Appendix: R Reference - R in a Nutshell

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Appendix: R Reference - R in a Nutshell
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boot

This package provides functions for bootstrapresampling.

Functions

Function	Description
EEF.profile	Calculates the log-likelihood for a mean using anempirical exponential family likelihood.
EL.profile	Calculates the log-likelihood for a mean using anempirical likelihood.
abc.ci	Calculates equitailed two-sided nonparametricapproximate bootstrap confidence intervals for a parameter, given a set of data and an estimator of the parameter, usingnumerical differentiation.
boot	Generates `R`bootstrap replicates of a statistic applied to data.
boot.array	Takes a bootstrap object calculated by one of thefunctions `boot`, `censboot`, or `tilt.boot` and returns the frequency(or index) array for the bootstrap resamples.
boot.ci	Generates five different types of equitailed two-sidednonparametric confidence intervals. These are the first-ordernormal approximation, the basic bootstrap interval, theStudentized bootstrap interval, the bootstrap percentileinterval, and the adjusted bootstrap percentile (BCa)interval. All or a subset of these intervals can begenerated.
censboot	Applies types of bootstrap resampling that have beensuggested to deal with right-censored data. It can alsoperform model-based resampling using a Cox regressionmodel.
control	Finds control variate estimates from a bootstrap outputobject.
corr	Calculates the weighted correlation given a data setand a set of weights.
cum3	Calculates an estimate of the third cumulant, orskewness, of a vector. Also, if more than one vector isspecified, a product-moment of order 3 is estimated.
cv.glm	Calculates the estimated K-foldcross-validation prediction error for generalized linearmodels.
empinf	Calculates the empirical influence values for astatistic applied to a data set.
envelope	Calculates overall and pointwise confidence envelopesfor a curve based on bootstrap replicates of the curveevaluated at a number of fixed points.
exp.tilt	Calculates exponentially tilted multinomialdistributions such that the resampling distributions of thelinear approximation to a statistic have the requiredmeans.
freq.array	Takes a matrix of indices for nonparametric bootstrapresamples and returns the frequencies of the originalobservations in each resample.
glm.diag	Calculates jackknife deviance residuals, standardizeddeviance residuals, standardized Pearson residuals, approximate Cook statistic, leverage, and estimated dispersion.
glm.diag.plots	Makes plot of jackknife deviance residuals againstlinear predictor, normal scores plots of standardized devianceresiduals, plot of approximate Cook statistics againstleverage/(1 − leverage), and case plot of Cookstatistic.
imp.moments, imp.prob, imp.quantile	Central moment, tail probability, and quantileestimates for a statistic under importance resampling.
imp.weights	Calculates the importance sampling weight required tocorrect for simulation from a distribution with probabilities`p` when estimates arerequired assuming that simulation was from an alternativedistribution with probabilities `q`.
inv.logit	Given a numeric object, returns the inverse logit ofthe values.
jack.after.boot	Calculates the jackknife influence values from abootstrap output object and plots the correspondingjackknife-after-bootstrap plot.
k3.linear	Estimates the skewness of a statistic from itsempirical influence values.
lik.CI	Function for use with the practicals in Davison andHinkley (1997), Bootstrap Methods and TheirApplications, Cambridge Series in Statistical andProbabilistic Mathematics, No. 1.
linear.approx	Takes a bootstrap object and, for each bootstrapreplicate, calculates the linear approximation to thestatistic of interest for that bootstrap sample.
logit	Calculates the logit of proportions.
nested.corr	Function for use with the practicals in Davison andHinkley (1997), Bootstrap Methods and TheirApplications, Cambridge Series in Statistical andProbabilistic Mathematics, No. 1.
norm.ci	Using the normal approximation to a statistic, calculates equitailed two-sided confidence intervals.
saddle	Calculates a saddlepoint approximation to thedistribution of a linear combination of Wat a particular point `u`, where W is a vector of randomvariables.
saddle.distn	Approximates an entire distribution using saddlepointmethods.
simplex	This function will optimize the linear function`a\%\%x` subject to theconstraints `A1\%\%x <=b1`, `A2\%\%x >=b2`, `A3\%\%x =b3`, and `x >=0`. Either maximization or minimization is possiblebut the default is minimization.
smooth.f	Uses the method of frequency smoothing to find adistribution on a data set that has a required value, `theta`, of the statistic ofinterest.
tilt.boot	This function will run an initial bootstrap with equalresampling probabilities (if required) and will use the outputof the initial run to find resampling probabilities that putthe value of the statistic at required values. It then runs animportance resampling bootstrap using the calculatedprobabilities as the resampling distribution.
tsboot	Generates `R`bootstrap replicates of a statistic applied to a time series.The replicate time series can be generated using fixed orrandom block lengths or can be model-based replicates.
var.linear	Estimates the variance of a statistic from itsempirical influence values.

