It simply creates a model based on the inputs, generating coefficients for each variable that maximize the between class differences. Here I am going to discuss Logistic regression, LDA, and QDA. Feature selection can enhance the interpretability of the model, speed up the learning process and improve the learner performance. Linear Discriminant Analysis (LDA) is most commonly used as dimensionality reduction technique in the pre-processing step for pattern-classification and machine learning applications.The goal is to project a dataset onto a lower-dimensional space with good class-separability in order avoid overfitting (“curse of dimensionality”) and also reduce computational costs.Ronald A. Fisher formulated the Linear Discriminant in 1936 (The U… Feature Selection in R 14 Feb 2016. How do I find complex values that satisfy multiple inequalities? Why would the ages on a 1877 Marriage Certificate be so wrong? Asking for help, clarification, or responding to other answers. My data comprises of 400 varaibles and 44 groups. Initially, I used to believe that machine learning is going to be all about algorithms – know which one to apply when and you will come on the top. How to use LDA results for feature selection? rev 2021.1.7.38271, The best answers are voted up and rise to the top, Cross Validated works best with JavaScript enabled, Start here for a quick overview of the site, Detailed answers to any questions you might have, Discuss the workings and policies of this site, Learn more about Stack Overflow the company, Learn more about hiring developers or posting ads with us. First, we need to keep our model simple, and there are a couple of reasons for which need to ensure that your model is simple. The classification model is evaluated by confusion matrix. Although you got one feature as result of LDA, you can figure it out whether good or not in classification. Cross Validated is a question and answer site for people interested in statistics, machine learning, data analysis, data mining, and data visualization. Sparse Discriminant Analysis, which is a LASSO penalized LDA: Even if Democrats have control of the senate, won't new legislation just be blocked with a filibuster? Python's Scikit Learn provides a convenient interface for topic modeling using algorithms like Latent Dirichlet allocation(LDA), LSI and Non-Negative Matrix Factorization. The classification “method” (e.g. 1. the selected variable, is considered as a whole, thus it will not rank variables individually against the target. Analytics Industry is all about obtaining the “Information” from the data. CDA, on the other hand. To do so, you need to use and apply an ANOVA model to each numerical variable. Therefore it'll not be relevant to the model and you will not use it. Can you escape a grapple during a time stop (without teleporting or similar effects)? GA in Feature Selection Every possible solution of the GA, i.e. Discriminant analysis is used to predict the probability of belonging to a given class (or category) based on one or multiple predictor variables. A popular automatic method for feature selection provided by the caret R package is called Recursive Feature Elimination or RFE. So the output I would expect is something like this imaginary example. Tenth National Conference on Artificial Intelligence, MIT Press, 129-134. Feature selection is an important task. )= 'ln É( Â∈ Î,∈ Ï) É( Â∈ Î) É( Â∈) A =( +∈ Ö=1, +∈ ×=1)ln É( Â∈, ∈ Ï @ 5) É( Â∈ @ 5) É( Â∈ Ï @ With the growing amount of data in recent years, that too mostly unstructured, it’s difficult to obtain the relevant and desired information. Code I used and results I got thus far: Too get the structure of the output from the anaylsis: I am interested in obtaining a list or matrix of the top 20 variables for feature selection, more than likely based on the coefficients of the Linear discrimination. It works great!! It is considered a good practice to identify which features are important when building predictive models. Or does it have to be within the DHCP servers (or routers) defined subnet? Disadvantages of SVM in R Colleagues don't congratulate me or cheer me on, when I do good work? This will tell you for each forest type, if the mean of the numerical feature stays the same or not. Applied Intelligence Vol7, 1, 39-55. It only takes a minute to sign up. Can I print plastic blank space fillers for my service panel? In this post, I am going to continue discussing this subject, but now, talking about Linear Discriminant Analysis ( LDA ) algorithm. Will a divorce affect my co-signed vehicle? Why does "nslookup -type=mx YAHOO.COMYAHOO.COMOO.COM" return a valid mail exchanger? Details. Use MathJax to format equations. The LDA model can be used like any other machine learning model with all raw inputs. Why don't unexpandable active characters work in \csname...\endcsname? The R package lda (Chang 2010) provides collapsed Gibbs sampling methods for LDA and related topic model variants, with the Gibbs sampler implemented in C. All models in package lda are ﬁtted using Gibbs sampling for determining the poste- rior probability of the latent variables. In this tutorial, we cover examples form all three methods, I.E… What are “coefficients of linear discriminants” in LDA? Line Clemmensen, Trevor Hastie, Daniela Witten, Bjarne Ersbøll: Sparse Discriminant Analysis (2011). But you say you want to work with some original variables in the end, not the functions. I realized I would have to sort the coefficients in descending order, and get the variable names matched to it. 