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lot cumulative periodogram cutree cut a tree into groups of data decompose classical seasonal decomposition by moving averages delete response modify terms objects dendrapply apply a function to all nodes of a dendrogram dendrogram general tree structures density kernel density estimation deriv symbolic and algorithmic derivatives of simple expressions deviance model deviance df residual residual degrees of freedom diffinv discrete integration inverse of differencing dist distance matrix computation distributions distributions in the stats package dummy coef extract coefficients in original coding ecdf empirical cumulative distribution function eff aovlist compute efficiencies of multistratum analysis of variance effects effects from fitted model embed embedding a time series expand model frame add new variables to a model frame exponential the exponential distribution extractaic extract aic from a fitted model factanal factor analysis factor scope compute allowed changes in adding to or dropping from a family family objects for models fdist the f distribution fft fast discrete fourier transform fft filter linear filtering on a time series fisher test fisher s exact test for count data fitted values extract model fitted values fivenum tukey five number summaries fligner test fligner killeen test of homogeneity of variances formula model formulae formula nls extract model formula from nls object friedman test friedman rank sum test ftable flat contingency tables ftable formula formula notation for flat contingency tables gammadist the gamma distribution geometric the geometric distribution getinitial get initial parameter estimates glm fitting generalized linear models glm control auxiliary for controlling glm fitting glm summaries accessing generalized linear model fits hclust hierarchical clustering heatmap draw a heat map holtwinters holt winters filtering hypergeometric the hypergeometric distribution identify hclust identify clusters in a dendrogram influence measures regression deletion diagnostics integrate integration of one dimensional functions interaction plot two way interaction plot iqr the interquartile range is empty test if a model s formula is empty isoreg isotonic monotone regression kalmanlike kalman filtering kernapply apply smoothing kernel kernel smoothing kernel objects kmeans k means clustering kruskal test kruskal wallis rank sum test ksmooth kernel regression smoother ks test kolmogorov smirnov tests lag lag a time series lag plot time series lag plots line robust line fitting listof a class for lists of parts of model fits lm fitting linear models lmfit fitter functions for linear models lm influence regression diagnostics lm summaries accessing linear model fits loadings print loadings in factor analysis loess local polynomial regression fitting loess control set parameters for loess logistic the logistic distribution loglik extract log likelihood loglin fitting log linear models lognormal the log normal distribution lowess scatter plot smoothing ls diag compute diagnostics for lsfit regression results lsfit find the least squares fit ls print print lsfit regression results mad median absolute deviation mahalanobis mahalanobis distance make link create a link for glm families makepredictcall utility function for safe prediction manova multivariate analysis of variance mantelhaen test cochran mantel haenszel chi squared test for count data mauchly test mauchly s test of sphericity mcnemar test mcnemar s chi squared test for count data median median value medpolish median polish robust twoway decomposition of a matrix model extract extract components from a model frame model frame extracting the model frame from a formula or fit model matrix construct design matrices model tables compute tables of results from an aov model fit monthplot plot a seasonal or other subseries from a time series mood test mood two sample test of scale multinom the multinomial distribution na action na action na contiguous find longest contiguous stretch of non nas na fail handle missing values in objects nafns adjust for missing values naprint adjust for missing values negbinomial the negative binomial distribution nextn find highly composite numbers nlm non linear minimization nlminb optimization using port routines nls nonlinear least squares nls control control the iterations in nls nlsstasymptotic fit the asymptotic regression model nlsstclosestx inverse interpolation nlsstlfasymptote horizontal asymptote on the left side nlsstrtasymptote horizontal asymptote on the right side nobs extract the number of observations from a fit normal the normal distribution numericderiv evaluate derivatives numerically offset include an offset in a model formula oneway test test for equal means in a one way layout optim general purpose optimization optimize one dimensional optimization order dendrogram ordering or labels of the leaves in a dendrogram p adjust adjust p values for multiple