Data Sets

Data Set	Class	Description
acme	data.frame	The `acme` data framehas 60 rows and 3 columns. The excess returns for the AcmeCleveland Corporation, along with those for all stocks listedon the New York and American Stock Exchanges, were recordedover a 5-year period. These excess returns are relative to thereturn on a riskless investment such as U.S. Treasurybills.
aids	data.frame	The `aids` data framehas 570 rows and 6 columns. Although all cases of AIDS inEngland and Wales must be reported to the Communicable DiseaseSurveillance Centre, there is often a considerable delaybetween the time of diagnosis and the time that it isreported. In estimating the prevalence of AIDS, account mustbe taken of the unknown number of cases that have beendiagnosed but not reported. The data set here records thereported cases of AIDS diagnosed from July 1983 until the endof 1992. The data is cross-classified by the date of diagnosisand the time delay in the reporting of the cases.
aircondit	data.frame	Proschan reported on the times between failures of theair-conditioning equipment in 10 Boeing 720 aircraft. The`aircondit` data framecontains the intervals for the ninth aircraft, while `aircondit7` contains those for theseventh aircraft. Both data frames have just one column. Notethat the data has been sorted into increasing order.
aircondit7	data.frame	Proschan reported on the times between failures of theair-conditioning equipment in 10 Boeing 720 aircraft. The`aircondit` data framecontains the intervals for the ninth aircraft, while `aircondit7` contains those for theseventh aircraft. Both data frames have just one column. Notethat the data has been sorted into increasing order.
amis	data.frame	The `amis` data framehas 8, 437 rows and 4 columns. In a study into the effect thatwarning signs have on speeding patterns, Cambridgeshire CountyCouncil considered 14 pairs of locations. The locations werepaired to account for factors such as traffic volume and typeof road. One site in each pair had a sign erected warning ofthe dangers of speeding and asking drivers to slow down. Noaction was taken at the second site. Three sets ofmeasurements were taken at each site. Each set of measurementswas nominally of the speeds of 100 cars, but not all siteshave exactly 100 measurements. These speed measurements weretaken before the erection of the sign, shortly after theerection of the sign, and again after the sign had been inplace for some time.
aml	data.frame	The `aml` data framehas 23 rows and 3 columns. A clinical trial to evaluate theefficacy of maintenance chemotherapy for acute myelogenousleukemia was conducted by Embury et al. at StanfordUniversity. After reaching a stage of remission throughtreatment by chemotherapy, patients were randomized into twogroups. The first group received maintenance chemotherapy, andthe second group did not. The aim of the study was to see ifmaintenance chemotherapy increased the length of theremission. The data here formed a preliminary analysis thatwas conducted in October 1974.
beaver	ts	The `beaver` dataframe has 100 rows and 4 columns. It is a multivariate timeseries of class `"ts"` andalso inherits from class `"data.frame"`. This data set is partof a long study into body temperature regulation in beavers.Four adult female beavers were live-trapped and had atemperature-sensitive radio transmitter surgically implanted.Readings were taken every 10 minutes. The location of thebeaver was also recorded, and her activity level wasdichotomized by whether she was in the retreat or outside ofit, since high-intensity activities only occur outside of theretreat. The data in this data frame comes from those readingsfor one of the beavers on a day in autumn.
bigcity	data.frame	The `bigcity` dataframe has 49 rows and 2 columns. The `city` data frame has 10 rows and 2columns. The measurements are the populations (in 1000s) of 49U.S. cities in 1920 and 1930. The 49 cities are a randomsample taken from the 196 largest cities in 1920. The `city` data frame consists of thefirst 10 observations in `bigcity`.
brambles	data.frame	The `brambles` dataframe has 823 rows and 3 columns. The location of livingbramble canes in a 9-m square plot was recorded. We take 9 mto be the unit of distance so that the plot can be thought ofas a unit square. The bramble canes were also classified bytheir age.
breslow	data.frame	The `breslow` dataframe has 10 rows and 5 columns. In 1961, Doll and Hill sentout a questionnaire to all men on the British Medical Registerinquiring about their smoking habits. Almost 70% of the menreplied. Death certificates were obtained for medicalpractitioners, and causes of death were assigned on the basisof these certificates. The `breslow` data set contains theperson-years of observations and deaths from coronary arterydisease accumulated during the first 10 years of thestudy.
calcium	data.frame	The `calcium` dataframe has 27 rows and 2 columns. Howard Grimes of the BotanyDepartment, North Carolina State University, conducted anexperiment for biochemical analysis of intracellular storageand transport of calcium across plasma membrane. Cells weresuspended in a solution of radioactive calcium for a certainlength of time, and then the amount of radioactive calciumthat was absorbed by the cells was measured. The experimentwas repeated independently with nine different times ofsuspension each replicated three times.
cane	data.frame	The `cane` data framehas 180 rows and 5 columns. The data frame represents arandomized block design with 45 varieties of sugarcane and 4blocks. The aim of the experiment was to classify thevarieties into resistant, intermediate, and susceptible to adisease called "coal of sugarcane" (carvao dacana-de-acucar). This is a disease that is commonin sugar-cane plantations in certain areas of Brazil. For eachplot, 50 pieces of sugarcane stem were put in a solutioncontaining the disease agent, and then some were planted inthe plot. After a fixed period of time, the total number ofshoots and the number of diseased shoots wererecorded.
capability	data.frame	The `capability` dataframe has 75 rows and 1 column. The data consists of simulatedsuccessive observations from a process in equilibrium. Theprocess is assumed to have specification limits (5.49, 5.79).
catsM	data.frame	The `catsM` data framehas 97 rows and 3 columns. One hundred and forty-four adult(over 2 kg in weight) cats used for experiments with the drugdigitalis had their heart and body weight recorded.Forty-seven of the cats were female, and 97 were male. The`catsM` data frame consistsof the data for the male cats. The full data can be found indata set `\link[MASS]{cats`}in package `MASS`.
cav	data.frame	The `cav` data framehas 138 rows and 2 columns. The data gives the positions ofthe individual caveolae in a square region with sides oflength 500 units. This grid was originally on a 2.65μm squareof muscle fiber. The data consist of those points falling inthe lower-left quarter of the region used for the data set`caveolae.dat`.
cd4	data.frame	The `cd4` data framehas 20 rows and 2 columns. CD4 cells are carried in the bloodas part of the human immune system. One of the effects of thehuman immunodeficiency virus (HIV) is that these cells die.The count of CD4 cells is used in determining the onset offull-blown AIDS in a patient. In this study of theeffectiveness of a new antiviral drug on HIV, 20 HIV-positivepatients had their CD4 counts recorded and then were put on acourse of treatment with this drug. After using the drug for 1year, their CD4 counts were again recorded. The aim of theexperiment was to show that patients taking the drug hadincreased CD4 counts, which is not generally seen in HIV-positive patients.
cd4.nested	boot	This is an example of a nested bootstrap for thecorrelation coefficient of the `cd4` data frame.
channing	data.frame	The `channing` dataframe has 462 rows and 5 columns. Channing House is aretirement center in Palo Alto, California. The data wascollected between the opening of the house in 1964 until July1, 1975. During that time, 97 men and 365 women passed throughthe center. For each of these, their age on entry and also onleaving or death was recorded. A large number of theobservations were censored mainly due to the resident beingalive on July 1, 1975, when the data was collected. Over thecourse of the study, 130 women and 46 men died at ChanningHouse. Differences between the survival of the sexes, takingage into account, was one of the primary concerns of thisstudy.
city	data.frame	The `bigcity` dataframe has 49 rows and 2 columns. The `city` data frame has 10 rows and 2columns. The measurements are the populations (in 1000s) of 49U.S. cities in 1920 and 1930. The 49 cities are a randomsample taken from the 196 largest cities in 1920. The `city` data frame consists of thefirst 10 observations in `bigcity`.
claridge	data.frame	The `claridge` dataframe has 37 rows and 2 columns. The data comes from anexperiment that was designed to look for a relationshipbetween a certain genetic characteristic and handedness. The37 subjects were women who had a son with mental retardationdue to inheriting a defective X-chromosome. For each suchmother, a genetic measurement of her DNA was made. Largervalues of this measurement are known to be linked to thedefective gene, and it was hypothesized that larger valuesmight also be linked to a progressive shift away fromright-handedness. Each woman also filled in a questionnaireregarding which hand she used for various tasks. From thesequestionnaires, a measure of hand preference was found foreach mother. The scale of this measure goes from 1, indicating women who alwaysfavor their right hand, to 8, indicating women who alwaysfavor their left hand. Between these two extremes are womenwho favor one hand for some tasks and the other for othertasks.
cloth	data.frame	The `cloth` data framehas 32 rows and 2 columns.
co.transfer	data.frame	The `co.transfer` dataframe has 7 rows and 2 columns. Seven smokers with chickenpoxhad their levels of carbon monoxide transfer measured uponbeing admitted to the hospital and then again after 1 week.The main question was whether 1 week of hospitalization hadchanged the carbon monoxide transfer factor.
coal	data.frame	The `coal` data framehas 191 rows and 1 column. This data frame gives the dates of191 explosions in coal mines that resulted in 10 or morefatalities. The time span of the data is from March 15, 1851, until March 22, 1962.
darwin	data.frame	The `darwin` dataframe has 15 rows and 1 column. Charles Darwin conducted anexperiment to examine the superiority of cross-fertilizedplants over self-fertilized plants. Fifteen pairs of plantswere used. Each pair consisted of one cross-fertilized plantand one self-fertilized plant that germinated at the same timeand grew in the same pot. The plants were measured at a fixedtime after planting, and the differences in heights betweenthe cross- and self-fertilized plants were recorded in eighthsof an inch.
dogs	data.frame	The `dogs` data framehas 7 rows and 2 columns. Data on the cardiac oxygenconsumption and left ventricular pressure was gathered onseven domestic dogs.
downs.bc	data.frame	The `downs.bc` dataframe has 30 rows and 3 columns. Down's syndrome is a geneticdisorder caused by an extra chromosome 21 or a part ofchromosome 21 being translocated to another chromosome. Theincidence of Down's syndrome is highly dependent on themother's age and rises sharply after age 30. In the 1960s, alarge-scale study of the effect of maternal age on theincidence of Down's syndrome was conducted at the BritishColumbia Health Surveillance Registry. This data frameconsists of the data that was collected in that study. Motherswere classified by age. Most groups correspond to the age inyears, but the first group comprises all mothers aged 15–17and the last is those aged 46–49. No data for mothers over 50or below 15 was collected.