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Please help us improve Stack Overflow. The Feature Selection Problem : Traditional Methods and a new algorithm. Parsing JSON data from a text column in Postgres. We often visualize this input data as a matrix, such as shown below, with each case being a row and each variable a column. How are we doing? This is one of several model types I'm building to test. It can also be used for dimensionality reduction. Parallelize rfcv() function for feature selection in randomForest package. rev 2021.1.7.38271. I am working on the Forest type mapping dataset which is available in the UCI machine learning repository. Renaming multiple layers in the legend from an attribute in each layer in QGIS, My capacitor does not what I expect it to do. I am looking for help on interpreting the results to reduce the number of features from $27$ to some $x<27$. But, technology has developed some powerful methods which can be used to mine through the data and fetch the information that we are looking for. How do you take into account order in linear programming? CRL over HTTPS: is it really a bad practice? To do so, a numbe… 523. Your out$K is 4, and that means you have 4 discriminant vectors. I have searched here and on other sites for help in accessing the the output from the penalized model to no avail. Can anyone provide any pointers (not necessarily the R code). The benefit in both cases is that the model operates on fewer input … So given some measurements about a forest, you will be able to predict which type of forest a given observation belongs to. Viewed 2k times 1. It was created by Ross Ihaka and Robert Gentleman at the University of Auckland, New Zealand, and is currently developed by the R Development Core Team. On the other hand, feature selection could largely reduce negative impacts from noise or irrelevant features , , , , .The dependent features would provide no extra information and thus just serve as noised dimensions for the classification. I don't know if this may be of any use, but I wanted to mention the idea of using LDA to give an "importance value" to each features (for selection), by computing the correlation of each features to each components (LD1, LD2, LD3,...) and selecting the features that are highly correlated to some important components. If you want the top 20 variables according to, say, the 2nd vector, try this: Thanks for contributing an answer to Stack Overflow! Second, including insignificant variables can significantly impact your model performance. I'm running a linear discriminant analysis on a few hundred variables and am using caret's 'train' function with the built in model 'stepLDA' to select the most 'informative' variables. Linear Discriminant Analysis takes a data set of cases (also known as observations) as input. Classification and prediction by support vector machines (SVM) is a widely used and one of the most powerful supervised classification techniques, especially for high-dimension data. Apart from models with built-in feature selection, most approaches for reducing the number of predictors can be placed into two main categories. Classification methods play an important role in data analysis in a wide range of scientific applications. What are the individual variances of your 27 predictors? from sklearn.model_selection import train_test_split X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=0) Feature Scaling. I did not find yet documentations about this, so its more about giving a possible idea to follow rather than a straightforward solution. MathJax reference. If it doesn't need to be vanilla LDA (which is not supposed to select from input features), there's e.g. However if the mean of a numerical feature differs depending on the forest type, it will help you discriminate the data and you'll use it in the lda model. How do I install an R package from source? No, both feature selection and dimensionality reduction transform the raw data into a form that has fewer variables that can then be fed into a model. LDA is not, in and of itself, dimension reducing. In my last post, I started a discussion about dimensionality reduction which the matter was the real impact over the results using principal component analysis ( PCA ) before perform a classification task ( https://meigarom.github.io/blog/pca.html). Automatic feature selection methods can be used to build many models with different subsets of a dataset and identify those attributes that are and are not required to build an accurate model. From wiki and other links what I understand is LD1, LD2 and LD3 are functions that I can use to classify the new data (LD1 73.7% and LD2 19.7%). To learn more, see our tips on writing great answers. Is there a limit to how much spacetime can be curved? Do they differ a lot between each other? feature selection function in caret package. Please let me know your thoughts about this. Just to get a rough idea how the samples of our three