Multicollinearity tutoral

I just posted brief multicollinearity tutorial on my other blog (loosely based on the material from the Serious Stats book).

You can read it here.

R functions for serious stats

UPDATE: Some problems arose with my previous host so I have now updated the links here and elsewhere on the blog.

The companion web site for Serious Stats has a zip file with R scripts for each chapter. This contains examples of R code and and all my functions from the book (and a few extras). This is a convenient form for working through the examples. However, if you just want to access the functions it is more convenient to load them all in at once.

The functions can be downloaded as a text file from:

http://www2.ntupsychology.net/seriousstats/SeriousStatsAllfunctions.txt

More conveniently, you can load them directly into R with the following call:

source('http://www2.ntupsychology.net/seriousstats/SeriousStatsAllfunctions.txt')

In addition to the Serious Stats functions, a number of other functions are contained in the text file. These include functions published on this blog for comparing correlations or confidence intervals for independent measures ANOVA and functions my paper on confidence intervals for repeated measures ANOVA.

N.B. R code formatted via Pretty R at inside-R.org

Comparing correlations: independent and dependent (overlapping or non-overlapping)

In Chapter 6 (correlation and covariance) I consider how to construct a confidence interval (CI) for the difference between two independent correlations.  The standard approach uses the Fisher z transformation to deal with boundary effects (the squashing of the distribution and increasing asymmetry as r approaches -1 or 1). As zr is approximately normally distributed (which r is decidedly not) you can create a standard error for the difference by summing the sampling variances according to the variance sum law (see chapter 3).

This works well for the CI around a single correlation (assuming the main assumptions – bivariate normality and homogeneity of variance – broadly hold) or for differences between means, but can perform badly when looking at the difference between two correlations. Zou (2007) proposed modification to the standard approach that uses the upper and lower bounds of the CIs for individual correlations to calculate a CI for their difference. He considered three cases: independent correlations and two types of dependent correlations (overlapping and non-overlapping). He also considered differences in R2 (not relevant here).

Independent correlations

In section 6.6.2 (p. 224) I illustrate Zou’s approach for independent correlations and provide R code in sections 6.7.5 and 6.7.6 to automate the calculations. Section 6.7.5 shows how to write a simple R function and illustrates it with a function to calculate a CI for Pearson’s r using the Fisher transformation. Whilst writing the book I encountered several functions do do exactly this. The cor.test() function in the base package does this for raw data (along with computing the correlation and usual NHST). A number of functions compute it using the usual text book formula. My function relies on R primitive hyperbolic functions (as the Fisher z transformation is related to the geometry of hyperbolas), which may be useful if you need to use it intensively (e.g., for simulations):

rz.ci <- function(r, N, conf.level = 0.95) {
    zr.se <- 1/(N - 3)^0.5
    moe <- qnorm(1 - (1 - conf.level)/2) * zr.se
    zu <- atanh(r) + moe
    zl <- atanh(r) - moe
    tanh(c(zl, zu))
}

The function is 6.7.6 uses the rz.ci() function to construct a CI for the difference between two independent correlations. See section 6.6.2 of Serious stats or Zou (2007) for further details and a worked example. My function from section 6.7.6 is reproduced here:

r.ind.ci <- function(r1, r2, n1, n2=n1, conf.level = 0.95) {
    L1 <- rz.ci(r1, n1, conf.level = conf.level)[1]
    U1 <- rz.ci(r1, n1, conf.level = conf.level)[2]
    L2 <- rz.ci(r2, n2, conf.level = conf.level)[1]
    U2 <- rz.ci(r2, n2, conf.level = conf.level)[2]
    lower <- r1 - r2 - ((r1 - L1)^2 + (U2 - r2)^2)^0.5
    upper <- r1 - r2 + ((U1 - r1)^2 + (r2 - L2)^2)^0.5
    c(lower, upper)
}

The call the function use the two correlation coefficients an sample as input (the default is to assume equal n and a 95% CI).

A caveat

As I point out in chapter 6, just because you can compare two correlation coefficients doesn’t mean it is a good idea. Correlations are standardized simple linear regression coefficients and even if the two regression coefficients measure the same effect, it doesn’t follow that their standardized counterparts do. This is not merely the problem that it may be meaningless to compare, say, a correlation between height and weight with a correlation between anxiety and neuroticism. Two correlations between the same variables in different samples might not be meaningfully comparable (e.g., because of differences in reliability, range restriction and so forth).

Dependent overlapping correlations

In many cases the correlations you want to compare aren’t independent. One reason for this is that the correlations share a common variable. For example if you correlate X with Y and X with Z you might be interested in whether the correlation rXY is larger than rXZ. As X is common to both variables the correlations are not independent. Zou (2007) describes how to adjust the interval to account for this correlation. In essence the sampling variances of the correlations are tweaked using a version of the variance sum law (again see chapter 3).

