Appendix: R Reference - R in a Nutshell

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Appendix: R Reference - R in a Nutshell
Pages: 1, 2, 3, 4, 5

MASS

This is the main package of Venables and Ripley'sMASS.

Functions

Function	Description
Null	Given a matrix `M`, finds a matrix `N` giving abasis for the null space. That is, `t(N) \%*\% M` is the 0, and `N` has the maximum number of linearlyindependent columns.
Shepard	One form of nonmetric multidimensional scaling.
addterm	Tries fitting all models that differ from the currentmodel by adding a single term from those supplied, maintainingmarginality.
area	Integrates a function of one variable over a finiterange using a recursive adaptive method. This function ismainly for demonstration purposes.
as.fractions	Finds rational approximations to the components of areal numeric object using a standard continued fractionmethod.
bandwidth.nrd	A well-supported rule of thumb for choosing thebandwidth of a Gaussian kernel density estimator.
bcv	Uses biased cross-validation to select the bandwidth ofa Gaussian kernel density estimator.
boxcox	Computes and optionally plots profile log-likelihoodsfor the parameter of the Box-Cox power transformation.
con2tr	Converts lists to data frames for use bylattice.
contr.sdif	A coding for unordered factors based on successivedifferences.
corresp	Finds the principal canonical correlation andcorresponding row and column scores from a correspondenceanalysis of a two-way contingency table.
cov.mcd, cov.mve, cov.rob	Compute a multivariate location and scale estimate witha high breakdown point. This can be thought of as estimatingthe mean and covariance of the `good` part of the data. `cov.mve` and `cov.mcd` are compatibilitywrappers.
cov.trob	Estimates a covariance or correlation matrix assumingthe data came from a multivariatet-distribution: this provides some degreeof robustness to outliers without giving a high breakdownpoint.
denumerate	`loglm` allowsdimension numbers to be used in place of names in the formula.`denumerate` modifies such aformula into one that `terms`can process.
dose.p	Calibrates binomial assays, generalizing thecalculation of LD50.
dropterm	Tries fitting all models that differ from the currentmodel by dropping a single term, maintainingmarginality.
eqscplot	Version of a scatter plot with scales chosen to beequal on both axes, i.e., 1 cm represents the same units oneach.
fitdistr	Maximum likelihood fitting of univariate distributions, allowing parameters to be held fixed, if desired.
fractions	Finds rational approximations to the components of areal numeric object using a standard continued fractionmethod.
gamma.dispersion	A frontend to `gamma.shape` for convenience. Findsthe reciprocal of the estimate of the shape parameteronly.
gamma.shape	Finds the maximum likelihood estimate of the shapeparameter of the gamma distribution after fitting a `Gamma` generalized linearmodel.
ginv	Calculates the Moore-Penrose generalized inverse of amatrix `X`.
glm.convert	Modifies an output object from `glm.nb()` to one that looks like theoutput from `glm()` with anegative binomial family. This allows it to be updated keepingthe theta parameter fixed.
glm.nb	A modification of the system function `glm()` to include estimation of theadditional parameter, `theta`, for a negative binomialgeneralized linear model.
glmmPQL	Fits a generalized linear mixed model (GLMM) withmultivariate normal random effects, using penalizedquasi-likelihood.
hist.FD	Plots a histogram with automatic bin width selection, using the Scott or Freedman-Diaconis formula.
hist.scott	Plots a histogram with automatic bin width selection, using the Scott or Freedman-Diaconis formula.
huber	Finds the Huber M-estimator of location with the medianabsolute deviation (MAD) scale.
hubers	Finds the Huber M-estimator for location with scalespecified, scale with location specified, or both if neitheris specified.
is.fractions	Finds rational approximations to the components of areal numeric object using a standard continued fractionmethod.
isoMDS	One form of nonmetric multidimensional scaling.
kde2d	Two-dimensional kernel density estimation with anaxis-aligned bivariate normal kernel, evaluated on a squaregrid.
lda	Linear discriminant analysis.
ldahist	Plots histograms or density plots of data on a singleFisher linear discriminant.
lm.gls	Fits linear models by generalized leastsquares.
lm.ridge	Fits a linear model by ridge regression.
lmsreg	Fits a regression to the goodpoints in the data set, thereby achieving a regressionestimator with a high breakdown point. (`lmsreg` is a compatibility wrapperfor `lqs`.)
lmwork	The standardized residuals. These are normalized tounit variance, fitted including the current datapoint.
loglm	Provides a frontend to the standard function, `loglin`, to allow log-linear modelsto be specified and fitted in a manner similar to that ofother fitting functions, such as `glm`.
logtrans	Finds and optionally plots the marginal (profile)likelihood for alpha for a transformation model of the form`log(y + alpha) ~ x1 + x2 +...`.
lqs, lqs.formula	Fit a regression to the goodpoints in the data set, thereby achieving a regressionestimator with a high breakdown point. `lmsreg` and `ltsreg` are compatibilitywrappers.
ltsreg	A compatibility wrapper for `lqs`.
mca	Computes a multiple-correspondence analysis of a set offactors.
mvrnorm	Produces one or more samples from the specifiedmultivariate normal distribution.
negative.binomial	Specifies the information required to fit a negativebinomial generalized linear model, with known `theta` parameter, using `glm()`.
parcoord	Parallel coordinates plot.
polr	Fits a logistic or probit regression model to anordered factor response. The default logistic case isproportional odds logistic regression, after which the function is named.
psi.bisquare, psi.hampel, psi.huber	Psi functions for `rlm`.
qda	Fits quadratic discriminant analysis models.
rational	Finds rational approximations to the components of areal numeric object using a standard continued fractionmethod.
renumerate	`denumerate` convertsa formula written using the conventions of `loglm` into one that `terms` is able to process. `renumerate` converts it back again toa form like the original.
rlm	Fits a linear model by robust regression using anM-estimator.
rms.curv	Calculates the root mean square parameter effects andintrinsic relative curvatures, c^θ andc^ι, for afitted nonlinear regression.
rnegbin	Generates random outcomes from a negative binomialdistribution, with mean `mu`and variance `mu + mu^2/theta`.
sammon	One form of nonmetric multidimensional scaling.
select	Fits a linear model by ridge regression.
stdres	The standardized residuals. These are normalized tounit variance, fitted including the current datapoint.
stepAIC	Performs stepwise model selection by AIC.
studres	Extracts the Studentized residuals from a linearmodel.
theta.md, theta.ml, theta.mm	Given the estimated mean vector, estimate `theta` of the negative binomialdistribution.
truehist	Creates a histogram on the current graphicsdevice.
ucv	Uses unbiased cross-validation to select the bandwidthof a Gaussian kernel density estimator.
width.SJ	Uses the method of Sheather and Jones to select thebandwidth of a Gaussian kernel density estimator.
write.matrix	Writes a matrix or data frame to a file or the console, using column labels and a layout respecting columns.