comparisons pair construct paired data object pairwise prop test pairwise comparisons for proportions pairwise table tabulate p values for pairwise comparisons pairwise t test pairwise t tests pairwise wilcox test pairwise wilcoxon rank sum tests plot acf plot autocovariance and autocorrelation functions plot density plot method for kernel density estimation plot holtwinters plot function for holtwinters objects plot isoreg plot method for isoreg objects plot lm plot diagnostics for an lm object plot ppr plot ridge functions for projection pursuit regression fit plot profile nls plot a profile nls object plot spec plotting spectral densities plot stepfun plot step functions plot ts plotting time series objects poisson the poisson distribution poisson test exact poisson tests poly compute orthogonal polynomials power create a power link object power anova test power calculations for balanced one way analysis of variance power prop test power calculations for two sample test for proportions power t test power calculations for one and two sample t tests ppoints ordinates for probability plotting ppr projection pursuit regression pp test phillips perron test for unit roots prcomp principal components analysis predict model predictions predict arima forecast from arima fits predict glm predict method for glm fits predict holtwinters prediction function for fitted holt winters models predict lm predict method for linear model fits predict loess predict loess curve or surface predict nls predicting from nonlinear least squares fits predict smooth spline predict from smoothing spline fit preplot pre computations for a plotting object princomp principal components analysis printcoefmat print coefficient matrices print power htest print methods for hypothesis tests and power calculation print ts printing and formatting of time series objects profile generic function for profiling models profile nls method for profiling nls objects proj projections of models prop test test of equal or given proportions prop trend test test for trend in proportions qqnorm quantile quantile plots quade test quade test quantile sample quantiles r2dtable random 2 way tables with given marginals read ftable manipulate flat contingency tables rect hclust draw rectangles around hierarchical clusters relevel reorder levels of factor reorder dendrogram reorder a dendrogram reorder factor reorder levels of a factor replications number of replications of terms reshape reshape grouped data residuals extract model residuals runmed running medians robust scatter plot smoothing rwishart random wishart distributed matrices scatter smooth scatter plot with smooth curve fitted by loess screeplot screeplots sd standard deviation se contrast standard errors for contrasts in model terms selfstart construct self starting nonlinear models setnames set the names in an object shapiro test shapiro wilk normality test sigma extract residual standard deviation sigma signrank distribution of the wilcoxon signed rank statistic simulate simulate responses smooth tukey s running median smoothing smoothends end points smoothing for running medians smooth spline fit a smoothing spline sortedxydata create a sortedxydata object spec ar estimate spectral density of a time series from ar fit spec pgram estimate spectral density of a time series by a smoothed spec taper taper a time series by a cosine bell spectrum spectral density estimation splinefun interpolating splines ssasymp self starting nls asymptotic regression model ssasympoff self starting nls asymptotic regression model with an offset ssasymporig self starting nls asymptotic regression model through the ssbiexp self starting nls biexponential model ssd ssd matrix and estimated variance matrix in multivariate ssfol self starting nls first order compartment model ssfpl self starting nls four parameter logistic model ssgompertz self starting nls gompertz growth model sslogis self starting nls logistic model ssmicmen self starting nls michaelis menten model ssweibull self starting nls weibull growth curve model start encode the terminal times of time series stat anova glm anova statistics stats defunct defunct functions in package stats stats deprecated deprecated functions in package stats stats package the r stats package step choose a model by aic in a stepwise algorithm stepfun step functions creation and class stl seasonal decomposition of time series by loess stlmethods methods for stl objects structts fit structural time series summary aov summarize an analysis of variance model summary glm summarizing generalized linear model fits summary lm summarizing linear model fits summary manova summary method for multivariate analysis of variance summary nls summarizing non linear least squares model fits summary princomp summary method for principal components analysis supsmu friedman s supersmoother symnum symbolic number coding tdist the student t distribution termplot plot regression terms terms model terms terms formula construct