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VGAM (version 1.1-1)

Vector Generalized Linear and Additive Models

Description

An implementation of about 6 major classes of statistical regression models. The central algorithm is Fisher scoring and iterative reweighted least squares. At the heart of this package are the vector generalized linear and additive model (VGLM/VGAM) classes. VGLMs can be loosely thought of as multivariate GLMs. VGAMs are data-driven VGLMs that use smoothing. The book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) gives details of the statistical framework and the package. Currently only fixed-effects models are implemented. Many (150+) models and distributions are estimated by maximum likelihood estimation (MLE) or penalized MLE. 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; see the NEWS and ChangeLog files for latest changes.

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Version

Install

install.packages('VGAM')

Monthly Downloads

31,077

Version

1.1-1

License

GPL-3

Maintainer

Thomas Yee

Last Published

February 18th, 2019

Functions in VGAM (1.1-1)

Link functions for VGLM/VGAM/etc. families

Mark the Baseline of Row and Column on a Matrix data

The AB-Ab-aB-ab Blood Group System

The ABO Blood Group System

Table 1 of Huggins (1989)

The Inverse Gaussian Distribution

Asymmetric Laplace Distribution Family Functions

The Laplace Distribution

Auckland University Undergraduate Counts Data

Analysis of Deviance for Vector Generalized Linear Model Fits

The A1A2A3 Blood Group System

The AA-Aa-aa Blood Group System

Computation of the Exact EIM of an Order-1 Autoregressive Process

Coef.rrvglm-class

Class ``Coef.rrvglm''

Returns Important Matrices etc. of a RR-VGLM Object

Seemingly Unrelated Regressions Family Function

Benford's Distribution

Select Variables for a Formula Response or the RHS of a Formula

Akaike's Information Criterion

Autoregressive Process with Order-1 Family Function

Benini Distribution Family Function

Clayton Copula (Bivariate) Distribution

Extract Model Coefficients for VLM Objects

CommonVGAMffArguments

Common VGAM Family Function Arguments

Vector Generalized Linear and Additive Models and Associated Models

The AR-1 Autoregressive Process

Ordinal Regression with Adjacent Categories Probabilities

Farlie-Gumbel-Morgenstern's Bivariate Distribution Family Function

Asymmetric Least Squares Quantile Regression

Bivariate Probit Model (Family Function)

The Pareto Distribution

Quasi-variances Preprocessing Function

Bivariate Probit Model

Gaussian Copula (Bivariate) Distribution

Poisson Regression by Asymmetric Maximum Likelihood Estimation

Plackett's Bivariate Copula Family Function

calibrate.qrrvglm

Calibration for CQO and CAO models

calibrate.qrrvglm.control

Control Function for CQO/CAO Calibration

Beta-binomial Distribution Family Function

Censored Normal Distribution

Beta-binomial Distribution Family Function

Censored Poisson Family Function

The Beta-Prime Distribution

Extract Model Coefficients of a vgam() Object

Ali-Mikhail-Haq Distribution Family Function

Extract Model Coefficients

Crashes on New Zealand Roads in 2009

Utility Functions for the VGAM Package

V1 Flying-Bombs Hits in London

Bivariate Student-t Family Function

The Two-parameter Beta Distribution Family Function

Ordinal Regression with Continuation Ratios

The Beta-Geometric Distribution

Bivariate Student-t Distribution Cumulative Distribution Function

Differenced Zeta Distribution

Fitting a Dirichlet Distribution

Farlie-Gumbel-Morgenstern's Bivariate Distribution

Takeuchi's Information Criterion

Bivariate Farlie-Gumbel-Morgenstern Exponential Distribution Family Function

Bayesian Information Criterion

Cystic Fibrosis Data

Bivariate Logistic Distribution Family Function

Bivariate Logistic Distribution

Computes Model Coefficients and Quantities

Birnbaum-Saunders Distribution Family Function

Coef.qrrvglm-class

Class ``Coef.qrrvglm''

Redirects the user to cqo

Returns Important Matrices etc. of a QO Object

Confidence Intervals for Parameters of VGLMs

The Birnbaum-Saunders Distribution

Body Mass Index of New Zealand Adults Data

Error Function, and variants

Constraint Matrices

Borel-Tanner Distribution Family Function

Fitting Constrained Additive Ordination (CAO)

Control Function for RR-VGAMs (CAO)

