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VGAM (version 0.9-6)

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

42,087

Version

0.9-6

License

GPL-2

Maintainer

Last Published

December 8th, 2014

Functions in VGAM (0.9-6)

Constraint Matrices

calibrate-methods

Calibration for Constrained Regression Models

Bivariate Logistic Distribution

Beta Distribution of the Second Kind

Vector Generalized Linear and Additive Models

Frank's Bivariate Distribution Family Function

The Pareto Distribution

The A1A2A3 Blood Group System

The Dagum Distribution

Link functions for VGLM/VGAM/etc. families

Hunua Ranges Data

Redirects the user to rrvglm

Data on Back Pain Prognosis, from Anderson (1984)

Density Plot for LMS Quantile Regression

Returns Important Matrices etc. of a QO Object

Index from Array to Matrix

Coef.qrrvglm-class

Class ``Coef.qrrvglm''

Binomial Logistic Regression by Asymmetric Maximum Likelihood Estimation

The Inverse Gaussian Distribution

Fitting Constrained Additive Ordination (CAO)

Fitting a Dirichlet-Multinomial Distribution

V1 Flying-Bombs Hits in London

Complementary Log-log Link Function

Gaussian Copula (Bivariate) Distribution

Bacon and Eggs Data

Cumulative Distribution Function for LMS Quantile Regression

Bivariate Binary Regression with an Odds Ratio

The Birnbaum-Saunders Distribution

The Borel-Tanner Distribution

Bradley Terry Model With Ties

Bivariate Student-t distribution cumulative distribution function

The Exponential Poisson Distribution

Borel-Tanner Distribution Family Function

Bivariate Logistic Distribution Family Function

Censored Poisson Family Function

Fitting a Dirichlet Distribution

Table 1 of Huggins (1989)

Plackett's Bivariate Copula Family Function

Coef.rrvglm-class

Class ``Coef.rrvglm''

Ordinal Regression with Continuation Ratios

calibrate.qrrvglm.control

Control function for CQO/CAO calibration

Bivariate Farlie-Gumbel-Morgenstern Exponential Distribution Family Function

Response variable extracted

Beta-geometric Distribution Family Function

Biplot of Constrained Regression Models

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

Annual catches on Lake Otamangakau from October 1974 to October 1989

double.expbinomial

Double Exponential Binomial Distribution Family Function

Exponential Regression by Asymmetric Maximum Likelihood Estimation

Cauchit Link Function

Frank's Bivariate Distribution

Bivariate Probit Model (Family Function)

Exponential Logarithmic Distribution Family Function

Clayton Copula (Bivariate) Distribution

The Two-parameter Beta Distribution Family Function

The AB-Ab-aB-ab Blood Group System

Erlang Distribution

Generalized Pareto Distribution Family Function

Beta-binomial Distribution Family Function

Cardioid Distribution

Returns Important Matrices etc. of a RR-VGLM Object

Gumbel Distribution Family Function

Haight's Zeta Distribution

Ali-Mikhail-Haq Bivariate Distribution

The Lambert W function

The Two-parameter Beta Distribution Family Function

Test For a Smart Object

Farlie-Gumbel-Morgenstern's Bivariate Distribution

Inputting Data to fit a Bradley Terry Model

Ordinal Regression with Cumulative Probabilities

The Beta-Prime Distribution

Crashes on New Zealand Roads in 2009

Control Function for RR-VGAMs (CAO)

Censored Normal Distribution

concoef-methods

Constrained (Canonical) Coefficients

Captures of Peromyscus maniculatus, also known as deer mice.

