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VGAM (version 0.9-8)

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. 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, 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

43,625

Version

0.9-8

License

GPL-2

Maintainer

Thomas Yee

Last Published

May 11th, 2015

Functions in VGAM (0.9-8)

The Positive-Normal Distribution

Control function for vglm

Yule-Simon Family Function

Positive Normal Distribution Family Function

Reciprocal Inverse Gaussian distribution

Reciprocal link function

A Short-tailed Symmetric Distribution

The Dirichlet distribution

Rhobit Link Function

The Two-stage Sequential Binomial Distribution Family Function

Truncated Weibull Distribution Family Function

Class ``rrvglm''

Venice Maximum Sea Levels Data

Control function for vgam

The Triangle Distribution

Power Link Function

Smart Prediction

Zero-Altered Negative Binomial Distribution

Upper Record Values from a Univariate Normal Distribution

The Singh-Maddala Distribution

Yellow-bellied Prinia

Proportional Odds Model for Ordinal Regression

Nested reduced-rank autoregressive models for multiple time series

rrvglm.optim.control

Control function for rrvglm() calling optim()

The Tobit Distribution

Quantile Plot for Gumbel Regression

quasibinomialff

Quasi-Binomial Family Function

Student t Distribution

von Mises Distribution Family Function

undocumented-methods

Undocumented Methods Functions

Zero-Altered Geometric Distribution

Quasi-variances Extraction Function

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

Zero-Inflated Poisson Distribution Family Function

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

Probit Link Function

Waitakere Ranges Data

The Skellam Distribution

Zero-Altered Poisson Distribution

Trajectory plot for QRR-VGLMs

The Rayleigh Distribution

Scaled Student t Distribution with 2 df Family Function

Prentice (1974) Log-gamma Distribution

Riemann's Zeta Function

Defining smooths in VGAM formulae

Vector cubic smoothing spline

Upper Record Values from a 1-parameter Exponential Distribution

Fitting Vector Generalized Linear Models

Quantile Plot for LMS Quantile Regression

Predict Method for a VGLM fit

Positive Poisson Distribution Family Function

University California Berkeley Graduate Admissions

Positive-Negative Binomial Distribution

Yule-Simon Distribution

Quasi-Poisson Family Function

Zero-Inflated Geometric Distribution

Asymmetric Laplace Distribution Family Functions

Smart Prediction Setup

Positive-Poisson Distribution

Rutherford-Geiger Polonium Data

Zero-Inflated Binomial Distribution

The Truncated Pareto Distribution

Wald Distribution Family Function

double.cens.normal

Univariate Normal Distribution with Double Censoring

Zipf Distribution Family Function

Fitting Vector Generalized Additive Models

Fitting a Dirichlet Distribution

Rice Distribution Family Function

Probability Plots for Categorical Data Analysis

F Distribution Family Function

The zero Argument in VGAM Family Functions

Haight's Zeta Distribution

Zero-Inflated Binomial Distribution Family Function

Toxoplasmosis Data

Generalized Poisson distribution

Zero-Altered Negative Binomial Distribution

Return Level Plot for GEV Fits

calibrate.qrrvglm

Calibration for CQO and CAO models

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

Exponential Logarithmic Distribution Family Function

Log link function, and variants

Beta-geometric Distribution Family Function

Bivariate Probit Model (Family Function)

Number of Parameters

Ordinal Regression with Stopping Ratios

Farlie-Gumbel-Morgenstern's Bivariate Distribution

Class ``vglmff''