Erlang Distribution

Ordinal Regression with Cumulative Probabilities

The Bell Distribution

Bell Distribution Family Function

Dagum Distribution Family Function

Family Function Name

Beta-geometric Distribution Family Function

Chest Pain in NZ Adults Data

Expectiles-Normal

Expectiles of the Normal Distribution

Chinese Population in New Zealand 1867--2001 Data

The Beta-Normal Distribution

Bivariate Gamma: McKay's Distribution

concoef-methods

Constrained (Canonical) Coefficients

Extract Model Constrained/Canonical Coefficients

Create a Survival Object

The Dagum Distribution

Gumbel's Type I Bivariate Distribution Family Function

Captures of Peromyscus maniculatus (Also Known as Deer Mice).

Expectiles-Uniform

Expectiles of the Uniform Distribution

Felix Distribution Family Function

Exponentiated Exponential Distribution

Plackett's Bivariate Copula

Mortality of Flour Beetles from Carbon Disulphide

Exponential Poisson Distribution Family Function

Binomial Logistic Regression by Asymmetric Maximum Likelihood Estimation

Model Formulae and Term Names for VGLMs

The Folded-Normal Distribution

Biplot of Constrained Regression Models

Frechet Distribution Family Function

calibrate-methods

Calibration for Constrained Regression Models

The Frechet Distribution

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

Model Calibrations

The Exponential Poisson Distribution

Generally-Altered Poisson Distribution

Cauchit Link Function

Exponential Regression by Asymmetric Maximum Likelihood Estimation

The Fisk Distribution

Generalized Poisson distribution

Generalized Rayleigh Distribution Family Function

Cauchy Distribution Family Function

Generally-Altered Poisson Distribution Family Function

aux.posbernoulli.t

Auxiliary Function for the Positive Bernoulli Family Function with Time Effects

Data on Back Pain Prognosis, from Anderson (1984)

Generally-Truncated Binomial Distribution Family Function

Fitted Values of a VLM object

Generally-Inflated Binomial Distribution

1-parameter Gamma Distribution

Cumulative Distribution Function for LMS Quantile Regression

The Two-parameter Beta Distribution Family Function

Bacon and Eggs Data

Generally-Truncated Poisson Distribution

Hat Values and Regression Deletion Diagnostics

Hauck-Donner Effects: A Detection Test for Wald Tests

Hypergeometric Family Function

The Bell Series of Integers

2-parameter Gamma Distribution

Censored Gumbel Distribution

Complementary Log-log Link Function

The Beta-Binomial Distribution

Generally-Inflated Poisson Distribution

Bivariate Binary Regression with an Odds Ratio (Family Function)

Hyperbolic Secant Distribution Family Function

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

Does the Fitted Object Suffer from a Known Bug?

get.smart.prediction

Retrieves ``.smart.prediction''

Generalized Gamma distribution family function

The Gompertz Distribution

The Benini Distribution

Beta Distribution of the Second Kind

Gamma-Ordinal Link Function

Bivariate Binary Regression with an Odds Ratio

Ali-Mikhail-Haq Bivariate Distribution

Clayton Copula (Bivariate) Family Function

Parallelism Constraint Matrices

The Generalized Gamma Distribution

Frank's Bivariate Distribution Family Function

Haight's Zeta Distribution

Haight's Zeta Family Function

Binomial Family Function

The Lambert W Function

Frank's Bivariate Distribution

Laplace Distribution

Generalized Extreme Value Distribution Family Function

The Generalized Extreme Value Distribution

Breathlessness and Wheeze Amongst Coalminers Data

Bivariate Normal Distribution Cumulative Distribution Function

Bivariate Normal Distribution Family Function

Test For a Smart Object

The Borel-Tanner Distribution

Zero Constraint Matrices

Gaussian Copula (Bivariate) Family Function

double.cens.normal

Univariate Normal Distribution with Double Censoring

Leipnik Distribution Family Function

The Lindley Distribution

1-parameter Gamma Distribution

Logarithms with an Unit Offset and Exponential Term

Inputting Data to fit a Bradley Terry Model

double.expbinomial

Double Exponential Binomial Distribution Family Function

Bradley Terry Model With Ties

The Exponential Integral and Variants

The Exponential Geometric Distribution

Grain Prices Data in USA

Lerch Phi Function

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

Bradley Terry Model

Natural Exponential Family Generalized Hyperbolic Secant Distribution Family Function

The Felix Distribution

Link Functions for VGLMs

F Distribution Family Function

Generally-Inflated Poisson Distribution Family Function

calibrate.rrvglm

Calibration for CLO models (RR-VGLMs)

calibrate.rrvglm.control

Control Function for CLO (RR-VGLM) Calibration

Chi-squared Distribution

log F Distribution

Cardioid Distribution

Loglinear Model for Two Binary Responses

Loglinear Model for Three Binary Responses

The Generalized Poisson Distribution

Extract Log-likelihood for VGLMs/VGAMs/etc.

