Appendix: R Reference - R in a Nutshell

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Appendix: R Reference - R in a Nutshell
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stats

This package contains functions to perform a wide varietyof statistical analyses.

Functions

Function	Description
AIC	Generic function for calculating the Akaike informationcriterion for one or several fitted model objects for which alog-likelihood value can be obtained, according to the formula−2 ∗ log-likelihood + k ∗n_par, wheren_par representsthe number of parameters in the fitted model, and k= 2 for the usual AIC, or k =log(n) (n is thenumber of observations) for the so-called Bayesian informationcriterion (BIC) or Schwarz's Bayesian criterion (SBC).
ARMAacf	Computes the theoretical autocorrelation function orpartial autocorrelation function for an autoregressive movingaverage (ARMA) process.
ARMAtoMA	Converts an ARMA process to an infinite moving average(MA) process.
Box.test	Computes the Box-Pierce or Ljung-Box test statistic forexamining the null hypothesis of independence in a given timeseries. These are sometimes known as "portmanteau"tests.
C	Sets the `"contrasts"`attribute for the factor.
D	Computes derivatives of simple expressions, symbolically.
Gamma	Family object for Gamma distributions (used byfunctions such as `glm`).
HoltWinters	Computes Holt-Winters filtering of a given time series.Unknown parameters are determined by minimizing the squaredprediction error.
IQR	Computes the interquartile range of the `x` values.
KalmanForecast, KalmanLike, KalmanRun, KalmanSmooth	Use Kalman filtering to find the (Gaussian)log-likelihood, or for forecasting or smoothing.
NLSstAsymptotic	Fits the asymptotic regression model, in the form`b0 + b1(1-exp(-exp(lrc) x)`, to the `xy`data. This can be used as a building block in determiningstarting estimates for more complicated models.
NLSstClosestX	Uses inverse linear interpolation to approximate the`x` value at which thefunction represented by `xy`is equal to `yval`.
NLSstLfAsymptote	Provides an initial guess at the horizontal asymptoteon the left side (i.e., small values of `x`) of the graph of `y` versus `x` from the `xy` object. Primarily used within`initial` functions forself-starting nonlinear regression models.
NLSstRtAsymptote	Provides an initial guess at the horizontal asymptoteon the right side (i.e., large values of `x`) of the graph of `y` versus `x` from the `xy` object. Primarily used within`initial` functions forself-starting nonlinear regression models.
PP.test	Computes the Phillips-Perron test for the nullhypothesis that `x` has aunit root against a stationary alternative.
SSD	Function to compute the matrix of residual sums ofsquares and products, or the estimated variance matrix formultivariate linear models.
SSasymp	This `selfStart` modelevaluates the asymptotic regression function and its gradient.It has an `initial` attributethat will evaluate initial estimates of the parameters`Asym`, `R0`, and `lrc` for a given set of data.
SSasympOff	This `selfStart` modelevaluates an alternative parametrization of the asymptoticregression function and the gradient with respect to thoseparameters. It has an `initial` attribute that createsinitial estimates of the parameters `Asym`, `lrc`, and `c0`.
SSasympOrig	This `selfStart` modelevaluates the asymptotic regression function through theorigin and its gradient. It has an `initial` attribute that will evaluateinitial estimates of the parameters `Asym` and `lrc` for a given set of data.
SSbiexp	This `selfStart` modelevaluates the biexponential model function and its gradient.It has an `initial` attributethat creates initial estimates of the parameters `A1`, `lrc1`, `A2`, and `lrc2`.
SSfol	This `selfStart` modelevaluates the first-order compartment function and itsgradient. It has an `initial`attribute that creates initial estimates of the parameters`lKe`, `lKa`, and `lCl`.
SSfpl	This `selfStart` modelevaluates the four-parameter logistic function and itsgradient. It has an `initial`attribute that will evaluate initial estimates of theparameters `A`, `B`, `xmid`, and `scal` for a given set ofdata.
SSgompertz	This `selfStart` modelevaluates the Gompertz growth model and its gradient. It hasan `initial` attribute thatcreates initial estimates of the parameters `Asym`, `b2`, and `b3`.
SSlogis	This `selfStart` modelevaluates the logistic function and its gradient. It has an`initial` attribute thatcreates initial estimates of the parameters `Asym`, `xmid`, and `scal`.
SSmicmen	This `selfStart` modelevaluates the Michaelis-Menten model and its gradient. It hasan `initial` attribute that willevaluate initial estimates of the parameters `Vm` and `K`.
SSweibull	This `selfStart` modelevaluates the Weibull model for growth curve data and itsgradient. It has an `initial`attribute that will evaluate initial estimates of theparameters `Asym`, `Drop`, `lrc`, and `pwr` for a given set of data.
StructTS	Fits a structural model for a time series by maximumlikelihood.
TukeyHSD	Creates a set of confidence intervals on thedifferences between the means of the levels of a factor withthe specified family-wise probability of coverage. Theintervals are based on the Studentized range statistic, Tukey's honest significant difference method. There is a`plot` method.
TukeyHSD.aov	Creates a set of confidence intervals on thedifferences between the means of the levels of a factor withthe specified family-wise probability of coverage. Theintervals are based on the Studentized range statistic, Tukey's honest significant difference method. There is a`plot` method.
acf	The function `acf`computes (and by default plots) estimates of theautocovariance or autocorrelation function. The function`pacf` is the function usedfor partial autocorrelations. The function `ccf` computes the cross-correlationor cross-covariance oftwo univariate series.
acf2AR	Computes an AR process exactly fitting anautocorrelation function.
add.scope	`add.scope` and`drop.scope` compute thoseterms that can be individually added to or dropped from amodel while respecting the hierarchy of terms.
add1	Computes all the single terms in the `scope` argument that can be added toor dropped from the model, fits those models, and computes atable of the changes in fit.
addmargins	For a given table, one can specify which of theclassifying factors to expand by one or more levels to holdmargins to be calculated. One may, for example, form sums andmeans over the first dimension and medians over the second.The resulting table will then have two extra levels for thefirst dimension and one extra level for the second. Thedefault is to sum over all margins in the table. Otherpossibilities may give results that depend on the order inwhich the margins are computed. This is flagged in the printedoutput from the function.
aggregate	Splits the data into subsets, computes summarystatistics for each, and returns the result in a convenientform.
alias	Finds aliases (linearly dependent terms) in a linearmodel specified by a formula.
anova	Computes analysis of variance (or deviance) tables forone or more fitted model objects.
anova.lmlist	Computes an analysis of variance table for one or morelinear model fits.
ansari.test	Performs the Ansari-Bradley two-sample test for adifference in scale parameters.
aov	Fits an analysis of variance model by a call to`lm` for eachstratum.
approx	Returns a list of points that linearly interpolategiven data points, or a function performing the linear (orconstant) interpolation.
approxfun	Returns a list of points that linearly interpolategiven data points, or a function performing the linear (orconstant) interpolation.
ar	Fits an autoregressive time series model to the data, by default selecting the complexity by AIC.
arima	Fits an ARIMA model to a univariate timeseries.
arima.sim	Simulates from an ARIMA model.
arima0	Fits an ARIMA model to a univariate time series andforecasts from the fitted model.
as.dendrogram	Coerces an object to class `"dendrogram"` (which provides generalfunctions for handling treelike structures).
as.dist	Coerces to a dist object (a matrix returned by the distfunction).
as.formula	The generic function `formula` and its specific methodsprovide a way of extracting formulas that have been includedin other objects. `as.formula` is almost identical, additionally preserving attributes when `object` already inherits from`"formula"`.
as.hclust	Converts objects from other hierarchical clusteringfunctions to class `"hclust"`.
as.stepfun	Given the vectors (x[1], ..., x[n]) and (y[0], y[1], ..., y[n]) (one value more!), `stepfun(x, y, ...)` returns an interpolating "step" function, say`fn`. That is, fn(t) = c_i{[i]}(constant) for t in (x[i], x[i+1]) and at the abscissa values, if (by default) `right =FALSE`, fn(x_i) = y_i{fn(x[i]) =y[i]} and for `right = TRUE`, fn(x[i]) = y[i-1], for i=1, ..., n.
as.ts	Coerces an object to a `ts` object.
asOneSidedFormula	Names, expressions, numeric values, and characterstrings are converted to one-sided formulas. If `object` is a formula, it must be onesided, in which case it is returned unaltered.
ave	Subsets of `x[]` areaveraged, where each subset consists of those observationswith the same factor levels.
