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VGAM (version 0.7-8)

Vector Generalized Linear and Additive Models

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.

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Version

Install

install.packages('VGAM')

Monthly Downloads

43,625

Version

0.7-8

License

GPL-2

Maintainer

Thomas Yee

Last Published

February 12th, 2025

Functions in VGAM (0.7-8)

CommonVGAMffArguments

Common VGAM family function Arguments

The Fisk Distribution

Create a Survival Object

The Benini Distribution

The Two-parameter Beta Distribution Family Function

Bivariate Logistic Distribution

Poisson Regression by Asymmetric Maximum Likelihood Estimation

Beta-binomial Distribution Family Function

Constraint Matrices

DeLury's Method for Population Size Estimation

Ordinal Regression with Cumulative Probabilities

Inputting Data to fit a Bradley Terry Model

The Dagum Distribution

The ABO Blood Group System

Fitting Constrained Quadratic Ordination (CQO)

Computes Model Coefficients and Quantities

Coef.rrvglm-class

Class ``Coef.rrvglm''

Coef.qrrvglm-class

Class ``Coef.qrrvglm''

Returns Important Matrices etc. of a QO Object

Ordinal Regression with Continuation Ratios

The G1G2G3 Blood Group System

The Lomax Distribution

Control Function for RR-VGAMs (CAO)

Exponential Regression by Asymmetric Maximum Likelihood Estimation

Bradley Terry Model With Ties

Binomial Logistic Regression by Asymmetric Maximum Likelihood Estimation

The Inverse Lomax Distribution

Extract Model Constrained/Canonical Coefficients

Univariate Normal Distribution with Double Censoring

Density Plot for LMS Quantile Regression

Fitting a Dirichlet-Multinomial Distribution

Vector Generalized Linear and Additive Models

The MNSs Blood Group System

Link functions for VGLM/VGAM/etc. families

Complementary Log-log Link Function

The Laplace Distribution

The AA-Aa-aa Blood Group System

The Paralogistic Distribution

The Two-parameter Beta Distribution Family Function

The Folded-Normal Distribution

Exponential Distribution

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

Asymmetric Laplace Distribution Family Functions

Gaussian (normal) Family Function

Double Exponential Binomial Distribution Family Function

The Generalized Pareto Distribution

F Distribution Family Function

The Rayleigh Distribution

Gamma Hyperbola Bivariate Distribution

Bivariate Logistic Distribution Family Function

Extract Model Coefficients for VLM Objects

2-parameter Gamma Distribution

Generalized Pareto Distribution Family Function

Hunua Ranges Data

Ali-Mikhail-Haq Distribution Distribution Family Function

Bivariate Probit Model (Family Function)

The Borel-Tanner Distribution

Benford's Distribution

GARMA (Generalized Autoregressive Moving-Average) Models

Borel-Tanner Distribution Family Function

The Birnbaum-Saunders Distribution

Inverse Gaussian Distribution Family Function

Chest Pain in NZ Adults

Hunting Spider Data

Logistic Distribution Family Function

Fitting Constrained Additive Ordination (CAO)

