Information on package ‘VGAM’ Description: Package: VGAM Version: 0.8-4 Date: 2011-11-04 Title: Vector Generalized Linear and Additive Models Author: Thomas W. Yee Maintainer: Thomas Yee Depends: R (>= 2.11.1), splines, methods, stats, stats4 Description: Vector generalized linear and additive models, and associated models (Reduced-Rank VGLMs, Quadratic RR-VGLMs, Reduced-Rank VGAMs). This package fits many models and distribution by maximum likelihood estimation (MLE) or penalized MLE. Also fits constrained ordination models in ecology. License: GPL-2 URL: http://www.stat.auckland.ac.nz/~yee/VGAM LazyLoad: yes LazyData: yes Packaged: 2011-11-04 01:06:31 UTC; tyee001 Built: R 2.14.0; i686-pc-linux-gnu; 2011-11-04 01:06:48 UTC; unix Index: AA.Aa.aa The AA-Aa-aa Blood Group System AB.Ab.aB.ab The AB-Ab-aB-ab Blood Group System AB.Ab.aB.ab2 The AB-Ab-aB-ab2 Blood Group System ABO The ABO Blood Group System AICvlm Akaike's Information Criterion Amh Ali-Mikhail-Haq Distribution's Bivariate Distribution Benford Benford's Distribution Benini The Benini Distribution Betabinom The Beta-Binomial Distribution Betageom The Beta-Geometric Distribution Betanorm The Beta-Normal Distribution Binom2.or Bivariate Binary Regression with an Odds Ratio Binom2.rho Bivariate Probit Model Bisa The Birnbaum-Saunders Distribution Bort The Borel-Tanner Distribution Brat Inputting Data to fit a Bradley Terry Model Card Cardioid Distribution Coef Computes Model Coefficients and Quantities Coef.qrrvglm Returns Important Matrices etc. of a QO Object Coef.qrrvglm-class Class "Coef.qrrvglm" Coef.rrvglm Returns Important Matrices etc. of a RR-VGLM Object Coef.rrvglm-class Class "Coef.rrvglm" Coef.vlm Extract Model Coefficients for VLM Objects CommonVGAMffArguments Common VGAM family function Arguments Dagum The Dagum Distribution DeLury DeLury's Method for Population Size Estimation Expectiles-Exponential Expectiles of the Exponential Distribution Expectiles-Koenker Expectiles/Quantiles of the Koenker Distribution Expectiles-Normal Expectiles of the Normal Distribution Expectiles-Uniform Expectiles of the Uniform Distribution Felix The Felix Distribution Fgm Farlie-Gumbel-Morgenstern's Bivariate Distribution Fisk The Fisk Distribution Fnorm The Folded-Normal Distribution Frank Frank's Bivariate Distribution Frechet The Frechet Distribution G1G2G3 The G1G2G3 Blood Group System Hzeta Haight's Zeta Function Inv.gaussian The Inverse Gaussian Distribution Invlomax The Inverse Lomax Distribution Invparalogistic The Inverse Paralogistic Distribution Kumar The Kumaraswamy Distribution Links Link functions for VGLM/VGAM/etc. families Lino The Generalized Beta Distribution (Libby and Novick, 1982) Log Logarithmic Distribution Lomax The Lomax Distribution MNSs The MNSs Blood Group System Max Maxima Maxwell The Maxwell Distribution Nakagami Nakagami Distribution Opt Maxima Paralogistic The Paralogistic Distribution Pareto The Pareto Distribution ParetoIV The Pareto(IV/III/II) Distributions Plackett Plackett's Bivariate Distribution Polono The Poisson Lognormal Distribution Posbinom Positive-Binomial Distribution Posnegbin Positive-Negative Binomial Distribution Posnorm The Positive-Normal Distribution Pospois Positive-Poisson Distribution Qvar Quasi-variances Preprocessing Function Rayleigh The Rayleigh Distribution Rcam Mark the Baseline of Row and Column on a Matrix data Rice The Rice Distribution Sinmad The Singh-Maddala Distribution Skellam The Skellam Distribution Slash Slash Distribution SurvS4 Create a Survival Object SurvS4-class Class "SurvS4" Tikuv A Short-tailed Symmetric Distribution Tobit The Tobit Distribution Tol Tolerances Tpareto The Truncated Pareto Distribution Triangle The Triangle Distribution VGAM-package Vector