bandwidth.kernel	Returns the equivalent bandwidth for a `tskernel` object.
bartlett.test	Performs Bartlett's test of the null that the variancesin each of the groups (samples) are the same.
binom.test	Performs an exact test of a simple null hypothesisabout the probability of success in a Bernoulliexperiment.
binomial	Family function for binomial distributions (used byfunctions such as `glm`).
biplot	Plots a biplot on the current graphics device.
bw.SJ, bw.bcv, bw.nrd, bw.nrd0, bw.ucv	Bandwidth selectors for Gaussian kernels in `density`.
cancor	Computes the canonical correlations between two datamatrices.
case.names	Simple utility returning (nonmissing) case names and(noneliminated) variable names.
ccf	The function `acf`computes (and by default plots) estimates of theautocovariance or autocorrelation function. The function`pacf` is the function usedfor partial autocorrelations. The function `ccf` computes the cross-correlationor cross-covariance oftwo univariate series.
chisq.test	Performs chi-squared contingency table tests andgoodness-of-fit tests.
clearNames	Sets the `names`attribute of `object` to`NULL` and returns theobject.
cmdscale	Classical multidimensional scaling of a data matrix.Also known as principal coordinatesanalysis.
coef, coefficients	`coef` is a genericfunction that extracts model coefficients from objectsreturned by modeling functions. `coefficients` is an alias forit.
complete.cases	Returns a logical vector indicating which cases arecomplete, i.e., have no missing values.
confint	Computes confidence intervals for one or moreparameters in a fitted model.
constrOptim	Minimizes a function subject to linear inequalityconstraints using an adaptive barrier algorithm.
contr.SAS, contr.helmert, contr.poly, contr.sum, contr.treatment	Return a matrix of contrasts.
contrasts, contrasts<-	Set and view the contrasts associated with afactor.
convolve	Uses the fast Fourier transform to compute the severalkinds of convolutions of two sequences.
cooks.distance	Computes "Cook's distance" on a model object.
cophenetic	Computes the cophenetic distances for a hierarchicalclustering.
cor	Computes the correlation of two vectors, or the columnsof two matrices.
cor.test	Tests for association between paired samples, using oneof Pearson's product-moment correlation coefficient, Kendall'stau, or Spearman's rho.
cov	Computes the covariance of two vectors, or the columnsof two matrices.
cov.wt	Returns a list containing estimates of the weightedcovariance matrix and the mean of the data and optionally ofthe (weighted) correlation matrix.
cov2cor	`var`, `cov`, and `cor` compute the variance of `x` and the covariance or correlationof `x` and `y` if these are vectors. If `x` and `y` are matrices, then the covariances(or correlations) between the columns of `x` and the columns of `y` are computed. `cov2cor` scales a covariance matrixinto the corresponding correlation matrixefficiently.
covratio	Returns the covariance ratio (for regressiondiagnostics) on a model object.
cpgram	Plots a cumulative periodogram.
cutree	Cuts a tree, e.g., resulting from `hclust`, into several groups byspecifying either the desired number(s) of groups or the cutheight(s).
cycle	`time` creates thevector of times at which a time series was sampled. `cycle` gives the positions in thecycle of each observation. `frequency` returns the number ofsamples per unit time, and `deltat` gives the timeinterval between observations (see `ts`).
dbeta	Density function for the Beta distribution.
dbinom	Density function for the binomial distribution.
dcauchy	Density function for the Cauchy distribution.
dchisq	Density function for the chi-squareddistribution.
decompose	Decomposes a time series into seasonal, trend, andirregular components using moving averages. Deals withadditive or multiplicative seasonal components.
delete.response	Returns a `terms`object for the same model but with no responsevariable.
deltat	`time` creates thevector of times at which a time series was sampled. `cycle` gives the positions in thecycle of each observation. `frequency` returns the number ofsamples per unit time, and `deltat` gives the timeinterval between observations (see `ts`).
dendrapply	Applies function `FUN`to each node of a `dendrogram` recursively. When`y <- dendrapply(x, fn)`, then `y` is a dendrogram ofthe same graph structure as `x` and for each node, `y.node[j] <- FUN(x.node[j], ...)`(where `y.node[j]` is an(invalid!) notation for the jth node of y).
density	The (S3) generic function `density` computes kernel densityestimates. Its default method does so with the given kerneland bandwidth for univariate observations.
density.default	The (S3) generic function `density` computes kernel densityestimates. Its default method does so with the given kerneland bandwidth for univariate observations.
deriv, deriv3	Compute derivatives of simple expressions, symbolically.
deviance	Returns the deviance of a fitted model object.
dexp	Density function for the exponentialdistribution.
df	Density, distribution function, quantile function, andrandom generation for the F-distributionwith `df1` and `df2` degrees of freedom (and optionalnoncentrality parameter `ncp`).
df.kernel	The `"tskernel"` classis designed to represent discrete symmetric normalizedsmoothing kernels. These kernels can be used to smoothvectors, matrices, or time series objects. There are `print`, `plot`, and `[` methods for these kernelobjects.
df.residual	Returns the residual degrees of freedom extracted froma fitted model object.
dfbeta	Returns dfbeta for a model object (for regressiondiagnostics).
dfbetas	Returns dfbetas for a model object (for regressiondiagnostics).
dffits	Returns dffits for a model object (for regressiondiagnostics).
dgamma	Density function for the Gamma distribution.
dgeom	Density, distribution function, quantile function, andrandom generation for the geometric distribution withparameter `prob`.
dhyper	Density function for the hypergeometricdistribution.
diff.ts	Methods for objects of class `"ts"`, typically the result of`ts`.
diffinv	Computes the inverse function of the lagged differencesfunction `diff`.
dist	Computes and returns the distance matrix computed byusing the specified distance measure to compute the distancesbetween the rows of a data matrix.
dlnorm	Density function for the log-normaldistribution.
dlogis	Density function for the logistic distribution.
dmultinom	Generates multinomially distributed random numbervectors and computes multinomialprobabilities.
dnbinom	Density function for the negative binomialdistribution.
dnorm	Density function for the normal distribution.
dpois	Density function for the Poisson distribution.
drop.scope	`add.scope` and`drop.scope` compute thoseterms that can be individually added to or dropped from amodel while respecting the hierarchy of terms.
drop.terms	`delete.response`returns a `terms` object forthe same model, but with no response variable. `drop.terms` removes variables fromthe righthand side of the model. There is also a `"[.terms"` method to perform the samefunction (with `keep.response=TRUE`). `reformulate` creates aformula from a character vector.
drop1	Computes all the single terms in the `scope` argument that can be added toor dropped from the model, fits those models, and computes atable of the changes in fit.
dsignrank	Density, distribution function, quantile function, andrandom generation for the distribution of the Wilcoxon signedrank statistic obtained from a sample with size `n`.
dt	Density, distribution function, quantile function, andrandom generation for the t-distributionwith `df` degrees of freedom(and optional noncentrality parameter `ncp`).
dummy.coef	Extracts coefficients in terms of the original levelsof the coefficients rather than the coded variables.
dunif	Density function for the uniform distribution.
dweibull	Density function for the Weibull distribution.
dwilcox	Density function for the distribution of the Wilcoxonrank sum statistic.
ecdf	Computes or plots an empirical cumulative distributionfunction.
eff.aovlist	Computes the efficiencies of fixed-effects terms in ananalysis of variance model with multiple strata.
effects	Returns (orthogonal) effects from a fitted model, usually a linear model. This is a generic function, butcurrently only has a method for objects inheriting fromclasses `"lm"` and `"glm"`.
embed	Embeds the time series `x` into a low-dimensional Euclideanspace.
end	Extracts and encodes the times the first and lastobservations were taken. Provided only for compatibility withS version 2.
estVar	Function to compute matrix of residual sums of squaresand products, or the estimated variance matrix formultivariate linear models.
expand.model.frame	Evaluates new variables as if they had been part of theformula of the specified model. This ensures that the same`na.action` and `subset` arguments are applied andallows, for example, `x` tobe recovered for a model using `sin(x)` as a predictor.
extractAIC	Computes the (generalized) Akaike information criterionfor a fitted parametric model.
factanal	Performs maximum likelihood factor analysis on acovariance matrix or data matrix.
family	Family objects provide a convenient way to specify thedetails of the models used by functions such as `glm`. See the documentation for`glm` for the details on howsuch model fitting takes place.