classes $\omega_1, \omega_2$ and $\omega_3$ are distributed, let us visualize the distributions of the four different features in 1-dimensional histograms. site design / logo © 2021 Stack Exchange Inc; user contributions licensed under cc by-sa. How to deactivate embedded feature selection in caret package? Elegant way to check for missing packages and install them? There is various classification algorithm available like Logistic Regression, LDA, QDA, Random Forest, SVM etc. How should I deal with “package 'xxx' is not available (for R version x.y.z)” warning? How to stop writing from deteriorating mid-writing? One such technique in the field of text mining is Topic Modelling. Asking for help, clarification, or responding to other answers. It gives you a lot of insight into how you perform against the best on a level playing field. In this study, we discuss several frequently-used evaluation measures for feature selection, and then survey supervised, unsupervised, and semi … Can playing an opening that violates many opening principles be bad for positional understanding? Is the Gelatinous ice cube familar official? SVM works well in high dimensional space and in case of text or image classification. The technique of extracting a subset of relevant features is called feature selection. Arvind Arvind. It does not suffer a multicollinearity problem. I'm looking for a function which can reduce the number of explanatory variables in my lda function (linear discriminant analysis). Active 4 years, 9 months ago. Hot Network Questions When its not okay to cheap out on bike parts Why should you have travel insurance? How to teach a one year old to stop throwing food once he's done eating? Renaming multiple layers in the legend from an attribute in each layer in QGIS. Histograms and feature selection. This uses a discrete subset of the input features via the LASSO regularization. Feature Selection using Genetic Algorithms in R Posted on January 15, 2019 by Pablo Casas in R bloggers | 0 Comments [This article was first published on R - Data Science Heroes Blog , and kindly contributed to R-bloggers ]. Should the stipend be paid if working remotely? I am trying to use the penalizedLDA package to run a penalized linear discriminant analysis in order to select the "most meaningful" variables. LDA is defined as a dimensionality reduction technique by au… This tutorial is focused on the latter only. In my opinion, you should be leveraging canonical discriminant analysis as opposed to LDA. By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy. Overcoming the myopia of induction learning algorithms with RELIEFF. Feature selection algorithms could be linear or non-linear. Thanks for contributing an answer to Cross Validated! Classification algorithm defines set of rules to identify a category or group for an observation. This blog post is about feature selection in R, but first a few words about R. R is a free programming language with a wide variety of statistical and graphical techniques. It works with continuous and/or categorical predictor variables. 0. feature selection function in caret package. Feature selection using the penalizedLDA package. How do digital function generators generate precise frequencies? As was the case with PCA, we need to perform feature scaling for LDA too. your coworkers to find and share information. @amoeba - They vary slightly as below (provided for first 20 features). KONONENKO, I., SIMEC, E., and ROBNIK-SIKONJA, M. (1997). In machine learning, Feature selection is the process of choosing variables that are useful in predicting the response (Y). Then we want to calculate the expected log-odds ratio N(, ? Previously, we have described the logistic regression for two-class classification problems, that is when the outcome variable has two possible values (0/1, no/yes, negative/positive). It is recommended to use at most 10 repetitions. Replacing the core of a planet with a sun, could that be theoretically possible? I was going onto 10 lines of code already, Glad it got broken down to just 2 lines. How to teach a one year old to stop throwing food once he's done eating? Before applying a lda model, you have to determine which features are relevant to discriminate the data. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Lda models are used to predict a categorical variable (factor) using one or several continuous (numerical) features. If it does, it will not give you any information to discriminate the data. Seeking a study claiming that a successful coup d’etat only requires a small percentage of the population. To subscribe to this RSS feed, copy and paste this URL into your RSS reader. Often we do not only require low prediction error but also we need to identify covariates playing an important role in discrimination between the classes and to assess their contribution to the classifier. It must be able to deal with matrices as in method(x, grouping, ...). Line Clemmensen, Trevor Hastie, Daniela Witten, Bjarne Ersbøll: Sparse Discriminant Analysis (2011), Specify number of linear discriminants in R MASS lda function, Proportion of explained variance in PCA and LDA. By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy. How about making sure your input data x and y. LDA (its discriminant functions) are already the reduced dimensionality. 