Data Sets

Data Set	Class	Description
Aids2	data.frame	Data on patients diagnosed with AIDS inAustralia before July 1, 1991.
Animals	data.frame	Average brain and body weights for 28 species of landanimals.
Boston	data.frame	The `Boston` dataframe has 506 rows and 14 columns.
Cars93	data.frame	The `Cars93` dataframe has 93 rows and 27 columns.
Cushings	data.frame	Cushing's syndrome is a hypertensive disorderassociated with oversecretion of cortisol by the adrenalgland. The observations are urinary excretion rates of twosteroid metabolites.
DDT	numeric	A numeric vector of 15 measurements by differentlaboratories of the pesticide DDT in kale, in ppm (parts permillion), using the multiple pesticide residuemeasurement.
GAGurine	data.frame	Data was collected on the concentration of the chemicalglycosaminoglycan (GAG) in the urine of 314 children aged 0 to17 years. The aim of the study was to produce a chart to helpa pediatrican to assess if a child's GAG concentration is"normal."
Insurance	data.frame	The data given in data frame `Insurance` consists of the numbers ofpolicyholders of an insurance company who were exposed torisk, and the numbers of car insurance claims made by thosepolicyholders in the third quarter of 1973.
Melanoma	data.frame	The `Melanoma` dataframe has data on 205 patients in Denmark with malignantmelanoma.
OME	data.frame	Experiments were performed on children on their abilityto differentiate a signal in broadband noise. The noise wasplayed from a pair of speakers, and a signal was added to justone channel; the subject had to turn his/her head to thechannel with the added signal. The signal was either coherent(the amplitude of the noise was increased for a period) orincoherent (independent noise was added for the same period toform the same increase in power). The threshold used in theoriginal analysis was the stimulus loudness needed to get 75%correct responses. Some of the children had suffered fromotitis media with effusion (OME).
Pima.te	data.frame	A population of women who were at least 21 years old, of Pima Indian heritage, and living near Phoenix, Arizona, wastested for diabetes according to World Health Organizationcriteria. The data was collected by the National Institute ofDiabetes and Digestive and Kidney Diseases. A total of 532complete records was used, after dropping the (mainly missing)data on serum insulin.
Pima.tr	data.frame	A population of women who were at least 21 years old, of Pima Indian heritage, and living near Phoenix, Arizona, wastested for diabetes according to World Health Organizationcriteria. The data was collected by the National Institute ofDiabetes and Digestive and Kidney Diseases. A total of 532complete records was used, after dropping the (mainly missing)data on serum insulin.
Pima.tr2	data.frame	A population of women who were at least 21 years old, of Pima Indian heritage, and living near Phoenix, Arizona, wastested for diabetes according to World Health Organizationcriteria. The data was collected by the National Institute ofDiabetes and Digestive and Kidney Diseases. A total of 532complete records was used, after dropping the (mainly missing)data on serum insulin.
Rabbit	data.frame	Five rabbits were studied on two occasions, aftertreatment with saline (control) and after treatment with the5-HT_3 antagonist MDL 72222. After each treatment, ascendingdoses of phenylbiguanide were injected intravenously at10-minute intervals and the responses of mean blood pressuremeasured. The goal was to test whether the cardiogenic chemoreflex elicited byphenylbiguanide depends on the activation of 5-HT_3receptors.
Rubber	data.frame	Data frame from accelerated testing of tirerubber.
SP500	numeric	Returns of the Standard & Poors 500 Index in the1990s.
Sitka	data.frame	The `Sitka` data framehas 395 rows and 4 columns. It gives repeated measurements onthe log-size of 79 Sitka spruce trees, 54 of which were grownin ozone-enriched chambers and 25 were controls. The size wasmeasured five times in 1988, at roughly monthly intervals.
Sitka89	data.frame	The `Sitka89` dataframe has 632 rows and 4 columns. It gives repeatedmeasurements on the log-size of 79 Sitka spruce trees, 54 ofwhich were grown in ozone-enriched chambers and 25 werecontrols. The size was measured eight times in 1989, atroughly monthly intervals.
Skye	data.frame	The `Skye` data framehas 23 rows and 3 columns.
Traffic	data.frame	An experiment was performed in Sweden in 1961–1962 toassess the effect of a speed limit on the highway accidentrate. The experiment was conducted on 92 days in each year, matched so that day `j` in1962 was comparable to day `j` in 1961. On some days, the speedlimit was in effect and enforced, while on other days therewas no speed limit and cars tended to be driven faster. Thespeed limit days tended to be in contiguous blocks.
UScereal	data.frame	The `UScereal` dataframe has 65 rows and 11 columns. The data comes from the 1993American Statistical Association (ASA) Statistical GraphicsExposition and is taken from the mandatory Food and DrugAdministration (FDA) food label. The data has been normalizedhere to a portion of one American cup.
UScrime	data.frame	Criminologists are interested in the effect ofpunishment regimes on crime rates. This has been studied usingthe aggregate data on 47 states of the United States for 1960given in this data frame. The variables seem to have beenrescaled to convenient numbers.
VA	data.frame	Veteran's Administration lung cancer trial fromKalbfleisch and Prentice.
abbey	numeric	A numeric vector of 31 determinations of nickel content(ppm) in a Canadian syenite rock.
accdeaths	ts	A regular time series giving the monthly totals ofaccidental deaths in the United States.
anorexia	data.frame	The `anorexia` dataframe has 72 rows and 3 columns. Weight change data for youngfemale anorexia patients.
bacteria	data.frame	Tests of the presence of the bacteria H.influenzae in children with otitis media in theNorthern Territory of Australia.
beav1	data.frame	Reynolds describes a small part of a study of thelong-term temperature dynamics of the beaver (Castorcanadensis) in north-central Wisconsin. Bodytemperature was measured by telemetry every 10 minutes forfour females, but data from a one period of less than a dayfor each of two animals is used here.