ducks	data.frame	The `ducks` data framehas 11 rows and 2 columns. Each row of the data framerepresents a male duck that is a second-generation crossbetween a mallard and a pintail. For 11 such ducks, abehavioral index and plumage index were calculated. These weremeasured on scales devised for this experiment, which was toexamine whether there was any link between which species theducks resembled physically and which they resembled inbehavior. The scale for physical appearance ranged from 0(identical in appearance to a mallard) to 20 (identical to apintail). The behavioral traits of the ducks were on a scaleof 0 to 15, with lower numbers indicating more mallard-likebehavior.
fir	data.frame	The `fir` data framehas 50 rows and 3 columns. The number of balsam-fir seedlingsin each quadrant of a grid of 50 five-foot-square quadrantswere counted. The grid consisted of 5 rows of 10 quadrants ineach row.
frets	data.frame	The `frets` data framehas 25 rows and 4 columns. The data consists of measurementsof the length and breadth of the heads of pairs of adultbrothers in 25 randomly sampled families. All measurements areexpressed in millimeters.
grav	data.frame	The `gravity` dataframe has 81 rows and 2 columns. The `grav` data set has 26 rows and 2columns. Between May 1934 and July 1935, the U.S. NationalBureau of Standards conducted a series of experiments toestimate the acceleration due to gravity, g, at Washington, DC. Each experimentproduced a number of replicate estimates ofg using the same methodology. Althoughthe basic method remained the same for all experiments, thatof the reversible pendulum, there were changes inconfiguration. The `gravity`data frame contains the data from all eight experiments. The`grav` data frame containsthe data from experiments 7 and 8. The data is expressed asdeviations from 980.000 in centimeters per secondsquared.
gravity	data.frame	The `gravity` dataframe has 81 rows and 2 columns. The `grav` data set has 26 rows and 2columns. Between May 1934 and July 1935, the U.S. NationalBureau of Standards conducted a series of experiments toestimate the acceleration due to gravity, g, at Washington, DC. Each experimentproduced a number of replicate estimates ofg using the same methodology. Althoughthe basic method remained the same for all experiments, thatof the reversible pendulum, there were changes inconfiguration. The `gravity`data frame contains the data from all eight experiments. The`grav` data frame containsthe data from experiments 7 and 8. The data is expressed asdeviations from 980.000 in centimeters per secondsquared.
hirose	data.frame	The `hirose` dataframe has 44 rows and 3 columns. PET film is used inelectrical insulation. In this accelerated life test, thefailure times for 44 samples in gas-insulated transformerswere estimated. Four different voltage levels wereused.
islay	data.frame	The `islay` data framehas 18 rows and 1 column. Measurements were taken of paleocurrent azimuths from theJura Quartzite on the Scottish island of Islay.
manaus	ts	The `manaus` timeseries is of class `"ts"` andhas 1, 080 observations on one variable. The data values aremonthly averages of the daily stages (heights) of the RioNegro at Manaus. Manaus is 18 km upstream from the confluenceof the Rio Negro with the Amazon but because of the tiny slopeof the water surface and the lower courses of its flatlandaffluents, they may be regarded as a good approximation of thewater level in the Amazon at the confluence. The data herecovers 90 years from January 1903 until December 1992. TheManaus gauge is tied in with an arbitrary benchmark of 100mset in the steps of the Municipal Prefecture; gauge readingsare usually referred to sea level, on the basis of a mark onthe steps leading to the Parish Church (Matriz), which isassumed to lie at an altitude of 35.874 m according toobservations made many years ago under the direction of SamuelPereira, an engineer in charge of the Manaus SanitationCommittee Whereas such an altitude cannot, by any means, beconsidered to be a precise datum point, observations have beenprovisionally referred to it. The measurements are inmeters.
melanoma	data.frame	The `melanoma` dataframe has 205 rows and 7 columns. The data consists of measurements made on patientswith malignant melanoma. Each patient had his or her tumorsurgically removed at the Department of Plastic Surgery, University Hospital of Odense, Denmark, during the period1962–1977. The surgery consisted of complete removal of thetumor together with about 2.5 cm of the surrounding skin.Among the measurements taken were the thickness of the tumorand whether it was ulcerated or not. These are thought to beimportant prognostic variables in that patients with a thickand/or ulcerated tumor have an increased chance of death frommelanoma. Patients were followed until the end of1977.
motor	data.frame	The `motor` data framehas 94 rows and 4 columns. The rows were obtained by removingreplicate values of `time`from the data set `mcycle`.Two extra columns were added to allow for strata with adifferent residual variance in each stratum.
neuro	matrix	`neuro` is a matrixcontaining times of observed firing of a neuron in windows of250 ms either side of the application of a stimulus to a humansubject. Each row of the matrix is a replication of theexperiment, and there are a total of 469 replicates.
nitrofen	data.frame	The `nitrofen` dataframe has 50 rows and 5 columns. Nitrofen is a herbicide thatwas used extensively for the control of broad-leaved and grassweeds in cereals and rice. Although it is relatively nontoxicto adult mammals, nitrofen is a significant teratogen andmutagen. It is also acutely toxic and reproductively toxic tocladoceran zooplankton. Nitrofen is no longer incommercial use in the United States, having been the firstpesticide to be withdrawn due to teratogenic effects. The datahere comes from an experiment to measure the reproductivetoxicity of nitrofen on a species of zooplankton(Ceriodaphnia dubia). Fifty animals wererandomized into batches of 10, and each batch was put in asolution with a measured concentration of nitrofen. Then thenumber of live offspring in each of the three broods of eachanimal was recorded.
nodal	data.frame	The `nodal` data framehas 53 rows and 7 columns. The treatment strategy for apatient diagnosed with prostate cancer depends highly onwhether the cancer has spread to the surrounding lymph nodes.It is common to operate on the patient to get samples from thenodes, which can then be analyzed under a microscope, butclearly it would be preferable if an accurate assessment ofnodal involvement could be made without surgery. For a sampleof 53 prostate cancer patients, a number of possible predictorvariables were measured before surgery. The patients then hadsurgery to determine nodal involvement. The point of the studywas to see if nodal involvement could be accurately predictedfrom the predictor variables and which ones were mostimportant.
nuclear	data.frame	The `nuclear` dataframe has 32 rows and 11 columns. The data relates to theconstruction of 32 light-water reactor (LWR) plantsconstructed in the United States in the late 1960s and early1970s. The data was collected with the aim of predicting thecost of construction of additional LWR plants. Six of thepower plants had partial turnkey guarantees, and it ispossible that, for these plants, some manufacturers' subsidiesmay be hidden in the quoted capital costs.
paulsen	data.frame	The `paulsen` dataframe has 346 rows and 1 column. Sections were prepared fromthe brain of adult guinea pigs. Spontaneous currents thatflowed into individual brain cells were then recorded and thepeak amplitude of each current measured. The aim of theexperiment was to see if the current flow was quantal innature (i.e., that it is not a single burst but instead isbuilt up of many smaller bursts of current). If the currentwas indeed quantal, then it would be expected that thedistribution of the current amplitude would be multimodal withmodes at regular intervals. The modes would be expected todecrease in magnitude for higher current amplitudes.
poisons	data.frame	The `poisons` dataframe has 48 rows and 3 columns. The data form a 3 × 4factorial experiment, the factors being three poisons and fourtreatments. Each combination of the two factors was used onfour animals, the allocation to animals having been completelyrandomized.
polar	data.frame	The `polar` data framehas 50 rows and 2 columns. The data consists of the polepositions from a paleomagnetic study of New Caledonianlaterites.
remission	data.frame	The `remission` dataframe has 27 rows and 3 columns.
salinity	data.frame	The `salinity` dataframe has 28 rows and 4 columns. Biweekly averages of thewater salinity and river discharge in Pamlico Sound, NorthCarolina, were recorded between the years 1972 and 1977. Thedata in this set consists only of those measurements in March, April, and May.
survival	data.frame	The `survival` dataframe has 14 rows and 2 columns. The data measured thesurvival percentages of batches of rats who were given varyingdoses of radiation. At each of six doses there were two orthree replications of the experiment.
tau	data.frame	The `tau` data framehas 60 rows and 2 columns. The tau particle is a heavyelectron-like particle discovered in the 1970s by Martin Perlat the Stanford Linear Accelerator Center. Soon after itsproduction, the tau particle decays into various collectionsof more stable particles. About 86% of the time, the decayinvolves just one charged particle. This rate has beenmeasured independently 13 times. The one-charged-particleevent is made up of four major modes of decay as well as acollection of other events. The four main types of decay aredenoted rho, pi, e, and mu. These rates have been measuredindependently 6, 7, 14, and 19 times, respectively. Due tophysical constraints, each experiment can only estimate thecomposite one-charged-particle decay rate or the rate of oneof the major modes of decay. Each experiment consists of amajor research project involving many years' work. One of thegoals of the experiments was to estimate the rate of decay dueto events other than the four main modes of decay. These areuncertain events and so cannot themselves be observeddirectly.
tuna	data.frame	The `tuna` data framehas 64 rows and 1 column. The data comes from an aerial linetransect survey of southern bluefin tuna in the GreatAustralian Bight. An aircraft with two spotters on board flewrandomly allocated line transects. Each school of tuna sightedwas counted and its perpendicular distance from the transectmeasured. The survey was conducted in summer when tuna tend tostay on the surface.
urine	data.frame	The `urine` data framehas 79 rows and 7 columns. Seventy-nine urine specimens wereanalyzed in an effort to determine if certain physicalcharacteristics of the urine might be related to the formationof calcium oxalate crystals.
wool	ts	`wool` is a timeseries of class `"ts"` andcontains 309 observations. Each week that the market was open, the Australian Wool Corporation set a floor price thatdetermined its policy on intervention and was therefore areflection of the overall price of wool for the week inquestion. Actual prices paid varied considerably about thefloor price. The series here is the log of the ratio betweenthe price for fine-grade wool and the floor price, each marketweek between July 1976 and June 1984.

