list of some useful R functions

Charles DiMaggio

February 27, 2013

1 help
• help() opens help page (same as ?topic)
• apropos()displays all objects matching topic (same as ??topic)
• library(help=packageName) help on a specific package
• example() ; demo()
• vignette(package=”packageName”); vignette(package=”topic”)
• RSiteSearch(”packageName”)
• ?NA - handling missing data values
• args() - arguments for a function
• functionName - just writing the name of the function returns the function source code
• help with math:
– ?Control - Help on control flow statements (e.g. if, for, while)
– ?Extract - Help on operators acting to extract or replace subsets of vectors
– ?Logic - Help on logical operators
– ?regex - Help on regular expressions used in R
– ?Syntax - Help on R syntax and giving the precedence of operators

2 General
• append() - add elements to a vector
• cbind() - Combine vectors by row/column
• grep() - regular expressions

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 • identical() - test if 2 objects are exactly equal
• length() - no. of elements in vector
• ls() - list objects in current environment
• range(x) - minimum and maximum
• rep(x,n) - repeat the number x, n times
• rev(x) - elements of x in reverse order
• seq(x,y,n) - sequence (x to y, spaced by n)
• sort(x) - sort the vector x
• order(x) - list the sorted element numbers of x
• tolower(),toupper() - Convert string to lower/upper case letters
• unique(x) - remove duplicate entries from vector
• round(x), signif(x), trunc(x) - rounding functions
• getwd() - return working directory
• setwd() - set working directory
• choose.files() - get path to a file (useful for virtual machines)
• month.abb/month.name - abbreviated and full names for months
• pi,letters,(e.g. letters[7] = ”g”) LETTERS

3 Math
• sqrt(),sum()
• log(x),log10(),,exp(),sqrt()
• cos(),sin(),tan(),
• %% modulus
• %/% integer divisilln
• %*% matrix multiplication
• %o% outer product (a%o% equivalent to outer(a,b,”*”))
• union(),intersect(),setdiff(),setequal() - set operations
• eigen() - eigenvalues and eigenvectors
• deriv() - symbolic and algorithmic derivatives of simple expressions

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 • integrate() - adaptive quadrature over a finite or infinite interval.

4 Plotting
• plot() - generic R object plotting
• par() - set or query graphical parameters
• curve(equation,add=T) - plot an equation as a curve
• points(x,y) - add additional set of points to an existing graph
• arrows() - draw arrows
• abline() - ddd a straight line to an existing graph
• lines() - join specified points with line segments
• segments() - draw line segments between pairs of points
• hist() - histogram
• pairs() - plot matrix of scatter plots
• matplot() - plot columns of matrices
• persp() - perspective plot
• contour() - contour plot
• image() - plot an image file
• loess(), lowess() - scatter plot smoothing
• splinefun() - spline interpolation
• smooth.spline() - Fits a cubic smoothing spline
• jitter() - Add a small amount of noise to a numeric vector
• pdf()/ png() / jpeg() - send plot to .pdf / .png / .jpeg file

5 Statistics
• help(package=stats) - list all stats functions
• lm - fit linear model
• glm - fit generalized linear model
• cor.test() - correlation test

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 • cumsum() cumprod() - cumuluative functions for vectors
• density(x) - kernel density estimates
• ks.test() - one or two sample Kolmogorov-Smirnov tests
• mean(x), weighted.mean(x), median(x), min(x), max(x), quantile(x)
• rnorm(), runif() - generate random data with Gaussian/uniform distribution
• sd() - standard deviation
• summary(x) - a summary of x (mean, min, max)
• t.test() - Student’s t-test
• var() - variance
• sample() - random samples
• qqplot() - quantile-quantile plot

6 regression
(Functions in italics, packages in quotation marks.)
• Linear models
– aov (”stats”), Anova() (”car”): ANOVA models
– coef : extract model coefficients (”stats”)
– confint: Computes confidence intervals for one or more parameters in a fitted
model. (”stats”)
– fitted : extracts fitted values (”stats”)
– lm: fit linear models. (”stats”)
– model.matrix : creates a design matrix (”stats”)
– predict: predicted values based on linear model object (”stats”)
– residuals: extracts model residuals (”stats”)
– summary summary method for class ”lm” (stats)
– vcov : variance-covariance matrix of the main parameters of a fitted model object
(”stats”)
– AIC : Akaike information criterion for one or several fitted model objects (”stats”)
– extractAIC : Computes the (generalized) Akaike An Information Criterion for a
fitted parametric model (”stats”)

