STAT 4020/MSA 5020, FALL 2014

R FUNCTIONS FOR REGRESSIO ANALYSIS

Here are some helpful R functions for regression analysis grouped by what they do. Not all these
functions will load when you open R. You need to download additional packages for some of these
functions. The name of package is in parentheses. The best way to use these functions is to first run lm()
and save the result into an object.name. Any function can then be applied to object.name, such as
anova(object.name). There are way more functions than needed in STAT 4020. However, I wanted to
provide a more complete collection.

Linear Model

anova: Compute an analysis of variance table for one or more linear model fits (stasts)

coef: is a generic function which extracts model coefficients from objects returned
by modeling functions. coefficients is an alias for it (stasts)

coeftest: Testing Estimated Coefficients (lmtest)

confint: Computes confidence intervals for one or more parameters in a fitted model.
Base has a method for objects inheriting from class "lm" (stasts)

deviance: Returns the deviance of a fitted model object (stats)

effects: Returns (orthogonal) effects from a fitted model, usually a linear model. This is a
generic function, but currently only has a methods for objects inheriting from classes "lm" and
"glm" (stasts)

fitted: is a generic function which extracts fitted values from objects returned by
modeling functions fitted.values is an alias for it (stasts)

formula: provide a way of extracting formulae which have been included in other objects
(stasts)

linear.hypothesis: Test Linear Hypothesis (car)

lm: is used to fit linear models. It can be used to carry out regression, single stratum
analysis of variance and analysis of covariance (stasts)

model.matrix: creates a design matrix (stasts)

predict: Predicted values based on linear model object (stasts)

residuals: is a generic function which extracts model residuals from objects returned by
modeling functions (stasts)

vcov: Returns the variance-covariance matrix

add1: Compute all the single terms in the scope argument that can be added to or
dropped from the model, fit those models and compute a table of the changes in fit (stats)

AIC: Generic function calculating the Akaike information criterion for one or
several fitted model objects for which a log-likelihood value can be obtained, according to the
formula -2*log-likelihood + k*npar, where npar represents the number of parameters in the
fitted model, and k = 2 for the usual AIC, or k = log(n) (n the number of observations) for
the so-called BIC or SBC (Schwarz's Bayesian criterion) (stats)

Cpplot: Cp plot (faraway)

drop1: Compute all the single terms in the scope argument that can be added to or
dropped from the model, fit those models and compute a table of the changes in fit( stats)

extractAIC: Computes the (generalized) Akaike An Information Criterion for a fitted parametric
model (stats)

leaps: Subset selection by `leaps and bounds' (leaps)

maxadjr: Maximum Adjusted R-squared

offset: An offset is a term to be added to a linear predictor, such as in a generalized linear

step: Select a formula-based model by AIC (stats)

update.formula: is used to update model formulae. This typically involves adding or dropping
terms, but updates can be more general (stats)

Diagnostics

cooks.distance: Cooks distance

covratio: covariance ratio (stats)

dfbeta: DBETA (stats)

dfbetas: DBETAS (stats)

dffits: DFFTITS (stats)

hatvalues: diagonal elements of the hat matrix (stats)

influence.measures: This suite of functions can be used to compute some of the regression
(leave-one-out deletion) diagnostics for linear and generalized linear models (stats)
 lm.influence: This function provides the basic quantities which are used in forming
a wide variety of diagnostics for checking the quality of regression fits (stats)

ls.diag: Computes basic statistics, including standard errors, t- and p-values for the regression
coefficients (stats)

outlier.test: Bonferroni Outlier Test (car)

rstandard: standardized residuals

rstudent: studentized residuals (stats)

vif: Variance Inflation Factor (car)

Graphics

ceres.plots: Ceres Plots (car)

cr.plots: Component+Residual (Partial Residual) Plots (car)

influence.plot: Regression Influence Plot (car)

leverage.plots: Regression Leverage Plots (car)

panel.car: Panel Function Coplots (car)

plot.lm: Four plots (selectable by which) are currently provided: a plot of residuals against
fitted values, a Scale-Location plot of sqrt{| residuals |} against fitted values, a Normal Q-Q plot,
and a plot of Cook's distances versus row labels (stats)
prplot: Partial Residual Plot (faraway)

qq.plot: Quantile-Comparison Plots (car)

qqline: adds a line to a normal quantile-quantile plot which passes through the first and
third quartiles (stats)
qqnorm: is a generic function the default method of which produces a normal QQ plot
of the values in y (stats)

reg.line: Plot Regression Line (car)

scatterplot.matrix: Scatterplot Matrices (car)

scatterplot: Scatterplots with Boxplots (car)

spread.level.plot: Spread-Level Plots (car)

ad.test: Anderson-Darling test for normality (nortest)

bartlett.test: Performs Bartlett's test of the null that the variances in each of the groups
(samples) are the same (stats)
bgtest: Breusch-Godfrey Test (lmtest)

bptest: Breusch-Pagan Test (lmtest)

cvm.test: Cramer-von Mises test for normality (nortest)

durbin.watson: Durbin-Watson Test for Autocorrelated Errors (car)

dwtest: Durbin-Watson Test (lmtest)

levene.test: Levene's Test (car)

lillie.test: Lilliefors (Kolmogorov-Smirnov) test for normality (nortest)

ncv.test: Score Test for Non-Constant Error Variance (car)

pearson.test: Pearson chi-square test for normality (nortest)

sf.test: Shapiro-Francia test for normality (nortest)

shapiro.test: Performs the Shapiro-Wilk test of normality (stats)

Variables Transformations

box.cox: Box-Cox Family of Transformations (car)

boxcox: Box-Cox Transformations for Linear Models (MASS)

box.cox.powers: Multivariate Unconditional Box-Cox Transformations (car)

box.tidwell: Box-Tidwell Transformations (car)

box.cox.var: Constructed Variable for Box-Cox Transformation (car)

Ridge Regression

lm.ridge: ridge regression (MASS)

segmented: Segmented relationships in regression models (segmented)

slope.segmented: Summary for slopes of segmented relationships (segmented)

Generalized Least Squares (GLS)

ACF.gls: Autocorrelation Function for gls Residuals (nlme)

anova.gls: Compare Likelihoods of Fitted Objects (nlme)

gls: Fit Linear Model Using Generalized Least Squares (nlme)

intervals.gls: Confidence Intervals on gls Parameters (nlme)

lm.gls: fit Linear Models by Generalized Least Squares (MASS)

plot.gls: Plot a gls Object (nlme)

predict.gls: Predictions from a gls Object (nlme)

qqnorm.gls: Normal Plot of Residuals from a gls Object (nlme)

residuals.gls: Extract gls Residuals (nlme)

summary.gls: Summarize a gls Object (nlme)