class

This package provides functions for classification.

Functions

Function	Description
SOM, batchSOM	Kohonen's self-organizing maps (SOMs) are a crude formof multidimensional scaling.
condense	Condenses training set fork-nearest-neighbor(k-NN) classifier.
knn	k-nearest-neighbor classificationfor test set from training set. For each row of the test set, the `k`-nearest (in Euclideandistance) training set vectors are found, and theclassification is decided by majority vote, with ties brokenat random. If there are ties for the `k`th nearest vector, allcandidates are included in the vote.
knn.cv	k-nearest-neighborcross-validatory classification from training set.
knn1	Nearest-neighbor classification for test set fromtraining set. For each row of the test set, the nearestneighbor (by Euclidean distance) training set vector is found, and its classification used. If there is more than one nearestneighbor, a majority vote is used, with ties broken atrandom.
lvq1, lvq2, lvq3	Moves examples in a codebook to better represent thetraining set.
lvqinit	Constructs an initial codebook for learning vectorquantization (LVQ) methods.
lvqtest	Classifies a test set by 1-NN from a specified LVQcodebook.
multiedit	Multiedit for k-NNclassifier.
olvq1	Moves examples in a codebook to better represent thetraining set.
reduce.nn	Reduces training set for a k-NNclassifier. Used after `condense`.
somgrid	Plotting functions for SOM results.

cluster

This package provides functions for clusteranalysis.

Functions

Function	Description
agnes	Computes agglomerative hierarchical clustering of thedata set.
bannerplot	Draws a "banner, " i.e., basically a horizontal `barplot` visualizing the(agglomerative or divisive) hierarchical clustering or another binary dendrogram structure.
clara	Computes a `"clara"`object, a list representing a clustering of the data into`k`clusters.
clusplot	Draws a two-dimensional (2D) "clusplot" on the currentgraphics device.
coef.hclust	Computes the "agglomerative coefficient, " measuring theclustering structure of the data set.
daisy	Computes all the pairwise dissimilarities (distances)between observations in the data set.
diana	Computes a divisive hierarchical clustering of the dataset, returning an object of class `diana`.
ellipsoidPoints	Computes points on the ellipsoid boundary, mostly fordrawing.
ellipsoidhull	Computes the "ellipsoid hull" or "spanning ellipsoid, "i.e., the ellipsoid of minimal volume ("area" in 2D) such thatall given points lie just inside or on the boundary of theellipsoid.
fanny	Computes a fuzzy clustering of the data into`k`clusters.
lower.to.upper.tri.inds	Computes index vectors for extracting or reordering oflower or upper triangular matrices that are stored ascontiguous vectors.
mona	Returns a list representing a divisive hierarchicalclustering of a data set with binary variables only.
pam	Partitioning (clustering) of the data into`k`clusters "around medoids, " a more robust version ofk-means clustering.
pltree	Generic function drawing a clustering tree (`"dendrogram"`) on the currentgraphics device. There is a `twins` method; see `pltree.twins` for usage andexamples.
predict.ellipsoid	Computes points on the ellipsoid boundary, mostly fordrawing.
silhouette	Computes silhouette information according to a givenclustering in k clusters.
sizeDiss	Returns the number of observations (samplesize) corresponding to a dissimilarity-like objector, equivalently, the number of rows or columns of a matrixwhen only the lower or upper triangular part (withoutdiagonal) is given. It is nothing else but the inversefunction of f(n)= n(n −1)/2.
sortSilhouette	Computes silhouette information according to a givenclustering in k clusters.
upper.to.lower.tri.inds	Computes index vectors for extracting or reordering oflower or upper triangular matrices that are stored ascontiguous vectors.
volume	Computes the volume of a planar object. This is ageneric function and a method for `ellipsoid` objects.

Data Sets

Data Set	Class	Description
agriculture	data.frame	Gross national product (GNP) per capita and percentageof the population working in agriculture for each countrybelonging to the European Union in 1993.
animals	data.frame	This data set considers 6 binary attributes for 20animals.
chorSub	matrix	This is a small rounded subset of the C-horizondata.
flower	data.frame	This data set consists of 8 characteristics for 18popular flowers.
plantTraits	data.frame	This data set constitutes a description of 136 plantspecies according to biological attributes (morphological orreproductive).
pluton	data.frame	The `pluton` dataframe has 45 rows and 4 columns, containing percentages ofisotopic composition of 45 plutonium batches.
ruspini	data.frame	The Ruspini data set, consisting of 75 points in 4groups, is popular for illustrating clustering techniques.
votes.repub	data.frame	A data frame with the percents of votes given to theRepublican candidates in presidential elections from 1856 to1976. Rows represent the 50 states, and columns the 31elections.
xclara	data.frame	An artificial data set consisting of 3, 000 points in 3well-separated clusters of size 1, 000 each.

codetools

This package provides tools for analyzing R code. It ismainly intended to support the other tools in this package and byte codecompilation. See the help file for more information.

foreign

This package provides functions for reading data stored byMinitab, S, SAS, SPSS, Stata, Systat, dBase, and so forth.