beav2	data.frame	Reynolds describes a small part of a study of thelong-term temperature dynamics of the beaver (Castorcanadensis) in north-central Wisconsin. Bodytemperature was measured by telemetry every 10 minutes forfour females, but data from a period of less than a day foreach of two animals is used here.
biopsy	data.frame	This breast cancer database was obtained from theUniversity of Wisconsin Hospitals, Madison, from Dr. WilliamH. Wolberg. He assessed biopsies of breast tumors for 699patients up to July 15, 1992; each of nine attributes has beenscored on a scale of 1 to 10, and the outcome is also known.There are 699 rows and 11 columns.
birthwt	data.frame	The `birthwt` dataframe has 189 rows and 10 columns. The data was collected atBaystate Medical Center, Springfield, Massachusetts, during1986.
cabbages	data.frame	The `cabbages` dataset has 60 observations and 4 variables.
caith	data.frame	Data on the cross-classification of people inCaithness, Scotland, by eye and hair color. This region of theUnited Kingdom is particularly interesting as there is amixture of people of Nordic, Celtic, and Anglo-Saxonorigin.
cats	data.frame	The heart and body weights of samples of male andfemale cats used for digitalis experiments. The cats were alladult, over 2 kg in body weight.
cement	data.frame	Experiment on the heat evolved in the setting of eachof 13 cements.
chem	numeric	A numeric vector of 24 determinations of copper inwholemeal flour, in parts per million.
coop	data.frame	Seven specimens were sent to six laboratories in threeseparate batches and each analyzed for analyte. Each analysiswas duplicated.
cpus	data.frame	A relative performance measure and characteristics of209 CPUs.
crabs	data.frame	The `crabs` data framehas 200 rows and 8 columns, describing 5 morphologicalmeasurements on 50crabs, each of two color forms and both sexes, of the speciesLeptograpsusvariegatus, collected at Fremantle, Western Australia.
deaths	ts	A time series giving the monthly deaths frombronchitis, emphysema, and asthma in the United Kingdom, 1974–1979, for both sexes.
drivers	ts	A regular time series giving the monthly totals of cardrivers in Great Britain killed or seriously injured fromJanuary 1969 to December 1984. Compulsory wearing of seatbelts was introduced on January 31, 1983.
eagles	data.frame	Knight and Skagen collected data during a field studyon the foraging behavior of wintering bald eagles inWashington State. The data concerned 160 attempts by one(pirating) bald eagle to steal a chum salmon from another(feeding) bald eagle.
epil	data.frame	Thall and Vail give a data set on 2-week seizure countsfor 59 epileptics. The number of seizures was recorded for abaseline period of 8 weeks, and then patients were randomlyassigned to a treatment group or a control group. Counts werethen recorded for four successive 2-week periods. Thesubject's age is the only covariate.
farms	data.frame	The `farms` data framehas 20 rows and 4 columns. The rows are farms on the Dutchisland of Terschelling, and the columns are factors describingthe management of grassland.
fgl	data.frame	The `fgl` data framehas 214 rows and 10 columns. It was collected by B. German onfragments of glass collected in forensic work.
forbes	data.frame	A data frame with 17 observations on the boiling pointof water and barometric pressure, in inches ofmercury.
galaxies	numeric	A numeric vector of velocities, in kilometers/second, of 82 galaxies from 6 well-separated conic sections of an`unfilled` survey of theCorona Borealis region. Multimodality in such surveys isevidence for voids and superclusters in the faruniverse.
gehan	data.frame	A data frame from a trial of 42 leukemia patients. Somewere treated with the drug 6-mercaptopurine, and the rest werecontrols. The trial was designed as matched pairs, bothwithdrawn from the trial when either came out ofremission.
genotype	data.frame	Data from a foster feeding experiment with rat mothersand litters of four different genotypes: `A`, `B`, `I` and `J`. Rat litters were separated fromtheir natural mothers at birth and given to foster mothers torear.
geyser	data.frame	A version of the eruptions data from the Old Faithfulgeyser in Yellowstone National Park, Wyoming. This versioncomes from Azzalini and Bowman and is of continuousmeasurement from August 1 to August 15, 1985. Some nocturnalduration measurements were coded as 2, 3, or 4 minutes, havingoriginally been described as "short, " "medium, " or"long."
gilgais	data.frame	This data set was collected on a line transect surveyin gilgai territory in New South Wales, Australia. Gilgais arenatural gentle depressions in otherwise flat land, andsometimes they seem to be regularly distributed. The datacollection was stimulated by the question: are these patternsreflected in soil properties? At each of 365 samplinglocations on a linear grid of 4 meters, spacing, samples weretaken at depths 0–10 cm, 30–40 cm, and 80–90 cm below thesurface. pH, electrical conductivity, and chloride contentwere measured on a 1:5 soil:water extract from eachsample.
hills	data.frame	The record times in 1984 for 35 Scottish hillraces.
housing	data.frame	The `housing` dataframe has 72 rows and 5 variables.
immer	data.frame	The `immer` data framehas 30 rows and 4 columns. Five varieties of barley were grownin six locations in 1931 and in 1932.
leuk	data.frame	A data frame of data from 33 leukemia patients.
mammals	data.frame	A data frame with average brain and body weights for 62species of land mammals.
mcycle	data.frame	A data frame giving a series of measurements of headacceleration in a simulated motorcycle accident; used to testcrash helmets.
menarche	data.frame	Proportions of female children at various ages duringadolescence who have reached menarche.
michelson	data.frame	Measurements of the speed of light in air, made betweenJune 5, and July 2, 1879. The data consists of 5 experiments, each consisting of 20 consecutive runs. The response is thespeed of light, in kilometers/second, less 299, 000. Thecurrently accepted value, on this scale of measurement, is734.5.
minn38	data.frame	Minnesota high school graduates of 1938 were classifiedaccording to four factors. The `minn38` data frame has 168 rows and 5columns.
