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VGAM (version 0.9-7)

Vector Generalized Linear and Additive Models

Description

An implementation of about 6 major classes of statistical regression models. At the heart of it are the vector generalized linear and additive model (VGLM/VGAM) classes. Many (150+) models and distributions are estimated by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring. VGLMs can be loosely thought of as multivariate GLMs. VGAMs are data-driven VGLMs (i.e., with smoothing). The other classes are RR-VGLMs (reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs, RCIMs (row-column interaction models)---these classes perform constrained and unconstrained quadratic ordination (CQO/UQO) models in ecology, as well as constrained additive ordination (CAO). Note that these functions are subject to change, especially before version 1.0.0 is released; see the NEWS file for latest changes.

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Version

Install

install.packages('VGAM')

Monthly Downloads

31,223

Version

0.9-7

License

GPL-2

Maintainer

Thomas Yee

Last Published

March 6th, 2015

Functions in VGAM (0.9-7)

The AB-Ab-aB-ab Blood Group System

The Inverse Gaussian Distribution

The AA-Aa-aa Blood Group System

The ABO Blood Group System

Bivariate normal distribution cumulative distribution function

The A1A2A3 Blood Group System

Akaike's Information Criterion

Bivariate Gamma: McKay's Distribution

V1 Flying-Bombs Hits in London

Bacon and Eggs Data

Computes Model Coefficients and Quantities

Quasi-variances Preprocessing Function

Create a Survival Object

Bivariate Logistic Distribution

Beta-binomial Distribution Family Function

Farlie-Gumbel-Morgenstern's Bivariate Distribution

CommonVGAMffArguments

Common VGAM family function Arguments

The Beta-Prime Distribution

Bivariate Binary Regression with an Odds Ratio

Bivariate Farlie-Gumbel-Morgenstern Exponential Distribution Family Function

The Pareto Distribution

The MNSs Blood Group System

Bivariate Logistic Distribution Family Function

Select variables for a formula response or the RHS of a formula

The Beta-Geometric Distribution

Clayton Copula (Bivariate) Family Function

Bayesian Information Criterion

Asymmetric Least Squares Quantile Regression

The Laplace Distribution

Link functions for VGLM/VGAM/etc. families

aux.posbernoulli.t

Auxiliary Function for the Positive Bernoulli Family Function with Time Effects

The Two-parameter Beta Distribution Family Function

Mark the Baseline of Row and Column on a Matrix data

Ali-Mikhail-Haq Bivariate Distribution

Frank's Bivariate Distribution

The Borel-Tanner Distribution

Plackett's Bivariate Copula Family Function

Poisson Regression by Asymmetric Maximum Likelihood Estimation

Benford's Distribution

Returns Important Matrices etc. of a QO Object

Gaussian Copula (Bivariate) Family Function

The Beta-Normal Distribution

Coef.qrrvglm-class

Class ``Coef.qrrvglm''

Table 1 of Huggins (1989)

Vector Generalized Linear and Additive Models

Seemingly Unrelated Regressions

Auckland University Undergraduate Counts Data

Asymmetric Laplace Distribution Family Functions

Bivariate Probit Model (Family Function)

Beta-geometric Distribution Family Function

Binomial Family Function

Borel-Tanner Distribution Family Function

Dagum Distribution Family Function

Bivariate Student-t Family Function

The Beta-Binomial Distribution

Cumulative Distribution Function for LMS Quantile Regression

The Exponential Logarithmic Distribution

Cardioid Distribution

Fitting Constrained Additive Ordination (CAO)

Cauchit Link Function

Censored Gumbel Distribution

Redirects the user to cqo

Corbet's Butterfly Data

Ordinal Regression with Cumulative Probabilities

Exponential Link Function

Expectiles-Exponential

Expectiles of the Exponential Distribution

Mortality of Flour Beetles from Carbon Disulphide

Gamma Hyperbola Bivariate Distribution

Creates a Matrix of Appropriate Dimension

Folded Normal Distribution Family Function

The Exponential Geometric Distribution

Constraint Matrices

Bradley Terry Model

Exponential Regression by Asymmetric Maximum Likelihood Estimation

Captures of Peromyscus maniculatus, also known as deer mice.

