1. Tukey's Test for Post-Hoc Analysis

After a multivariate test, it is often desired to know more about the specific groups to find out if they are significantly different or similar. This step after analysis is referred to as 'post-hoc analysis' and is a major step in hypothesis testing. One common and popular method of post-hoc analysis is Tukey's Test. The test is known by several different names. Tukey's test compares the means of all treatments to the mean of every other treatment and is considered the best available method in cases when confidence intervals are desired or if sample sizes are unequal.

Tagged as : R statistics
2. Kruskal-Wallis One-Way Analysis of Variance of Ranks

The Kruskal-Wallis test extends the Mann-Whitney-Wilcoxon Rank Sum test for more than two groups. The test is nonparametric similar to the Mann-Whitney test and as such does not assume the data are normally distributed and can, therefore, be used when the assumption of normality is violated. This example will employ the Kruskal-Wallis test on the PlantGrowth dataset as used in previous examples. Although the data appear to be approximately normally distributed as seen before, the Kruskal-Wallis test performs just as well as a parametric test.

Tagged as : R statistics
3. Quadratic Discriminant Analysis of Several Groups

Quadratic discriminant analysis for classification is a modification of linear discriminant analysis that does not assume equal covariance matrices amongst the groups ($$\Sigma_1, \Sigma_2, \cdots, \Sigma_k$$). Similar to LDA for several groups, quadratic discriminant analysis for several groups classification seeks to find the group that maximizes the quadratic classification function and assign the observation vector $$y$$ to that group.

4. Quadratic Discriminant Analysis of Two Groups

LDA assumes the groups in question have equal covariance matrices ($$\Sigma_1 = \Sigma_2 = \cdots = \Sigma_k$$). Therefore, when the groups do not have equal covariance matrices, observations are frequently assigned to groups with large variances on the diagonal of its corresponding covariance matrix (Rencher, n.d., pp. 321). Quadratic discriminant analysis is a modification of LDA that does not assume equal covariance matrices amongst the groups. In quadratic discriminant analysis, the respective covariance matrix $$S_i$$ of the $$i^{th}$$ group is employed in predicting the group membership of an observation, rather than the pooled covariance matrix $$S_{p1}$$ in linear discriminant analysis.

5. Linear Discriminant Analysis for the Classification of Several Groups

Similar to the two-group linear discriminant analysis for classification case, LDA for classification into several groups seeks to find the mean vector that the new observation $$y$$ is closest to and assign $$y$$ accordingly using a distance function. The several group case also assumes equal covariance matrices amongst the groups ($$\Sigma_1 = \Sigma_2 = \cdots = \Sigma_k$$).

6. Linear Discriminant Analysis for the Classification of Two Groups

In this post, we will use the discriminant functions found in the first post to classify the observations. We will also employ cross-validation on the predicted groups to get a realistic sense of how the model would perform in practice on new observations. Linear classification analysis assumes the populations have equal covariance matrices ($$\Sigma_1 = \Sigma_2$$) but does not assume the data are normally distributed.

7. Discriminant Analysis for Group Separation

Discriminant analysis assumes the two samples or populations being compared have the same covariance matrix $$\Sigma$$ but distinct mean vectors $$\mu_1$$ and $$\mu_2$$ with $$p$$ variables. The discriminant function that maximizes the separation of the groups is the linear combination of the $$p$$ variables. The linear combination denoted $$z = a′y$$ transforms the observation vectors to a scalar. The discriminant functions thus take the form:

8. Discriminant Analysis of Several Groups

Discriminant analysis is also applicable in the case of more than two groups. In the first post on discriminant analysis, there was only one linear discriminant function as the number of linear discriminant functions is $$s = min(p, k − 1)$$, where $$p$$ is the number of dependent variables and $$k$$ is the number of groups. In the case of more than two groups, there will be more than one linear discriminant function, which allows us to examine the groups' separation in more than one dimension.