motors	data.frame	The `motors` dataframe has 40 rows and 3 columns. It describes an acceleratedlife test at each of four temperatures of 10 motorettes andhas rather discrete times.
muscle	data.frame	The purpose of this experiment was to assess theinfluence of calcium in solution on the contraction of heartmuscle in rats. The left auricle of 21 rat hearts wasisolated, and on several occasions a constant-length strip oftissue was electrically stimulated and dipped into variousconcentrations of calcium chloride solution, after which theshortening of the strip was accurately measured as theresponse.
newcomb	numeric	A numeric vector giving the "Third Series" ofmeasurements of the passage time of light recorded by Newcombin 1882. The given values divided by 1, 000 plus 24 give thetime, in millionths of a second, for light to traverse a knowndistance. The "true" value is now considered to be33.02.
nlschools	data.frame	Snijders and Bosker use as a running example a study of2, 287 eighth-grade pupils (aged about 11) in 132 classes in131 schools in the Netherlands. Only the variables used intheir examples are supplied.
npk	data.frame	A classical N, P, K (nitrogen, phosphate, potassium)factorial experiment on the growth of peas conducted on sixblocks. Each half of a fractional factorial design confoundingthe NPK interaction was used on three of the plots.
npr1	data.frame	Data on the locations, porosity, and permeability (ameasure of oil flow) on 104 oil wells in the U.S. NavalPetroleum Reserve No. 1 in California.
oats	data.frame	The yield of oats from a split-plot field trial usingthree varieties and four levels of manurial treatment. Theexperiment was laid out in six blocks of three main plots, each split into four subplots. The varieties were applied tothe main plots and the manurial treatments to thesubplots.
painters	data.frame	The subjective assessment, on an integer scale of 0 to20, of 54 classical painters. The painters were assessed onfour characteristics: composition, drawing, color, andexpression. The data is due to the 18th-century art critic, dePiles.
petrol	data.frame	The yield of a petroleum refining process with fourcovariates. The crude oil appears to come from only 10distinct samples. This data was originally used by Prater tobuild an estimation equation for the yield of the refiningprocess of crude oil to gasoline.
phones	list	A list object with the annual number of telephone callsin Belgium.
quine	data.frame	The `quine` data framehas 146 rows and 5 columns. Children from Walgett, New SouthWales, Australia, were classified by culture, age, sex, andlearner status, and the number of days absent from school in aparticular school year was recorded.
road	data.frame	A data frame with the annual deaths in road accidentsfor half the U.S. states.
rotifer	data.frame	The data give the numbers of rotifers falling out ofsuspension for different fluid densities.
ships	data.frame	Data frame giving the number of damage incidents andaggregate months of service by ship type, year ofconstruction, and period of operation.
shoes	list	A list of two vectors, giving the wear of shoes ofmaterials A and B for one foot each of 10 boys.
shrimp	numeric	A numeric vector with 18 determinations by differentlaboratories of the amount (percentage of the declared totalweight) of shrimp in shrimp cocktail.
shuttle	data.frame	The `shuttle` dataframe has 256 rows and 7 columns. The first six columns arecategorical variables giving example conditions; the seventhis the decision. The first 253 rows are the training set, thelast 3 the test conditions.
snails	data.frame	Groups of 20 snails were held for periods of 1, 2, 3, or 4 weeks under carefully controlled conditions oftemperature and relative humidity. There were two species ofsnail, A and B, and the experiment was designed as a4-by-3-by-4-by-2 completely randomized design. At the end ofthe exposure time, the snails were tested to see if they hadsurvived; the process itself is fatal for the animals. Theobject of the exercise was to model the probability ofsurvival in terms of the stimulus variables and, inparticular, to test for differences between species. The data areunusual in that, in most cases, fatalities during theexperiment were fairly small.
steam	data.frame	Temperature and pressure in a saturated steam-drivenexperimental device.
stormer	data.frame	The stormer viscometer measures the viscosity of afluid by measuring the time taken for an inner cylinder in themechanism to perform a fixed number of revolutions in responseto an actuating weight. The viscometer is calibrated bymeasuring the time taken with varying weights while themechanism is suspended in fluids of accurately knownviscosity. The data comes from such a calibration, andtheoretical considerations suggest a nonlinear relationshipamong time, weight, and viscosity of the form `Time = (B1 * Viscosity)/(Weight - B2) +E`, where `B1` and`B2` are unknown parametersto be estimated, and `E` iserror.
survey	data.frame	This data frame contains the responses of 237Statistics I students at the University of Adelaide to anumber of questions.
synth.te	data.frame	The `synth.tr` dataframe has 250 rows and 3 columns. The `synth.te` data frame has 100 rows and3 columns. It is intended that `synth.tr` be used from training and`synth.te` fortesting.
synth.tr	data.frame	The `synth.tr` dataframe has 250 rows and 3 columns. The `synth.te` data frame has 100 rows and3 columns. It is intended that `synth.tr` be used from training and`synth.te` fortesting.
topo	data.frame	The `topo` data framehas 52 rows and 3 columns, of topographic heights within a310-foot square.
waders	data.frame	The `waders` dataframe has 15 rows and 19 columns. The entries are counts ofwaders in summer.
whiteside	data.frame	Mr. Derek Whiteside of the UK Building Research Stationrecorded the weekly gas consumption and average externaltemperature at his own house in southeast England for twoheating seasons, one of 26 weeks before, and one of 30 weeksafter cavity-wall insulation was installed. The object of theexercise was to assess the effect of the insulation on gasconsumption.
wtloss	data.frame	This data frame gives the weight, in kilograms, of anobese patient at 52 time points over an 8-month period of aweight rehabilitation program.