Toxicity trial for insects

F Distribution Family Function

Bivariate normal distribution family function

Haight's Zeta Distribution

Freund's (1961) Bivariate Extension of the Exponential Distribution

The Felix Distribution

Exponentiated Exponential Distribution

The Benini Distribution

Generalized Beta Distribution of the Second Kind

concoef-methods

Constrained (Canonical) Coefficients

Row-Column Interaction Models including Goodman's RC Association Model and Unconstrained Quadratic Ordination

Extract Model Constrained/Canonical Coefficients

Biplot of Constrained Regression Models

Ordinal Regression with Adjacent Categories Probabilities

Gaussian (normal) Family Function

The Two-parameter Beta Distribution Family Function

calibrate.qrrvglm.control

Control function for CQO/CAO calibration

Exponential Geometric Distribution Family Function

Binomial Logistic Regression by Asymmetric Maximum Likelihood Estimation

Frank's Bivariate Distribution Family Function

Censored Normal Distribution

The Birnbaum-Saunders Distribution

Gumbel's Type I Bivariate Distribution Family Function

Chest Pain in NZ Adults Data

Generalized Gamma distribution family function

Censored Poisson Family Function

Fisk Distribution family function

Expectiles-Uniform

Expectiles of the Uniform Distribution

double.expbinomial

Double Exponential Binomial Distribution Family Function

Extract Model Coefficients

Redirects the user to rrvglm

Density Plot for LMS Quantile Regression

Complementary Log-log Link Function

Error Function, and variants

Control Function for RR-VGAMs (CAO)

Hat Values and Regression Deletion Diagnostics

calibrate.qrrvglm

Calibration for CQO and CAO models

Data on Back Pain Prognosis, from Anderson (1984)

Inverse Gaussian Distribution Family Function

Plackett's Bivariate Copula

Crashes on New Zealand Roads in 2009

Breathlessness and Wheeze Amongst Coalminers Data

Gompertz Distribution Family Function

Likelihood Ratio Test of Nested Models

Beta-binomial Distribution Family Function

Gaussian Copula (Bivariate) Distribution

The Exponential Integral and Variants

Frechet Distribution Family Function

calibrate-methods

Calibration for Constrained Regression Models

1-parameter Gamma Distribution

Folded Square Root Link Function

Fisher's Z Link Function

Log-gamma Distribution Family Function

Inverse Binomial Distribution Family Function

Generalized Poisson distribution

Gamma-Ordinal Link Function

The Generalized Pareto Distribution

The Generalized Rayleigh Distribution

Hypergeometric Family Function

Marginal effects for the multinomial logit and cumulative models

The Generalized Gamma Distribution

Logistic Distribution Family Function

Response variable extracted

New Zealand Marital Data.

Fitting a Dirichlet-Multinomial Distribution

The Kumaraswamy Distribution

GARMA (Generalized Autoregressive Moving-Average) Models

The Generalized Beta Distribution (Libby and Novick, 1982)

Huber's least favourable distribution

McCullagh (1989) Distribution Family Function

Fitted Values of a VLM object

Laplace Distribution

Expectiles-Normal

Expectiles of the Normal Distribution

Erlang Distribution

Residual Degrees-of-Freedom

Latent Variable Plot for QO models

Exponentiated Exponential Distribution

Chinese Population in New Zealand 1867--2001 Data

The Generalized Extreme Value Distribution

Zero Constraint Matrices

Link Functions for VGLMs

Exponential Poisson Distribution Family Function

Latent Variable Plot for RR-VGLMs

Geometric (Truncated and Untruncated) Distributions

Positive-Binomial Distribution

get.smart.prediction

Retrieves ``.smart.prediction''

Generalized Extreme Value Distribution Family Function

Huber's least favourable distribution family function

Machinists Accidents

Fitting Constrained Quadratic Ordination (CQO)

melbmaxtemp daily maximum temperatures

Acute Myelogenous Leukemia Survival Data

Grain Prices Data in USA

Perspective plot for QRR-VGLMs

Model Calibrations

Power Link Function

Leipnik Distribution Family Function

Pareto and Truncated Pareto Distribution Family Functions

Prentice (1974) Log-gamma Distribution

Chi-squared Distribution

Hyperbolic Secant Distribution Family Function

Lomax Distribution Family Function

Logit Link Function

Fitting a Dirichlet-Multinomial Distribution

Cauchy Distribution Family Function

Hunua Ranges Data

Cardioid Distribution Family Function

Gumbel Distribution Family Function

Ordinal Regression with Continuation Ratios

The Log-Gamma Distribution

Fitting a Dirichlet Distribution

The Lindley Distribution

Log link function, and variants

The Exponential Poisson Distribution

Exponential Logarithmic Distribution Family Function

model.matrixvlm

Construct the Design Matrix of a VLM Object

Identity Link Function

double.cens.normal

Univariate Normal Distribution with Double Censoring

Gumbel-II Distribution Family Function

notdocumentedyet

Undocumented and Internally Used Functions and Classes

Multinomial Logit Model

Nakagami Distribution Family Function

Coef.rrvglm-class

Class ``Coef.rrvglm''