Identity Link Function

McKay's Bivariate Gamma Distribution

Beta Distribution of the Second Kind

The AB-Ab-aB-ab Blood Group System

Gumbel Distribution Family Function

calibrate-methods

Calibration for Constrained Regression Models

Levy Distribution Family Function

Constrained (Canonical) Coefficients

Cauchy Distribution Family Function

Invparalogistic

The Inverse Paralogistic Distribution

Kumaraswamy Distribution Family Function

LMS Quantile Regression with a Yeo-Johnson Transformation to Normality

Michaelis-Menten Model

Fitting a Dirichlet-Multinomial Distribution

Bivariate Binary Regression with an Odds Ratio

Model Calibrations

Laplace Distribution

1-parameter Gamma Distribution

Cumulative Distribution Function for LMS Quantile Regression

The Pareto(IV/III/II) Distributions

Mixture of Two Univariate Normal Distributions

Fitting a Dirichlet Distribution

Positive Normal Distribution Family Function

Redirects the user to rrvglm

Cauchit Link Function

Logarithmic Distribution

Univariate normal distribution

Felix Distribution Family Function

Ordinal Regression with Adjacent Categories Probabilities

The Zeta Distribution

The Beta-Geometric Distribution

Censored Poisson Family Function

Pareto and Truncated Pareto Distribution Family Functions

Breathlessness and Wheeze Amongst Coalminers

Probit Link Function

Fisher's Z Link Function

Exponentiated Exponential Distribution

Creates a Matrix of Appropriate Dimension

The Frechet Distribution

Upper Record Values from a 1-parameter Exponential Distribution

Complementary-log Link Function

Skellam Distribution Family Function

The Generalized Extreme Value Distribution

Perspective plot for QRR-VGLMs

model.matrixvlm

Construct the Design Matrix of a VLM Object

Nakagami Distribution Family Function

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

Folded Normal Distribution Family Function

2-parameter Gamma Distribution

Lerch Phi Function

LMS Quantile Regression with a Box-Cox Transformation to Normality

Loglinear Model for Three Binary Responses

The Generalized Gamma Distribution

Generalized Gamma distribution family function

Control function for rrvglm

Body Mass Index of New Zealand Adults

Geometric Distribution

Index from Array to Matrix

Positive Negative Binomial Distribution Family Function

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

Slash Distribution Family Function

Gumbel's Type I Bivariate Distribution Family Function

Inverse Binomial Distribution Family Function

calibrate.qrrvglm

Calibration for CQO, UQO and CAO models

get.smart.prediction

Retrieves ``.smart.prediction''

The AB-Ab-aB-ab2 Blood Group System

Reciprocal Inverse Gaussian distribution

Vector cubic smoothing spline

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

Latent Variable Plot

Biplot of Constrained Regression Models

Frank's Bivariate Distribution

Skew-Normal Distribution

Generalized Poisson distribution

General Electric and Westinghouse Data

Loglinear Model for Two Binary Responses

Determine What Mode the Smart Prediction is In

Returns Important Matrices etc. of a RR-VGLM Object

Point System for the 2008 World Fly Fishing Championships

Cleans Up After Smart Prediction

undocumented-methods

Undocumented Methods Functions

Haight's Zeta Function

The Gumbel Distribution

A Short-tailed Symmetric Distribution

Latent Variable Plot for QO models

McCullagh (1989) Distribution Family Function

Trajectory Plot

The Beta-Normal Distribution

Yeo-Johnson Transformation

Generalized Extreme Value Distribution Family Function

The Pareto Distribution

Zero-Altered Poisson Distribution

Zero-Inflated Negative Binomial Distribution Family Function

Zeta Distribution Family Function

Multinomial Logit Model

Binomial Family Function

Venice Maximum Sea Levels

Plackett's Bivariate Distribution Family Function

Mixture of Two Exponential Distributions

Zero-Altered Negative Binomial Distribution

The Laplace Distribution

The zero Argument in VGAM Family Functions

Folded Square Root Link Function

Log-gamma Distribution Family Function

Censored Gumbel Distribution

Zero-Inflated Poisson Distribution

Hyperbolic Secant Distribution Family Function

Hypergeometric Family Function

Default VGAM Plotting

Logit Link Function

Log-log Link Function

plotqtplot.lmscreg

Quantile Plot for LMS Quantile Regression

Poisson-Ordinal Link Function

The Generalized Beta Distribution (Libby and Novick, 1982)

Log link function

2008 World Fly Fishing Championships

Yule-Simon Distribution

Negative Binomial-Ordinal Link Function

Minimizing the L-q norm Family Function

Zero-Inflated Binomial Distribution

Lognormal Distribution

Mean Excess Plot

The Poisson Lognormal Distribution

Constrained Quadratic Ordination

Morgenstern's Bivariate Distribution Family Function

Latent Variables

Maxwell Distribution Family Function

The Truncated Pareto Distribution

Quasi-Poisson Family Function

Rutherford-Geiger Polonium Data

Cardioid Distribution Family Function

Class ``rrvglm''