Constraint Matrices

Bivariate Logistic Distribution

inv.paralogistic

Inverse Paralogistic Distribution Family Function

Akaike's Information Criterion

Censored Normal Distribution

Folded Square Root Link Function

Univariate Normal Distribution

Pregnant Rats Toxological Experiment Data

Cleans Up After Smart Prediction

The Rice Distribution

Create a Survival Object

Zero-Altered Binomial Distribution

Cumulative Distribution Function for LMS Quantile Regression

Chinese Population in New Zealand 1867--2001 Data

Frank's Bivariate Distribution Family Function

Ordinal Regression with Continuation Ratios

Fisk Distribution family function

Bivariate Student-t distribution cumulative distribution function

Benford's Distribution

The Two-parameter Beta Distribution Family Function

Ordinal Regression with Cumulative Probabilities

Identity Link Function

The AR-1 Autoregressive Process

Felix Distribution Family Function

Latent Variable Plot

The Pareto Distribution

The A1A2A3 Blood Group System

Zero-Altered Binomial Distribution

General Electric and Westinghouse Data

Gamma Hyperbola Bivariate Distribution

The Inverse Gaussian Distribution

Binomial Logistic Regression by Asymmetric Maximum Likelihood Estimation

Zero-Inflated Negative Binomial Distribution

Vector Generalized Linear and Additive Models

calibrate.qrrvglm.control

Control function for CQO/CAO calibration

Gumbel's Type I Bivariate Distribution Family Function

The Generalized Gamma Distribution

The AB-Ab-aB-ab Blood Group System

Generalized Beta Distribution Family Function

The MNSs Blood Group System

Redirects the user to rrvglm

Gompertz Distribution Family Function

Generalized Gamma distribution family function

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

Exponential Poisson Distribution Family Function

Generalized Extreme Value Distribution Family Function

Generalized Pareto Distribution Family Function

Biplot of Constrained Regression Models

plotqtplot.lmscreg

Quantile Plot for LMS Quantile Regression

Latent Variable Plot for QO models

Complementary Log-log Link Function

The Generalized Beta II Distribution

Mortality of Flour Beetles from Carbon Disulphide

The AA-Aa-aa Blood Group System

Positive-Binomial Distribution

Gamma-Ordinal Link Function

Bivariate normal distribution family function

Beta-binomial Distribution Family Function

Bacon and Eggs Data

aux.posbernoulli.t

Auxiliary Function for the Positive Bernoulli Family Function with Time Effects

Log link function with an offset

Clayton Copula (Bivariate) Distribution

2008 and 2012 Summer Olympic Final Medal Count Data

The Exponential Geometric Distribution

Inverse Binomial Distribution Family Function

The Birnbaum-Saunders Distribution

Ali-Mikhail-Haq Distribution Family Function

CommonVGAMffArguments

Common VGAM family function Arguments

The Exponential Integral and Variants

Benini Distribution Family Function

Bivariate Farlie-Gumbel-Morgenstern Exponential Distribution Family Function

Logarithmic Distribution

Chi-squared Distribution

Cauchy Distribution Family Function

Frank's Bivariate Distribution

Bayesian Information Criterion

V1 Flying-Bombs Hits in London

Response variable extracted

Skew-Normal Distribution

Coef.qrrvglm-class

Class ``Coef.qrrvglm''

Extract Model Coefficients

Breathlessness and Wheeze Amongst Coalminers Data

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

Plackett's Bivariate Copula

Exponential Link Function

Gumbel Distribution Family Function

Inputting Data to fit a Bradley Terry Model

Exponential Regression by Asymmetric Maximum Likelihood Estimation

Lognormal Distribution

Bivariate Binary Regression with an Odds Ratio (Family Function)

Constrained Quadratic Ordination

Exponential Geometric Distribution Family Function

2-parameter Gamma Distribution

Negative Binomial-Ordinal Link Function

The Generalized Rayleigh Distribution

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

Data on Back Pain Prognosis, from Anderson (1984)

The Two-parameter Beta Distribution Family Function

Hunua Ranges Data

The Gumbel-II Distribution

Mark the Baseline of Row and Column on a Matrix data

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

Plackett's Bivariate Copula Family Function

The Benini Distribution

The Kumaraswamy Distribution

Creates a Matrix of Appropriate Dimension

Positive Bernoulli Family Function with Time Effects

Crashes on New Zealand Roads in 2009

Hunting Spider Data

Extract Model Coefficients for VLM Objects

Prior and Working Weights of a VGLM fit

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

The Frechet Distribution

Exponentiated Exponential Distribution

Univariate Normal Distribution as a Varying-Coefficient Model

negbinomial.size

Negative Binomial Distribution Family Function With Known Size

Binomial Family Function

melbmaxtemp daily maximum temperatures

plotvgam.control

Control Function for plotvgam()