Functions

Function	Description
data.restore	Reads binary data files or `data.dump` files that were producedin S version 3.
lookup.xport	Scans a file as a SAS XPORT format library and returnsa list containing information about the SAS library.
read.S	Reads binary data files or `data.dump` files that were producedin S version 3.
read.arff	Reads data from Weka Attribute-Relation File Format(ARFF) files.
read.dbf	Reads a DBF file into a data frame, convertingcharacter fields to factors and trying to respect `NULL` fields.
read.dta	Reads a file in Stata version 5–10 binary format into adata frame.
read.epiinfo	Reads data files in the `.REC` format used by Epi Infoversions 6 and earlier and by EpiData. Epi Info is apublic-domain database and statistics package produced by theU.S. Centers for Disease Control and Prevention, and EpiDatais a freely available data entry and validationsystem.
read.mtp	Returns a list with the data stored in a file as aMinitab Portable Worksheet.
read.octave	Reads a file in Octave text data format into alist.
read.spss	Reads a file stored by the SPSS `save` or `export` commands.
read.ssd	Generates a SAS program to convert the ssd contents toSAS transport format and then uses `read.xport` to obtain a dataframe.
read.systat	Reads a rectangular data file stored by the Systat`SAVE` command as (legacy)`.sys` or, more recently, `.syd` files.
read.xport	Reads a file as a SAS XPORT format library and returnsa list of data.frames.
write.arff	Writes data into Weka Attribute-Relation File Format(ARFF) files.
write.dbf	Tries to write a data frame to a DBF file.
write.dta	Writes the data frame to file in the Stata binaryformat. Does not write array variables unless they can be`drop`-ed to avector.
write.foreign	Exports simple data frames to other statisticalpackages by writing the data as free-format text and writing aseparate file of instructions for the other package to readthe data.

grDevices

This package provides functions for graphics devices andsupport for base and grid graphics.

Functions

Function	Description
CIDFont	Used to define the translation of an R graphics fontfamily name to a Type 1 or CID font description, used by both the`postscript` and the `pdf` graphics devices.
Type1Font	Used to define the translation of an R graphics fontfamily name to a Type 1 or CID font description, used by both the`postscript` and the `pdf` graphics devices.
X11	Starts a graphics device driver for the X Window System(version 11). This can only be done on machines/accounts thathave access to an X server.
X11.options	Sets options for an X11 device.
X11Font, X11Fonts	Handle the translation of a device-independent Rgraphics font family name to an X11 font description.
as.graphicsAnnot	Coerces an R object into a form suitable for graphicsannotation.
bitmap	Generates a graphics file. `dev2bitmap` copies the currentgraphics device to a file in a graphics format.
bmp	Graphics device for generating BMP(bitmap)files.
boxplot.stats	This function is typically called by another functionto gather the statistics necessary for producing box plots, but may be invoked separately.
cairo_pdf	A Cairo-based graphics device for generating PDFfiles.
cairo_ps	A Cairo-based graphics device for generating PostScriptfiles.
check.options	Utility function for setting options with someconsistency checks. The `attributes` of the new settings in`new` are checked forconsistency with the model (oftendefault) list in `name.opt`.
chull	Computes the subset of points that lie on the convexhull of the set of points specified.
cm	Translates from inches to centimeters (cm).
cm.colors	Creates a vector of `n` contiguouscolors.
col2rgb	R color to RGB (red/green/blue) conversion.
colorConverter	Specifies color spaces for use in `convertColor`.
colorRamp, colorRampPalette	These functions return functions that interpolate a setof given colors to create new color palettes (like `topo.colors`) and color ramps, functions that map the interval [0, 1] to colors (like`gray`).
colors, colours	Returns the built-in color names that R knowsabout.
contourLines	Calculates contour lines for a given set ofdata.
convertColor	Converts colors between standard color spacerepresentations. This function is experimental.
densCols	Produces a vector containing colors that encode thelocal densities at each point in a scatter plot.
dev.control	Allows the user to control the recording of graphicsoperations in a device.
dev.copy	Copies the graphics contents of the current device tothe device specified by `which` or to a new device that hasbeen created by the function specified by `device` (it is an error to specifyboth `which` and `device`).
dev.copy2eps	Copies the graphics contents of the current device toan Encapsulated PostScript Format (EPSF) output file inportrait orientation (`horizontal =FALSE`).
dev.copy2pdf	Copies the graphics contents of the current device to aPDF output file in portrait orientation (`horizontal = FALSE`).
dev.cur	Returns a named integer vector of length 1, giving thenumber and name of the active device, or 1, the null device, if none is active.
dev.interactive	Tests if the current graphics device (or that whichwould be opened) is interactive.
dev.list	Returns the numbers of all open devices, except device1, the null device. This is a numeric vector with a namesattribute giving the device names, or `NULL` if there is no opendevice.
dev.new	Opens a new graphics device.
dev.next	Returns the number and name of the next device in thelist of devices.
dev.off	Shuts down the specified (by default the current)graphics device.
dev.prev	Returns the number and name of the previous device inthe list of devices.
dev.print	Copies the graphics contents of the current device to anew device that has been created by the function specified by`device` and then shuts thenew device.
dev.set	Makes the specified graphics device the activedevice.
dev.size	Finds the dimensions of the device surface of thecurrent device.
dev2bitmap	`bitmap` generates agraphics file. `dev2bitmap`copies the current graphics device to a file in a graphicsformat.
devAskNewPage	Used to control (for the current device) whether theuser is prompted before starting a new page of output.
deviceIsInteractive	Tests if the current graphics device (or that whichwould be opened) is interactive.
embedFonts	Runs Ghostscript to process a PDF or PostScript fileand embed all fonts in the file.
extendrange	Extends a numeric range by a small percentage, i.e., fraction, on both sides.
getGraphicsEvent	Waits for input from a graphics window in the form of amouse or keyboard event.
graphics.off	Provides control over multiple graphicsdevices.
gray	Creates a vector of colors from a vector of graylevels.
gray.colors	Creates a vector of `n` gamma-corrected graycolors.
grey	Creates a vector of colors from a vector of graylevels.
grey.colors	Creates a vector of `n` gamma-corrected graycolors.
hcl	Creates a vector of colors from vectors specifying hue, chroma, and luminance.
heat.colors	Creates a vector of `n` contiguous colors.
hsv	Creates a vector of colors from vectors specifying hue, saturation, and value.
jpeg	Creates a graphics device for generating JPEG formatfiles.
make.rgb	Specifies color spaces for use in `convertColor`.
n2mfrow	Easy setup for plotting multiple figures (in arectangular layout) on one page. This computes a sensibledefault for `par(mfrow)`.
nclass.FD	Computes the number of classes for a histogram usingthe Freedman-Diaconis choice based on the interquartile range(IQR), unless that's 0, where it reverts to `mad(x, constant = 2), and` when thatis 0 as well, returns 1.
nclass.Sturges	Computes the number of classes for a histogram usingSturges's formula, implicitly basing bin sizes on the range ofthe data.
nclass.scott	Computes the number of classes for a histogram usingScott's choice for a normal distribution based on the estimateof the standard error, unless that is 0 where it returns1.
palette	Views or manipulates the color palette that is usedwhen a `col=` has a numericindex.
pdf	Starts the graphics device driver for producing PDFgraphics.
pdf.options	The auxiliary function `pdf.options` can be used to set orview (if called without arguments) the default values for someof the arguments to `pdf`.
pdfFonts	Lists existing mapping for PDF fonts or creates newmappings.
pictex	Produces graphics suitable for inclusion in TeX andLaTeX documents.
png	Creates a new graphics device for producing PortableNetwork Graphics (PNG) files.
postscript	Starts the graphics device driver for producingPostScript graphics.
postscriptFonts	Lists existing mapping for PostScript fonts or createsnew mappings.
ps.options	The auxiliary function `ps.options` can be used to set orview (if called without arguments) the default values for someof the arguments to `postscript`.
quartz	Starts a graphics device driver for the Mac OS Xsystem.
quartz.options	Sets options for a quartz device.
quartzFont	Translates from a device-independent R graphics fontfamily name to a quartz font description.
quartzFonts	Lists existing mappings of device-independent Rgraphics to a quartz font description, or defines newmappings.
rainbow	Creates a vector of `n` contiguous colors.
recordGraphics	Records arbitrary code on the graphics engine displaylist. Useful for encapsulating calculations with graphicaloutput that depends on the calculations. Intendedonly for expert use.
recordPlot, replayPlot	Functions to save the current plot in an R variable andto replay it.
rgb	Creates colors corresponding to the given intensities(between 0 and `max`) of thered, green, and blue primaries.
rgb2hsv	Transforms colors from RGB space (red/green/blue) intoHSV space (hue/saturation/value).
savePlot	Saves the current page of a Cairo X11() device to afile.
setEPS	A wrapper to ps.options that sets defaults appropriatefor figures for inclusion in documents (the default size is 7inches square unless width or height is supplied).
setPS	A wrapper to ps.options to set defaults appropriate forfigures for spooling to a PostScript printer.
svg	Creates a new graphics device for outputting graphicsin Scalable Vector Graphics (SVG) format.
terrain.colors	Creates a vector of `n` contiguous colors.
tiff	Creates a new graphics device for outputting graphicsin Tagged Image File Format (TIFF) format.
topo.colors	Creates a vector of `n` contiguous colors.
trans3d	Projection of three-dimensional to two-dimensionalpoints using a 4 × 4 viewing transformation matrix.
x11	A synonym for X11 (which opens a new X11 device forplotting graphics).
xfig	Starts the graphics device driver for producing XFig(version 3.2) graphics.
xy.coords	Used by many functions to obtain x and y coordinatesfor plotting. The use of this common mechanism across allrelevant R functions produces a measure ofconsistency.
xyTable	Given (x, y) points, determines theirmultiplicity—checking for equality only up to some (crude kindof) noise. Note that this is a special kind of 2Dbinning.
xyz.coords	Utility for obtaining consistent x, y, and zcoordinates and labels for three-dimensional (3D)plots.