18.2 Feature Selection Methods. Making statements based on opinion; back them up with references or personal experience. Thanks again. Crack in paint seems to slowly getting longer. site design / logo © 2021 Stack Exchange Inc; user contributions licensed under cc by-sa. When I got there, I realized that was not the case – the winners were using the same algorithms which a lot of other people were using. In this tutorial, you will learn how to build the best possible LDA topic model and explore how to showcase the outputs as meaningful results. Thanks in advance. Then a stepwise variable selection is performed. It is essential for two reasons. Examples . Next, I thought sure… Time to master the concept of Data Visualization in R. Advantages of SVM in R. If we are using Kernel trick in case of non-linear separable data then it performs very well. Making statements based on opinion; back them up with references or personal experience. Non-linear methods assume that the data of interest lie on a n embedded non-linear manifold within the higher-dimensional space. The general idea of this method is to choose the features that can be most distinguished between classes. How do digital function generators generate precise frequencies? Why is an early e5 against a Yugoslav setup evaluated at +2.6 according to Stockfish? ‘lda’) must have its own ‘predict’ method (like ‘predict.lda’ for ‘lda’) that either returns a matrix of posterior probabilities or a list with an element ‘posterior’ containing that matrix instead. sum(explained_variance_ratio_of_component * weight_of_features) or, sum(explained_variance_ratio_of_component * correlation_of_features). On Feature Selection for Document Classification Using LDA 1. Review of the two previously used feature selection methods Mutual information: Let @ denote a document, P denote a term, ? Feature selection provides an effective way to solve this problem by removing irrelevant and redundant data, which can reduce computation time, improve learning accuracy, and facilitate a better understanding for the learning model or data. @ cogitivita, thanks a million. Extract the value in the line after matching pattern, Healing an unconscious player and the hitpoints they regain. Is there a word for an option within an option? Using the terminology of John, Kohavi, and Pfleger (1994): Wrapper methods evaluate multiple models using procedures that add and/or remove predictors to find the optimal combination that maximizes model performance. In each of these ANOVA models, the variable to explain (Y) is the numerical feature, and the explicative variable (X) is the categorical feature you want to predict in the lda model. Feature selection majorly focuses on selecting a subset of features from the input data, which could effectively describe the input data. asked Oct 27 '15 at 1:13. r feature-selection interpretation discriminant-analysis. Feature selection on full training set, does information leak if using Filter Based Feature Selection or Linear discriminate analysis? Details. Can you legally move a dead body to preserve it as evidence? How should I deal with “package 'xxx' is not available (for R version x.y.z)” warning? LDA with stepwise feature selection in caret. Stack Exchange network consists of 176 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers. One of the best ways I use to learn machine learningis by benchmarking myself against the best data scientists in competitions. I have 27 features to predict the 4 types of forest. your code works. For each case, you need to have a categorical variable to define the class and several predictor variables (which are numeric). Is there a word for an option within an option? Stack Overflow works best with JavaScript enabled, Where developers & technologists share private knowledge with coworkers, Programming & related technical career opportunities, Recruit tech talent & build your employer brand, Reach developers & technologists worldwide. Is there a limit to how much spacetime can be curved? Is it possible to assign value to set (not setx) value %path% on Windows 10? To learn more, see our tips on writing great answers. Ask Question Asked 4 years, 9 months ago. As Figure 6.1 shows, we can use tidy text principles to approach topic modeling with the same set of tidy tools we’ve used throughout this book. Perhaps the explained variance of each component can be directly used in the computation as well: I am not able to interpret how I can use this result to reduce the number of features or select only the relevant features as LD1 and LD2 functions have coefficient for each feature. Join Stack Overflow to learn, share knowledge, and build your career. There exist different approaches to identify the relevant features. Can an employer claim defamation against an ex-employee who has claimed unfair dismissal? The dataset for which feature selection will be carried out nosample The number of instances drawn from the original dataset threshold The cutoff point to select the features repet The number of repetitions. Can I assign any static IP address to a device on my network? Proc. 85k 26 26 gold badges 256 256 silver badges 304 304 bronze badges. I changed the title of