Loglinear Model for Two Binary Responses

The Beta-Normal Distribution

Link functions for VGLM/VGAM/etc. families

Chest Pain in NZ Adults Data

Expectiles-Exponential

Expectiles of the Exponential Distribution

Index from Array to Matrix

The Generalized Poisson Distribution

pgamma.deriv.unscaled

Derivatives of the Incomplete Gamma Integral (Unscaled Version)

Mixture of Two Exponential Distributions

log F Distribution

Expectiles-Uniform

Expectiles of the Uniform Distribution

2-parameter Gamma Distribution

Expectiles-sc.t2

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

Pareto and Truncated Pareto Distribution Family Functions

Geometric (Truncated and Untruncated) Distributions

Acute Myelogenous Leukemia Survival Data

Zero Constraint Matrices

The Lomax Distribution

Exponential Distribution

Hyperbolic Secant Distribution Family Function

The Exponential Logarithmic Distribution

Ordinal Regression with Adjacent Categories Probabilities

Nakagami Distribution

Returns Important Matrices etc. of a RR-VGLM Object

Generalized Rayleigh Distribution Family Function

Coef.rrvglm-class

Class ``Coef.rrvglm''

1-parameter Gamma Distribution

Log-gamma Distribution Family Function

GARMA (Generalized Autoregressive Moving-Average) Models

Redirects the user to cqo

Lerch Phi Function

Zero-Inflated Poisson Distribution

Fisher's Z Link Function

The Generalized Extreme Value Distribution

Fitting Constrained Quadratic Ordination (CQO)

get.smart.prediction

Retrieves ``.smart.prediction''

Folded Normal Distribution Family Function

Kendall's Tau Statistic

Borel-Tanner Distribution Family Function

Natural Exponential Family Generalized Hyperbolic Secant Distribution Family Function

Censored Poisson Family Function

Laplace Distribution

Oxford Temperature Data

Relative Frequencies of Serum Proteins in white Pekin ducklings

Link Functions for VGLMs

Logit Link Function

Hormone Assay Data

Test For a Smart Object

Grain Prices Data in USA

McCullagh (1989) Distribution Family Function

Zero-Altered Geometric Distribution

Determine What Mode the Smart Prediction is In

Autoregressive Process with Order-1 Family Function

Bradley Terry Model With Ties

The Beta-Binomial Distribution

Minimizing the L-q norm Family Function

Asymmetric Least Squares Quantile Regression

The Lambert W function

Logarithmic Distribution

Levy Distribution Family Function

double.expbinomial

Double Exponential Binomial Distribution Family Function

Toxicity trial for insects

Low-iron Rat Teratology Data

The Lindley Distribution

The Maxwell Distribution

Extract Log-likelihood for VGLMs/VGAMs/etc.

posbernoulli.tb

Positive Bernoulli Family Function with Time and Behavioural Effects

The ABO Blood Group System

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

Exponentiated Exponential Distribution

Poisson-Ordinal Link Function

Zero-Altered Poisson Distribution

Latent Variables

Beta-binomial Distribution Family Function

model.matrixvlm

Construct the Design Matrix of a VLM Object

Makeham Distribution Family Function

Huber's least favourable distribution family function

Default VGAM Plotting

Erlang Distribution

Machinists Accidents

Cystic Fibrosis Data

LMS Quantile Regression with a Yeo-Johnson Transformation to Normality

Parallelism Constraint Matrices

Negative Binomial Distribution Family Function

Density Plot for LMS Quantile Regression

Gaussian (normal) Family Function

The Generalized Pareto Distribution

plotdeplot.lmscreg

Density Plot for LMS Quantile Regression

Logistic Distribution Family Function

Body Mass Index of New Zealand Adults Data

Plots for VGLMs

Positive-geometric Distribution

Inverse Lomax Distribution Family Function

Table 1 of Huggins (1989)

Hat Values and Regression Deletion Diagnostics

Pareto(IV/III/II) Distribution Family Functions

Gaussian Copula (Bivariate) Family Function

Seemingly Unrelated Regressions

Auckland University Undergraduate Counts Data

notdocumentedyet

Undocumented and Internally Used Functions and Classes

The Laplace Distribution

The Paralogistic Distribution

Positive Negative Binomial Distribution Family Function

Captures of Peromyscus maniculatus, also known as deer mice.