Data Sets

Data Set	Class	Description
Hershey	list	If the `family`graphical parameter (see `par`) has been set to one of theHershey fonts, Hershey vector fonts are used to render text.When using the `text` and`contour` functions, Hersheyfonts may be selected via the `vfont` argument, which is a charactervector of length 2. This allows Cyrillic to be selected, whichis not available via the font families.
blues9	character	`densCols` produces avector containing colors that encode the local densities ateach point in a scatter plot.
colorspaces	list	Converts colors between standard color spacerepresentations. This function is experimental.

graphics

This package contains functions for base graphics. Basegraphics are traditional S graphics, as opposed to the newer gridgraphics.

Functions

Function	Description
Axis	Generic function to add a suitable axis to the currentplot.
abline	Adds one or more straight lines through the currentplot.
arrows	Draws arrows between pairs of points.
assocplot	Produces a Cohen-Friendly association plot indicatingdeviations from independence of rows and columns in atwo-dimensional contingency table.
axTicks	Computes pretty tick mark locations, the same way as Rdoes internally. This is only nontrivial whenlog coordinates are active. By default, gives the `at` values that`axis(side)` woulduse.
axis	Adds an axis to the current plot, allowing thespecification of the side, position, labels, and otheroptions.
barplot	Creates a bar plot with vertical or horizontalbars.
box	Draws a box around the current plot in a given colorand line type. The `bty`parameter determines the type of box drawn. See `par` for details.
boxplot	Produces box-and-whisker plot(s) of the given (grouped)values.
boxplot.matrix	Interprets the columns (or rows) of a matrix asdifferent groups and draws a box plot for each.
bxp	Draws box plots based on the given summaries in`z`. It is usually calledfrom within `boxplot`, butcan be invoked directly.
cdplot	Computes and plots conditional densities describing howthe conditional distribution of a categorical variable`y` changes over a numericvariable `x`.
clip	Sets clipping region in user coordinates.
close.screen	Removes the specified screen definition(s) created by`split.screen`.
co.intervals	Produces two variants of theconditioning plots.
contour	Creates a contour plot or adds contour lines to anexisting plot. Methods include `contour.default`.
coplot	Produces two variants of theconditioning plots.
curve	Draws a curve corresponding to a given function or, for`curve()`, also an expression(in `x`) over the interval`[from, to]`.
dotchart	Draws a Cleveland dot plot.
erase.screen	Used to clear a single screen (when using `split.screen`), which it does byfilling with the background color.
filled.contour	Produces a contour plot with the areas between thecontours filled in solid color (Cleveland calls this a levelplot).
fourfoldplot	Creates a fourfold display of a2-by-2-by-k contingency table on thecurrent graphics device, allowing for the visual inspection ofthe association between two dichotomous variables in one orseveral populations (strata).
frame	This function (`frame`is an alias for `plot.new`)causes the completion of plotting in the current plot (ifthere is one) and an advance to a new graphics frame.
grconvertX, grconvertY	Convert between graphics coordinate systems.
grid	Adds an `nx`-by-`ny` rectangular grid to an existingplot.
hist	The generic function `hist` computes a histogram of thegiven data values. If `plot=TRUE`, the resulting object of`\link[base]{class`"histogram"} is plotted by `plot.histogram`, before it isreturned. Methods include `hist.default`.
identify	Reads the position of the graphics pointer when the(first) mouse button is pressed. It then searches thecoordinates given in `x` and`y` for the point closest tothe pointer. If this point is close enough to the pointer, itsindex will be returned as part of the value of thecall.
image	Creates a grid of colored or grayscale rectangles withcolors corresponding to the values in `z`.
layout, layout.show	`layout` divides thedevice up into as many rows and columns as there are in matrix`mat`, with the column widthsand the row heights specified in the respective arguments.
lcm	`layout` divides thedevice up into as many rows and columns as there are in matrix`mat`, with the column widthsand the row heights specified in the respective arguments.
legend	Used to add legends to plots. Note that a call to thefunction `locator(1)` can beused in place of the `x` and`y` arguments.
lines	A generic function taking coordinates given in variousways and joining the corresponding points with line segments.Methods include `lines.default` and `lines.ts`.
locator	Reads the position of the graphics cursor when the(first) mouse button is pressed.
matlines, matplot, matpoints	Plot the columns of one matrix against the columns ofanother.
mosaicplot	Plots a mosaic on the current graphics device.
mtext	Text is written in one of the four margins of thecurrent figure region or one of the outer margins of thedevice region.
pairs	A matrix of scatter plots is produced.
panel.smooth	An example of a simple useful `panel` function to be used as anargument in, e.g., `coplot`or `pairs`.
par	Used to set or query graphical parameters.
persp	Draws perspective plots of surfaces over thex–y plane.
pie	Draws a pie chart.
plot	Generic function for plotting R objects.
plot.design	Plots univariate effects of one or more `factor`s, typically for a designedexperiment as analyzed by `aov()`.
plot.new	This function (`plot.new` is an alias for `frame`) causes the completion ofplotting in the current plot (if there is one) and an advanceto a new graphics frame.
plot.window	Sets up the world coordinate system for a graphicswindow. It is called by higher-level functions such as`plot.default`(after `plot.new`).
plot.xy	This is the internal function thatdoes the basic plotting of points and lines. Usually, oneshould rather use the higher-level functions instead and referto their help pages for explanation of the arguments.
points	A generic function to draw a sequence of points at thespecified coordinates. The specified character(s) are plotted, centered at the coordinates. Methods include `points.default`.
polygon	Draws the polygons whose vertices are given in `x` and `y`.
rect	Draws a rectangle (or sequence of rectangles) with thegiven coordinates, fill, and border colors.
rug	Adds a rug representation (1Dplot) of the data to the plot.
screen	Used to select which screen to draw in (when usingsplit.screen).
segments	Draws line segments between pairs of points.
smoothScatter	Produces a smoothed color density representation of thescatter plot, obtained through a kernel densityestimate.
spineplot	Spine plots are a special case of mosaic plots and canbe seen as a generalization of stacked (or highlighted) barplots. Analogously, spinograms are an extension ofhistograms.
split.screen	Defines a number of regions within the current devicethat can, to some extent, be treated as separate graphicsdevices. It is useful for generating multiple plots on asingle device.
stars	Draws star plots or segment diagrams of a multivariatedata set. With one single location, also draws "spider" (or"radar") plots.
stem	Produces a stem-and-leaf plot of the values in `x`.
strheight	Computes the height of the given strings ormathematical expressions `s[i]` on the current plotting devicein user coordinates, inches, or as a fraction of the figurewidth `par("fin")`.
stripchart	Produces one-dimensional scatter plots (or dot plots)of the given data. These plots are a good alternative to boxplots when sample sizes are small.
strwidth	Computes the width of the given strings or mathematicalexpressions `s[i]` on thecurrent plotting devicein user coordinates, inches, or as a fraction of the figurewidth `par("fin")`.
sunflowerplot	Multiple points are plotted as "sunflowers" withmultiple leaves ("petals") such that overplotting isvisualized instead of accidental and invisible.
symbols	Draws symbols on a plot. One of six symbols, circles, squares, rectangles, stars, thermometers, and boxplots, can be plotted at a specified set of x and ycoordinates.
text	Draws the strings given in the vector `labels` at the coordinates given by`x` and `y`. `y` may be missing since `xy.coords(x, y)` is used forconstruction of the coordinates.
title	Used to add labels to a plot.
xinch, xyinch, yincch	`xinch` and `yinch` convert the specified numberof inches given as their arguments into the correct units forplotting with graphics functions. Usually, this only makessense when normal coordinates are used, i.e., no `log`scale (see the `log` argumentto `par`). `xyinch` does the same for a pair ofnumbers `xy`, simultaneously.
xspline	Draws an X-spline, a curve drawn relative to controlpoints.