The following functions (not in the book) compute the correlation between the correlations and use it to adjust the CI for the difference in correlations to account for overlap (a shared predictor). Note that both functions and  rz.ci() must be loaded into R. Also included is a calls to the main function  that reproduces the output from example 2 of Zou (2007).

rho.rxy.rxz <- function(rxy, rxz, ryz) {
	num <- (ryz-1/2*rxy*rxz)*(1-rxy^2-rxz^2-ryz^2)+ryz^3
	den <- (1 - rxy^2) * (1 - rxz^2)
	num/den
	}

r.dol.ci <- function(r12, r13, r23, n, conf.level = 0.95) {
    L1 <- rz.ci(r12, n, conf.level = conf.level)[1]
    U1 <- rz.ci(r12, n, conf.level = conf.level)[2]
    L2 <- rz.ci(r13, n, conf.level = conf.level)[1]
    U2 <- rz.ci(r13, n, conf.level = conf.level)[2]
    rho.r12.r13 <- rho.rxy.rxz(r12, r13, r23)
    lower <- r12-r13-((r12-L1)^2+(U2-r13)^2-2*rho.r12.r13*(r12-L1)*(U2- r13))^0.5
    upper <- r12-r13+((U1-r12)^2+(r13-L2)^2-2*rho.r12.r13*(U1-r12)*(r13-L2))^0.5
    c(lower, upper)
} 

# input from example 2 of Zou (2007, p.409)
r.dol.ci(.396, .179, .088, 66)

The r.dol.ci() function takes three correlations as input – the correlations of interest (e.g., rXY and rXZ) and the correlation between the non-overlapping variables (e.g., rYZ). Also required is the sample size (often identical for both correlations).

Dependent non-overlapping correlations

Overlapping correlations are not the only cause of dependency between correlations. The samples themselves could be correlated. Zou (2007) gives the example of a correlation between two variables for a sample of mothers. The same correlation could be computed for their children. As the children and mothers have correlated scores on each variable, the correlation between the same two variables will be correlated (but not overlapping in the sense used earlier). The following functions compute the CI for the difference in correlations  between dependent non-overlapping correlations. Also included is a call to the main function that reproduces Zou (2007) example 3.

rho.rab.rcd <- function(rab, rac, rad, rbc, rbd, rcd) {
	num <- 1/2*rab*rcd * (rac^2 + rad^2 + rbc^2 + rbd^2) + rac*rbd + rad*rbc - (rab*rac*rad + rab*rbc*rbd + rac*rbc*rcd + rad*rbd*rcd)
	den <- (1 - rab^2) * (1 - rcd^2)
	num/den
	}

r.dnol.ci <- function(r12, r13, r14, r23, r24, r34, n12, n34=n12, conf.level=0.95) {
    L1 <- rz.ci(r12, n12, conf.level = conf.level)[1]
    U1 <- rz.ci(r12, n12, conf.level = conf.level)[2]
    L2 <- rz.ci(r34, n34, conf.level = conf.level)[1]
    U2 <- rz.ci(r34, n34, conf.level = conf.level)[2]
    rho.r12.r34 <- rho.rab.rcd(r12, r13, r14, r23, r24, r34)
    lower <- r12 - r34 - ((r12 - L1)^2 + (U2 - r34)^2 - 2 * rho.r12.r34 * (r12 - L1) * (U2 - r34))^0.5
    upper <- r12 - r34 + ((U1 - r12)^2 + (r34 - L2)^2 - 2 * rho.r12.r34 * (U1 - r12) * (r34 - L2))^0.5
    c(lower, upper)
} 

# from example 3 of Zou (2007, p.409-10)

r.dnol.ci(.396, .208, .143, .023, .423, .189, 66)

Although this call reproduces the final output for example 3 it produces slightly different intermediate results (0.0891 vs. 0.0917) for the correlation between correlations. Zou (personal communication) confirms that this  is either a typo or rounding error (e.g., arising from hand calculation) in example 3 and that the function here produces accurate output. The input here requires the correlations from every possible correlation between the four variables being compared (and the relevant sample size for the correlations being compared). The easiest way to get the correlations is from a correlation matrix of the four variables.

Robust alternatives

Wilcox (2009) describes a robust alternative to these methods for independent correlations and modifications to Zou’s  method that make the dependent correlation methods robust to violations of bivariate normality and (in particular) homogeneity of variance assumptions. Wilcox provides R functions for these approaches on his web pages. His functions take raw data as input and are computationally intensive. For instance the dependent correlation methods use Zou’s approach but take boostrap CIs for the individual correlations as input (rather than the simpler Fisher z transformed versions).

The relevant functions are twopcor() for the independent case, TWOpov() for the dependent overlapping case and TWOpNOV() for the non-overlapping case.