Redirects the User to rrvglm()

has.interceptvlm

Has a Fitted VGLM Got an Intercept Term?

Corbet's Butterfly Data

Fitting Constrained Quadratic Ordination (CQO)

Density Plot for LMS Quantile Regression

The Generalized Rayleigh Distribution

Cardioid Distribution Family Function

Generally-Truncated-Binomial Distribution

Lognormal Distribution

Residual Degrees-of-Freedom

Differenced Zeta Distribution Family Function

Log Link Function with an Offset

Relative Frequencies of Serum Proteins in White Pekin Ducklings

Expectiles-Exponential

Expectiles of the Exponential Distribution

Latent Variable Plot for QO models

Latent Variable Plot for RR-VGLMs

Response Variable Extracted

Exponential Link Function

Fitting a Dirichlet-Multinomial Distribution

The Maxwell Distribution

New Zealand Marital Data

Fitting a Dirichlet-Multinomial Distribution

Gumbel Distribution Family Function

The Exponential Logarithmic Distribution

Exponentiated Exponential Distribution

McCullagh (1989) Distribution Family Function

Exponential Geometric Distribution Family Function

Mixture of Two Exponential Distributions

Inverse Binomial Distribution Family Function

Inverse Gaussian Distribution Family Function

Creates a Matrix of Appropriate Dimension

Exponential Logarithmic Distribution Family Function

Mixture of Two Univariate Normal Distributions

Maxwell Distribution Family Function

Toxicity trial for insects

Fisher's Z Link Function

The Laplace Distribution

Negative Binomial-Ordinal Link Function

Multi-logit Link Function

Exponential Distribution

Folded Normal Distribution Family Function

Latent Variables

Negative Binomial Distribution Family Function

Fisk Distribution family function

One-inflated Zipf Distribution Family Function

2-parameter Gamma Distribution

Gumbel-II Distribution Family Function

notdocumentedyet

Undocumented and Internally Used Functions and Classes

Gamma Hyperbola Bivariate Distribution

Number of Parameters

Folded Square Root Link Function

Hauck-Donner Effects: Severity Measures

One-Inflated Zipf Distribution

Generalized Pareto Distribution Family Function

Pareto(IV/III/II) Distribution Family Functions

One-inflated Logarithmic Distribution Family Function

GARMA (Generalized Autoregressive Moving-Average) Models

Generalized Beta Distribution Family Function

The Generalized Beta Distribution (Libby and Novick, 1982)

One-Inflated Logarithmic Distribution

One-truncated Poisson Distribution

The Generalized Pareto Distribution

The Log-Laplace Distribution

Log-Laplace and Logit-Laplace Distribution Family Functions

Hunting Spider Data

Hormone Assay Data

One-truncated Zeta Distribution Family Function

Derivatives of the Incomplete Gamma Integral

The Pareto(IV/III/II) Distributions

Generally-Altered Binomial Distribution

inv.paralogistic

Inverse Paralogistic Distribution Family Function

Inv.paralogistic

The Inverse Paralogistic Distribution

Lomax Distribution Family Function

Huber's Least Favourable Distribution Family Function

pgamma.deriv.unscaled

Derivatives of the Incomplete Gamma Integral (Unscaled Version)

Acute Myelogenous Leukemia Survival Data

Index from Array to Matrix

Identity Link Function

The Lomax Distribution

Default VGAM Plotting

plotvgam.control

Control Function for plotvgam()