fft	Performs the fast Fourier transform of anarray.
filter	Applies linear filtering to a univariate time series orto each series separately of a multivariate timeseries.
fisher.test	Performs Fisher's exact test for testing the null ofindependence of rows and columns in a contingency table withfixed marginals.
fitted, fitted.values	`fitted` is a genericfunction that extracts fitted values from objects returned bymodeling functions. `fitted.values` is an alias forit.
fivenum	Returns Tukey's five-number summary (minimum, lower-hinge, median, upper-hinge, maximum) for the inputdata.
fligner.test	Performs a Fligner-Killeen (median) test of the nullthat the variances in each of the groups (samples) are thesame.
formula	The generic function `formula` and its specific methodsprovide a way of extracting formulas that have been includedin other objects.
frequency	Returns the number of samples per unit time from a`ts` object.
friedman.test	Performs a Friedman rank sum test with unreplicatedblocked data.
ftable	Creates "flat" contingency tables.
gaussian	Family object for Gaussian functions (used by functionssuch as `glm`).
getInitial	Evaluates initial parameter estimates for a nonlinearregression model.
get_all_vars	Returns a data.frame containing the variables used informula plus those specified. Unlike `model.frame.default`, it returns theinput variables and not those resulting from function calls informula.
glm	Used to fit generalized linear models, specified bygiving a symbolic description of the linear predictor and adescription of the error distribution.
glm.control	Auxiliary function as user interface for `glm` fitting. Typically only usedwhen calling `glm` or`glm.fit`.
glm.fit	`glm` is used to fitgeneralized linear models, specified by giving a symbolicdescription of the linear predictor and a description of theerror distribution.
hasTsp	`tsp` returns the`tsp` attribute (or `NULL`). It is included forcompatibility with S version 2. `tsp<-` sets the `tsp` attribute. `hasTsp` ensures `x` has a `tsp` attribute, by adding one ifneeded.
hat, hatvalues, hatvalues.lm	Return the hat matrix for a model object (forregression diagnostics).
hclust	Hierarchical cluster analysis on a set ofdissimilarities and methods for analyzing it.
heatmap	Plots a heat map object (an image with an accompanyingdendrogram).
influence	Provides the basic quantities that are used in forminga wide variety of diagnostics for checking the quality ofregression fits.
influence.measures	Produces a class "infl" object tabular display showingthe DFBETAS for each model variable, DFFITS, covarianceratios, Cook's distances, and the diagonal elements of the hatmatrix.
integrate	Adaptive quadrature of functions of one variable over afinite or infinite interval.
interaction.plot	Plots the mean (or other summary) of the response fortwo-way combinations of factors, thereby illustrating possibleinteractions.
inverse.gaussian	Family object for inverse Gaussian distributions (usedby functions such as `glm`).
is.empty.model	R model notation allows models with no intercept and nopredictors. These require special handling internally.`is.empty.model()` checkswhether an object describes an empty model.
is.leaf	Class `"dendrogram"`provides general functions for handling treelike structures.It is intended as a replacement for similar functions inhierarchical clustering and classification/regression trees, such that all of these can use the same engine for plotting orcutting trees. The code is still in the testing stage, and theAPI may change in the future.
is.mts	Tells whether an object is of class `mts`.
is.stepfun	Tells whether an object is a function of class `stepfun`.
is.ts	Tells whether an object is of class `ts`.
is.tskernel	Tells whether an object is of class `tskernel`.
isoreg	Computes the isotonic (monotonically increasingnonparametric) least squares regression that is piecewiseconstant.
kernapply	Computes the convolution between an input sequence anda specific kernel.
kernel	Constructs a general kernel or named specific kernels(returns a "tskernel" object).
kmeans	Performs k-means clustering on adata matrix.
knots	Extracts the knots from a step function (returned by`stepfun`).
kruskal.test	Performs a Kruskal-Wallis rank sum test.
ks.test	Performs one- or two-sample Kolmogorov-Smirnovtests.
ksmooth	The Nadaraya-Watson kernel regression estimate.
lag	Computes a lagged version of a time series, shiftingthe time base back by a given number of observations.
lag.plot	Plots time series against lagged versions ofthemselves. Helps visualizing "autodependence" even whenautocorrelations vanish.
line	Fits a line robustly.
lines.ts	Plotting method for objects inheriting from class`"ts"`.
lm	`lm` is used to fitlinear models. It can be used to carry out regression, single-stratum analysis of variance, and analysis ofcovariance (although `aov`may provide a more convenient interface for these).
lm.fit	Basic computing engines called by `lm` and used to fit linear models.These should usually not be used directlyunless by experienced users.
lm.influence	Provides the basic quantities that are used in forminga wide variety of diagnostics for checking the quality ofregression fits.
lm.wfit	Basic computing engines called by `lm` and used to fit linear models.These should usually not be used directlyunless by experienced users.
loadings	Extracts or prints loadings in factor analysis (orprincipal components analysis).
loess	Fits a polynomial surface determined by one or morenumerical predictors, using local fitting.
loess.control	Sets control parameters for `loess` fits.
loess.smooth	Plots and adds a smooth curve computed by `loess` to a scatter plot.
logLik	Extracts the log-likelihood value from an object(usually a model).
loglin	Used to fit log-linear models to multidimensionalcontingency tables by iterative proportional fitting.
lowess	Performs the computations for locally weighted scatterplot smoothing (LOWESS), smoother which uses locally weightedpolynomial regression.
ls.diag	Computes basic statistics, including standard errors, t-, and p-values, for the regression coefficients.
ls.print	Computes basic statistics, including standard errors, t-, and p-values, for the regression coefficients and prints them if `print.it` is `TRUE`.
lsfit	Finds the least squares estimate of β in the modelY = Xβ + ε.
mad	Computes the median absolute deviation, i.e., the(lo-/hi-) median of the absolute deviations from the medianand (by default) adjusts by a factor for asymptotically normalconsistency.
mahalanobis	Returns the squared Mahalanobis distance of all rows in`x` and the vectorμ = `center` with respect to Σ= `cov`. This is(for vector `x`) defined asD² = (x - μ)'Σ^-1 (x - μ).
make.link	This function is used with the `family` functions in `glm()`. Given the name of a link, itreturns a link function, an inverse link function, thederivative dμ / dη and a function fordomain checking.
makeARIMA	Uses Kalman filtering to find the (Gaussian)log-likelihood, or for forecasting or smoothing.
makepredictcall	Utility to help `model.frame.default` create the rightmatrices when predicting from models with terms like `poly` or `ns`.
manova	A class for the multivariate analysis ofvariance.
mantelhaen.test	Performs a Cochran-Mantel-Haenszel chi-squared test ofthe null that two nominal variables are conditionallyindependent in each stratum, assuming that there is nothree-way interaction.
mauchly.test	Tests whether a Wishart-distributed covariance matrix(or transformation thereof) is proportional to a givenmatrix.
mcnemar.test	Performs McNemar's chi-squared test for symmetry ofrows and columns in a two-dimensional contingencytable.
median	Computes the sample median.
median.default	Computes the sample median.
medpolish	Fits an additive model using Tukey's median polishprocedure.
model.extract	Returns the response, offset, subset, weights, or otherspecial components of a model frame passed as optionalarguments to `model.frame`.
model.frame	`model.frame` (ageneric function) and its methods return a `data.frame` with the variables neededto use `formula` and any`...` arguments.
model.matrix	Creates a design matrix.
model.offset	Returns the offset of a model frame.
model.response	Returns the response of a model frame.
model.tables	Computes summary tables for model fits, especiallycomplex `aov` fits.
model.weights	Returns the weights of a model frame.
monthplot	Plots seasonal (or other) subseries from a timeseries.
mood.test	Performs Mood's two-sample test for a difference inscale parameters.
mvfft	Performs the fast Fourier transform of anarray.
na.action	Extracts information on the NA action used to create anobject.
na.contiguous	Finds the longest consecutive stretch of nonmissingvalues in a time series object. (In the event of a tie, thefirst such stretch.)
na.exclude	`na.exclude` returnsthe object with incomplete cases removed and with the `na.action` attribute set to"exclude". (Usually used as an `na.action` argument for a modelingfunction.)
na.fail	Returns the object if it does not contain any missingvalues and signals an error otherwise. (Usually used as an`na.action` argument for amodeling function.)