grid

This package is a low-level graphics system that providesa great deal of control and ﬂexibility in the appearance and arrangementof graphical output. It does not provide high-level functions thatcreate complete plots. What it does provide is a basis for developingsuch high-level functions (e.g., the lattice package), the facilities forcustomizing and manipulating lattice output, the ability to producehigh-level plots or non-statistical images from scratch, and the abilityto add sophisticated annotations to the output from base graphicsfunctions (see the gridBase package).For more information, see the help files for grid.

KernSmooth

This package provides functions for kernelsmoothing.

Functions

Function	Description
bkde	Returns x andy coordinates of the binned kerneldensity estimate of the probability density of thedata.
bkde2D	Returns the set of grid points in each coordinatedirection, and the matrix of density estimates over the meshinduced by the grid points. The kernel is the standardbivariate normal density.
bkfe	Returns an estimate of a binned approximation to thekernel estimate of the specified density function. The kernelis the standard normal density.
dpih	Uses direct plug-in methodology to select the bin widthof a histogram.
dpik	Uses direct plug-in methodology to select the bandwidthof a kernel density estimate.
dpill	Uses direct plug-in methodology to select the bandwidthof a local linear Gaussian kernel regression estimate.
locpoly	Estimates a probability density function, regressionfunction, or their derivatives using local polynomials. A fastbinned implementation over an equally spaced grid isused.

lattice

Trellis graphics is a framework for data visualizationdeveloped at Bell Labs by Richard Becker, William Cleveland, et al., extending ideas presented inBill Cleveland's 1993 book Visualizing Data.

Lattice is best thought of as an implementation of Trellisgraphics for R. It is built upon the grid graphics engine and requiresthe grid add-on package. It is not (readily) compatible with traditionalR graphics tools. The public interface is based on the implementation inS-PLUS, but features several extensions, in addition toincompatibilities introduced through the use of grid. To the extentpossible, care has been taken to ensure that existing Trellis codewritten for S-PLUS works unchanged (or with minimal change) in lattice.If you are having problems porting S-PLUS code, read the entry for panelin the documentation for xyplot. Mosthigh-level Trellis functions in S-PLUS are implemented, with theexception of piechart.