methods

This package contains formally defined methods and classesfor R objects, plus other programming tools.

Functions

Function	Description
@<-	Gets or sets information about the individual slots inan object.
MethodAddCoerce	Possibly modifies one or more methods to explicitlycoerce this argument to `methodClass`, the class forwhich the method is explicitly defined.
Quote	These are utilities, currently in the `methods` package, that either providesome functionality needed by the package (e.g., elementmatching by name) or add compatibility with S-PLUS, orboth.
S3Class, S3Class<-	`S3Class` extracts orreplaces the S3-style class from an S4 class that was createdfrom an S3 class through `setOldClass`.
S3Part, S3Part<-	The function `S3Part`extracts or replaces the S3 part of such an object.
addNextMethod	Generic function that finds the next method for thesignature of the method definition method and caches thatmethod in the method definition.
allNames	Returns the character vector of names (unlike names(), never returns `NULL`) for amethod.
as, as<-	Manage the relations that allow coercing an object to agiven class.
asMethodDefinition	Turns a function definition into an object of class`MethodDefinition`, corresponding to the given signature (by default, generates adefault method with empty signature).
assignClassDef	Assigns the definition of the class to the speciallynamed object.
assignMethodsMetaData	Utility to assign the metadata object recording themethods defined in a particular package.
balanceMethodsList	Called from setMethod to ensure that all nodes in thelist have the same depth (i.e., the same number of levels ofarguments).
body<-	Sets the body of a method.
cacheGenericsMetaData, cacheMetaData	Utilities for ensuring that the internal informationabout class and method definitions is up to date. Shouldnormally be called automatically whenever needed (e.g., when amethod or class definition changes or when a package isattached or detached).
cacheMethod	Stores the definition for this function and signaturein the method metadata for the function.
callGeneric	The name and package of the current generic function isstored in the environment of the method definitionobject.
callNextMethod	A call to `callNextMethod` can only appearinside a method definition. It then results in a call to thefirst inherited method after the current method, with thearguments to the current method passed down to the nextmethod. The value of that method call is the value of `callNextMethod`.
canCoerce	Tests if an object can be coerced to a given S4class.
cbind2	Combines two matrix-like R objects by columns (`cbind2`) or rows (`rbind2`). These are (S4) genericfunctions with default methods.
checkSlotAssignment	Checks that the value provided is allowed for thisslot, by consulting the definition of the class. Called fromthe C code that assigns slots.
classMetaName	A name for the object storing this class'sdefinition.
classesToAM	Given a vector of class names or a list of classdefinitions, returns an adjacency matrix of the superclassesof these classes; i.e., a matrix with class names as the rowand column names and with element [i, j] being 1 if the classin column j is a direct superclass of the class in row i, and0 otherwise.
coerce, coerce<-	Manage the relations that allow coercing an object to agiven class.
completeClassDefinition	Completes the definition of Class, relative to theclass definitions visible from environment where. If doExtendsis TRUE, completes the super- and subclass information.
completeExtends	Completes the extends information in the classdefinition, by following transitive chains.
completeSubclasses
conformMethod	If the formal arguments, mnames, are not identical tothe formal arguments to the function, fnames, conformMethoddetermines whether the signature and the two sets of argumentsconform and returns the signature, possibly extended.
defaultDumpName	Default name to be used for dumping a method.
defaultPrototype	The prototype for a class that will have slots, is nota virtual class, and does not extend one of the basic classes.Both its class and its (R internal) type, `typeof()`, are "S4."
doPrimitiveMethod	Performs a primitive call to built-in function name thedefinition and call provided, and carried out in the specifiedenvironment.
dumpMethod	Dumps the method for this generic function andsignature.
dumpMethods	Dumps all the methods for this generic.
elNamed, elNamed<-	Get or set the element of the vector corresponding toname.
existsFunction	Is there a function of this name? If generic is FALSE, generic functions are not counted.
existsMethod	Tests for the existence of a method corresponding to agiven generic function and signature.
extends	Function to test inheritance relationships between anobject and a class (`is`) orbetween two classes (`extends`) and to establish suchrelationships (`setIs`, anexplicit alternative to the `contains=` argument to `setClass`).
findClass	Function to find and manipulate classdefinitions.
findFunction	Returns a list of either the positions on the searchlist or the current top-level environment on which a functionobject for name exists.
findMethod	Returns the package(s) in the search list (or in thepackages specified by the `where` argument) that contain amethod for this function and signature.
findMethodSignatures	Returns a character matrix whose rows are the classnames from the signature of the corresponding methods; itoperates either from a list returned by `findMethods` or by computing such alist itself, given the same arguments as `findMethods`.
findMethods	Returns a list of the method definitions currentlyexisting for generic function `f`, limited to the methods defined inenvironment `where` if thatargument is supplied and possibly limited to those includingone or more of the specified `classes` in the methodsignature.
findUnique	Returns the list of environments (or equivalent) havingan object named what, using environment where and its parentenvironments.
fixPre1.8	Beginning with R version 1.8.0, the class of an objectcontains the identification of the package in which the classis defined. The function `fixPre1.8` fixes and reassignsobjects missing that information (typically because they wereloaded from a file saved with a previous version ofR).
formalArgs	Returns the names of the formal arguments of thisfunction.
functionBody, functionBody<-	These are utilities, currently in the methods package, that either provide some functionality needed by the package(e.g., element matching by name) or add compatibility withS-PLUS, or both.
generic.skeleton	Utility functions to support the definition and use offormal methods. Most of these functions will not normally becalled directly by the user.
getAllSuperClasses	Gets the names of all the classes that this classdefinition extends.
getClass, getClassDef	Get the definition of a class.
getClasses	Function to find and manipulate classdefinitions.
getDataPart	Utility called to implement `object@.Data`.
getFromClassDef	Extracts one of the intrinsically defined classdefinition properties (".Properties", etc.). Strictly autility function.