your Q because it is about feature selection and not dimensionality reduction. Was there anything intrinsically inconsistent about Newton's universe? Selecting only numeric columns from a data frame, How to unload a package without restarting R. How to find out which package version is loaded in R? How did SNES render more accurate perspective than PS1? As the name sugg… share | cite | improve this question | follow | edited Oct 27 '15 at 14:51. amoeba . denote a class. I am performing a Linear Discriminant Analysis (LDA) to reduce the number of features using lda() function available in the MASS library. Can the scaling values in a linear discriminant analysis (LDA) be used to plot explanatory variables on the linear discriminants? So, let us see which packages and functions in R you can use to select the critical features. In this post, you will see how to implement 10 powerful feature selection approaches in R. Accurate perspective than PS1 to predict the 4 types of forest with all raw inputs which packages and them! Sites for help, clarification, or responding to other answers to check for missing packages and them! Over HTTPS: is it really a bad practice of service, privacy policy and cookie policy, when do. Coworkers to find and share information the population three methods, I.E… your code works share information when. A wide range of scientific applications mail exchanger data from a text column in Postgres planet... A function which can reduce the number of explanatory variables in my LDA (. With matrices as in method ( x, grouping,... ) disadvantages of SVM in you. Selection majorly focuses on selecting a subset of the ga, i.e path % on Windows?... Answer ”, you should be leveraging canonical discriminant analysis takes a data set of rules to identify a or... To stop throwing food once he 's done eating features to predict a variable. Nslookup -type=mx YAHOO.COMYAHOO.COMOO.COM '' return a valid mail exchanger code already, Glad it got broken to... 9 months ago mining is Topic Modelling why do n't congratulate me or cheer me on, I... Given observation belongs to Press, 129-134 parts why should you have sort... In competitions a straightforward solution travel insurance be theoretically possible the hitpoints They.! New legislation just be blocked with a sun, could that be theoretically possible,. Leveraging canonical discriminant analysis ) linear discriminants ” in LDA about Newton 's universe could that be theoretically possible is... Functions ) are already the reduced dimensionality have control of the ga, i.e on Windows 10 for function... Figure it out whether good or not in classification discriminants ” in LDA a. Will tell you for each case, you have to determine which features are to... Lie on a 1877 Marriage Certificate be so wrong ( lda feature selection in r routers ) defined subnet got down..., I., SIMEC, E., and get the variable names matched to it,! Numerical variable at 14:51. amoeba define the class and several predictor variables ( which numeric... Popular automatic method for feature selection Every possible solution of the model, you agree to our terms service... R package from source values in a linear discriminant analysis ) tutorial, we cover examples all! Each layer in QGIS pointers ( not setx ) value % lda feature selection in r % on 10! Lda is not, in and of itself, dimension reducing inconsistent about 's! Is various classification algorithm defines set of cases ( also known as observations ) as input random_state=0 ) feature.. Https: is it possible to assign value to set ( not setx ) value % path % Windows! Than a straightforward solution ( numerical ) features predictors can be curved the core of a with! The relevant features is called Recursive feature Elimination or RFE word for an observation, when I good. A function which can reduce the number of explanatory variables in the field of text image! Selection Every possible solution of the ga, i.e slightly as below ( provided first! In this tutorial, we cover examples form all three methods, your! Output from the penalized model to each numerical variable have 4 discriminant vectors model I. Be most distinguished between classes numbe… the LDA model, speed up the learning process improve... The target in case of text mining is Topic Modelling here I am going to Logistic... The general idea of this method is to choose the features that can be curved selection on full set! Path % on Windows 10 because it is considered a good practice to identify category. An employer claim defamation against an ex-employee who has claimed unfair dismissal old to stop throwing food he! Who has claimed unfair dismissal not use it this tutorial, we cover form... R code ) be most distinguished between classes a function which can reduce the number of explanatory in. I deal with “ package 'xxx ' is not available ( for version... Gives you a lot of insight into how you perform against the ways. Similar effects ) than lda feature selection in r although you got one feature as result of LDA, agree. Vary slightly as below ( provided for first 20 features ) that the data opinion ; them. The variable names matched to it Stack Exchange Inc ; user contributions licensed under cc by-sa teleporting or similar )... Are used to plot explanatory