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VGAM (version 1.0-1)

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, and the book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) gives details of the statistical framework and VGAM package. Currently only fixed-effects models are implemented, i.e., no random-effects models. 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; see the NEWS and ChangeLog files for latest changes.

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Version

Install

install.packages('VGAM')

Monthly Downloads

42,087

Version

1.0-1

License

GPL-2 | GPL-3

Maintainer

Last Published

March 15th, 2016

Functions in VGAM (1.0-1)

Annual catches on Lake Otamangakau from October 1974 to October 1989

The Beta-Prime Distribution

Trajectory Plot

The Kumaraswamy Distribution

Clayton Copula (Bivariate) Family Function

Poisson Family Function

The Gumbel-II Distribution

The AR-1 Autoregressive Process

V1 Flying-Bombs Hits in London

Bayesian Information Criterion

Akaike's Information Criterion

The Inverse Gaussian Distribution

Pareto and Truncated Pareto Distribution Family Functions

The A1A2A3 Blood Group System

Autoregressive Process with Order-1 Family Function

The AA-Aa-aa Blood Group System

Data on Back Pain Prognosis, from Anderson (1984)

Seemingly Unrelated Regressions Family Function

The Beta-Geometric Distribution

Extract Model Coefficients for VLM Objects

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

Slash Distribution

Coef.qrrvglm-class

Class ``Coef.qrrvglm''

The MNSs Blood Group System

The Pareto Distribution

Table 1 of Huggins (1989)

Zero-Altered Negative Binomial Distribution

The Beta-Binomial Distribution

Waitakere Ranges Data

Quasi-variances Preprocessing Function

The AB-Ab-aB-ab Blood Group System

Cauchy Distribution Family Function

Erlang Distribution

Exponential Logarithmic Distribution Family Function

The ABO Blood Group System

Zero-Altered Binomial Distribution

Asymmetric Laplace Distribution Family Functions

aux.posbernoulli.t

Auxiliary Function for the Positive Bernoulli Family Function with Time Effects

Gumbel's Type I Bivariate Distribution Family Function

Body Mass Index of New Zealand Adults Data

Bivariate Logistic Distribution Family Function

Link functions for VGLM/VGAM/etc. families

concoef-methods

Constrained (Canonical) Coefficients

Frank's Bivariate Distribution Family Function

Expectiles-Exponential

Expectiles of the Exponential Distribution

Expectiles-Normal

Expectiles of the Normal Distribution

The Two-parameter Beta Distribution Family Function

Computes Model Coefficients and Quantities

Positive-Binomial Distribution

Utility Functions for the VGAM Package

Returns Important Matrices etc. of a QO Object

Returns Important Matrices etc. of a RR-VGLM Object

Beta Distribution of the Second Kind

Beta-binomial Distribution Family Function

Frank's Bivariate Distribution

Bivariate Farlie-Gumbel-Morgenstern Exponential Distribution Family Function

Bradley Terry Model

Bivariate Probit Model (Family Function)

Create a Survival Object

CommonVGAMffArguments

Common VGAM family function Arguments

Plackett's Bivariate Copula Family Function

Bradley Terry Model With Ties

Auckland University Undergraduate Counts Data

Bivariate Student-t Family Function

Censored Normal Distribution

Cardioid Distribution

The Benini Distribution

Ordinal Regression with Continuation Ratios

Response variable extracted

Lomax Distribution Family Function

Chest Pain in NZ Adults Data

The Pareto(IV/III/II) Distributions

The Laplace Distribution

Coef.rrvglm-class

Class ``Coef.rrvglm''

Bacon and Eggs Data

The Two-parameter Beta Distribution Family Function

Beta-geometric Distribution Family Function

Bivariate Logistic Distribution

Plackett's Bivariate Copula

Mark the Baseline of Row and Column on a Matrix data

Ali-Mikhail-Haq Bivariate Distribution

Farlie-Gumbel-Morgenstern's Bivariate Distribution Family Function

The Exponential Poisson Distribution

Extract Model Coefficients of a vgam() Object

Gaussian Copula (Bivariate) Distribution

Bivariate Gamma: McKay's Distribution

Bivariate normal distribution family function

Borel-Tanner Distribution Family Function

Benini Distribution Family Function

Bivariate Binary Regression with an Odds Ratio (Family Function)