getFunction	These are utilities, currently in the methods package, that either provide some functionality needed by the package(e.g., element matching by name) or add compatibility withS-PLUS, or both.
getGeneric	Returns the definition of the function named `f` as a generic.
getGenerics	Returns the names of the generic functions that havemethods defined on where; this argument can be an environmentor an index into the search list.
getGroup	Returns the groups to which this generic belongs, searching from environment where (the global environmentnormally by default).
getGroupMembers	Returns all the members of the group generic functionnamed group.
getMethod	Returns the method corresponding to a given genericfunction and signature.
getMethods	An older alternative to `findMethods`, returning informationin the form of an object of class `MethodsList`, previously used formethod dispatch.
getMethodsForDispatch	Support routine for computations on formalmethods.
getMethodsMetaData	Utility to get the metadata object recording themethods defined in a particular package.
getPackageName	Returns the package associated with a particularenvironment or position on the search list, or the packagecontaining a particular function.
getSlots	Returns a named character vector. The names are thenames of the slots; the values are the classes of thecorresponding slots.
getValidity	The validity of `object` related to its classdefinition is tested. If the object is valid, `TRUE` is returned; otherwise, eithera vector of strings describing validity failures is returnedor an error is generated (according to whether `test` is `TRUE`).
hasArg	Returns `TRUE` if`name` corresponds to anargument in the call, either a formal argument to the functionor a component of `...`, and`FALSE` otherwise.
hasMethod	Tests for the existence of a method corresponding to agiven generic function and signature.
hasMethods	Returns `TRUE` or`FALSE` according to whetherthere is a nonempty table of methods for function `f` in the environment or searchposition `where` (or anywhereon the search list if `where`is missing).
implicitGeneric	Returns the implicit generic version.
initialize	Given the name or the definition of a class, plusoptionally data to be included in the object, initializereturns an object from that class.
is	Function to test inheritance relationships between anobject and a class (`is`) orbetween two classes (`extends`) and to establish suchrelationships (`setIs`, anexplicit alternative to the `contains=` argument to `setClass`).
isClass	Function to find and manipulate classdefinitions.
isClassDef	Is object a representation of a class?
isClassUnion	Tests if a class is a "ClassUnion".
isGeneric	Is there a function named `f`, and, if so, is it ageneric?
isGroup	Manages collections of methods associated with ageneric function, as well as providing information about thegeneric functions themselves.
isSealedClass, isSealedMethod	Check for either a method or a class that has beensealed when it was defined and thereforecannot be redefined.
isVirtualClass	Is the named class a virtual class?
isXS3Class	Old-style (S3) classes may be registered as S4 classes(by calling `setOldClass`), and many have been. These classes can then be contained in(i.e., superclasses of) regular S4 classes, allowing formalmethods and slots to be added to the S3 behavior. The function`S3Part` extracts or replacesthe S3 part of such an object. `S3Class` extracts or replaces theS3-style class. `S3Class`also applies to objects from an S4 class with `S3methods=TRUE` in the call to`setClass`.
listFromMethods	Support routine for computations on formalmethods.
makeClassRepresentation	Constructs an object of class `classRepresentation` to describe aparticular class. Mostly a utility function, but you can callit to create a class definition without assigning it, as`setClass` would do.
makeExtends	Converts the argument to a list defining the extensionmechanism.
makeGeneric	Makes a generic function object corresponding to thegiven function name, optional definition, and optional defaultmethod.
makePrototypeFromClassDef	Makes the prototype implied by the classdefinition.
makeStandardGeneric	A utility function that makes a valid function calling`standardGeneric` for name`f`.
matchSignature	Matches the signature object (a partially or completelynamed subset of the signature arguments of the genericfunction object fun) and returns a vector of all the classesin the order specified by `fun@signature`.
metaNameUndo	As its name implies, this function undoes the namemangling used to produce metadata object names and returns anobject of class `ObjectsWithPackage`.
method.skeleton	Writes a source file containing a call to `setMethod` to define a method for thegeneric function and signature supplied. By default, themethod definition is in line in the call, but can be made anexternal (previously assigned) function.
methodSignatureMatrix	Returns a matrix with the contents of the specifiedslots as rows.
methodsPackageMetaName	A name-mangling device to hide metadata defining methodand class information.
missingArg	Returns `TRUE` if thesymbol supplied is missing from the call corresponding to theenvironment supplied (by default, environment of the call to`missingArg`).
new	Given the name or the definition of a class, plusoptionally data to be included in the object, `new` returns an object from thatclass.
newBasic	The implementation of the function `new` for basic classes that don'thave a formal definition.
newClassRepresentation	Various functions to support the definition and use offormal classes. Most of them are rarely suitable to be calleddirectly. Others are somewhat experimental and/or partiallyimplemented only. Do refer to `setClass` for normal codedevelopment.
newEmptyObject	Utility function to create an empty object into whichslots can be set.
packageName	Returns the character-string name of the package(without the extraneous "package:" found in the searchlist).
packageSlot, packageSlot<-	Return or set the package name slot (currently anattribute, not a formal slot, but this may changesomeday).
possibleExtends	Finds the information that says whether one classextends another, directly or indirectly.
prohibitGeneric	Prevents your function from being made generic.
promptClass	Creates a help file for a class definition containingall relevant slot and method information for a class, withminimal markup for Rd processing; no QC facilities atpresent.
promptMethods	Generates a shell of documentation for the methods of ageneric function.
prototype	In calls to `setClass`, this function constructsthe `prototype`argument.
rbind2	Combines two matrix-like R objects by columns (`cbind2`) or rows (`rbind2`). These are (S4) genericfunctions with default methods.
reconcilePropertiesAndPrototype	Makes a list or a structure look like a prototype forthe given class.
registerImplicitGenerics	Saves a set of implicit generic definitions in thecached table of the current session.
rematchDefinition	If the specified method in a call to setMethodspecializes the argument list (by replacing ...), then`rematchDefinition`constructs the actual method stored.
removeClass	Function to find and manipulate classdefinitions.