a terms object from a formula terms object description of terms objects time sampling times of time series toeplitz form symmetric toeplitz matrix ts time series objects tsdiag diagnostic plots for time series fits ts methods methods for time series objects tsp tsp attribute of time series like objects ts plot plot multiple time series tssmooth use fixed interval smoothing on time series ts union bind two or more time series t test student s t test tukey the studentized range distribution tukeyhsd compute tukey honest significant differences uniform the uniform distribution uniroot one dimensional root zero finding update update and re fit a model call update formula model updating varimax rotation methods for factor analysis var test f test to compare two variances vcov calculate variance covariance matrix for a fitted model weibull the weibull distribution weighted mean weighted arithmetic mean weighted residuals compute weighted residuals weights extract model weights wilcoxon distribution of the wilcoxon rank sum statistic wilcox test wilcoxon rank sum and signed rank tests window time series windows xtabs cross tabulation zc sets contrasts for a factor stats4 coef methods methods for function coef in package stats4 confint methods methods for function confint in package stats4 loglik methods methods for function loglik in package stats4 mle maximum likelihood estimation mle class class mle for results of maximum likelihood estimation plot methods methods for function plot in package stats4 profile methods methods for function profile in package stats4 profile mle class class profile mle profiling information for mle show methods methods for function show in package stats4 stats4 package statistical functions using s4 classes summary methods methods for function summary in package stats4 summary mle class class summary mle summary of mle objects update methods methods for function update in package stats4 vcov methods methods for function vcov in package stats4 tcltk tclinterface low level tcl tk interface tclservicemode allow tcl events to be serviced or not tcltk defunct defunct functions in package tcltk tcltk package tcl tk interface tk_choose dir choose a folder interactively tk_choose files choose a list of files interactively tkcommands tk non widget commands tk_messagebox tk message box tkpager page file using tk text widget tkprogressbar progress bars via tk tk_select list select items from a list tkstartgui tcl tk gui startup tkwidgetcmds tk widget commands tkwidgets tk widgets tools add_datalist add a datalist file to a source package assertcondition asserting error conditions bibstyle select or define a bibliography style buildvignette build one vignette buildvignettes list and build package vignettes charsets conversion tables between character sets checkff check foreign function calls checkmd5sums check and create md5 checksum files check_packages_in_dir check source packages and their reverse dependencies checkpofiles check translation files for inconsistent format strings checkrd check an rd object checkrdafiles report on details of saved images or re saves them checktnf check r packages or code for t f checkvignettes check package vignettes codoc check code documentation consistency compactpdf compact pdf files crantools cran package repository tools delimmatch delimited pattern matching dependsonpkgs find reverse dependencies encoded translate non ascii text to latex escapes fileutils file utilities find_gs_cmd find a ghostscript executable getvignetteinfo get information on installed vignettes htmlheader generate a standard html header for r help htmllinks collect html links from package documentation loadrdmacros load user defined rd help system macros makelazyloading lazy loading of packages make_translations_pkg package the current translations in the r sources makevars user and site compilation variables md5sum compute md5 checksums package_dependencies computations on the dependency hierarchy of packages package_native_routine_registration_skeleton write skeleton for adding native routine registration to a parselatex experimental functions to work with latex code parse_rd parse an rd file print via format printing utilities pskill kill a process psnice get or set the priority niceness of a process qc qc checks for r code and or documentation rcmd r cmd interface rd2html rd converters rd2txt_options set formatting options for text help rdiff difference r output files rdindex generate index from rd files rdtextfilter select text in an rd file rdutils rd utilities read 00index read 00index style files shownonascii pick out non ascii characters startdynamichelp start the dynamic html help system sweavetexfilter strip r code out of sweave file testinstalledpackage test installed packages texi2dvi compile latex files tohtml display an object in html tools defunct defunct objects in package tools tools deprecated deprecated objects in package tools tools 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