9. Introduction to Rpoet

The Rpoet package is a wrapper of the PoetryDB API, which enables developers and other users to extract a vast amount of English-language poetry from nearly 130 authors. The package provides a simple R interface for interacting and accessing the PoetryDB database. This vignette will introduce the basic functionality of Rpoet and some example usages of the package.

Tagged as : R APIs poetry
10. Calculating and Performing One-way Multivariate Analysis of Variance (MANOVA)

MANOVA, or Multiple Analysis of Variance, is an extension of Analysis of Variance (ANOVA) to several dependent variables. The approach to MANOVA is similar to ANOVA in many regards and requires the same assumptions (normally distributed dependent variables with equal covariance matrices).

Tagged as : R statistics
11. Calculating and Performing One-way Analysis of Variance (ANOVA)

ANOVA, or Analysis of Variance, is a commonly used approach to testing a hypothesis when dealing with two or more groups. One-way ANOVA, which is what will be explored in this post, can be considered an extension of the t-test when more than two groups are being tested. The factor, or categorical variable, is often referred to as the 'treatment' in the ANOVA setting. ANOVA involves partitioning the data's total variation into variation between and within groups. This procedure is thus known as Analysis of Variance as sources of variation are examined separately.

Tagged as : R statistics
12. Computing Working-Hotelling and Bonferroni Simultaneous Confidence Intervals

There are two procedures for forming simultaneous confidence intervals, the Working-Hotelling and Bonferroni procedures. Each estimates intervals of the mean response using a family confidence coefficient. The Working-Hotelling coefficient is defined by $$W$$ and Bonferroni $$B$$. In practice, it is recommended to perform both procedures to determine which results in a tighter interval. The Bonferroni method will be explored first.

Tagged as : R statistics
13. Predicting Cat Genders with Logistic Regression

Consider a data set of 144 observations of household cats. The data contains the cats' gender, body weight and height. Can we model and accurately predict the gender of a cat based on previously observed values using logistic regression?

Tagged as : R statistics
14. PetfindeR, R Wrapper for the Petfinder API, Introduction Part Two

The first post introduced and explored the basic usage of the PetfindeR library. In this post, we take a quick look at some of the additional uses of the library and its methods to extract data from the Petfinder database.

Tagged as : R PetfindeR APIs
15. PetfindeR, R Wrapper for the Petfinder API, Introduction Part One

The goal of the PetfindeR package is to provide a simple and straightforward interface for interacting with the Petfinder API through R. The Petfinder database contains approximately 300,000 adoptable pet records and 11,000 animal welfare organization records, which makes it a handy and valuable source of data for those in the animal welfare community. However, the outputs from the Petfinder API are in messy JSON format and thus it makes it more time-consuming and often frustrating to coerce the output data into a form that is workable with R.

Tagged as : R PetfindeR APIs
16. Analyzing Nationwide Utility Rates with R, SQL and Plotly

R and SQL make excellent complements for analyzing data due to their respective strengths. The sqldf package provides an interface for working with SQL in R by querying data from a database into an R data.frame. This post will demonstrate how to query and analyze data using the sqldf package in conjunction with the graphing libraries plotly and ggplot2 as well as some other packages that provide useful statistical tests and other functions.

Tagged as : R Plotly SQL
17. Cartesian Product and Ordered and Unordered Pairs

A pair set is a set with two members, for example, {2, 3}, which can also be thought of as an unordered pair, in that {2, 3}={3, 2}. However, we seek a more a strict and rich object that tells us more about two sets and how their elements are ordered.

Tagged as : R set theory
18. Algebra of Sets with R

The set operations, union and intersection, the relative complement − and the inclusion relation (subsets) are known as the algebra of sets. The algebra of sets can be used to find many identities related to set relations.

Tagged as : R set theory
19. N-Union and Intersection Set Operations

Set unions and intersections can be extended to any number of sets. This post introduces notation to simplify the expression of n-sets and the set union and intersection operations themselves with R.