removeGeneric	Removes all the methods for the generic function ofthis name and the function itself.
removeMethod	Creates and saves a formal method for a given functionand list of classes.
removeMethods	Removes all the methods for the generic function ofthis name.
representation	In calls to `setClass`, this function constructsthe `representation`argument.
requireMethods	Requires a subclass to implement methods for thegeneric functions, for this signature.
resetClass	Function to find and manipulate classdefinitions.
resetGeneric	Support routine for computations on formalmethods.
sealClass	Function to find and manipulate classdefinitions.
selectMethod	Returns a method corresponding to a given genericfunction and signature.
selectSuperClasses	Returns superclasses of `ClassDef`, possibly only nonvirtualor direct or simple ones. This function is designed to be fastand, consequently, only works with the `contains` slot of the correspondingclass definitions.
sessionData	Returns the index of the session data in the searchlist, attaching it if it is not attached.
setAs	Manages the relations that allow coercing an object toa given class.
setClass	Creates a class definition, specifying therepresentation (the slots) and/or the classes contained inthis one (the superclasses), plus other optionaldetails.
setClassUnion	A class may be defined as theunion of other classes, i.e., as avirtual class defined as a superclass of several otherclasses.This function creates class unions.
setDataPart	Utility called to implement `object@.Data`. Calls to `setDataPart` are also used to mergethe data part of a superclass prototype.
setGeneric	Creates a new generic function of the given name, i.e., a function that dispatches methods according to the classes ofthe arguments, from among the formal methods defined for thisfunction.
setGenericImplicit	Turns a generic implicit.
setGroupGeneric	Creates a new generic function of the given name, i.e., a function that dispatches methods according to the classes ofthe arguments, from among the formal methods defined for thisfunction.
setIs	Function to test inheritance relationships between anobject and a class (`is`) orbetween two classes (`extends`) and to establish suchrelationships (`setIs`, anexplicit alternative to the `contains=` argument to `setClass`).
setMethod	Creates and saves a formal method for a given functionand list of classes.
setOldClass	Registers an old-style ("S3") class as a formallydefined class. The `Classes`argument is the character vector used as the `class` attribute; in particular, ifthere is more than one string, old-style class inheritance ismimicked. Registering via `setOldClass` allows S3 classes toappear in method signatures, as a slot in an S4 class or as asuperclass of an S4 class.
setPackageName	Used to establish a package name in an environment thatwould otherwise not have one. This allows you to createclasses and/or methods in an arbitrary environment, but it isusually preferable tocreate packages by the standard R programming tools (`package.skeleton`, etc.).
setPrimitiveMethods	Utility functions to support the definition and use offormal methods. Most of these functions will not normally becalled directly by the user.
setReplaceMethod	Manages collections of methods associated with ageneric function, as well as providing information about thegeneric functions themselves.
setValidity	Sets the validity method of a class (but more normally, this method will be supplied as the `validity` argument to `setClass`).
show	Displays the object, by printing, plotting, or whateversuits its class. This function exists to be specialized bymethods. The default method calls `showDefault`. Formal methods for`show` will usually beinvoked for automatic printing (see the details).
showClass	Prints the information about a classdefinition.
showDefault	Utility used to enable show methods to be called by theautomatic printing (via `print.default`).
showExtends	Prints the elements of the list of extensions; for`printTo = FALSE`, returns alist with components what and how; this is used, e.g., by`promptClass()`.
showMethods	Shows a summary of the methods for one or more genericfunctions, possibly restricted to those involving specifiedclasses.
sigToEnv	Turns the signature (a named vector of classes) into anenvironment with the classes assigned to the names.
signature	Returns a named list of classes to be matched toarguments of a generic function.
slot, slot<-	Return or set information about the individual slots inan object.
slotNames	Returns or sets information about the individual slotsin an object.
slotsFromS3	Old-style (S3) classes may be registered as S4 classes(by calling `setOldClass`), and many have been. These classes can then be contained in(i.e., superclasses of) regular S4 classes, allowing formalmethods and slots to be added to the S3 behavior. The function`S3Part` extracts or replacesthe S3 part of such an object. `S3Class` extracts or replaces theS3-style class. `S3Class`also applies to objects from an S4 class with `S3methods=TRUE` in the call to`setClass`.
substituteDirect	Substitutes for the variables named in the secondargument the corresponding objects; substituting into `object`.
standardGeneric	Dispatches a method from the current function call forthe generic function.
substituteFunctionArgs	Utility function to support the definition and use offormal methods. Most of these functions will not normally becalled directly by the user.
superClassDepth	`superClassDepth`, which is called from `getAllSuperClasses`, returns the sameinformation, but as a list with components label and depth, the latter for the number of generations back each class is inthe inheritance tree.
testInheritedMethods	A set of distinct inherited signatures is generated totest inheritance for all the methods of a specified genericfunction. If method selection is ambiguous for some of these, a summary of the ambiguities is attached to the returnedobject. This test should be performed by package authorsbefore releasing a package.
testVirtual	Tests for a virtual class.
traceOff	The functions `traceOn` and `traceOff` have been replaced byextended versions of the functions `trace` and `untrace` and should not beused.
traceOn	The functions `traceOn` and `traceOff` have been replaced byextended versions of the functions `trace` and `untrace` and should not beused.
tryNew, trySilent	Tries to generate a new element from this class, but ifthe attempt fails (as, e.g., when the class is undefined orvirtual) just returns `NULL`.
unRematchDefinition	Using knowledge of how rematchDefinition works, `unRematchDefinition`reverses the procedure; if given a function or methoddefinition that does not correspond to this form, it justreturns its argument.
validObject	The validity of an object related to its classdefinition is tested. If the object is valid, `TRUE` is returned; otherwise, eithera vector of strings describing the validity failures isreturned or an error is generated (according to whether`test` is `TRUE`).
validSlotNames	Returns names unless one of the names is reserved, inwhich case there is an error. (As of this writing, "class" isthe only reserved slot name.)