Melbourne Daily Maximum Temperatures

Mean Excess Plot

Generalized Beta Distribution of the Second Kind

Inverse Lomax Distribution Family Function

The Generalized Beta II Distribution

Generally-Truncated Poisson Distribution Family Function

Levy Distribution Family Function

Nakagami Distribution

Negative Binomial Canonical Link Function

Geometric (Truncated and Untruncated) Distributions

General Electric and Westinghouse Data

One-Inflated Positive Binomial Distribution

One-Inflated Positive Binomial Distribution Family Function

2008 and 2012 Summer Olympic Final Medal Count Data

Gompertz Distribution Family Function

The Inverse Lomax Distribution

Low-iron Rat Teratology Data

Logarithmic Distribution

Plots for VGLMs

The Gumbel-II Distribution

The Gumbel Distribution

Ordinal Poisson Family Function

Paralogistic Distribution Family Function

The Paralogistic Distribution

Huber's Least Favourable Distribution

Positive Bernoulli Family Function with Behavioural Effects

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

Kendall's Tau Statistic

Hunua Ranges Data

Logistic Distribution Family Function

Pneumoconiosis in Coalminers Data

plotdeplot.lmscreg

Density Plot for LMS Quantile Regression

Kumaraswamy Distribution Family Function

Positive Bernoulli Family Function with Time Effects

Log Link Function, and Variants

Logarithmic Distribution

Model Diagnostic Plots for QRR-VGLMs

The Kumaraswamy Distribution

Annual catches on Lake Otamangakau from October 1974 to October 1989

Complementary-log Link Function

The Log-Gamma Distribution

Log-log and Log-log-log Link Functions

Minimizing the L-q norm Family Function

Prentice (1974) Log-gamma Distribution

Yellow-bellied Prinia

Likelihood Ratio Test of Nested Models

Log-gamma Distribution Family Function

LMS Quantile Regression with a Box-Cox Transformation to Normality

LMS Quantile Regression with a Yeo-Johnson Transformation to Normality

Likelihood Ratio Test Statistics Evaluated at the Null Values

Logit Link Function

posbernoulli.tb

Positive Bernoulli Family Function with Time and Behavioural Effects

Quantile Plot for Gumbel Regression

Latent Variable Plot

Mixture of Two Poisson Distributions

Construct the Model Frame of a VLM Object

logitoffsetlink

Logit-with-an-Offset Link Function

The Makeham Distribution

One-Altered Logarithmic Distribution

Machinists Accidents

Marginal Effects for Several Categorical Response Models

model.matrixqrrvglm

Construct the Model Matrix of a QRR-VGLM Object

University California Berkeley Graduate Admissions

Positive-Binomial Distribution

Makeham Distribution Family Function

Michaelis-Menten Model

Quantile Plot for LMS Quantile Regression

Nested Reduced-rank Autoregressive Models for Multiple Time Series

Yule-Simon Family Function

Probit Link Function

Method for Profiling vglm Objects

One-Altered Positive-Poisson Distribution

One-truncated Logarithmic Distribution

Class ``rrvglm''

rrvglm.optim.control

Control Function for rrvglm() Calling optim()