Censored Gumbel Distribution

Complementary Log-log Link Function

Control Function for RR-VGAMs (CAO)

Residual Degrees-of-Freedom

Censored Poisson Family Function

Breathlessness and Wheeze Amongst Coalminers Data

Cardioid Distribution Family Function

calibrate.qrrvglm

Calibration for CQO and CAO models

Exponential Regression by Asymmetric Maximum Likelihood Estimation

Folded Normal Distribution Family Function

Confidence Intervals for VGLM Parameters

1-parameter Gamma Distribution

Ordinal Regression with Cumulative Probabilities

Poisson Regression by Asymmetric Maximum Likelihood Estimation

Ordinal Regression with Adjacent Categories Probabilities

The Felix Distribution

Exponentiated Exponential Distribution

2-parameter Gamma Distribution

Fitted Values of a VLM object

Extract Model Coefficients

Fitting a Dirichlet-Multinomial Distribution

The Exponential Integral and Variants

The Dagum Distribution

Exponential Link Function

GARMA (Generalized Autoregressive Moving-Average) Models

Relative Frequencies of Serum Proteins in white Pekin ducklings

General Electric and Westinghouse Data

Benford's Distribution

Inverse Binomial Distribution Family Function

Beta-binomial Distribution Family Function

Frechet Distribution Family Function

Gamma Hyperbola Bivariate Distribution

The Exponential Logarithmic Distribution

Constraint Matrices

Creates a Matrix of Appropriate Dimension

Generalized Beta Distribution of the Second Kind

Gaussian (normal) Family Function

Exponential Distribution

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

Mortality of Flour Beetles from Carbon Disulphide

has.interceptvlm

Has a Fitted VGLM Got an Intercept Term?

Fisk Distribution family function

Generalized Rayleigh Distribution Family Function

The Generalized Gamma Distribution

F Distribution Family Function

calibrate-methods

Calibration for Constrained Regression Models

Hyperbolic Secant Distribution Family Function

Hormone Assay Data

Model Formulae and Term Names for VGLMs

Generalized Extreme Value Distribution Family Function

Generalized Poisson distribution

Captures of Peromyscus maniculatus, also known as deer mice.

Expectiles-Uniform

Expectiles of the Uniform Distribution

Gaussian Copula (Bivariate) Family Function

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

Haight's Zeta Family Function

The Birnbaum-Saunders Distribution

double.expbinomial

Double Exponential Binomial Distribution Family Function

Fitting a Dirichlet-Multinomial Distribution

Geometric (Truncated and Untruncated) Distributions

The Borel-Tanner Distribution

Biplot of Constrained Regression Models

Error Function, and variants

calibrate.qrrvglm.control

Control function for CQO/CAO calibration

The Exponential Geometric Distribution

Fitting Constrained Additive Ordination (CAO)

The Folded-Normal Distribution

Redirects the user to rrvglm

Crashes on New Zealand Roads in 2009

Cauchit Link Function

get.smart.prediction

Retrieves ``.smart.prediction''

The Generalized Rayleigh Distribution

Cumulative Distribution Function for LMS Quantile Regression

The Generalized Extreme Value Distribution

Generalized Gamma distribution family function

Gamma-Ordinal Link Function

The Generalized Poisson Distribution

Folded Square Root Link Function

The Gompertz Distribution

Hypergeometric Family Function

Chinese Population in New Zealand 1867--2001 Data

Chi-squared Distribution

Fitting Constrained Quadratic Ordination (CQO)