UPDATE

Zou’s modified asymptotic method is easy enough that you can run it in Excel. I’ve added an Excel spreadsheet to the blog resources that should implement the methods (and matches the output to R fairly closely). As it uses Excel it may not cope gracefully with some calculations (e.g., with extremely small or large values or r or other extreme cases) – and I have more confidence in the R code.

References

Baguley, T. (2012, in press). Serious stats: A guide to advanced statistics for the behavioral sciences. Basingstoke: Palgrave.

Zou, G. Y. (2007). Toward using confidence intervals to compare correlations. Psychological Methods, 12, 399-413.

Wilcox, R. R. (2009). Comparing Pearson correlations: Dealing with heteroscedascity and non-normality. Communications in Statistics – Simulation & Computation, 38, 2220-2234.

N.B. R code formatted via Pretty R at inside-R.org

Serious stats – a quick chapter summary

Here is a list of the contents by chapter with quick notes on chapter content …

0. Preface (About the book; notes on software, mathematics and types of boxed sections)

1. Data, Samples and Statistics (A gentle review of measures of central tendency and dispersion with a little more depth in places – flagging up the distinction between descriptive and inferential formulas and perhaps introducing a few unfamiliar statistics such the geometric mean)

2. Probability Distributions (A background chapter giving a whirlwind tour of the main probability distributions – discrete and continuous – that crop up in later chapters. It also introduces important concepts such probability mass functions, probability density functions and cumulative density functions and characteristics of distributions such as skew, kurtosis and whether they are bounded. From a statistical point of view it is a quick overview missing out a lot of the difficult stuff. )

3. Confidence Intervals (This chapter introduces interval estimation using confidence intervals (CIs) and gives examples for discrete and continuous distributions – particularly those for means and differences between independent or paired means using the t distribution. This chapter also introduces Monte Carlo methods – with emphasis on the bootstrap.)

4. Significance Tests (This chapter introduces significance tests. These are deliberately covered after CIs – which are less popular in the behavioral sciences but generally more useful. A number of common tests are covered – notably t tests and chi-square tests. The chapter ends with some comments on the appropriate use of significance tests – a point picked up again in chapter 11.)

5. Regression (This chapter introduces regression – with an emphasis on simple linear regression. Later chapters draw heavily on this basic material including concepts such as prediction, leverage and influence. The versatility of regression approaches is shown by illustrating how an independent t test is a simple regression model and how a linear model can fit some curvilinear relationships.)

6. Correlation and Covariance (Introduces covariance and correlation with emphasis on the link between Pearson’s r and simple linear regression. The chapter also introduces standardization and problems of working with standardized quantities such as boundary effects, range restriction and small sample bias. Methods for inference with correlation coefficients and comparing correlations (e.g., using the Fisher z distribution) are considered. Some alternatives to Pearson’s r are also introduced.)

7. Effect Size (This chapter focuses on effect size, starting with an overview of the different uses of effect size metrics. The chapter gives a tour of different types of effect size metrics, distinguishing between: continuous and discrete metrics; simple (unstandardized) and standardized metrics; focused (1 df) and unfocused (multiple df) metrics; base rate sensitive and base rate insensitive metrics. I argue that standardized metrics whether based on differences or correlations (d family or r family) are not good measures of the practical, clinical or theoretical importance of an effect because they confound the magnitude of an effect with its variability – though they may be useful in some situations.)

8. Statistical Power (This chapter introduces statistical power – starting by explaining the link between the effect size and statistical power, illustrating why standardized effect size (by combining the magnitude of an effect with its variability) is often a convenient way to summarize an effect in order to estimate statistical power or the sample size required to detect an effect. Problems and pitfalls in statistical power and sample size estimation are discussed. Later sections introduce the accuracy in parameter estimation approach to power in relation to the width of a confidence interval.)

9. Exploring Messy Data (This chapter looks at exploratory analysis of data with emphasis on graphical methods for checking statistical assumptions.)

10. Dealing with Messy Data (This chapter surveys approaches to dealing with violations of statistical assumptions with particular emphasis on robust methods and transformations.)

11. Alternatives to Classical Statistical Inference (This chapter looks at criticism of classical, frequentist methods of inference and considers frequentist responses and three alternative approaches: likelihood, Bayesian and information-theoretic methods. I illustrate each of the alternatives both here and in later chapters.)

12. Multiple Regression and the General Linear Model (This chapter extends regression to models with multiple predictors. The problem of fitting these models when predictors are not orthogonal (i.e., when they are correlated) is introduced and a solution is illustrated using matrix algebra. The rest of the chapter introduces partial and semi-partial correlation and focuses on interpreting a multiple regression model and related issues such as collinearity and suppression.)

