower price than PLS toolbox . However , Solo does not have some features that are specific to MATLAB such as code editing , debugging , scripting , etc. To get this option , you need to buy it from Eigenvector Research https://eigenvector.com/software/solo/ .


How to use PLS toolbox?




To illustrate how to use PLS toolbox , we will show you a simple example of performing a PCA analysis with PLS toolbox . PCA is a method that reduces the dimensionality of a data set by finding a few linear combinations (called principal components) that capture most of the variation in the data . PCA can help you to explore your data , visualize your data , remove noise from your data , compress your data , etc.


Step 1: Load data




The first step is to load your data into MATLAB . You can import your data from different sources such as Excel files , text files , binary files , databases , etc. You can also generate your own data using MATLAB commands . For this example , we will use a built-in data set called NIRcorn that contains near-infrared spectra of corn samples with different moisture levels . To load this data set , type the following command in MATLAB :


nircorn = load('nircorn');


This command will create a variable called nircorn that contains two fields : nircorn.data which is a matrix with 80 rows (samples) and 700 columns (variables) , and nircorn.labels which is a cell array with 80 elements (sample names) . You can view these fields by typing :


nircorn.data


nircorn.labels Continuing the article:


Step 2: Preprocess data




The next step is to preprocess your data to improve the quality and accuracy of your PCA analysis. You can use PLS toolbox to apply various preprocessing methods to your data such as centering, scaling, smoothing, derivatizing, etc. For this example, we will use mean centering and autoscaling. Mean centering subtracts the mean of each variable from each observation, making the data have zero mean. Autoscaling divides each variable by its standard deviation, making the data have unit variance. To preprocess your data with PLS toolbox , type the following commands in MATLAB :


preproc = preprocess ('default','autoscale'); % create a preprocessing object with autoscaling option nircornp = applypreprocess (nircorn.data,preproc); % apply the preprocessing object to the data matrix


This will create a new variable called nircornp that contains the preprocessed data matrix.


Step 3: Perform PCA




The next step is to perform PCA on your preprocessed data using PLS toolbox . You can use the pca function to create a PCA model object that contains all the information and results of the PCA analysis. To perform PCA with PLS toolbox , type the following command in MATLAB :


pcamodel = pca (nircornp); % create a PCA model object from the preprocessed data matrix


This will create a variable called pcamodel that contains a PCA model object. You can view the properties and methods of this object by typing :


pcamodel


methods (pcamodel)


You can also use the display function to show a summary of the PCA model object :


display (pcamodel)


This will show you some information such as the number of components, the explained variance, the scores, the loadings, etc.


Step 4: Interpret PCA




The next step is to interpret your PCA results and understand what they mean. You can use PLS toolbox to access and manipulate various properties and methods of the PCA model object. For example, you can use the following commands to get some information about your PCA model :


pcamodel.ncomp % get the number of components pcamodel.ssqresiduals % get the sum of squared residuals for each component pcamodel.cumexpvar % get the cumulative explained variance for each component pcamodel.scores % get the scores matrix pcamodel.loadings % get the loadings matrix pcamodel.residuals % get the residuals matrix pcamodel.predict (nircornp) % get the predicted values for each component


You can also use some methods to perform some calculations or tests on your PCA model. For example, you can use the following commands to do some analysis on your PCA model :


pcamodel.hotellingt2test % perform a Hotelling's T-squared test for outliers pcamodel.crossval ('random',10) % perform a 10-fold cross-validation pcamodel.permutetest (1000) % perform a permutation test with 1000 permutations


Step 5: Visualize PCA




The final step is to visualize your PCA results and display them in a graphical way. You can use PLS toolbox to create different plots and graphs that show your PCA results. For example, you can use the following commands to create some plots for your PCA model :


plot (pcamodel) % create a default plot with scores and loadings plot (pcamodel,'scores',1:2) % create a scores plot for components 1 and 2 plot (pcamodel,'loadings',1:2) % create a loadings plot for components 1 and 2 plot (pcamodel,'explainedvariance') % create an explained variance plot plot (pcamodel,'residuals') % create a residuals plot plot (pcamodel,'t2') % create a Hotelling's T-squared plot plot (pcamodel,'crossval') % create a cross-validation plot plot (pcamodel,'permutationtest') % create a permutation test plot


You can also customize your plots by using various options and arguments. For example, you can use the following commands to modify some plots for your PCA model :


plot (pcamodel,'scores',1:2,'colorby',nircorn.labels) % color the scores by sample names plot (pcamodel,'loadings',1:2,'labels',1:50:700) % label every 50th variable on the loadings plot plot (pcamodel,'explainedvariance','cumulative',true) % show cumulative explained variance instead of individual explained variance


Conclusion




In this article, we have shown you how to use PLS toolbox for matlab free download . We have explained what PLS toolbox is, why you should use it, how to get it and how to use it with a simple example of performing a PCA analysis. We hope that this article has helped you to understand and appreciate PLS toolbox as a powerful and versatile software for multivariate analysis and machine learning. If you want to learn more about PLS toolbox , you can visit their website https://eigenvector.com/software/pls-toolbox/ or check their documentation https://eigenvector.com/docs/pls_toolbox/ . You can also contact them for technical support or training https://eigenvector.com/contact/ . Thank you for reading this article and happy analyzing!


FAQs




  • Q: What are the system requirements for PLS toolbox?



  • A: PLS toolbox requires MATLAB version R2014b or later and at least 4 GB of RAM. It also requires an internet connection for activation and updates.



  • Q: How can I update my PLS toolbox?



  • A: You can update your PLS toolbox by using the updatepls function in MATLAB . This function will check for updates online and download them if available.



  • Q: How can I cite PLS toolbox?



  • A: You can cite PLS toolbox by using the following reference: Wise BM, Gallagher NB, Bro R, et al., PLS_Toolbox 8.8.1 for use with MATLAB , Eigenvector Research Inc., Manson WA USA , 2020.



  • Q: What are some alternatives to PLS toolbox?



  • A: Some alternatives to PLS toolbox are Solo , which is a standalone product that does not require MATLAB , Unscrambler , which is a commercial software for chemometrics and multivariate analysis , or scikit-learn , which is an open source Python library for machine learning.



  • Q: How can I learn more about PLS toolbox?



  • A: You can learn more about PLS toolbox by visiting their website https://eigenvector.com/software/pls-toolbox/ or checking their documentation https://eigenvector.com/docs/pls_toolbox/ . You can also watch their videos https://eigenvector.com/videos/ or attend their courses https://eigenvector.com/courses/ .




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