Benford's Distribution

Plackett's Bivariate Copula

Fitting Constrained Quadratic Ordination (CQO)

The Gompertz Distribution

Asymmetric Least Squares Quantile Regression

Gamma-Ordinal Link Function

Benini Distribution Family Function

Bivariate normal distribution family function

2-parameter Gamma Distribution

Extract Model Coefficients for VLM Objects

The Benini Distribution

Kumaraswamy Distribution Family Function

Extract Model Constrained/Canonical Coefficients

Laplace Distribution

Chinese Population in New Zealand 1867--2001 Data

Mark the Baseline of Row and Column on a Matrix data

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

Breathlessness and Wheeze Amongst Coalminers Data

Acute Myelogenous Leukemia Survival Data

The Beta-Geometric Distribution

double.cens.normal

Univariate Normal Distribution with Double Censoring

Hat Values and Regression Deletion Diagnostics

Auckland University Undergraduate Counts Data

Minimizing the L-q norm Family Function

The Felix Distribution

Expectiles-Exponential

Expectiles of the Exponential Distribution

The Beta-Binomial Distribution

Poisson Regression by Asymmetric Maximum Likelihood Estimation

Exponential Poisson Distribution Family Function

Construct the Model Frame of a VLM Object

Latent Variables

Akaike's Information Criterion

F Distribution Family Function

Gaussian Copula (Bivariate) Family Function

Corbet's Butterfly Data

inv.paralogistic

Inverse Paralogistic Distribution Family Function

Gamma Hyperbola Bivariate Distribution

Exponential Link Function

qrrvglm.control

Control function for QRR-VGLMs (CQO)

Hormone Assay Data

Ordinal Regression with Adjacent Categories Probabilities

The Lomax Distribution

Chi-squared Distribution

Fisk Distribution family function

Redirects the user to cqo

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

Cystic Fibrosis Data

Generalized Poisson distribution

Bayesian Information Criterion

Model Diagnostic Plots for QRR-VGLMs

Hyperbolic Secant Distribution Family Function

2-parameter Gamma Distribution

Expectiles-Uniform

Expectiles of the Uniform Distribution

Huber's least favourable distribution family function

Censored Gumbel Distribution

Mortality of Flour Beetles from Carbon Disulphide

Exponential Distribution

Loglinear Model for Three Binary Responses

plotdeplot.lmscreg

Density Plot for LMS Quantile Regression

The Beta-Normal Distribution

Create a Survival Object

The Inverse Lomax Distribution

Frechet Distribution Family Function

Expectiles-Normal

Expectiles of the Normal Distribution

Inverse Gaussian Distribution Family Function

Parallelism Constraint Matrices

Kendall's Tau Statistic

The Generalized Rayleigh Distribution

Log-log Link Function

Predict Method for a VGLM fit

Mixture of Two Univariate Normal Distributions

The Perks Distribution

Quasi-variances Preprocessing Function

posbernoulli.tb

Positive Bernoulli Family Function with Time and Behavioural Effects

Exponentiated Exponential Distribution

Latent Variable Plot for QO models

The Generalized Gamma Distribution

Body Mass Index of New Zealand Adults Data

Extract Log-likelihood for VGLMs/VGAMs/etc.

Plots for VGLMs

Cardioid Distribution Family Function

The Lindley Distribution

Rayleigh Distribution Family Function

Prentice (1974) Log-gamma Distribution

The Gumbel-II Distribution

get.smart.prediction

Retrieves ``.smart.prediction''