Extract Model Constrained/Canonical Coefficients

Hat Values and Regression Deletion Diagnostics

2-parameter Gamma Distribution

Index from Array to Matrix

Gumbel Distribution Family Function

Exponential Poisson Distribution Family Function

Corbet's Butterfly Data

Fitting a Dirichlet Distribution

Huber's least favourable distribution family function

Inverse Gaussian Distribution Family Function

The Gumbel Distribution

double.cens.normal

Univariate Normal Distribution with Double Censoring

Hunua Ranges Data

Exponentiated Exponential Distribution

Gumbel-II Distribution Family Function

Exponential Geometric Distribution Family Function

Toxicity trial for insects

Huber's least favourable distribution

Vector Generalized Linear and Additive Models

Binomial Logistic Regression by Asymmetric Maximum Likelihood Estimation

The Beta-Normal Distribution

Asymmetric Least Squares Quantile Regression

Binomial Family Function

Bivariate normal distribution cumulative distribution function

Model Calibrations

Redirects the user to cqo

Cystic Fibrosis Data

Density Plot for LMS Quantile Regression

Fisher's Z Link Function

Grain Prices Data in USA

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

Generalized Pareto Distribution Family Function

The Generalized Pareto Distribution

Hunting Spider Data

Inverse Lomax Distribution Family Function

Log-gamma Distribution Family Function

Generalized Beta Distribution Family Function

Inv.paralogistic

The Inverse Paralogistic Distribution

The Log-Gamma Distribution

Mean Excess Plot

Acute Myelogenous Leukemia Survival Data

Zero-Inflated Poisson Distribution Family Function

Test For a Smart Object

Zero Constraint Matrices

Nakagami Distribution

Log link function with an offset

Prior and Working Weights of a VGLM fit

Lerch Phi Function

The Laplace Distribution

Number of Parameters

McCullagh (1989) Distribution Family Function

Multi-logit Link Function

The Rayleigh Distribution

Positive-geometric Distribution

Loglinear Model for Three Binary Responses

Likelihood Ratio Test of Nested Models

Kendall's Tau Statistic

melbmaxtemp daily maximum temperatures

The Paralogistic Distribution

Logarithms with an Unit Offset and Exponential Term

Natural Exponential Family Generalized Hyperbolic Secant Distribution Family Function

negbinomial.size

Negative Binomial Distribution Family Function With Known Size

Negative Binomial-Ordinal Link Function

Positive Bernoulli Sequence Model

Scaled Student t Distribution with 2 df Family Function

smart.expression

S Expression for Smart Functions

Logarithmic Distribution

Class ``rrvglm''

Positive Poisson Distribution Family Function

Maxwell Distribution Family Function

Marginal effects for several categorical response models

Log link function, and variants

Identity Link Function

Mixture of Two Exponential Distributions

Does the fitted object suffer from a known bug?

Complementary-log Link Function

Extract Log-likelihood for VGLMs/VGAMs/etc.

Mixture of Two Univariate Normal Distributions

Perspective plot for QRR-VGLMs

New Zealand Marital Data.

notdocumentedyet

Undocumented and Internally Used Functions and Classes

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

Latent Variables

Positive Normal Distribution Family Function

Probability Plots for Categorical Data Analysis

1-parameter Gamma Distribution

Rhobit Link Function

Michaelis-Menten Model

Log-log Link Function

LMS Quantile Regression with a Box-Cox Transformation to Normality

Log-Laplace and Logit-Laplace Distribution Family Functions

Univariate Normal Distribution as a Varying-Coefficient Model

Default VGAM Plotting

Wald Distribution Family Function

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

Yule-Simon Family Function

Smart Prediction Setup

log F Distribution

The Two-stage Sequential Binomial Distribution Family Function

Expectiles-sc.t2

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

Minimizing the L-q norm Family Function

Pregnant Rats Toxological Experiment Data

Logit Link Function

Quasi-Poisson Family Function

Negative binomial canonical link function

Smart Prediction

Machinists Accidents

Positive Negative Binomial Distribution Family Function

Quantile Plot for LMS Quantile Regression

Rice Distribution Family Function

Reciprocal link function

Prentice (1974) Log-gamma Distribution

Power Link Function

Mixture of Two Poisson Distributions

Makeham Distribution Family Function

quasibinomialff

Quasi-Binomial Family Function

2008 and 2012 Summer Olympic Final Medal Count Data

Oxford Temperature Data

Ordinal Poisson Family Function

posbernoulli.tb

Positive Bernoulli Family Function with Time and Behavioural Effects

Latent Variable Plot

Perks Distribution Family Function

Low-iron Rat Teratology Data

Model Diagnostic Plots for QRR-VGLMs

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

The Log-Laplace Distribution

Latent Variable Plot for RR-VGLMs

Zeta Distribution Family Function

plotdeplot.lmscreg

Density Plot for LMS Quantile Regression

Probit Link Function

Truncated Weibull Distribution Family Function

The Dirichlet distribution

Latent Variable Plot for QO models

Lognormal Distribution

Rutherford-Geiger Polonium Data

Determine What Mode the Smart Prediction is In

Link Functions for VGLMs

A Short-tailed Symmetric Distribution

Poisson Points Distribution

Positive Bernoulli Family Function with Time Effects

The Zero/One-Inflated Beta Distribution

Negative Binomial Distribution Family Function

Class ``vglmff''