Generalized Linear and Additive Models Yules Yule-Simon Distribution Zanegbin Zero-Altered Negative Binomial Distribution Zapois Zero-Altered Poisson Distribution Zeta The Zeta Distribution Zibinom Zero-Inflated Binomial Distribution Zigeom Zero-Inflated Geometric Distribution Zinegbin Zero-Inflated Negative Binomial Distribution Zipf The Zipf Distribution Zipois Zero-Inflated Poisson Distribution acat Ordinal Regression with Adjacent Categories Probabilities alaplace1 Asymmetric Laplace Distribution Family Functions amh Ali-Mikhail-Haq Distribution Distribution Family Function amlbinomial Binomial Logistic Regression by Asymmetric Maximum Likelihood Estimation amlexponential Exponential Regression by Asymmetric Maximum Likelihood Estimation amlnormal Asymmetric Least Squares Quantile Regression amlpoisson Poisson Regression by Asymmetric Maximum Likelihood Estimation auuc Auckland University Undergraduate Counts Data backPain Data on Back Pain Prognosis, from Anderson (1984) benini Benini Distribution Family Function beta.ab The Two-parameter Beta Distribution Family Function betaII Beta Distribution of the Second Kind betabinomial Beta-binomial Distribution Family Function betabinomial.ab Beta-binomial Distribution Family Function betaff The Two-parameter Beta Distribution Family Function betageometric Beta-geometric Distribution Family Function betaprime The Beta-Prime Distribution bilogis4 Bivariate Logistic Distribution bilogistic4 Bivariate Logistic Distribution Family Function binom2.or Bivariate Binary Regression with an Odds Ratio (Family Function) binom2.rho Bivariate Probit Model (Family Function) binomialff Binomial Family Function binormal Bivariate normal distribution biplot,rrvglm-method Biplot of Constrained Regression Models bisa Birnbaum-Saunders Distribution Family Function bivgamma.mckay Bivariate Gamma: McKay's Distribution bminz Body Mass Index of New Zealand Adults Data borel.tanner Borel-Tanner Distribution Family Function brat Bradley Terry Model bratt Bradley Terry Model With Ties calibrate Model Calibrations calibrate,rrvglm-method Calibration for Constrained Regression Models calibrate.qrrvglm Calibration for CQO, UQO and CAO models calibrate.qrrvglm.control Control function for CQO/UQO/CAO calibration cao Fitting Constrained Additive Ordination (CAO) cao.control Control Function for RR-VGAMs (CAO) cardioid Cardioid Distribution Family Function cauchit Cauchit Link Function cauchy Cauchy Distribution Family Function ccoef Extract Model Constrained/Canonical Coefficients ccoef-method Constrained (Canonical) Coefficients cdf.lmscreg Cumulative Distribution Function for LMS Quantile Regression cennormal1 Censored Normal Distribution cenpoisson Censored Poisson Family Function cgo Redirects the user to cqo cgumbel Censored Gumbel Distribution chestnz Chest Pain in NZ Adults Data chisq Chi-squared Distribution clo Redirects the user to rrvglm cloglog Complementary Log-log Link Function coalminers Breathlessness and Wheeze Amongst Coalminers Data constraints Constraint Matrices cqo Fitting Constrained Quadratic Ordination (CQO) crashi Crashes on New Zealand Roads in 2009 cratio Ordinal Regression with Continuation Ratios cumulative Ordinal Regression with Cumulative Probabilities dagum Dagum Distribution Family Function dalap The Laplace Distribution dcennormal1 Univariate Normal Distribution with Double Censoring deplot.lmscreg Density Plot for LMS Quantile Regression depvar Response variable extracted dexpbinomial Double Exponential Binomial Distribution Family Function dgumbel The Gumbel Distribution dhuber Huber's least favourable distribution dirichlet Fitting a Dirichlet Distribution dirmul.old Fitting a Dirichlet-Multinomial Distribution dirmultinomial Fitting a