model.matrixvlm

Construct the Design Matrix of a VLM Object

One-Altered Logarithmic Distribution

Rutherford-Geiger Polonium Data

Singh-Maddala Distribution Family Function

Multinomial Logit Model

Nakagami Distribution Family Function

negbinomial.size

Negative Binomial Distribution Family Function With Known Size

The Dirichlet distribution

One-truncated Positive-Poisson Distribution

Upper Record Values from a 1-parameter Exponential Distribution

One-truncated Zeta Distribution

Univariate Normal Distribution as a Varying-Coefficient Model

Oxford Temperature Data

The Perks Distribution

Perspective plot for QRR-VGLMs

The Rice Distribution

Poisson Family Function

One-Altered Zeta Distribution

The Poisson Lognormal Distribution

Rice Distribution Family Function

The Singh-Maddala Distribution

One-Altered Logarithmic Distribution

Ordinal Superiority Measures

One-truncated Logarithmic Distribution

Pareto and Truncated Pareto Distribution Family Functions

One-Altered Logarithmic Distribution

smart.expression

S Expression for Smart Functions

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

Defining Smooths in VGAM Formulas

Plotting Functions for 'profile' Objects

Poisson Points Distribution

The Positive-Normal Distribution

Determine What Mode the Smart Prediction is In

One-Inflated Positive Poisson Distribution

Summarizing Vector Generalized Additive Model Fits

Positive-Negative Binomial Distribution

Positive Normal Distribution Family Function

Positive Negative Binomial Distribution Family Function

Residuals for a VGLM fit

Perks Distribution Family Function

One-inflated Positive Poisson Distribution Family Function

Scaled Student t Distribution with 2 df Family Function

Rhobit Link Function

Skew-Normal Distribution

Univariate Skew-Normal Distribution Family Function

Power Link Function

The Rayleigh Distribution

Pregnant Rats Toxological Experiment Data

Slash Distribution Family Function

One-inflated Zeta Distribution Family Function

Positive Binomial Distribution Family Function

Summarizing Vector Generalized Linear Model Fits

Slash Distribution

Truncated Weibull Distribution Family Function

One-Inflated Zeta Distribution

Smart Prediction Setup

Positive-Geometric Distribution

Simplex Distribution Family Function

Constrained Quadratic Ordination

plotqtplot.lmscreg

Quantile Plot for LMS Quantile Regression

Expectiles-sc.t2

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

Rao's Score Test Statistics Evaluated at the Null Values

The Skellam Distribution

Skellam Distribution Family Function

Reciprocal Inverse Gaussian distribution

Return Level Plot for GEV Fits

Smart Prediction

Proportional Odds Model for Ordinal Regression

Yule-Simon Distribution

Probability Plots for Categorical Data Analysis

Defining O'Sullivan Spline Smooths in VGAM Formulas

Ordinal Regression with Stopping Ratios

Main Effects Plot for a Row-Column Interaction Model (RCIM)

Fitting Vector Generalized Linear Models

Defining Penalized Spline Smooths in VGAM Formulas

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

Topp-Leone Distribution Family Function

undocumented-methods

Undocumented Methods Functions

Control Function for vgam()

Control Function for vglm()

The Topp-Leone Distribution

Zero-Altered Geometric Distribution

Trajectory plot for QRR-VGLMs

Zero-Altered Geometric Distribution

The Tobit Distribution

qrrvglm.control

Control Function for QRR-VGLMs (CQO)

The Truncated Pareto Distribution

Weibull Distribution Family Function

Zero-Inflated Poisson Distribution

Vector Cubic Smoothing Spline

The Zeta Distribution

The Zipf Distribution

Prior and Working Weights of a VGLM fit

Univariate Normal Distribution

Upper Record Values from a Univariate Normal Distribution

Reciprocal Link Function

The zero Argument in VGAM Family Functions

Hauck-Donner Effects: Segmented Lines Plot

Zeta Distribution Family Function

Yeo-Johnson Transformation

Poisson-Ordinal Link Function

Riemann's Zeta Function

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

Zero-Inflated Negative Binomial Distribution

Zero-Inflated Negative Binomial Distribution Family Function

The Two-stage Sequential Binomial Distribution Family Function

Positive Bernoulli Sequence Model

Positive-Poisson Distribution

Simplex Distribution

Positive Poisson Distribution Family Function

Predict Method for a CQO fit

Predict Method for a VGLM fit

Quasi-variances Extraction Function

Fitting Vector Generalized Additive Models

Simulate Responses for VGLMs and VGAMs

Rayleigh Distribution Family Function

Student t Distribution

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

Toxoplasmosis Data

Control Function for rrvglm()

Summarizing Penalized Vector Generalized Additive Model Fits

Waitakere Ranges Data

Short-tailed Symmetric Distribution Family Function

Triangle Distribution Family Function

The Triangle Distribution

Trivariate Normal Distribution Family Function

Wald Test Statistics Evaluated at the Null Values

A Short-tailed Symmetric Distribution

Trivariate Normal Distribution Density and Random Variates

Trajectory Plot

Class ``vglmff''

Calculate Variance-Covariance Matrix for a Fitted VLM or RR-VGLM or QRR-VGLM Object

Zero-Altered Poisson Distribution

von Mises Distribution Family Function

Venice Maximum Sea Levels Data

Zero-Altered Poisson Distribution

Bitterness in Wine Data

Cleans Up After Smart Prediction

Zero-Altered Binomial Distribution

Wald Distribution Family Function

The Zero/One-Inflated Beta Distribution

Zero-Altered Binomial Distribution

Zero-Inflated Binomial Distribution

Weibull Distribution Family Function, Parameterized by the Mean

Zero-Inflated Binomial Distribution Family Function

Zero-Altered Negative Binomial Distribution

Exchangeable Bivariate cloglog Odds-ratio Model From a Zero-inflated Poisson Distribution

Zero-Altered Negative Binomial Distribution

Zero-Inflated Geometric Distribution

Zipf Distribution Family Function

Zero-Inflated Geometric Distribution Family Function

Zero-Inflated Poisson Distribution Family Function

Zero- and One-Inflated Beta Distribution Family Function

R-squared for Latent Variable Models

The MNSs Blood Group System