mgcv

This package provides functions for generalized additivemodeling and generalized additive mixed modeling. The term GAM is takento include any GLM estimated by quadratically penalized (possiblyquasi-) likelihood maximization. For more information on this package, see the help file.

nlme

This package provides functions for linear and nonlinearmixed-effects models. See the help file for more information.

nnet

This package provides functions for feed-forward neuralnetworks and multinomial log-linear models.

Functions

Function	Description
class.ind	Generates a class indicator function from a givenfactor.
multinom	Fits multinomial log-linear models via neuralnetworks.
nnet	Fits single-hidden-layer neural network, possibly withskip-layer connections.
nnetHess	Evaluates the Hessian (matrix of second derivatives) ofthe specified neural network. Normally called via argument`Hess=TRUE` to `nnet` or via `vcov.multinom`.
which.is.max	Finds the maximum position in a vector, breaking tiesat random.

rpart

This package provides functions for recursive partitioningand regression trees.

Functions

Function	Description
meanvar	Creates a plot on the current graphics device of thedeviance of the node divided by the number of observations atthe node. Also returns the node number.
na.rpart	Handles missing values in an `rpart` object.
path.rpart	Returns a names list, where each element contains thesplits on the path from the root to the selected nodes.
plotcp	Gives a visual representation of the cross-validationresults in an `rpart`object.
post	Generates a PostScript presentation plot of an `rpart` object.
printcp	Displays the `cp`table for a fitted `rpart`object.
prune	Determines a nested sequence of subtrees of thesupplied `rpart` object byrecursively `snipping` offthe least important splits, based on the complexity parameter(`cp`).
rpart	Fits an `rpart`model.
rpart.control	Various parameters that control aspects of the `rpart` fit.
rpconvert	Rpart objects changed (slightly) in their internalformat in order to accommodate the changes for user-writtensplit functions. This routine updates an old object to the newformat.
rsq.rpart	Produces two plots. The first plots ther-square (apparent and apparent − fromcross-validation) versus the number of splits. The secondplots the relative error(cross-validation) +/− 1 − SE fromcross-validation versus the number of splits.
snip.rpart	Creates a "snipped" rpart object, containing the nodesthat remain after selected subtrees have been snipped off. Theuser can snip nodes using the toss argument or interactivelyby clicking the mouse button on specified nodes within thegraphics window.
xpred.rpart	Gives the predicted values for an `rpart` fit, under cross-validation, for a set of complexity parameter values.

Data Sets

Data Set	Class	Description
car.test.frame	data.frame	The `car.test.frame` data frame has 60rows and 8 columns, giving data on makes of cars taken fromthe April 1990 issue of Consumer Reports.This is part of a larger data set, some columns of which aregiven in `cu.summary`.
cu.summary	data.frame	The `cu.summary` dataframe has 117 rows and 5 columns, giving data on makes of carstaken from the April 1990 issue of ConsumerReports.
kyphosis	data.frame	The `kyphosis` dataframe has 81 rows and 4 columns, representing data on children who have had correctivespinal surgery.
solder	data.frame	The `solder` dataframe has 720 rows and 6 columns, representing a balancedsubset of a designed experiment varying 5 factors on thesoldering of components on printed-circuit boards.

spatial

This package provides functions for Kriging and pointpattern analysis.

Functions

Function	Description
Kaver	Forms the average of a series of (usually simulated)`K` functions.
Kenvl	Computes envelope (upper and lower limits) and averageof simulations of `K` functions.
Kfn	Actually computes L = sqrt(K/pi).
Psim	Simulates binomial spatial point process.
SSI	Simulates SSI (sequential spatial inhibition) pointprocess.
Strauss	Simulates Strauss spatial point process.
anova.trls	Computes analysis of variance tables for one or morefitted trend surface model objects; where `anova.trls` is called with multipleobjects, it passes on the arguments to `anovalist.trls`.
anovalist.trls	Computes analysis of variance tables for one or morefitted trend surface model objects; where `anova.trls` is called with multipleobjects, it passes on the arguments to `anovalist.trls`.
correlogram	Computes spatial correlograms of spatial data orresiduals.
expcov	Spatial covariance function for use with `surf.gls`.
gaucov	Spatial covariance function for use with `surf.gls`.
plot.trls	Provides the basic quantities used in forming a varietyof diagnostics for checking the quality of regression fits for trendsurfaces calculated by `surf.ls`.
ppgetregion	Retrieves the rectangular domain `(xl, xu)` x `(yl, yu)` from the underlying Ccode.
ppinit	Reads a file in standard format and creates a pointprocess object.
pplik	Pseudolikelihood estimation of a Strauss spatial pointprocess.
ppregion	Sets the rectangular domain `(xl, xu)` x `(yl, yu)`.
predict.trls	Predicted values based on trend surface modelobject.
prmat	Evaluates Kriging surface over a grid.
semat	Evaluates Kriging standard error of prediction over agrid.
sphercov	Spatial covariance function for use with `surf.gls`.
surf.gls	Fits a trend surface by generalized leastsquares.
surf.ls	Fits a trend surface by least squares.
trls.influence	Provides the basic quantities used in forming a varietyof diagnostics for checking the quality of regression fits fortrend surfaces calculated by `surf.ls`.
trmat	Evaluates trend surface over a grid.
variogram	Computes spatial (semi-)variogram of spatial data orresiduals.

splines

This package provides functions for working withregression splines using the B-spline basis, bs, and the natural cubic spline basis, ns.

Functions

Function	Description
as.polySpline	Creates the piecewise polynomial representation of aspline object.
asVector	This is a generic function. Methods for this functioncoerce objects of given classes to vectors.
backSpline	Creates a monotone inverse of a monotone naturalspline.
bs	Generates the B-spline basis matrix for a polynomialspline.
interpSpline	Creates an interpolation spline, either from `x` and `y` vectors or from aformula/data.frame combination.
ns	Generates the B-spline basis matrix for a natural cubicspline.
periodicSpline	Creates a periodic interpolation spline, either from`x` and `y` vectors or from aformula/data.frame combination.
polySpline	Creates the piecewise polynomial representation of aspline object.
spline.des	Evaluates the design matrix for the B-splines definedby `knots` at the values in`x`.
splineDesign	Evaluates the design matrix for the B-splines definedby `knots` at the values in`x`.
splineKnots	Returns the knot vector corresponding to a splineobject.
splineOrder	Returns the order of a spline object.
xyVector	Creates an object to represent a set ofx-y pairs.

Pages: 1, 2, 3, 4, 5

MASS

Functions

Data Sets

methods

Functions

mgcv

nlme

nnet

Functions

rpart

Functions

Data Sets

spatial

Functions

splines

Functions

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