na.omit	Returns the object with incomplete cases removed.(Usually used as an `na.action` argument for a modelingfunction.)
na.pass	Returns an object unchanged. (Usually used as an`na.action` argument for amodeling function.)
napredict	Uses missing value information to adjust residuals andpredictions.
naprint	Uses missing value information to report the effects ofan `na.action`.
naresid	Uses missing value information to adjust residuals andpredictions.
nextn	Returns the smallest integer, greater than or equal to`n`, that can be obtained asa product of powers of the values contained in `factors`.
nlm	Carries out a minimization of the function `f` using a Newton-typealgorithm.
nlminb	Unconstrained and constrained optimization using PORTroutines.
nls	Determines the nonlinear (weighted) least squaresestimates of the parameters of a nonlinear model.
nls.control	Allows the user to set some characteristics of thenonlinear least squares algorithm.
numericDeriv	Numerically evaluates the gradient of anexpression.
offset	An offset is a term to be added to a linear predictor, such as in a generalized linear model, with known coefficient1 rather than an estimated coefficient.
oneway.test	Tests whether two or more samples from normaldistributions have the same means. The variances are notnecessarily assumed to be equal.
optim	General-purpose optimization based on Nelder-Mead, quasi-Newton, and conjugate-gradient algorithms.It includes an option for box-constrained optimization andsimulated annealing.
optimise, optimize	The function `optimize` searches the interval from`lower` to `upper` for a minimum or maximum ofthe function `f` with respectto its first argument. `optimise` is an alias for `optimize`.
order.dendrogram	Returns the order (index) or the `"label"` attribute for the leaves ina dendrogram. These indices can then be used to access theappropriate components of any additional data.
p.adjust	Given a set of p-values, returnsp-values adjusted using one of severalmethods.
pacf	Computes partial autocorrelations.
pairwise.prop.test	Calculates pairwise comparisons between pairs ofproportions with correction for multiple testing.
pairwise.t.test	Calculates pairwise comparisons between group levelswith corrections for multiple testing.
pairwise.table	Creates a table of p-values forpairwise comparisons with corrections for multipletesting.
pairwise.wilcox.test	Calculates pairwise comparisons between group levelswith corrections for multiple testing.
pbeta	Distribution function for the Betadistribution.
pbinom	Distribution function for the binomialdistribution.
pbirthday	Computes the probability of a coincidence for ageneralized birthday paradox problem.
pcauchy	Distribution function for the Cauchydistribution.
pchisq	Distribution function for the chi-squareddistribution.
pexp	Distribution function for the exponentialdistribution.
pf	Distribution function for theF-distribution.
pgamma	Distribution function for the Gammadistribution.
pgeom	Distribution function for the geometricdistribution.
phyper	Distribution function for the hypergeometricdistribution.
plclust	Hierarchical cluster analysis on a set ofdissimilarities and methods for analyzing it.
plnorm	Distribution function for the log-normaldistribution.
plogis	Distribution function for the logisticdistribution.
plot.TukeyHSD	Creates a set of confidence intervals on thedifferences between the means of the levels of a factor withthe specified family-wise probability of coverage. Theintervals are based on the Studentized range statistic, Tukey's honest significant difference method. There is a`plot` method.
plot.density	The `plot` method fordensity objects.
plot.ecdf	Computes or plots an empirical cumulative distributionfunction.
plot.lm	Plots diagnostics for an lm object.
plot.mlm	Plots diagnostics for an mlm object.
plot.spec, plot.spec.coherency, plot.spec.phase	Plotting methods for objects of class `"spec"`. For multivariate timeseries, they plot the marginal spectra of the series or pairsplots of the coherency and phase of the cross-spectra.
plot.stepfun	Method of the generic `plot` for `stepfun` objects and utility forplotting piecewise-constant functions.
plot.ts	Plotting method for objects inheriting from class`"ts"`.
pnbinom	Distribution function for the negative binomialdistribution.
pnorm	Distribution function for the normaldistribution.
poisson	Family objects for Poisson distributions (used byfunctions such as `glm`).
poisson.test	Performs an exact test of a simple null hypothesisabout the rate parameter in a Poisson distribution or for theratio between two rate parameters.
poly, polym	Return or evaluate orthogonal polynomials of degree 1to `degree` over thespecified set of points `x`.These are all orthogonal to the constant polynomial of degree0. Alternatively, evaluate raw polynomials.
power	Creates a link object based on the link functionη =μ^λ.
power.anova.test	Computes power of test or determines parameters toobtain target power.
power.prop.test	Computes power of test or determines parameters toobtain target power.
power.t.test	Computes power of test or determines parameters toobtain target power.
ppoints	Generates the sequence of probability points `(1:m - a)/(m + (1-a)-a)`, where`m` is either `n`, if `length(n)==1`, or `length(n)`.
ppois	Distribution function for the Poissondistribution.
ppr	Fits a projection pursuit regression model.
prcomp	Performs a principal components analysis on the givendata matrix and returns the results as an object of class`prcomp`.
predict	Generic function for predictions from the results ofvarious model-fitting functions.
preplot	Computes an object to be used for plots relating to thegiven model object.
princomp	Performs a principal components analysis on the givennumeric data matrix and returns the results as an object ofclass `princomp`.
printCoefmat	Utility function to be used in higher-level `print` methods, such as `print.summary.lm`, `print.summary.glm`, and `print.anova`. The goal is to providea flexible interface with smart defaults such that often only`x` needs to bespecified.
profile	Investigates the behavior of an objective function nearthe solution.
proj	Returns a matrix or list of matrices giving theprojections of the data onto the terms of a linear model. Itis most frequently used for `aov` models.
promax	These functions "rotate" loading matrices in factoranalysis.
prop.test	Used for testing the null that the proportions(probabilities of success) in several groups are the same orthat they equal certain given values.
prop.trend.test	Performs a chi-squared test for trend in proportions, i.e., a test asymptotically optimal for local alternativeswhere the log odds vary in proportion with `score`. By default, `score` is chosen as the groupnumbers.
psignrank	Distribution function for the distribution of theWilcoxon signed rank statistic.
pt	Distribution function for thet-distribution.
ptukey	Distribution function for the Studentizedrange.
punif	These functions provide information about the uniformdistribution on the interval from `min` to `max`. `dunif` gives the density, `punif` gives the distributionfunction, `qunif` gives thequantile function, and `runif` generates randomdeviates.
pweibull	Distribution function for the Weibulldistribution.
pwilcox	Distribution function for the distribution of theWilcoxon rank sum statistic.
qbeta	Quantile function for the Beta distribution.
qbinom	Quantile function for the binomialdistribution.
qbirthday	Computes the number of observations needed to have aspecified probability of coincidence for a generalizedbirthday paradox problem.
qcauchy	Quantile function for the Cauchy distribution.
qchisq	Quantile function for the chi-squareddistribution.
qexp	Quantile function for the exponentialdistribution.
qf	Quantile function for theF-distribution.
qgamma	Quantile function for the Gamma distribution.
qgeom	Quantile function for the geometricdistribution.
qhyper	Quantile function for the hypergeometricdistribution.
qlnorm	Quantile function for the log-normaldistribution.
qlogis	Quantile function for the logisticdistribution.
qnbinom	Quantile function for the negative binomialdistribution.
qnorm	Quantile function for the normal distribution.
qpois	Quantile function for the Poisson distribution.
qqline	Adds a line to a normal Q-Q plot (usually generated byqqnorm or qqplot) that passes through the first and thirdquartiles.
qqnorm	Generic function the default method of which produces anormal Q-Q plot of the values in `y`.
qqplot	Produces a Q-Q plot of two data sets.
qsignrank	Density, distribution function, quantile function, andrandom generation for the distribution of the Wilcoxon signedrank statistic obtained from a sample with size `n`.
qt	Quantile function for thet-distribution.
qtukey	Function of the distribution of the Studentized range, R/s, where R is therange of a standard normal sample anddf∗s² isindependently distributed as chi-squared withdf degrees of freedom; see `pchisq`.
quade.test	Performs a Quade test with unreplicated blockeddata.
quantile	The generic function `quantile` produces sample quantilescorresponding to the given probabilities. The smallestobservation corresponds to a probability of 0 and the largestto a probability of 1.