Loglinear Model for Three Binary Responses

Pneumoconiosis in Coalminers Data

Gaussian Copula (Bivariate) Distribution

The Beta-Prime Distribution

Michaelis-Menten Model

smart.expression

S Expression for Smart Functions

Extract Model Constrained/Canonical Coefficients

Perspective plot for QRR-VGLMs

Ordinal Poisson Family Function

Poisson Points Distribution

Fitting Constrained Additive Ordination (CAO)

New Zealand Marital Data.

Cardioid Distribution

The Log-Gamma Distribution

The Laplace Distribution

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

Likelihood Ratio Test of Nested Models

The Beta-Geometric Distribution

Bivariate Logistic Distribution Family Function

Complementary-log Link Function

The Dagum Distribution

The Log-Laplace Distribution

LMS Quantile Regression with a Box-Cox Transformation to Normality

The Borel-Tanner Distribution

The Gumbel Distribution

The Folded-Normal Distribution

Univariate Skew-Normal Distribution Family Function

Perks Distribution Family Function

Inverse Gaussian Distribution Family Function

Cauchit Link Function

Gumbel-II Distribution Family Function

Simplex Distribution

Cardioid Distribution Family Function

Annual catches on Lake Otamangakau from October 1974 to October 1989

Beta Distribution of the Second Kind

Zero-Inflated Negative Binomial Distribution Family Function

concoef-methods

Constrained (Canonical) Coefficients

The Exponential Poisson Distribution

Log-log Link Function

Control function for rrvglm

Huber's least favourable distribution

Poisson Regression by Asymmetric Maximum Likelihood Estimation

Fitted Values of a VLM object

Bitterness in Wine Data

Does the fitted object suffer from a known bug?

Control Function for RR-VGAMs (CAO)

Fitting a Dirichlet-Multinomial Distribution

Error Function, and variants

Bivariate Gamma: McKay's Distribution

Yeo-Johnson Transformation

Mixture of Two Univariate Normal Distributions

Poisson Family Function

The Poisson Lognormal Distribution

Predict Method for a CQO fit

Censored Gumbel Distribution

Slash Distribution

Marginal effects for the multinomial logit and cumulative models

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

Leipnik Distribution Family Function

Fitting a Dirichlet-Multinomial Distribution

Returns Important Matrices etc. of a QO Object

Model Diagnostic Plots for QRR-VGLMs

Multinomial Logit Model

qrrvglm.control

Control function for QRR-VGLMs (CQO)

Positive Bernoulli Sequence Model

Mixture of Two Poisson Distributions

Zeta Distribution Family Function

Corbet's Butterfly Data

Logarithms with an Unit Offset and Exponential Term

Hypergeometric Family Function

Bivariate normal distribution cumulative distribution function

Multi-logit Link Function

Derivatives of the Incomplete Gamma Integral

Log-Laplace and Logit-Laplace Distribution Family Functions

Residual Degrees-of-Freedom

Positive Binomial Distribution Family Function

Construct the Model Frame of a VLM Object

Zero-Inflated Geometric Distribution Family Function

Mean Excess Plot

Latent Variable Plot for RR-VGLMs

calibrate-methods

Calibration for Constrained Regression Models

Model Calibrations

Weibull Distribution Family Function

Expectiles-Normal

Expectiles of the Normal Distribution

Trajectory Plot

Negative binomial canonical link function

Positive Bernoulli Family Function with Behavioural Effects

Computes Model Coefficients and Quantities

Simulate Responses for VGLMs and VGAMs