Latent Variable Plot for RR-VGLMs

calibrate.qrrvglm.control

Control function for CQO/UQO/CAO calibration

Fitting Goodman's RC Association Model

Fitting Unconstrained Quadratic Ordination (UQO)

Log link function with an offset

USA grain prices

Zero-Inflated Poisson Distribution Family Function

Ordinal Poisson Family Function

Rhobit Link Function

Negative Binomial Distribution Family Function

Positive Poisson Distribution Family Function

Mixture of Two Poisson Distributions

Chi-squared Distribution

quasibinomialff

Quasi-Binomial Family Function

Censored Normal Distribution

plotvgam.control

Control Function for plotvgam()

Control function for vglm

Model Diagnostic Plots for QRR-VGLMs

Akaike's An Information Criterion

The Log-Gamma Distribution

Return Level Plot for GEV Fits

Smart Prediction Setup

2008 World Fly Fishing Championships (Team results)

predict.qrrvglm

Predict Method for a CQO fit

Quantile Plot for LMS Quantile Regression

Farlie-Gumbel-Morgenstern's Bivariate Distribution Family Function

Quantile Plot for Gumbel Regression

Rice Distribution Family Function

Zero-Altered Poisson Distribution

Smart Prediction

Positive-Negative Binomial Distribution

Generalized Beta Distribution of the Second Kind

Positive-Binomial Distribution

Univariate Skew-Normal Distribution Family Function

Nested reduced-rank autoregressive models for multiple time series

The Rice Distribution

smart.expression

S Expression for Smart Functions

Student t Distribution

Reciprocal link function

Control Function for UQO models

Triangle Distribution Family Function

Zero-Inflated Binomial Distribution Family Function

Fitting Vector Generalized Additive Models

Fitting Vector Generalized Linear Models

Zipf Distribution Family Function

Acute Myelogenous Leukemia Survival Data

von Mises Distribution Family Function

Leipnik Distribution Family Function

Construct the Model Frame of a VLM Object

Waitakere Ranges Data

Low-iron Rat Teratology Data

notdocumentedyet

Undocumented and Internally Used Functions and Classes

Control function for vgam

Oxford Temperature Data

Toxoplasmosis Data

Weibull Distribution Family Function

2008 World Fly Fishing Championships (Individual results)

Yule-Simon Family Function

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

2008 World Fly Fishing Championships (Number of captures)

Chinese Population in New Zealand 1867--2001

Zero-Inflated Negative Binomial Distribution

Poisson Family Function

Pneumoconiosis amongst a group of coalminers

Positive-Poisson Distribution

Power Link Function

The Dirichlet distribution

Upper Record Values from a Univariate Normal Distribution

Defining smooths in VGAM formulae

Singh-Maddala Distribution Family Function

The Two-stage Sequential Binomial Distribution Family Function

rrvglm.optim.control

Control function for rrvglm() calling optim()

Trajectory plot for QRR-VGLMs

Ordinal Regression with Stopping Ratios

Prentice (1974) Log-gamma Distribution

Class ``vglmff''

Wald Distribution Family Function

Prior and Working Weights of a VGLM fit

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

The Inverse Gaussian Distribution

Asymmetric Least Squares Quantile Regression

Beta-binomial Distribution Family Function

The Beta-Binomial Distribution

The Beta-Prime Distribution

Beta-geometric Distribution Family Function

Cardioid Distribution

Auckland University Undergraduate Counts

Redirects the user to cqo

Exponentiated Exponential Distribution

Fitted Values of a VLM object

Erlang Distribution

Gamma-Ordinal Link Function

Test For a Smart Object

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

Logarithmic Distribution

The Matched Binomial Distribution Family Function

plotdeplot.lmscreg

Density Plot for LMS Quantile Regression

The Positive-Normal Distribution

Positive Binomial Distribution Family Function

Predict Method for a VGLM fit

qrrvglm.control

Control function for QRR-VGLMs (CQO)

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

Simplex distribution

Zero-Altered Negative Binomial Distribution