Functions

Function	Description
Rows	Convenience function to extract a subset of a list.Usually used in creating keys.
as.shingle, as.factorOrShingle	Functions to handle shingles.
axis.default	Default function for drawing axes in latticeplots.
banking	Calculates banking slope.
barchart	Draws bar charts.
bwplot	Draws box plots.
canonical.theme	Initialization of a display device with appropriategraphical parameters.
cloud	Generic function to draw 3D scatter plots and surfaces.The `"formula"` methods domost of the actual work.
col.whitebg	Initialization of a display device with appropriategraphical parameters.
contourplot	Draws level plots and contour plots.
current.column	Returns an integer index specifying which column in thelayout is currently active.
current.panel.limits	Used to retrieve a panel's x and y limits.
current.row	Returns an integer index specifying which row in thelayout is currently active.
densityplot	Draws histograms and kernel density plots, possiblyconditioned on other variables.
diag.panel.splom	This is the default superpanel function for `splom`.
do.breaks	Draws histograms and kernel density plots, possiblyconditioned on other variables.
dotplot	Draws Cleveland dot plots.
draw.colorkey	Produces (and possibly draws) a grid frame grob, whichis a color key that can be placed in other grid plots. Used inlevelplot.
draw.key	Produces (and possibly draws) a grid frame grob, whichis a legend (aka key) that can be placed in other gridplots.
equal.count	Function to handle shingles.
histogram	Draws histograms and kernel density plots, possiblyconditioned on other variables.
is.shingle	Function to handle shingles.
larrows, llines, lplot.xy, lpoints, lpolygon, lrect, lsegments, ltext, panel.points, panel.polygon, panel.rect, panel.segments, panel.text	These functions are intended to replace commonlow-level traditional graphics functions, primarily for use inpanel functions. The originals cannot be used (at least noteasily) because lattice panel functions need to use gridgraphics. Low-level drawing functions in grid can be useddirectly as well and are often more flexible. These functionsare provided for convenience and portability.
lattice.getOption, lattice.options	Functions to handle settings used by lattice. Theirmain purpose is to make code maintenance easier, and usersnormally should not need to use these functions. However, finecontrol at this level may be useful in certain cases.
latticeParseFormula	Used by high-level lattice functions like `xyplot` to parse the formula argumentand evaluate various components of the data.
level.colors	Calculates false colors from a numeric variable(including factors, using their numeric codes) given a colorscheme and break points.
levelplot	Draws level plots and contour plots.
ltransform3dMatrix, ltransform3dto3d	These are (related to) the default panel functions for`cloud` and `wireframe`.
make.groups	Combines two or more vectors, possibly of differentlengths, producing a data frame with a second columnindicating which of these vectors that row came from. This ismostly useful for getting data into a form suitable for use inhigh-level lattice functions.
oneway	Fits a one-way model to univariate data grouped by afactor, the result often being displayed using `rfs`.
packet.number	A function that identifies which packet eachobservation in the data is part of.
packet.panel.default	Default function in lattice to determine, given thecolumn, row, page, and other relevant information, the packet(if any) that should be used in a panel.
panel.3dscatter, panel	Default panel functions controlling `cloud` and `wireframe` displays.
panel.abline	Adds a line of the form y = a + bxor vertical and/or horizontal lines.
panel.average	Treats one of x andy as a factor (according to the value ofhorizontal), calculates fun applied to the subsets of theother variable determined by each unique value of the factor, and joins them by a line.
panel.arrows	Draws arrows in a panel.
panel.axis	The function used by lattice to draw axes. It istypically not used by users, except those wishing to createadvanced annotation. Keep in mind issues of clipping whentrying to use it as part of the panel function. `current.panel.limits` can be used toretrieve a panel's x andy limits.
panel.barchart	Default panel function for `barchart`.
panel.brush.splom	`panel.link.splom` ismeant for use with splom and requires a panel to be chosenusing `trellis.focus` beforeit is called. Clicking on a point causes that and thecorresponding projections in other pairwise scatter plots tobe highlighted.
panel.bwplot	Default panel function for `bwplot`.
panel.cloud	Default panel function controlling `cloud` and `wireframe` displays.
panel.contourplot	Default panel function for `levelplot`.
panel.curve	Adds a curve, similar to what curve does with `add=TRUE`. Graphical parameters forthe line are obtained from the `add.line` setting.
panel.densityplot	Default panel function for `densityplot`.
panel.dotplot	Default panel function for `dotplot`.
panel.error	Default handler used when an error occurs whileexecuting a panel function.
panel.fill	Fills the panel with a specified color.
panel.grid	Draws a reference grid.
panel.histogram	Default panel function for `histogram`.
panel.identify	Similar to identify. When called, it waits for the userto identify points (in the panel being drawn) via mouseclicks.
panel.levelplot	Default panel function for `levelplot`.
panel.linejoin	`panel.linejoin` is analias for `panel.average`that was retained for back-compatibility and may go away inthe future.
panel.lines	Plots lines in a panel.
panel.link.splom	The classic Trellis paradigm is to plot the wholeobject at once, without the possibility of interacting with itafterward. However, by keeping track of the grid viewportswhere the panels and strips are drawn, it is possible to goback to them afterward and enhance them one panel at a time.This function provides convenient interfaces to help in this.Note that this is still experimental and the exact details maychange in the future.
panel.lmline	`panel.lmline(x, y)`is equivalent to `panel.abline(lm(y~x))`.
panel.loess	Adds a smooth curve (fitted by `loess`).
panel.mathdensity	Plots a (usually theoretical) probability densityfunction.
panel.number	Returns an integer counting which panel is being drawn(starting from 1 for the first panel, aka the panelorder).
panel.pairs	Default superpanel function for `splom`.
panel.parallel	Default panel function for `parallel`.
panel.qq	Default panel function for `qq`.
panel.qqmath	Default panel function for `qqmath`.
panel.qqmathline	Useful panel function with `qqmath`. Draws a line passing throughthe points (usually) determined by the .25 and .75 quantilesof the sample and the theoretical distribution.
panel.refline	Similar to `panel.abline`, but uses the"reference.line" settings for the defaults.
panel.rug	Adds a rug representation of the (marginal) data to thepanel.
panel.smoothScatter	Allows the user to place `smoothScatter` plots in latticegraphics.
panel.splom	Default panel function for `splom`.
panel.stripplot	Default panel function for `stripplot`. Also see `panel.superpose`.
panel.superpose, panel.superpose.2	These are panel functions for Trellis displays, whichare useful when a grouping variable is specified for usewithin panels. The `x` (and`y` where appropriate)variables are plotted with different graphical parameters foreach distinct value of the grouping variable.
panel.tmd.default, panel.tmd.qqmath	Default panel functions for tmd.
panel.violin	This is a panel function that can create a violin plot.It is typically used in a high-level call to `bwplot`.
panel.wireframe	Default panel functions controlling `cloud` and `wireframe` displays.
panel.xyplot	Default panel function for `xyplot`.
parallel	Draws conditional scatter plot matrices and parallelcoordinate plots.
prepanel.default.bwplot, prepanel.default.cloud, prepanel.default.densityplot, prepanel.default.histogram, prepanel.default.levelplot, prepanel.default.parallel, prepanel.default.qq, prepanel.default.qqmath, prepanel.default.splom, prepanel.default.xyplot	These prepanel functions are used as fallback defaultsin various high-level plot functions in lattice. These arerarely useful to normal users, but may be helpful indeveloping new displays.
prepanel.lmline, prepanel.loess, prepanel.qqmathline	These are predefined prepanel functions available inlattice.
prepanel.tmd.default, prepanel.tmd.qqmath	`tmd` creates Tukeymean-difference plots from a `trellis` object returned by `xyplot`, `qq`, or `qqmath`. The prepanel and panelfunctions are used as appropriate. The `formula` method for `tmd` is provided for convenience andsimply calls `tmd` on theobject created by calling `xyplot` on that formula.
qq	Quantile-quantile plots for comparing twodistributions.
qqmath	Quantile-quantile plot of a sample and a theoreticaldistribution.
rfs	Plots fitted values and residuals (via `qqmath`) on a common scale for anyobject that has methods for fitted values andresiduals.
shingle	Function to handle shingle.
show.settings	Function used to query, display, and modify graphicalparameters for fine control of Trellis displays. Modificationsare made to the settings for the currently active deviceonly.
simpleKey	Simple interface to generate a list appropriate for`draw.key`.
simpleTheme	Simple interface to generate a list appropriate as atheme, typically used as the `par.settings` argument in ahigh-level call.
splom	Draws conditional scatter plot matrices and parallelcoordinate plots.
standard.theme	Initialization of a display device with appropriategraphical parameters.
strip.custom	Provides a convenient way to obtain new strip functionsthat differ from `strip.default` only in the defaultvalues of certain arguments.
strip.default	Function that draws the strips by default in Trellisplots. Users can write their own strip functions, but mostcommonly this involves calling `strip.default` with slightlydifferent arguments.
stripplot	Draws strip plots in lattice.
tmd	`tmd` creates Tukeymean-difference plots from a `trellis` object returned by `xyplot`, `qq`, or `qqmath`. The `formula` method for `tmd` is provided for convenience andsimply calls `tmd` on theobject created by calling `xyplot` on that formula.
trellis.currentLayout	Returns a matrix with as many rows and columns as inthe layout of panels in the current plot.
trellis.device	Initialization of a display device with appropriategraphical parameters.
trellis.focus, trellis.grobname	`trellis.focus` can beused to move to a particular panel or strip, identified by itsposition in the array of panels.
trellis.last.object	Updates method for objects of class `"trellis"` and is a way to retrievethe last printed `trellis`object (that was saved).
trellis.panelArgs	Once a panel or strip is in focus (e.g., by using`trellis.switchFocus`), `trellis.panelArgs` can beused to retrieve the arguments that were available to the`panel` function at thatposition.
trellis.par.get, trellis.par.set	Functions used to query, display, and modify graphicalparameters for fine control of Trellis displays. Modificationsare made to the settings for the currently active deviceonly.
trellis.switchFocus	A convenience function to switch from one viewport toanother, while preserving the current row and column.
trellis.unfocus	Unsets the focus and makes the top-level viewport thecurrent viewport.
trellis.vpname	Returns the name of a viewport.
which.packet	Returns the combination of levels of the conditioningvariables in the form of a numeric vector as long as thenumber of conditioning variables, with each element an integerindexing the levels of the corresponding variable.
wireframe	Generic function to draw 3D scatter plots and surfaces.The `"formula"` methods domost of the actual work.
xscale.components.default, yscale.components.default	Return a list of the form suitable as the componentsargument of `axis.default`.
xyplot	Produces conditional scatter plots.

Data Sets

Data Set	Class	Description
barley	data.frame	Total yield in bushels per acre for 10 varieties at 6sites in each of 2 years.
environmental	data.frame	Daily measurements of ozone concentration, wind speed, temperature, and solar radiation in New York City from May toSeptember of 1973.
ethanol	data.frame	Ethanol fuel was burned in a single-cylinder engine.For various settings of the engine compression and equivalenceratio, the emissions of nitrogen oxides were recorded.
melanoma	data.frame	This data from the Connecticut Tumor Registry presentsage-adjusted numbers of melanoma skin cancer incidences per100, 000 people in Connecticut for the years 1936–1972.
singer	data.frame	Heights, in inches, of the singers in the New YorkChoral Society in 1979. The data is grouped according to voicepart. The vocal range for each voice part increases in pitchaccording to the following order: Bass 2, Bass 1, Tenor 2, Tenor 1, Alto 2, Alto 1, Soprano 2, Soprano 1.

Pages: 1, 2, 3, 4, 5

boot

Functions

Data Sets

class

Functions

cluster

Functions

Data Sets

codetools

foreign

Functions

grDevices

Functions

Data Sets

graphics

Functions

grid

KernSmooth

Functions

lattice

Functions

Data Sets

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