Dirichlet-Multinomial Distribution dlaplace The Laplace Distribution dloglap The Log-Laplace Distribution dsimplex Simplex Distribution enzyme Enzyme Data erf Error Function erlang Erlang Distribution expexp Exponentiated Exponential Distribution expexp1 Exponentiated Exponential Distribution expgeom The Exponential Geometric Distribution expgeometric Exponential Geometric Distribution Family Function explink Exponential Link Function explog The Exponential Logarithmic Distribution explogarithmic Exponential Logarithmic Distribution Family Function exponential Exponential Distribution exppois The Exponential Poisson Distribution exppoisson Exponential Poisson Distribution Family Function felix Felix Distribution Family Function fff F Distribution Family Function fgm Farlie-Gumbel-Morgenstern's Bivariate Distribution Family Function fill Creates a Matrix of Appropriate Dimension finney44 Toxicity trial for insects fisherz Fisher's Z Link Function fisk Fisk Distribution family function fittedvlm Fitted Values of a VLM object fnormal1 Folded Normal Distribution Family Function frank Frank's Bivariate Distribution Family Function frechet2 Frechet Distribution Family Function freund61 Freund's (1961) Bivariate Extension of the Exponential Distribution fsqrt Folded Square Root Link Function gamma1 1-parameter Gamma Distribution gamma2 2-parameter Gamma Distribution gamma2.ab 2-parameter Gamma Distribution gammahyp Gamma Hyperbola Bivariate Distribution garma GARMA (Generalized Autoregressive Moving-Average) Models gaussianff Gaussian (normal) Family Function genbetaII Generalized Beta Distribution of the Second Kind gengamma Generalized Gamma distribution family function gengammaUC The Generalized Gamma Distribution genpoisson Generalized Poisson distribution genray The Generalized Rayleigh Distribution genrayleigh Generalized Rayleigh Distribution Family Function geometric Geometric Distribution get.smart Retrieve One Component of ".smart.prediction" get.smart.prediction Retrieves ".smart.prediction" gev Generalized Extreme Value Distribution Family Function gevUC The Generalized Extreme Value Distribution gew General Electric and Westinghouse Data golf Gamma-Ordinal Link Function gpd Generalized Pareto Distribution Family Function gpdUC The Generalized Pareto Distribution grc Row-Column Association Models including Goodman's RC Association Model gumbel Gumbel Distribution Family Function gumbelIbiv Gumbel's Type I Bivariate Distribution Family Function guplot Gumbel Plot hspider Hunting Spider Data huber Huber's least favourable distribution family function hued Harvard University Degrees Conferred by Student Ethnicity huggins91 Huggins (1991) Capture-recapture Model Family Function (approximation only) huggins91UC Huggins (1991) Capture-recapture Model huie Harvard University International Enrollments hunua Hunua Ranges Data huse Harvard University Numbers of Ladder Faculty by School and Ethnicity hyperg Hypergeometric Family Function hypersecant Hyperbolic Secant Distribution Family Function hzeta Haight's Zeta Family Function iam Index from Array to Matrix identity Identity Link Function inv.gaussianff Inverse Gaussian Distribution Family Function invbinomial Inverse Binomial Distribution Family Function invlomax Inverse Lomax Distribution Family Function invparalogistic Inverse Paralogistic Distribution Family Function is.smart Test For a Smart Object koenker Koenker's Distribution Family Function kumar Kumaraswamy Distribution Family Function lambertW The Lambert W function laplace Laplace Distribution leipnik Leipnik Distribution Family Function lerch Lerch Phi Function leukemia Acute Myelogenous Leukemia Survival Data levy Levy Distribution Family Function lgammaUC The Log-Gamma Distribution