13. ANOVA and ANCOVA with Independent Measures (This chapter introduces ANOVA and ANCOVA as special cases of multiple regression with categorical predictors (e.g., using dummy or effect coding). The chapter ends by introducing the multiple comparison problem in relation to differences between means for a factor in ANOVA or differences between adjusted means in ANCOVA. For the latter, the main focus is on modified Bonferroni procedures, though alternatives such as control of false discovery rate and information-theoretic approaches are briefly considered.)

14. Interactions (This chapter looks at modeling non-additive effects of predictors in multiple regression models through the inclusion of interaction terms. It starts by looking at the most general form of an interaction model in multiple regression (often termed a moderated multiple regression) before looking at polynomial terms in regression and interactions in the context of ANOVA and ANCOVA. The main emphasis is on interpreting and exploring interaction effects (e.g., through graphical methods). The chapter also looks at simple main effects and simple interaction effects.)

15. Contrasts (This chapter looks at the often neglected topic of contrasts – mainly in the context of ANOVA and ANCOVA models (where they are weighted combinations of differences in means or adjusted means). Methods for setting up contrasts to test hypotheses about patterns of means are explained for simple cases and extended for unbalanced designs, adjusted means and interaction effects.)

16. Repeated Measures ANOVA (This chapter introduces repeated measures and related (e.g., matched) designs. These increase statistical power by removing individual differences from the ANOVA error term, but at the cost of increased complexity (e.g., making stronger assumptions about the errors of the model). Again, the chapter focuses on checking and dealing with violations of assumptions and on the interpretation of the model. It also briefly considers MANOVA and repeated measures ANCOVA models and the use of gain scores).

17. Modelling Discrete Outcomes (This chapter explains how the regression approach of the general linear model can be extended to models with discrete outcomes using the generalized linear model and related approaches. The main focus is on logistic regression (including multinomial and ordered logistic regression) and Poisson regression, but negative binomial regression and models for excess zeroes (zero-inflated and hurdle models) are briefly reviewed. The chapter ends by considering the difficulty of modeling correlated observations in logistic regression.)

18. Multilevel Models (This chapter introduces multilevel models with particular emphasis on their application to the analysis repeated measures data. The chapter considers conventional nested designs (e.g., repeated measures within participants or children within schools) and moves on to fully crossed models and a brief overview of multilevel generalized linear models).

All chapters come with several examples within the chapter and R code (at the end). Most also have notes on SPSS syntax. I don’t include full SPSS instructions because these are often already available in popular texts. If they aren’t available it is generally because SPSS couldn’t readily implement these analyses. Also note that recent versions of SPSS can be set up to call R via syntax (though I find it easier to use R directly).

Online supplements

The book is around 800 pages long and some material cut from the final draft will be available in five online supplements. This material is either parenthetical (being too detailed than required) or self-contained sections that could stand alone and were perhaps not relevant for all readers.

OS1. Meta-analysis (This section was included in chapter 7 Effect size and introduces meta-analysis. Most meta-analytic approaches for continuous data use standardized effect size metrics. As the chapter argues that simple effect size metrics are often superior for summarizing and comparing effects this chapter uses meta-analysis of simple (raw) mean differences to illustrate fixed effect and random effects models. There is a nice link between random effects meta-analysis and multilevel models – so it was a shame to drop it.)

OS2. Dealing with missing data (An overview of methods for dealing with missing data that was part of chapter 10. The main focus is on multiple imputation – an extremely useful and underused approach in the behavioral sciences and a worked example is demonstrated for both R and SPSS. There are nice links between multiple imputation and meta-analysis – so it made sense to move this chapter out once I had decided to leave out meta-analysis. If you work with missing data and aren’t already familiar with multiple imputation you should take a careful look at this chapter – as most standard methods for dealing with missing data are biased and have low statistical power.)

OS3. Replication probabilities and prep (When I started writing the book there was quite an interest in replication probabilities and prep. in particular as an alternative to p values. This interest has largely faded and my (largely critical) take on prep is now mainly a historical curiosity. The main text now covers this topic briefly in chapter 11. )

OS4. Pseudo-R2 and related measures (A reader of the final draft of chapter 17 commented that given the problems with these measures and my own critical stance on standardized effect size metrics that my coverage of this topic was too detailed. I greatly reduced the emphasis on pseudo-R2 in the text by moving most of the material here. Of these measures my favourite is Zheng and Agresti’s predictive power measure – which I find most intuitive.)

OS5. Loglinear models (Loglinear models are models of contingency table data (closely related to Poisson regression, and under certain conditions equivalent). As Poisson models are generally more flexible, loglinear models were cut from the final draft. However, as they are quite popular in the behavioral sciences – this supplement is provided. Loglinear models are also a convenient way to parameterize a count model to make it more “chi-square-like”. Note: loglinear model can also be used in a more general sense to include models with log link functions or log transformations.)

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