Tagged as : R set theory
20. Combined Linear Congruential Generator for Pseudo-random Number Generation

Combined linear congruential generators, as the name implies, are a type of PRNG (pseudorandom number generator) that combine two or more LCGs (linear congruential generators). The combination of two or more LCGs into one random number generator can result in a marked increase in the period length of the generator which makes them better suited for simulating more complex systems.

21. Multiplicative Congruential Random Number Generators with R

Multiplicative congruential generators, also known as Lehmer random number generators, is a type of linear congruential generator for generating uniform pseudorandom numbers. The multiplicative congruential generator, often abbreviated as MLCG or MCG, is defined as a recurrence relation similar to the LCG.

22. Linear Congruential Generator for Pseudo-random Number Generation with R

Linear congruential generators (LCGs) are a class of pseudorandom number generator (PRNG) algorithms used for generating sequences of random-like numbers. The generation of random numbers plays a large role in many applications ranging from cryptography to Monte Carlo methods. Linear congruential generators are one of the oldest and most well-known methods for generating random numbers primarily due to their comparative ease of implementation and speed and their need for little memory.

23. Set Union and Intersections with R

The set operations 'union' and 'intersection' should ring a bell for those who've worked with relational databases and Venn Diagrams. The 'union' of two of sets A and B represents a set that comprises all members of A and B (or both).

Tagged as : R set theory
24. Introduction to Sets and Set Theory with R

Sets define a 'collection' of objects, or things typically referred to as 'elements' or 'members.' The concept of sets arises naturally when dealing with any collection of objects, whether it be a group of numbers or anything else.

Tagged as : R set theory
25. Hierarchical Clustering Nearest Neighbors Algorithm in R

Hierarchical clustering is a widely used and popular tool in statistics

Tagged as : R clustering statistics
26. Factor Analysis with the Iterated Factor Method and R

The iterated principal factor method is an extension of the principal

27. Factor Analysis with Principal Factor Method and R

As discussed in a previous post on the principal component method of factor analysis, the $$\hat{\Psi}$$ term in the estimated covariance matrix $$S$$, $$S = \hat{\Lambda} \hat{\Lambda}' + \hat{\Psi}$$, was excluded and we proceeded directly to factoring $$S$$ and $$R$$. The principal factor method of factor analysis (also called the principal axis method) finds an initial estimate of $$\hat{\Psi}$$ and factors $$S - \hat{\Psi}$$, or $$R - \hat{\Psi}$$ for the correlation matrix.

Tagged as : R factor analysis
28. Factor Analysis with the Principal Component Method and R Part Two

In the first post on factor analysis, we examined computing the estimated covariance matrix $$S$$ of the rootstock data and proceeded to find two factors that fit most of the variance of the data. However, the variables in the data are not on the same scale of measurement, which can cause variables with comparatively large variances to dominate the diagonal of the covariance matrix and the resulting factors. The correlation matrix, therefore, makes more intuitive sense to employ in factor analysis.

29. Factor Analysis with the Principal Component Method and R

The goal of factor analysis, similar to principal component analysis, is to reduce the original variables into a smaller number of factors that allows for easier interpretation. PCA and factor analysis still defer in several respects. One difference is principal components are defined as linear combinations of the variables while factors are defined as linear combinations of the underlying latent variables.

30. Principal Component Analysis with R Example

Often, it is not helpful or informative to only look at all the variables in a dataset for correlations or covariances. A preferable approach is to derive new variables from the original variables that preserve most of the information given by their variances. Principal component analysis is a widely used and popular statistical method for reducing data with many dimensions (variables) by projecting the data with fewer dimensions using linear combinations of the variables, known as principal components.

31. Image Compression with Singular Value Decomposition

The method of image compression with singular value decomposition is

32. Singular Value Decomposition and R Example

SVD underpins many statistical and real-world

33. How to Calculate the Inverse Matrix for 2×2 and 3×3 Matrices

The inverse of a number is its reciprocal. For example, the inverse of 8

Tagged as : R linear algebra matrices

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