quantile.default	The generic function `quantile` produces sample quantilescorresponding to the given probabilities. The smallestobservation corresponds to a probability of 0 and the largestto a probability of 1.
quasi	Family object for the quasi distribution (used byfunctions such as `glm`).
quasibinomial	Family object for the quasibinomial distribution (usedby functions such as `glm`).
quasipoisson	Family object for the quasi-Poisson distribution (usedby functions such as `glm`).
qunif	Quantile function for the uniform distribution.
qweibull	Quantile function for the Weibull distribution.
qwilcox	Quantile function for the Wilcoxon rank sumstatistic.
r2dtable	Generates random two-way tables with given marginalsusing Patefield's algorithm.
rbeta	Random number generation for the Betadistribution.
rbinom	Random number generation for the binomialdistribution.
rcauchy	Random number generation for the Cauchydistribution.
rchisq	Random number generation for the chi-squareddistribution.
read.ftable	Reads, writes, and coerces "flat" contingencytables.
rect.hclust	Draws rectangles around the branches of a dendrogram, highlighting the corresponding clusters. First, the dendrogramis cut at a certain level, and then a rectangle is drawnaround selected branches.
reformulate	Creates a formula from a character vector.
relevel	The levels of a factor are reordered so that the levelspecified by `ref` is first, and the others are moved down. This is useful for `contr.treatment` contrasts, whichtake the first level as the reference.
reorder	`reorder` is a genericfunction. Its `"factor"`method reorders the levels of a factor depending on values ofa second variable, usually numeric. The `"character"` method is a convenientalias.
replications	Returns a vector or a list of the number of replicatesfor each term in the formula.
reshape	Reshapes a data frame between "wide" format withrepeated measurements in separate columns of the same recordand "long" format with the repeated measurements in separaterecords.
resid	Generic function that extracts model residuals fromobjects returned by modeling functions. The abbreviated form`resid` is an alias for`residuals`.
residuals	Generic function that extracts model residuals fromobjects returned by modeling functions.
rexp	Random generation for the exponentialdistribution.
rf	Random generation for theF-distribution.
rgamma	Random generation for the Gamma distribution.
rgeom	Random generation for the geometricdistribution.
rhyper	Random generation for the hypergeometricdistribution.
rlnorm	Random generation for the log-normaldistribution.
rlogis	Random generation for the logisticdistribution.
rmultinom	Generates multinomially distributed random numbervectors and computes multinomialprobabilities.
rnbinom	Random generation for the negative binomialdistribution.
rnorm	Random generation for the normal distribution.
rpois	Random generation for the Poisson distribution.
rsignrank	Random generation for the distribution of the Wilcoxonsigned rank statistic.
rstandard	Returns the standardized residuals from a modelobject.
rstudent	Returns the Studentized residuals from a modelobject.
rt	Random generation for thet-distribution.
runif	Generates random numbers from the uniformdistribution.
runmed	Computes running medians of odd span. This is the "mostrobust" scatter plot smoothing possible. For efficiency (andhistorical reasons), you can use one of two differentalgorithms giving identical results.
rweibull	Random generation for the Weibull distribution.
rwilcox	Random generation for the distribution of the Wilcoxonrank sum statistic.
scatter.smooth	Plots and adds a smooth curve computed by `loess` to a scatter plot.
screeplot	Plots the variances against the number of the principalcomponent. This is also the `plot` method for classes `"princomp"` and `"prcomp"`.
sd	Computes the standard deviation of the values in`x`.
se.contrast	Returns the standard errors for one or more contrastsin an `aov` object.
selfStart	Constructs self-starting nonlinear models.
setNames	This is a convenience function that sets the names onan object and returns the object. It is most useful at the endof a function definition where one is creating the object to be returned andwould prefer not to store it under a name just so the namescan be assigned.
shapiro.test	Performs the Shapiro-Wilk test of normality.
simulate	Simulates one or more responses from the distributioncorresponding to a fitted model object.
smooth	Tukey's smoothers, 3RS3R, 3RSS, 3R, etc.
smooth.spline	Fits a cubic smoothing spline to the supplieddata.
smoothEnds	Smooths end points of a vector `y` using subsequently smaller mediansand Tukey's end point rule at the very end.
sortedXyData	This is a constructor function for the class of`sortedXyData` objects. Theseobjects are mostly usedin the `initial` function fora self-starting nonlinear regression model, which will be ofthe `selfStart` class.
spec.ar	Fits an AR model to `x` (or uses the existing fit) andcomputes (and by default plots) the spectral density of thefitted model.
spec.pgram	Calculates the periodogram using a fast Fouriertransform and optionally smooths the result with a series ofmodified Daniell smoothers (moving averages giving half weightto the end values).
spec.taper	Applies a cosine-bell taper to a time series.
spectrum	Estimates the spectral density of a timeseries.
spline	Performs cubic spline interpolation of given datapoints, returning either a list of points obtained by theinterpolation or a function performingthe interpolation. Returns a list containing components`x` and `y`, which give the ordinates whereinterpolation took place and the interpolated values.
splinefun	Performs cubic spline interpolation of given datapoints, returning either a list of points obtained by theinterpolation or a function performingthe interpolation. Returns a function with formal arguments`x` and `deriv`, the latter defaulting to0.
splinefunH	Performs Hermite spline interpolation of given datapoints, returning either a list of points obtained by theinterpolation or a function performingthe interpolation.
start	Extracts and encodes the times the first and lastobservations were taken. Provided only for compatibility withS version 2.
stat.anova	Utility function, used in `lm` and `glm` methods for `anova(..., test != NULL)` and shouldnot be used by the average user.
step	Selects a formula-based model by AIC.
stepfun	Returns an interpolating step function from two sets ofvectors.
stl	Decomposes a time series into seasonal, trend, andirregular components using `loess`.
supsmu	Smooths the (x, y) values by Friedman'ssupersmoother.
symnum	Symbolically encodes a given numeric or logical vectoror array. Particularly useful for visualization of structuredmatrices, e.g., correlation, sparse, or logical ones.
t.test	Performs one- and two-samplet-tests on vectors of data.
termplot	Plots regression terms against their predictors, optionally with standard errors and partial residualsadded.
terms	Generic function that can be used to extractterms objects from various kinds of Rdata objects.
time	Creates the vector of times at which a time series wassampled.
toeplitz	Forms a symmetric Toeplitz matrix given its firstrow.
ts	Used to create time series objects.
ts.intersect	Binds time series that have a common frequency.`ts.intersect` is restrictedto the time covered by all the series.
ts.plot	Plots several time series on a common plot. Unlike`plot.ts`, the series canhave different time bases, but they should have the samefrequency.
ts.union	Binds time series that have a common frequency.`ts.union` pads with `NA`s to the total timecoverage.
tsSmooth	Performs fixed-interval smoothing on a univariate timeseries via a state-space model.
tsdiag	Generic function to plot time seriesdiagnostics.
tsp, tsp<-	`tsp` returns the`tsp` attribute (or `NULL`). It is included forcompatibility with S version 2. `tsp<-` sets the `tsp` attribute.
uniroot	Searches the interval from `lower` to `upper` for a root (i.e., 0) of thefunction `f` with respect toits first argument.
update	Updates and (by default) refits a model. It does thisby extracting the call stored in the object, updating the calland (by default) evaluating that call.
var	Computes the variance of a vector.
var.test	Performs an F-test to compare thevariances of two samples from normal populations.
variable.names	Simple utility returning (nonmissing) case names and(noneliminated) variable names.
varimax	These functions "rotate" loading matrices in factoranalysis.
vcov	Returns the variance-covariance matrix of the mainparameters of a fitted model object.
weighted.mean	Computes a weighted mean of a numeric vector.
weighted.residuals	Computes weighted residuals from a linear modelfit.
weights	All these functions are `methods` for class `"lm"` objects.
wilcox.test	Performs one- and two-sample Wilcoxon tests on vectorsof data; the latter is also known as the Mann-Whitneytest.
window, window<-	`window` is a genericfunction that extracts the subset of the object `x` observed between the times`start` and `end`. If a frequency is specified, the series is then resampled at the new frequency.
write.ftable	Reads, writes, and coerces "flat" contingencytables.
xtabs	Creates a contingency table from cross-classifyingfactors, usually contained in a data frame, using a formulainterface.