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 – offset: An offset is a term to be added to a linear predictor, such as in a generalised
linear model
• Generalized Linear Models (GLM)
– glm: is used to fit generalized linear models (”stats”)
”family=” specify the details of the models used by glm (”stats”)
– glm.nb: fit a negative binomial generalized linear model (”MASS”)
• Diagnostics
– cookd : cook’s distances for linear and generalized linear models (”car”) ”cooks.distance”:
Cooks distance (”stats”)
– influence.measures: suite of functions to compute regression (leave-one-out dele-
tion) diagnostics for linear and generalized linear models (”stats”)
– lm.influence: provides the basic quantities used in diagnostics for checking the
quality of regression fits (”stats”)
– outlier.test: Bonferroni outlier test (”car”)
– rstandard : standardized residuals (”stats”)
– rstudent: studentized residuals (”stats”)
– vif : variance inflation factor (”car”)
• Graphics
– influence.plot: regression influence plot (”car”)
– leverage.plots: regression leverage plots (”car”)
– plot: four residual plots (”stats”)
– 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: normal QQ plot of the values in y (”stats”)
– reg.line: plot regression line (”car”)
– scatterplot: scatterplots with boxplots (”car”)
• Tests and Transformations
– 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”)

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 – pearson.test: Pearson chi-square test for normality (”nortest”)
– box.cox : Box-Cox family of transformations (”car”)
– boxcox : Box-Cox transformations for linear models (”MASS”)
• Survival analysis
– anova.survreg: ANOVA tables for survreg objects (”survival”)
– clogit: Conditional logistic regression (”survival”)
– cox.zph: Test the proportional hazards assumption of a Cox regression (”sur-
vival”)
– coxph: proportional hazards regression (”survival”)
– coxph.detail : details of a Cox model fit (”survival”)
– coxph.rvar : robust variance for a Cox model (”survival”)
– ridge: ridge regression (”survival”)
– survdiff : test survival curve differences (”survival”)
– survexp: compute expected survival (”survival”)
– survfit: compute a survival curve for censored data (”survival”)
– survreg: regression for a parametric survival model (”survival”)
• Linear and nonlinear mixed effects models
– ACF : autocorrelation function (”nlme”)
– ACF.lme: autocorrelation Function for lme Residuals (”nlme”)
– intervals: confidence intervals on coefficients (”nlme”)
– intervals.lme: confidence intervals on lme parameters (”nlme”)
– lme: linear mixed-effects models (”nlme”)
– nlme: nonlinear mixed-effects models (”nlme”)
– predict.lme: predictions from an lme object (”nlme”)
– predict.nlme: predictions from an nlme object (”nlme”)
– qqnorm.lme: normal plot of residuals or random effects from an lme object
(”nlme”)
– ranef.lme: extract lme random effects (”nlme”)
– residuals.lme: extract lme residuals (”nlme”)
– simulate.lme: simulate lme models (”nlme”)
– summary.lme: summarize an lme object (”nlme”)

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• Structural Equation, Principal Components, Partial Least Squares Regression Models
– sem: general structural equation models (”sem”)
– systemfit: fits a set of linear structural equations using ordinary least squares
– biplot.mvr : biplots of PLSR and PCR Models (”pls”)
– coefplot: plot regression coefficients of plsr and pcr models (”pls”)
– mvr : partial least squares and principal components regression (”pls”)
– scores: extract scores and loadings from plsr and pcr models (”pls”)
• Recursive Partitioning and Regression Trees
– cv.tree: cross-validation for choosing tree complexity (”tree”)
– deviance.tree: extract deviance from a tree object (”tree”)
– labels.rpar t: create split labels for an rpart object (”rpart”)
– misclass.tree: misclassifications by a classification tree (”tree”)
– partition.tree: plot the partitions of a simple tree model (”tree”)
– path.rpart: follow paths to selected nodes of an rpart object (rpart)
– plotcp: plot a complexity parameter table for an rpart fit (”rpart”)
– printcp: displays cp table for fitted rpart object (”rpart”)
– prune.misclass: cost-complexity pruning of tree by error rate (”tree”)
– rpart: recursive partitioning and regression trees (”rpart”)
– rsq.rpar t: plots the approximate r-square for the different splits (”rpart”)
– tile.tree: add class barplots to a classification tree plot (”tree”)
– tree.control : select parameters for tree (tree)
– tree.screens: split screen for plotting trees (”tree”)
– tree: fit a classification or regression tree (”tree”)

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This list is based on material posted online by Alastair Sanderson and Vito Ricci.