Return Level Plot for GEV Fits

Poisson-Ordinal Link Function

Constrained Quadratic Ordination

Zero-Altered Negative Binomial Distribution

Control function for rrvglm

LMS Quantile Regression with a Yeo-Johnson Transformation to Normality

Summarizing Vector Generalized Linear Model Fits

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

Control function for vgam

Derivatives of the Incomplete Gamma Integral

Positive Binomial Distribution Family Function

Zipf Distribution Family Function

Skellam Distribution Family Function

Triangle Distribution Family Function

Fitting Vector Generalized Additive Models

Predict Method for a VGLM fit

Zero-Altered Geometric Distribution

Plots for VGLMs

Simplex Distribution Family Function

Upper Record Values from a 1-parameter Exponential Distribution

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

The Rice Distribution

Ordinal Regression with Stopping Ratios

Quantile Plot for Gumbel Regression

undocumented-methods

Undocumented Methods Functions

Univariate Skew-Normal Distribution Family Function

Zero-Altered Poisson Distribution

Zero-Altered Geometric Distribution

Upper Record Values from a Univariate Normal Distribution

Zero-Inflated Geometric Distribution

Trajectory plot for QRR-VGLMs

Positive-Poisson Distribution

plotvgam.control

Control Function for plotvgam()

pgamma.deriv.unscaled

Derivatives of the Incomplete Gamma Integral (Unscaled Version)

Weibull Distribution Family Function

Zero-Inflated Binomial Distribution

Venice Maximum Sea Levels Data

The Singh-Maddala Distribution

Zero-Inflated Binomial Distribution Family Function

The Poisson Lognormal Distribution

The Truncated Pareto Distribution

logitoffsetlink

Logit-with-an-Offset Link Function

Zero-Altered Binomial Distribution

The Positive-Normal Distribution

Positive-Negative Binomial Distribution

Univariate Normal Distribution

Nested reduced-rank autoregressive models for multiple time series

Zero-Inflated Negative Binomial Distribution

Construct the Model Frame of a VLM Object

Multinomial Logit Model

model.matrixvlm

Construct the Design Matrix of a VLM Object

Defining smooths in VGAM formulae

The zero Argument in VGAM Family Functions

Vector cubic smoothing spline

Control function for vglm

Toxoplasmosis Data

University California Berkeley Graduate Admissions

Positive Bernoulli Family Function with Behavioural Effects

Yule-Simon Distribution

Fitting Vector Generalized Linear Models

Zero-Inflated Geometric Distribution Family Function

Reciprocal Inverse Gaussian distribution

Levy Distribution Family Function

Leipnik Distribution Family Function

Proportional Odds Model for Ordinal Regression

Skew-Normal Distribution

plotqtplot.lmscreg

Quantile Plot for LMS Quantile Regression

Logistic Distribution Family Function

Zero-Inflated Poisson Distribution

Predict Method for a CQO fit

Pneumoconiosis in Coalminers Data

Bitterness in Wine Data

Yeo-Johnson Transformation

The Zeta Distribution

Parallelism Constraint Matrices

Cleans Up After Smart Prediction

Laplace Distribution

qrrvglm.control

Control function for QRR-VGLMs (CQO)

Weibull Distribution Family Function, Parameterized by the Mean

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

Logarithmic Distribution

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

Student t Distribution

Loglinear Model for Two Binary Responses

Zero-Altered Poisson Distribution

Yellow-bellied Prinia

The Lambert W function

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

Zero-Inflated Negative Binomial Distribution Family Function

rrvglm.optim.control

Control function for rrvglm() calling optim()

von Mises Distribution Family Function

Simulate Responses for VGLMs and VGAMs