Data Set

Data Set	Class	Description
p.adjust.methods	character	Allowed methods for `p.adjust`.

stats4

This package contains statistical functions using S4methods and classes.

Functions

Function	Description
AIC	Calculates the Akaike information criterion for one orseveral fitted model objects for which a log-likelihood valuecan be obtained.
BIC	Calculates the Bayesian information criterion (BIC), also known as Schwarz's Bayesian criterion (SBC), for one orseveral fitted model objects for which a log-likelihood valuecan be obtained, according to the formula −2 ∗ log-likelihood+ n_par ∗log(n_obs), wheren_par representsthe number of parameters andn_obs the number ofobservations in the fitted model.
coef	Extracts model coefficients from objects returned bymodeling functions.
confint	Computes confidence intervals for one or moreparameters in a fitted model.
logLik	Extracts the log-likelihood from a modelobject.
mle	Estimates parameters by the method of maximumlikelihood.
plot	Generic function for plotting an R object.
profile	Investigates behavior of objective function near thesolution represented by fitted.
summary	Generic function used to produce result summaries ofthe results of various model-fitting functions.
update	Updates and (by default) refits a model.
vcov	Returns the variance-covariance matrix of the mainparameters of a fitted model object.

survival

This package contains functions for survivalanalysis.

Functions

Function	Description
Surv	Creates a survival object, usually used as a responsevariable in a model formula.
aareg	Returns an object of class `"aareg"` that represents an Aalenmodel.
attrassign	The `"assign"`attribute on model matrices describes which columns come fromwhich terms in the model formula.
basehaz	Computes the baseline survival curve for a Coxmodel.
cch	Returns estimates and standard errors from relativerisk regression fit to data from case-cohort studies, cohortdata, and Borgan II, a generalization of the Lin-Yingestimator.
clogit	Estimates a logistic regression model by maximizing theconditional likelihood.
cluster	This is a special function used in the context ofsurvival models. It identifies correlated groups ofobservations and is used on the righthand side of aformula.
cox.zph	Tests the proportional hazards assumption for a Coxregression model fit (`coxph`).
coxph	Fits a Cox proportional hazards regressionmodel.
coxph.control	Used to set various numeric parameters controlling aCox model fit. Typically, it would only be used in a call to`coxph`.
coxph.detail	Returns the individual contributions to the first andsecond derivative matrix, at each unique event time.
coxph.fit	Internal survival function.
dsurvreg	Density, cumulative probability, and quantiles for theset of distributions supported by the `survreg` function.
format.Surv	Creates a survival object, usually used as a responsevariable in a model formula.
frailty	Adds a simple random-effects term to a Cox or survregmodel.
is.Surv	Tests for a survival object.
is.na.Surv	Tests for NA values in a survival object.
is.na.ratetable	Matches variable names in data to those in a rate tablefor `survexp`.
is.ratetable	Verifies not only the `class` attribute but also thestructure of the object.
labels.survreg	Finds a suitable set of labels from a survival objectfor use in printing or plotting, for example.
pspline	Specifies a penalized spline basis for thepredictor.
psurvreg	Density, cumulative probability, and quantiles for theset of distributions supported by the `survreg` function.
pyears	Computes the person-years of follow-up time contributedby a cohort of subjects, stratified into subgroups.
qsurvreg	Density, cumulative probability, and quantiles for theset of distributions supported by the `survreg` function.
ratetable	Matches variable names in data to those in a rate tablefor `survexp`.
ridge	Specifies a ridge regression term when used in a coxphor survreg model formula.
strata	This is a special function used in the context of theCox survival model. It identifies stratification variableswhen they appear on the righthand side of a formula.
survConcordance	Computes the concordance between a right-censoredsurvival time and a single continuous covariate.
survSplit	Given a survival data set and a set of specified cuttimes, splits each record into multiple subrecords at each cuttime. The new data set will be in "counting process" format, with a start time, stop time, and event status for eachrecord.
survdiff	Tests if there is a difference between two or moresurvival curves using theG^ρ family oftests, or for a single curve against a knownalternative.
survexp	Returns either the expected survival of a cohort ofsubjects or the individual expected survival for eachsubject.
survfit	Computes an estimate of a survival curve for censoreddata using either the Kaplan-Meier or the Fleming-Harringtonmethod or computes the predicted survivor function.
survobrien	O'Brien's test for association of a single variablewith survival.
survreg	Fits a parametric survival regression model. These arelocation-scale models for an arbitrary transform of the timevariable; the most common cases use a log transformation, leading to accelerated failure time models.
survreg.control	Checks and packages the fitting options for `survreg`.
survreg.fit	Internal survival function.
survregDtest	This routine is called by `survreg` to verify that adistribution object is valid.
tcut	Attaches categories for person-year calculations to avariable without losing the underlying continuousrepresentation.
untangle.specials	Given a `terms`structure and a desired special name, this returns an indexappropriate for subscripting the `terms` structure and anotherappropriate for the data frame.

Data Sets

Data Set	Class	Description
aml	data.frame	Survival in patients with acute myelogenousleukemia. The question at the time was whether the standardcourse of chemotherapy should be extended ("maintenance") foradditional cycles.
bladder	data.frame	Data on recurrences of bladder cancer, used by manypeople to demonstrate methodology for recurrent eventmodeling. Bladder1 is the full data set from the study. Thisdata set contains only the 85 subjects with nonzero follow-upwho were assigned to either thiotepa or placebo.
bladder1	data.frame	Data on recurrences of bladder cancer, used by manypeople to demonstrate methodology for recurrent eventmodeling. Bladder1 is the full data set from the study. Itcontains all three treatment arms and all recurrences for 118subjects; the maximum observed number of recurrences is9.
bladder2	data.frame	Data on recurrences of bladder cancer, used by manypeople to demonstrate methodology for recurrent eventmodeling. Bladder2 uses the same subset of subjects asbladder, but formatted in the (start, stop] or Anderson-Gillstyle.
cancer	data.frame	Survival in patients with advanced lung cancer from theNorth Central Cancer Treatment Group. Performance scores ratehow well the patient can perform normal dailyactivities.
cgd	data.frame	Data is from a placebo controlled trial of gammainterferon in chronic granulotomous disease (CGD).
colon	data.frame	Data from one of the first successful trials ofadjuvant chemotherapy for colon cancer.
heart, jasa, jasa1	data.frame	Survival of patients on the waiting list for theStanford heart transplant program.
kidney	data.frame	Data on the recurrence times to infection, at the pointof insertion of the catheter, for kidney patients usingportable dialysis equipment.
leukemia	data.frame	Survival in patients with acute myelogenous leukemia.The question at the time was whether the standard course ofchemotherapy should be extended ("maintenance") for additionalcycles.
lung	data.frame	Survival in patients with advanced lung cancer from theNorth Central Cancer Treatment Group. Performance scores ratehow well the patient can perform normal dailyactivities.
mgus, mgus1, mgus2	data.frame	Natural history of 241 subjects with monoclonalgammapathy of undetermined significance (MGUS).
nwtco	data.frame	Missing data/measurement error example. Tumor histologypredicts survival, but prediction is stronger with central labhistology than with the local institutiondetermination.
ovarian	data.frame	Survival in a randomized trial comparing two treatmentsfor ovarian cancer.
pbc	data.frame	This data is from the Mayo Clinic trial in primarybiliary cirrhosis (PBC) of the liver conducted between 1974and 1984.
pbcseq	data.frame	This data is a continuation of the PBC data set andcontains the follow-up laboratory data for each studypatient.
rats	data.frame	Forty-eight rats were injected with a carcinogen andthen randomized to either drug or placebo. The number oftumors ranged from 0 to 13; all rats were censored at 6 months afterrandomization.
stanford2	data.frame	This contains the Stanford heart transplant data in adifferent format. The main data set is in `heart`.
survexp.mn	ratetable	Census data sets for the expected-survival andperson-year functions.
survexp.mnwhite	ratetable	Census data sets for the expected-survival andperson-year functions.
survexp.us	ratetable	Census data sets for the expected-survival andperson-year functions.
survexp.usr	ratetable	Census data sets for the expected-survival andperson-year functions.
survreg.distributions	list	List of distributions for accelerated failure models.These are location-scale families for some transformation oftime.
tobin	data.frame	Economists fit a parametric censored data model calledthe tobit. The data come from Tobin'soriginal paper.
veteran	data.frame	Randomized trial of two treatment regimens for lungcancer. This is a standard survival analysis data set.

tcltk

The package contains interface and language bindings toTcl/Tk GUI elements. Please see the online help for more details.

tools

This package provides tools for developingpackages.

Functions

Function	Description
Rd2HTML	This (experimental) function converts from an R helppage to an HTML document.
Rd2ex	This (experimental) function converts from an R helppage to the format used by example.
Rd2latex	This (experimental) function converts from an R helppage to a LaTeX document.
Rd2txt	This (experimental) function converts from an R helppage to a text document.
Rd_db	Builds a simple database of all R documentation (Rd)sources in a package, as a list of character vectors with thelines of the Rd files in the package.
Rdiff	Given two R output files, computes differences, ignoring headers, footers, and some encodingdifferences.
Rdindex	Prints a two-column index table with names and titlesfrom given R documentation files to a given output file orconnection. The titles are nicely formatted between two columnpositions (typically 25 and 72, respectively).
buildVignettes	Runs `Sweave` and`texi2dvi` on all vignettesof a package.
checkDocFiles	Checks, for all Rd files in a package, whether allarguments shown in the usage sections of the Rd file aredocumented in its arguments section.
checkDocStyle	Investigates how (S3) methods are shown in the usagesof the Rd files in a package.
checkFF	Performs checks on calls to compiled code from Rcode.
checkMD5sums	Checks the files against a file "MD5".
checkNEWS	Reads R's NEWS file or a similarly formatted one. Thisis an experimental feature, new in R 2.4.0, and may change inseveral ways.
checkRd	These experimental functions take the output of the`parse_Rd` function and checkit or produce a help page from it. Their interfaces (andexistence!) are subject to change.
checkReplaceFuns	Checks whether replacement functions or S3/S4replacement methods in the package R code have their finalargument named value.
checkS3methods	Checks whether all S3 methods defined in the package Rcode have all arguments of the corresponding generic, withpositional arguments of the generics in the same positions forthe method.
checkTnF	Checks the specified R package or code file foroccurrences of `T` or`F` and gathers theexpressions containing these.
checkVignettes	Checks all `Sweave`files of a package by running `Sweave` and/or `Stangle` on them.
codoc	Compares names and optionally also correspondingpositions and default values of the arguments offunctions.
codocClasses	Finds inconsistencies between actual and documented"structure" of R objects in a package. `codoc` compares names and optionallyalso corresponding positions and default values of thearguments of functions. `codocClasses` and `codocData` compare slot names of S4classes and variable names of data sets, respectively.
codocData	Compares slot names of S4 classes.
delimMatch	Matches delimited substrings in a character vector, with proper nesting.
dependsOnPkgs	Finds "reverse" dependencies of packages, i.e., thosepackages that depend on this one and (optionally) so onrecursively.
encoded_text_to_latex	Translates non-ASCII characters in text to LaTeX escapesequences.
file_path_as_absolute	Turns a possibly relative file path absolute, performing tilde expansion, if necessary.
file_path_sans_ext	Returns the file paths without extension.
findHTMLlinks	Finds HTML links in an R help file.
getDepList	Given a dependency matrix, creates a `DependsList` object for that package, which will include the dependencies for that matrix, whichones are installed, which unresolved dependencies were foundonline, which unresolved dependencies were not found online, and any R dependencies.
installFoundDepends	Takes the `Found`element of a `pkgDependsList`object and attempts to install all of the listed packages fromthe specified repositories.
list_files_with_exts	Returns the paths or names of the files in directorydir with extensions matching one of the elements ofexts.
list_files_with_type	Returns the paths of the files in dir of the given"type, " as determined by the extensions recognized byR.
md5sum	Computes the 32-byte MD5 checksums of one or morefiles.
package.dependencies	Parses and checks the dependencies of a package againstthe currently installed version of R (and otherpackages).
parse_Rd	Reads an Rd file and parses it, for processing by otherfunctions. It is experimental.
pkgDepends	Convenience function that wraps getDepList and takes asinput a package name.
pkgVignettes	Runs `Sweave` and`texi2dvi` on all vignettesof a package.
read.00Index	Reads item/description information from 00Index-stylefiles.
readNEWS	Read R's NEWS file or a similarly formatted one. Thisis an experimental feature, new in R 2.4.0, and may change inseveral ways.
showNonASCII	Prints elements of a character vector that containnon-ASCII bytes, printing such bytes as an escape like`<fc>`.
testInstalledBasic	Allows an installed package to be tested by running thebasic tests.
testInstalledPackage	Allows an installed package to be tested.
testInstalledPackages	Allows all base and recommended packages to betested.
texi2dvi	Runs `latex` and`bibtex` until allcross-references are resolved and creates either a deviceindependent (DVI) or a PDF file.
undoc	Finds the objects in a package that are undocumented, in the sense that they are visible to the user (or dataobjects or S4 classes provided by the package), but nodocumentation entry exists.
vignetteDepends	Given a vignette name, creates a DependsList objectthat reports information about the packages the vignettedepends on.
write_PACKAGES	Generates `PACKAGES`and `PACKAGES.gz` files for arepository of source or Mac/Windows binary packages.
xgettext, xgettext2pot, xngettext	For each file in the `R` directory (includingsystem-specific subdirectories) of a package, extract theunique arguments passed to `stop`, `warning`, `message`, `gettext`, and `gettextf`, or to `ngettext`.