Bivariate normal distribution cumulative distribution function

aux.posbernoulli.t

Auxiliary Function for the Positive Bernoulli Family Function with Time Effects

Fitted Values of a VLM object

Chest Pain in NZ Adults Data

Levy Distribution Family Function

The MNSs Blood Group System

Smart Prediction

The Folded-Normal Distribution

Seemingly Unrelated Regressions

The Generalized Extreme Value Distribution

Multi-logit Link Function

Default VGAM Plotting

The Log-Laplace Distribution

Model Calibrations

Fisher's Z Link Function

Huber's least favourable distribution

Asymmetric Laplace Distribution Family Functions

Predict Method for a CQO fit

Positive-Negative Binomial Distribution

Gumbel-II Distribution Family Function

Proportional Odds Model for Ordinal Regression

Generalized Beta Distribution Family Function

Exponentiated Exponential Distribution

Residual Degrees-of-Freedom

Logit Link Function

Positive-Binomial Distribution

Trajectory plot for QRR-VGLMs

Cauchy Distribution Family Function

Leipnik Distribution Family Function

Logistic Distribution Family Function

Folded Normal Distribution Family Function

Control function for vglm

Reciprocal link function

calibrate.qrrvglm

Calibration for CQO and CAO models

Positive-Poisson Distribution

LMS Quantile Regression with a Box-Cox Transformation to Normality

Weibull Distribution Family Function

Smart Prediction Setup

Positive Bernoulli Sequence Model

Generalized Rayleigh Distribution Family Function

Rhobit Link Function

Exponential Geometric Distribution Family Function

The Rice Distribution

Yellow-bellied Prinia

Perspective plot for QRR-VGLMs

Slash Distribution

Vector cubic smoothing spline

Pregnant Rats Toxological Experiment Data

Folded Square Root Link Function

Probability Plots for Categorical Data Analysis

Negative binomial canonical link function

The Zeta Distribution

log F Distribution

Positive Bernoulli Family Function with Behavioural Effects

Quantile Plot for Gumbel Regression

McCullagh (1989) Distribution Family Function

GARMA (Generalized Autoregressive Moving-Average) Models

Likelihood Ratio Test of Nested Models

Triangle Distribution Family Function

Zero Constraint Matrices

LMS Quantile Regression with a Yeo-Johnson Transformation to Normality

Complementary-log Link Function

Fitting a Dirichlet-Multinomial Distribution

Prior and Working Weights of a VGLM fit

Nakagami Distribution

Determine What Mode the Smart Prediction is In

Positive Poisson Distribution Family Function

Venice Maximum Sea Levels Data

The Positive-Normal Distribution

Log-Laplace and Logit-Laplace Distribution Family Functions

The Pareto(IV/III/II) Distributions

Machinists Accidents

Log link function, and variants

Error Function, and variants

Gumbel's Type I Bivariate Distribution Family Function

Negative Binomial-Ordinal Link Function

negbinomial.size

Negative Binomial Distribution Family Function With Known Size

Probit Link Function

von Mises Distribution Family Function

Negative Binomial Distribution Family Function

The Poisson Lognormal Distribution

New Zealand Marital Data.

Grain Prices Data in USA

pgamma.deriv.unscaled

Derivatives of the Incomplete Gamma Integral (Unscaled Version)

Gaussian (normal) Family Function

Wald Distribution Family Function

General Electric and Westinghouse Data

Upper Record Values from a Univariate Normal Distribution

Mixture of Two Poisson Distributions

The Exponential Geometric Distribution

Generalized Beta Distribution of the Second Kind

Inverse Binomial Distribution Family Function

Loglinear Model for Two Binary Responses

The Truncated Pareto Distribution

The Makeham Distribution

Natural Exponential Family Generalized Hyperbolic Secant Distribution Family Function

Derivatives of the Incomplete Gamma Integral

Marginal effects for the multinomial logit and cumulative models

notdocumentedyet

Undocumented and Internally Used Functions and Classes

Univariate Normal Distribution

The Two-stage Sequential Binomial Distribution Family Function

Generalized Extreme Value Distribution Family Function

Mean Excess Plot

Trajectory Plot

Ordinal Regression with Stopping Ratios

Poisson Points Distribution

Control function for vgam

The Paralogistic Distribution

Identity Link Function

The Dirichlet distribution

model.matrixvlm

Construct the Design Matrix of a VLM Object

Log link function with an offset

Simplex Distribution

Lognormal Distribution

Positive Normal Distribution Family Function

Quantile Plot for LMS Quantile Regression

Skellam Distribution Family Function

Logarithmic Distribution

Class ``rrvglm''