Michaelis-Menten Model

Hunting Spider Data

The Laplace Distribution

Relative Frequencies of Serum Proteins in white Pekin ducklings

Annual catches on Lake Otamangakau from October 1974 to October 1989

Number of Parameters

Extract Model Coefficients for VLM Objects

Mixture of Two Univariate Normal Distributions

Returns Important Matrices etc. of a RR-VGLM Object

The Log-Laplace Distribution

Extract Log-likelihood for VGLMs/VGAMs/etc.

Retrieve One Component of ``.smart.prediction''

The Folded-Normal Distribution

The Maxwell Distribution

The Lambert W function

Multi-logit Link Function

Exponential Distribution

2008 and 2012 Summer Olympic Final Medal Count Data

Complementary-log Link Function

Logarithms with an Unit Offset and Exponential Term

Pneumoconiosis in Coalminers Data

Negative binomial canonical link function

Oxford Temperature Data

2-parameter Gamma Distribution

LMS Quantile Regression with a Box-Cox transformation to a Gamma Distribution

The Poisson Lognormal Distribution

Poisson-points-on-a-plane/volume Distances Distribution

posbernoulli.tb

Positive Bernoulli Family Function with Time and Behavioural Effects

pgamma.deriv.unscaled

Derivatives of the Incomplete Gamma Integral (Unscaled Version)

2-parameter Gamma Distribution

Rayleigh Distribution Family Function

Index from Array to Matrix

Truncated Weibull Distribution Family Function

Generalized Rayleigh Distribution Family Function

The Perks Distribution

Control function for vgam

Hormone Assay Data

Log-Laplace and Logit-Laplace Distribution Family Functions

Derivatives of the Incomplete Gamma Integral

Ordinal Regression with Stopping Ratios

Positive Negative Binomial Distribution Family Function

log F Distribution

Zero-Altered Poisson Distribution

The Makeham Distribution

Generalized Pareto Distribution Family Function

negbinomial.size

Negative Binomial Distribution Family Function With Known Size

The Gumbel-II Distribution

Log link function with an offset

Test For a Smart Object

Inverse Lomax Distribution Family Function

Loglinear Model for Two Binary Responses

Reciprocal link function

Model Diagnostic Plots for QRR-VGLMs

Lognormal Distribution

Skew-Normal Distribution

Quantile Plot for Gumbel Regression

Yule-Simon Family Function

General Electric and Westinghouse Data

Vector cubic smoothing spline

Lerch Phi Function

Latent Variables

Negative Binomial-Ordinal Link Function

Positive Bernoulli Sequence Model

Exchangeable bivariate cloglog odds-ratio model from a zero-inflated Poisson distribution

plotdeplot.lmscreg

Density Plot for LMS Quantile Regression

plotvgam.control

Control Function for plotvgam()

Yule-Simon Distribution

plotqtplot.lmscreg

Quantile Plot for LMS Quantile Regression

Positive Bernoulli Family Function with Behavioural Effects

Probit Link Function

Univariate Normal Distribution as a Varying-Coefficient Model

Zero-Altered Poisson Distribution

Slash Distribution Family Function

Mixture of Two Poisson Distributions

Minimizing the L-q norm Family Function

Negative Binomial Distribution Family Function

Prior and Working Weights of a VGLM fit

Poisson Family Function

Probability Plots for Categorical Data Analysis

Inv.paralogistic

The Inverse Paralogistic Distribution

LMS Quantile Regression with a Yeo-Johnson Transformation to Normality

LMS Quantile Regression with a Box-Cox Transformation to Normality

Positive-geometric Distribution

Positive-Negative Binomial Distribution

Levy Distribution Family Function

Latent Variable Plot

The Gumbel Distribution

Upper Record Values from a 1-parameter Exponential Distribution

Mean Excess Plot

Mixture of Two Exponential Distributions

Trajectory plot for QRR-VGLMs

Proportional Odds Model for Ordinal Regression

Kendall's Tau Statistic

Positive Binomial Distribution Family Function

The Pareto(IV/III/II) Distributions

The Singh-Maddala Distribution

Yellow-bellied Prinia

University California Berkeley Graduate Admissions

The Rice Distribution

rrvglm.optim.control

Control function for rrvglm() calling optim()