Data Sets

Data Set	Class	Description
Adobe_glyphs	data.frame	A data frame that gives Adobe glyph names forUnicode points.
charset_to_Unicode	hexmode	A matrix of Unicode points with columns for the common8-bit encodings.

utils

This package contains a variety of utility functions forR, including package management, file reading and writing, andediting.

Functions

Function	Description
?	Documentation on a topic.
RShowDoc	Utility function to find and display Rdocumentation.
RSiteSearch	Searches for keywords or phrases in the R-help mailinglist archives, help pages, vignettes, or task views, using thesearch engine at http://search.r-project.org, and displays theresults in a web browser.
Rprof	Enables or disables profiling of the execution of Rexpressions.
Rprofmem	Enables or disables reporting of memory allocation inR.
Rtangle	A driver for `Stangle`that extracts R code chunks.
RtangleSetup	A driver for `Stangle`that extracts R code chunks.
RtangleWritedoc	These functions are handy for writing Sweave driversand currently not documented. Look at the source code of theSweave Latex driver (in this package) or the HTML driver (inthe R2HTML package from CRAN) to see how they can beused.
RweaveChunkPrefix	These functions are handy for writing Sweave driversand currently not documented. Look at the source code of theSweave Latex driver (in this package) or the HTML driver (inthe R2HTML package from CRAN) to see how they can beused.
RweaveEvalWithOpt	These functions are handy for writing Sweave driversand currently not documented. Look at the source code of theSweave Latex driver (in this package) or the HTML driver (inthe R2HTML package from CRAN) to see how they can beused.
RweaveLatex	A driver for `Sweave`that translates R code chunks in LaTeX files.
RweaveLatexFinish	These functions are handy for writing Sweave driversand currently not documented. Look at the source code of theSweave Latex driver (in this package) or the HTML driver (inthe R2HTML package from CRAN) to see how they can beused.
RweaveLatexOptions	These functions are handy for writing Sweave driversand currently not documented. Look at the source code of theSweave Latex driver (in this package) or the HTML driver (inthe R2HTML package from CRAN) to see how they can beused.
RweaveLatexSetup	A driver for `Sweave`that translates R code chunks in LaTeX files.
RweaveLatexWritedoc	These functions are handy for writing Sweave driversand currently not documented. Look at the source code of theSweave Latex driver (in this package) or the HTML driver (inthe R2HTML package from CRAN) to see how they can beused.
RweaveTryStop	These functions are handy for writing Sweave driversand currently not documented. Look at the source code of theSweave Latex driver (in this package) or the HTML driver (inthe R2HTML package from CRAN) to see how they can beused.
Stangle	A frontend to `Sweave`using a simple driver by default, which discards thedocumentation and concatenates all code chunks the current Sengine understands.
Sweave	`Sweave` provides aflexible framework for mixing text and S code for automaticreport generation. The basic idea is to replace the S codewith its output, such that the final document only containsthe text and the output of the statistical analysis.
SweaveSyntConv	This function converts the syntax of files in `Sweave` format to another Sweavesyntax definition.
URLdecode	Function to decode characters in URLs.
URLencode	Function to encode characters in URLs.
View	Invokes a spreadsheet-style data viewer on amatrix-like R object.
alarm	Gives an audible or visual signal to the user.
apropos	`apropos()` returns acharacter vector giving the names of all objects in the searchlist matching a specified value.
argsAnywhere	Returns the arguments for all functions with a namematching its argument, whether visible on the search path, registered as an S3 method, or in a namespace but notexported.
as.person	A class and utility method for holding informationabout persons such as name and email address.
as.personList	A class and utility method for holding informationabout persons such as name and email address.
as.relistable	`relist()` is an S3generic function with a few methods in order to allow easyinversion of `unlist(obj)`when that is used with an object of (S3) class `"relistable"`.
as.roman	Manipulates integers as roman numerals.
assignInNamespace	Utility function to access and replace the nonexportedfunctions in a namespace, for use in developing packages withnamespaces.
available.packages	Used to automatically compare the version numbers ofinstalled packages with the newest available version on therepositories and update outdated packages on the fly.
browseEnv	Opens a browser with list of objects currently in the`sys.frame()`environment.
browseURL	Loads a given URL into a web browser.
browseVignettes	Lists available vignettes in an HTML browser with linksto PDF, LaTeX/noweb source, and (tangled) R code (ifavailable).
bug.report	Invokes an editor to write a bug report and optionallymail it to the automated r-bugs repository atr-bugs@r-project.org. Some standardinformation on the current version and configuration of R areincluded automatically.
capture.output	Evaluates its arguments with the output being returnedas a character string or sent to a file. Related to `sink` in the same way that `with` is related to `attach`.
checkCRAN	Functions helping to maintain CRAN, some of which mayalso be useful to administrators of other repositorynetworks.
chooseCRANmirror	Interacts with the user to choose a CRANmirror.
citEntry	Creates "citation" objects, which are modeled afterBibTeX entries.
citFooter	Creates a footer in a CITATION file.
citHeader	Creates a header in a CITATION file.
citation	Shows how to cite R and R packages inpublications.
close.socket	Closes the socket and frees the space in the filedescriptor table. The port may not be freedimmediately.
combn	Generates all combinations of the elements of `x` taken `m` at a time. If `x` is a positive integer, returns allcombinations of the elements of `seq(x)` taken `m` at a time. If argument `FUN` is not `NULL`, applies a function given bythe argument to each point. If simplify is FALSE, returns alist; otherwise, returns an `array`, typically a `matrix`. `...` are passed unchanged to the`FUN` function, ifspecified.
compareVersion	Compares two package version numbers to see which islater.
contrib.url	Used to automatically compare the version numbers ofinstalled packages with the newest available version on therepositories and update outdated packages on the fly.
count.fields	Counts the number of fields, as separated by `sep`, in each of the lines of`file` read.
data	Loads specified data sets or lists the available datasets.
data.entry, dataentry, de, de.ncols, de.restore, de.setup	Spreadsheet-like editors for entering or editingdata.
debugger	Function to dump the evaluation environments (frames)and to examine dumpedframes.
demo	User-friendly interface for running some demonstrationR scripts. `demo()` gives thelist of available topics.
download.file	Used to download a file from the Internet.
download.packages	Used to automatically compare the version numbers ofinstalled packages with the newest available version on therepositories and update outdated packages on the fly.
dump.frames	Function to dump the evaluation environments (frames)and to examine dumpedframes.
edit	Invokes an editor on an R object.
emacs	Invokes the text editor emacs on an R object.
example	Runs all the R code from theExamples part of R's online help.
file.edit	Edits one or more files in a text editor.
file_test	Utility for shell-style file tests.
find	Returns a character vector giving the names of allobjects in the search list matching a given value.
fix	Invokes `edit` on`x` and assigns the new(edited) version of `x` inthe user's workspace.
fixInNamespace	Utility function to access and replace the nonexportedfunctions in a namespace, for use in developing packages withnamespaces.
flush.console	On the Mac OS X and Windows GUIs, ensures that thedisplay of output in the console is current, even if outputbuffering is on. (This does nothing except on console-basedversions of R.)
formatOL, formatUL	Format unordered (itemize) and ordered (enumerate)lists.
getAnywhere	Locates and returns all objects with a name matchingits argument, whether visible on the search path, registeredas an S3 method, or in a namespace but not exported.
getCRANmirrors	Interacts with the user to choose a CRANmirror.
getFromNamespace	Utility function to access and replace the nonexportedfunctions in a namespace, for use in developing packages withnamespaces.
getS3method	Gets a method for an S3 generic, possibly from anamespace.
getTxtProgressBar	Text progress bar in the R console.
glob2rx	Changes wildcard (akaglobbing) patterns into the correspondingregular expressions (`regexp`).
head	Returns the first or last parts of a vector, matrix, table, data frame, or function. Since `head()` and `tail()` are generic functions, theymay also have been extended to other classes.
help	The primary interface to R's help system.