lgammaff Log-gamma Distribution Family Function lino Generalized Beta Distribution Family Function lirat Low-iron Rat Teratology Data lms.bcg LMS Quantile Regression with a Box-Cox transformation to a Gamma Distribution lms.bcn LMS Quantile/Expectile Regression with a Box-Cox Transformation to Normality lms.yjn LMS Quantile Regression with a Yeo-Johnson Transformation to Normality logc Complementary-log Link Function loge Log link function logff Logarithmic Distribution logistic Logistic Distribution Family Function logit Logit Link Function loglaplace1 Log-Laplace and Logit-Laplace Distribution Family Functions loglinb2 Loglinear Model for Two Binary Responses loglinb3 Loglinear Model for Three Binary Responses loglog Log-log Link Function lognormal Lognormal Distribution logoff Log link function with an offset lomax Lomax Distribution Family Function lqnorm Minimizing the L-q norm Family Function lv Latent Variables lvplot Latent Variable Plot lvplot.qrrvglm Latent Variable Plot for QO models lvplot.rrvglm Latent Variable Plot for RR-VGLMs margeff Marginal effects for the multinomial logit and cumulative models maxwell Maxwell Distribution Family Function mbinomial The Matched Binomial Distribution Family Function mccullagh89 McCullagh (1989) Distribution Family Function meplot Mean Excess Plot micmen Michaelis-Menten Model mix2exp Mixture of Two Exponential Distributions mix2normal1 Mixture of Two Univariate Normal Distributions mix2poisson Mixture of Two Poisson Distributions model.framevlm Construct the Model Frame of a VLM Object model.matrixvlm Construct the Design Matrix of a VLM Object moffset Matrix Offset morgenstern Morgenstern's Bivariate Distribution Family Function multinomial Multinomial Logit Model nakagami Nakagami Distribution Family Function nbolf Negative Binomial-Ordinal Link Function negbinomial Negative Binomial Distribution Family Function normal1 Univariate Normal Distribution nzc Chinese Population in New Zealand 1867-2001 Data nzmarital New Zealand Marital Data. olympic 2008 Summer Olympic Final Medal Count Data ordpoisson Ordinal Poisson Family Function oxtemp Oxford Temperature Data paralogistic Paralogistic Distribution Family Function pareto1 Pareto and Truncated Pareto Distribution Family Functions paretoIV Pareto(IV/III/II) Distribution Family Functions perspqrrvglm Perspective plot for QRR-VGLMs plackett Plackett's Bivariate Distribution Family Function plotdeplot.lmscreg Density Plot for LMS Quantile Regression plotqrrvglm Model Diagnostic Plots for QRR-VGLMs plotqtplot.lmscreg Quantile Plot for LMS Quantile Regression plotrcam0 Main effects plot for a Row-Column Association Model (RCAM) plotvgam Default VGAM Plotting plotvgam.control Control Function for plotvgam() pneumo Pneumoconiosis in Coalminers Data poissonff Poisson Family Function poissonp Poisson-points-on-a-plane/volume Distances Distribution polf Poisson-Ordinal Link Function posbinomial Positive Binomial Distribution Family Function posnegbinomial Positive Negative Binomial Distribution Family Function posnormal1 Positive Normal Distribution Family Function pospoisson Positive Poisson Distribution Family Function powl Power Link Function predictqrrvglm Predict Method for a CQO fit predictvglm Predict Method for a VGLM fit prentice74 Prentice (1974) Log-gamma Distribution probit Probit Link Function propodds Proportional Odds Model for Ordinal Regression prplot Probability Plots for Categorical Data Analysis put.smart Adds a List to the End of the List ".smart.prediction" qrrvglm.control Control function for QRR-VGLMs (CQO) qtplot.gumbel Quantile Plot for Gumbel Regression qtplot.lmscreg Quantile Plot for LMS Quantile Regression quasibinomialff Quasi-Binomial Family Function quasipoissonff