Positive-Poisson Distribution

Fitting Reduced-Rank Vector Generalized Linear Models (RR-VGLMs)

Predict Method for a VGLM fit

Class ``vglmff''

quasibinomialff

Quasi-Binomial Family Function

Weibull Distribution Family Function

Natural Exponential Family Generalized Hyperbolic Secant Distribution Family Function

Zero-Inflated Geometric Distribution Family Function

Toxoplasmosis Data

Low-iron Rat Teratology Data

Main effects plot for a Row-Column Interaction Model (RCIM)

Control function for rrvglm

The Positive-Normal Distribution

Logarithmic Distribution

The Dirichlet distribution

Loglinear Model for Three Binary Responses

Riemann's Zeta Function

Paralogistic Distribution Family Function

smart.expression

S Expression for Smart Functions

Fitting Vector Generalized Additive Models

Yeo-Johnson Transformation

Scaled Student t Distribution with 2 df Family Function

Constrained Quadratic Ordination

Default VGAM Plotting

Poisson-Ordinal Link Function

Control function for vglm

Return Level Plot for GEV Fits

Logarithmic Distribution

Simplex Distribution Family Function

Predict Method for a CQO fit

Nested reduced-rank autoregressive models for multiple time series

Defining smooths in VGAM formulae

Cleans Up After Smart Prediction

Positive Normal Distribution Family Function

The zero Argument in VGAM Family Functions

Skellam Distribution Family Function

Fitting Vector Generalized Linear Models

Zero-Inflated Poisson Distribution (Yip (1988) algorithm)

Zeta Distribution Family Function

Zero-Inflated Binomial Distribution Family Function

Benini Distribution Family Function

Construct the Model Frame of a VLM Object

undocumented-methods

Undocumented Methods Functions

Zero-Altered Binomial Distribution

Venice Maximum Sea Levels Data

Univariate Skew-Normal Distribution Family Function

Zero-Altered Negative Binomial Distribution

Determine What Mode the Smart Prediction is In

Smart Prediction

The Truncated Pareto Distribution

Zero-Altered Geometric Distribution

Short-tailed Symmetric Distribution Family Function

Zero-Inflated Poisson Distribution Family Function

von Mises Distribution Family Function

Positive Bernoulli Family Function with Time Effects

Trajectory Plot

Rhobit Link Function

Rutherford-Geiger Polonium Data

Rice Distribution Family Function

Plots for VGLMs

Bitterness in Wine Data

Positive Poisson Distribution Family Function

Zipf Distribution Family Function

Smart Prediction Setup

Zero-Altered Binomial Distribution

Quasi-Poisson Family Function

Upper Record Values from a Univariate Normal Distribution

Univariate Normal Distribution

The Triangle Distribution

Student t Distribution

Zero-Inflated Negative Binomial Distribution Family Function

Zero-Altered Negative Binomial Distribution

The Two-stage Sequential Binomial Distribution Family Function

Zero-Inflated Binomial Distribution

Zero-Altered Geometric Distribution

Zero-Inflated Negative Binomial Distribution

Beta Distribution of the Second Kind

Quantile Plot for LMS Quantile Regression

Pregnant Rats Toxological Experiment Data

Class ``rrvglm''

Expectiles-sc.t2

Expectiles/Quantiles of the Scaled Student t Distribution with 2 Df

Body Mass Index of New Zealand Adults Data

Zero-Inflated Poisson Distribution

Wald Distribution Family Function

Bradley Terry Model With Ties

Cystic Fibrosis Data

Zero-Inflated Geometric Distribution

Parallelism Constraint Matrices

Log-log Link Function

Ordinal Poisson Family Function

Poisson Points Distribution

Adds a List to the End of the List ``.smart.prediction''

qrrvglm.control

Control function for QRR-VGLMs (CQO)

Reciprocal Inverse Gaussian distribution

Waitakere Ranges Data

Simulate Responses for VGLMs and VGAMs