help.request	Prompts users to check they have done all that isexpected of them before sending a post to the R-help mailinglist, provides a template for the post with sessioninformation included, and optionally sends the email (on Unixsystems).
help.search	Allows for searching the help system for documentationmatching a given character string in the (file) name, alias, title, concept, or keyword entries (or any combinationthereof), using either fuzzy matching or regular expressionmatching. Names and titles of the matched help entries aredisplayed nicely formatted.
help.start	Starts the hypertext (currently HTML) version of R'sonline documentation.
history	Loads or saves or displays the commandshistory.
index.search	Used to search the indexes for help files, possiblyunder aliases.
install.packages	Used to automatically compare version numbers ofinstalled packages with the newest available version on therepositories and update outdated packages on the fly.
installed.packages	Finds (or retrieves) details of all packages installedin the specified libraries.
is.relistable	`relist()` is an S3generic function with a few methods in order to allow easyinversion of `unlist(obj)`when that is used with an object of (S3) class `"relistable"`.
limitedLabels	Allows the user to browse directly on any of thecurrently active function calls and is suitable as an erroroption. The expression `options(error=recover)` will makethis the error option.
loadhistory	Loads or saves or displays the commandshistory.
localeToCharset	Aims to find a suitable coding for the locale named, bydefault the current locale, and if it is a UTF-8 locale, asuitable single-byte encoding.
ls.str, lsf.str	`ls.str` and `lsf.str` are variations of `ls` applying `str()` to each matched name.
make.packages.html	Updates HTML documentation files.
make.socket	With `server = FALSE`, attempts to open a client socket to the specified port andhost. With `server = TRUE`, listens on the specified port for a connection and thenreturns a server socket. It is a good idea to use `on.exit` to ensure that a socket isclosed, as you only get 64 of them.
makeRweaveLatexCodeRunner	These functions are handy for writing Sweave driversand currently not documented. Look at the source code of theSweave Latex driver (in this package) or the HTML driver (inthe R2HTML package from CRAN) to see how they can beused.
memory.limit	Gets or sets the memory limit on Microsoft Windowsplatforms.
memory.size	Checks the current memory usage on Microsoft Windowsplatforms.
menu	Presents the user with a menu of choices labeled from 1to the number of choices. To exit without choosing an item, select 0.
methods	Lists all available methods for an S3 generic functionor all methods for a class.
mirror2html	Functions helping to maintain CRAN, some of which mayalso be useful to administrators of other repositorynetworks.
modifyList	Modifies a possibly nested list recursively by changinga subset of elements at each level to match a secondlist.
new.packages	Used to automatically compare the version numbers ofinstalled packages with the newest available version on therepositories and update outdated packages on the fly.
normalizePath	Converts file paths to canonical form for the platform, to display them in a user-understandable form.
nsl	Interface to gethostbyname.
object.size	Provides an estimate of the memory that is being usedto store an R object.
old.packages	Used to automatically compare the version numbers ofinstalled packages with the newest available version on therepositories and update outdated packages on the fly.
package.skeleton	Automates some of the setup for a new source package.It creates directories; saves functions, data, and R codefiles to appropriate places; and creates skeleton help filesand a `Read-and-delete-me`file describing further steps in packaging.
packageDescription	Parses and returns the `DESCRIPTION` file of apackage.
packageStatus	Summarizes information about installed packages andpackages available at various repositories, and automaticallyupgrades outdated packages.
page	Displays a representation of the object named by`x` in a pager via `file.show`.
person	Creates a "person" object.
personList	Creates a "personList" object.
pico	Invokes a text editor on an R object.
prompt	Facilitates the construction of files documenting Robjects.
promptData	Generates a shell of documentation for a dataset.
promptPackage	Generates a shell of documentation for an installed orsource package.
read.DIF	Reads a file in Data Interchange Format (DIF) andcreates a data frame from it. DIF is a format for datamatrices such as single spreadsheets.
read.csv, read.csv2, read.delim, read.delim2	Read a file in table format and create a data framefrom it, with cases corresponding to lines and variables tofields in the file.
read.fortran	Reads fixed-format data files using FORTRAN-styleformat specifications.
read.fwf	Reads a table of fixed-width-formatted data into a`data.frame`.
read.socket	`read.socket` reads astring from the specified socket; `write.socket` writes to the specifiedsocket. There is very little error checking done byeither.
read.table	Reads a file in table format and creates a data framefrom it, with cases corresponding to lines and variables tofields in the file.
readCitationFile	The `CITATION` fileof R packages contains an annotated list of references thatshould be used for citing the packages.
recover	Allows the user to browse directly on any of thecurrently active function calls and is suitable as an erroroption. The expression `options(error=recover)` will makethis the error option.
relist	`relist()` is an S3generic function with a few methods in order to allow easyinversion of `unlist(obj)`when that is used with an object of (S3) class `"relistable"`.
remove.packages	Removes installed packages/bundles and updates indexinformation as necessary.
rtags	Provides etags-like indexing capabilities for R code, using R's own parser.
savehistory	Loads or saves or displays the commandshistory.
select.list	Selects item(s) from a character vector.
sessionInfo	Prints version information about R and attached orloaded packages.
setRepositories	Interacts with the user to choose the packagerepositories to be used.
setTxtProgressBar	Text progress bar in the R console.
stack	Stacking vectors concatenates multiple vectors into asingle vector along with a factor indicating where eachobservation originated; unstacking reverses this.
str	Compactly displays the internal structure of an Robject; the idea is to give reasonable output forany R object.
strOptions	`strOptions()` is aconvenience function for setting `options(str = .)`.
summaryRprof	Summarizes the output of the `Rprof` function to show the amount oftime used by different R functions.
tail	Returns the first or last parts of a vector, matrix, table, data frame, or function. Since `head()` and `tail()` are generic functions, theymay also have been extended to other classes.
timestamp	Loads or saves or displays the commandshistory.
toBibtex	Converts R objects to character vectors with BibTeXmarkup.
toLatex	Converts R objects to character vectors with LaTeXmarkup.
txtProgressBar	Text progress bar in the R console.
type.convert	Converts a character vector to logical, integer, numeric, complex, or factor, as appropriate.
unstack	Stacking vectors concatenates multiple vectors into asingle vector along with a factor indicating where eachobservation originated; unstacking reverses this.
unzip	Extracts files from or lists a zip archive.
update.packageStatus	Summarizes information about installed packages andpackages available at various repositories and automaticallyupgrades outdated packages.
update.packages	Used to automatically compare the version numbers ofinstalled packages with the newest available version on therepositories and update outdated packages on the fly.
upgrade	Summarizes information about installed packages andpackages available at various repositories and automaticallyupgrades outdated packages.
url.show	Extension of `file.show` to display text files froma remote server.
vi	Invokes a text editor on an R object.
vignette	Views a specified vignette or lists the availableones.
write.csv, write.csv2	Convenience wrappers to `write.table` for producing CSV filesfrom an R object.
write.socket	`read.socket` reads astring from the specified socket; `write.socket` writes to the specifiedsocket. There is very little error checking done byeither.
write.table	Prints its required argument `x` (after converting it to a dataframe if it is not one nor a matrix) to a file orconnection.
wsbrowser	The `browseEnv`function opens a browser with list of objects currently in the`sys.frame()`environment.
xedit	Invokes the xedit editor on an R object.
xemacs	Invokes the xemacs editor on an R object.
zip.file.extract	Extracts the file named `file` from the zip archive, ifpossible, and writes it in a temporary location.

stats

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stats4

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survival

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tcltk

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