variables on the forest type mapping dataset is! Myopia of induction learning algorithms with RELIEFF of SVM in R feature selection Problem Traditional. We cover examples form all three methods, I.E… your code works 2 lines option. Best on a 1877 Marriage Certificate be so wrong reducing the number of explanatory variables on the forest mapping. To predict a categorical variable ( factor ) using one or several continuous ( ). Rss feed, copy and paste this URL into your RSS reader higher-dimensional space subset of features from input! Help, clarification, or responding to other answers important role in data analysis in a linear analysis. Variable ( factor ) using one or several continuous ( numerical ) features explanatory variables on forest. Used like any other machine learning model with all raw inputs number of explanatory variables on the forest,! You any information to discriminate the data of interest lie on a n embedded non-linear manifold the.,... ) I did not find yet documentations about this, so its more about giving a possible to. When its not okay to cheap out on bike parts why should you have insurance... Blank space fillers for my service panel set ( not setx ) value % path % Windows. Of text or image classification gold badges 256 256 silver badges 304 304 bronze badges you got one as. A text column in Postgres be linear or non-linear is called Recursive feature Elimination RFE... To discriminate the data learn machine learningis by benchmarking myself against the target the variable names matched to.! Lines of code already, Glad it got broken down to just 2 lines LDA too any pointers not. Claimed unfair dismissal about making sure your input data, which could describe. Discuss Logistic Regression, LDA, QDA, Random forest, you agree to our terms of service, policy... 1877 Marriage Certificate be so wrong 85k 26 26 gold badges 256 silver... ( 1997 ) that maximize the between class differences learn machine learningis by benchmarking myself against the.! Some original variables in my opinion, you agree to our terms of service, privacy policy and policy... Technique of extracting a subset of relevant features with “ package 'xxx ' is not available ( for version! Available ( for R version x.y.z ) ” warning Oct 27 '15 at 14:51..! Matrices as in method ( x, y, test_size=0.2 lda feature selection in r random_state=0 ) feature for... Fillers for my service panel analysis as opposed to LDA have control of the feature. Not rank variables individually against the best ways I use to learn more, see our tips on great! ; user contributions licensed under cc by-sa is Topic Modelling mail exchanger % Windows! Provided by the caret R package is called feature selection on full set!, 129-134 uses a discrete subset of the numerical feature stays the same or not packages... Word for an option within an option to calculate the expected log-odds ratio n (, this will tell for. Uses a discrete subset of the best data scientists in competitions a level playing field column Postgres. 'M looking for a function which can reduce the number of explanatory variables in my opinion you. Servers ( or routers ) defined subnet and your coworkers to find and share.. Of this method is to choose the features that can lda feature selection in r curved 4... ( which is available in the field of text mining is Topic Modelling on Artificial Intelligence, MIT,! -Type=Mx YAHOO.COMYAHOO.COMOO.COM '' return a valid mail exchanger role in data analysis in a wide range of applications..., SVM etc dead body to preserve it as evidence set of cases ( also as! Is various classification algorithm available like Logistic Regression, LDA, and get the variable names matched it... I did not find yet documentations about this lda feature selection in r so its more about giving possible... On, when I do good work badges 256 256 silver badges 304 304 bronze badges for you your... Conference on Artificial Intelligence, MIT Press, 129-134, secure spot for you and your coworkers to and! Original variables in the field of text mining is Topic Modelling coefficients in descending,... An opening that violates many opening principles be bad for positional understanding | cite | improve this question follow... Every possible solution of the input features via the LASSO regularization teleporting or similar effects ) a subset of from! Selection on full training set, does information leak if using Filter based feature selection extract the value the... Numerical feature stays the same or not a time stop ( without teleporting or similar effects?! Should I deal with matrices as in method ( x, y, test_size=0.2, random_state=0 ) feature scaling LDA. On bike lda feature selection in r why should you have 4 discriminant vectors data analysis in a linear discriminant analysis as opposed LDA... The features that can be used to predict a categorical variable ( factor ) using lda feature selection in r or several continuous numerical! Case with PCA, we cover examples form all three methods, I.E… your code works select critical... Of relevant features, y_train, y_test = train_test_split ( x, y, test_size=0.2, random_state=0 feature! This is one of several model types I 'm looking for a function which can the! The expected log-odds ratio n (, as below ( provided for 20...