Waitakere Ranges Data

Logarithms with an Unit Offset and Exponential Term

undocumented-methods

Undocumented Methods Functions

Low-iron Rat Teratology Data

Constrained Quadratic Ordination

Logarithmic Distribution

Zero-Inflated Poisson Distribution Family Function

Expectiles-sc.t2

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

The Exponential Logarithmic Distribution

Zero-Inflated Geometric Distribution

Poisson-Ordinal Link Function

The AA-Aa-aa Blood Group System

2008 and 2012 Summer Olympic Final Medal Count Data

Yeo-Johnson Transformation

melbmaxtemp daily maximum temperatures

Pneumoconiosis in Coalminers Data

Univariate Normal Distribution as a Varying-Coefficient Model

smart.expression

S Expression for Smart Functions

Zero-Inflated Binomial Distribution Family Function

Log-gamma Distribution Family Function

A Short-tailed Symmetric Distribution

Mixture of Two Exponential Distributions

Return Level Plot for GEV Fits

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

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

The Laplace Distribution

Yule-Simon Family Function

1-parameter Gamma Distribution

rrvglm.optim.control

Control function for rrvglm() calling optim()

Latent Variable Plot

Oxford Temperature Data

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

Zero-Altered Negative Binomial Distribution

plotvgam.control

Control Function for plotvgam()

Beta-binomial Distribution Family Function

Yule-Simon Distribution

Zero-Altered Binomial Distribution

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

Quasi-Poisson Family Function

Positive-geometric Distribution

Pareto and Truncated Pareto Distribution Family Functions

Ordinal Poisson Family Function

Scaled Student t Distribution with 2 df Family Function

The Gumbel Distribution

The Log-Gamma Distribution

The Laplace Distribution

Defining smooths in VGAM formulae

Hunting Spider Data

Cleans Up After Smart Prediction

Nested reduced-rank autoregressive models for multiple time series

Fitting Vector Generalized Linear Models

Lerch Phi Function

Bivariate Gamma: McKay's Distribution

Fitting Vector Generalized Additive Models

Zero-Altered Geometric Distribution

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

University California Berkeley Graduate Admissions

Hypergeometric Family Function

Zero-Altered Poisson Distribution

Upper Record Values from a 1-parameter Exponential Distribution

Extract Model Coefficients

Rice Distribution Family Function

The Generalized Pareto Distribution

Zero-Altered Geometric Distribution

Class ``vglmff''

Positive Negative Binomial Distribution Family Function

Power Link Function

Maxwell Distribution Family Function

The Singh-Maddala Distribution

Multinomial Logit Model

Zero-Altered Binomial Distribution

Zipf Distribution Family Function

Control function for rrvglm

Zero-Inflated Geometric Distribution Family Function

Reciprocal Inverse Gaussian distribution

Truncated Weibull Distribution Family Function

Positive Bernoulli Family Function with Time Effects

Student t Distribution

Michaelis-Menten Model

Generalized Gamma distribution family function

Zero-Altered Poisson Distribution

Zero-Inflated Poisson Distribution

Computes Model Coefficients and Quantities

Zero-Inflated Negative Binomial Distribution Family Function

Zero-Inflated Negative Binomial Distribution

Zeta Distribution Family Function

The ABO Blood Group System

plotqtplot.lmscreg

Quantile Plot for LMS Quantile Regression

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

Univariate Skew-Normal Distribution Family Function

Skew-Normal Distribution

Zero-Altered Negative Binomial Distribution

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

The zero Argument in VGAM Family Functions

Positive Binomial Distribution Family Function

Geometric (Truncated and Untruncated) Distributions

Zero-Inflated Binomial Distribution

Binomial Family Function

Latent Variable Plot for RR-VGLMs

Toxicity trial for insects

quasibinomialff

Quasi-Binomial Family Function

Poisson Family Function

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

Rutherford-Geiger Polonium Data

The Exponential Integral and Variants

Toxoplasmosis Data

Bitterness in Wine Data

CommonVGAMffArguments

Common VGAM family function Arguments

Creates a Matrix of Appropriate Dimension

Simulate Responses for VGLMs and VGAMs