Quasi-Poisson Family Function rayleigh Rayleigh Distribution Family Function rcqo Constrained Quadratic Ordination rdiric The Dirichlet distribution recexp1 Upper Record Values from a 1-parameter Exponential Distribution reciprocal Reciprocal link function recnormal1 Upper Record Values from a Univariate Normal Distribution rhobit Rhobit Link Function riceff Rice Distribution Family Function rig Reciprocal Inverse Gaussian distribution rlplot.egev Return Level Plot for GEV Fits rrar Nested reduced-rank autoregressive models for multiple time series rrvglm Fitting Reduced-Rank Vector Generalized Linear Models (RR-VGLMs) rrvglm-class Class "rrvglm" rrvglm.control Control function for rrvglm rrvglm.optim.control Control function for rrvglm() calling optim() ruge Rutherford-Geiger Polonium Data s Defining smooths in VGAM formulae seq2binomial The Two-stage Sequential Binomial Distribution Family Function setup.smart Smart Prediction Setup simplex Simplex Distribution Family Function sinmad Singh-Maddala Distribution Family Function skellam Skellam Distribution Family Function skewnormal1 Univariate Skew-Normal Distribution Family Function slash Slash Distribution Family Function smart.expression S Expression for Smart Functions smart.mode.is Determine What Mode the Smart Prediction is In smartpred Smart Prediction snorm Skew-Normal Distribution sratio Ordinal Regression with Stopping Ratios studentt Student t Distribution tikuv Short-tailed Symmetric Distribution Family Function tobit Tobit Model toxop Toxoplasmosis Data triangle Triangle Distribution Family Function trplot Trajectory Plot trplot.qrrvglm Trajectory plot for QRR-VGLMs ugss Undergraduate Statistics Students Lifestyle Questionnaire uqo Fitting Unconstrained Quadratic Ordination (UQO) uqo.control Control Function for UQO models uscrime Estimated Crime in 2009 in USA usgrain Grain Prices Data in USA venice Venice Maximum Sea Levels Data vgam Fitting Vector Generalized Additive Models vgam-class Class "vgam" vgam.control Control function for vgam vglm Fitting Vector Generalized Linear Models vglm-class Class "vglm" vglm.control Control function for vglm vglmff-class Class "vglmff" vonmises von Mises Distribution Family Function vsmooth.spline Vector cubic smoothing spline waitakere Waitakere Ranges Data wald Wald Distribution Family Function weibull Weibull Distribution Family Function weightsvglm Prior and Working Weights of a VGLM fit wffc 2008 World Fly Fishing Championships Data wffc.P1 Point System for the 2008 World Fly Fishing Championships wffc.indiv 2008 World Fly Fishing Championships (Individual results) Data wffc.nc 2008 World Fly Fishing Championships (Number of captures) Data wffc.teams 2008 World Fly Fishing Championships (Team results) Data wrapup.smart Cleans Up After Smart Prediction yeo.johnson Yeo-Johnson Transformation yip88 Zero-Inflated Poisson Distribution (Yip (1988) algorithm) yulesimon Yule-Simon Family Function zanegbinomial Zero-Altered Negative Binomial Distribution zapoisson Zero-Altered Poisson Distribution zero The zero Argument in VGAM Family Functions zeta Riemann's Zeta Function zetaff Zeta Distribution Family Function zibinomial Zero-Inflated Binomial Distribution Family Function zigeometric Zero-Inflated Geometric Distribution Family Function zinegbinomial Zero-Inflated Negative Binomial Distribution Family Function zipebcom Exchangeable bivariate cloglog odds-ratio model from a zero-inflated Poisson distribution zipf Zipf Distribution Family Function zipoisson Zero-Inflated Poisson Distribution Family Function Further information is available in the following vignettes in directory ‘/usr/local/lib/Rstuff/myRlibs/VGAM/doc’: categoricalVGAM: The VGAM Package for Categorical Data Analysis (source, pdf)