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VGAM (version 0.9-4)

Vector Generalized Linear and Additive Models

Description

This package fits many (150+) models and distributions by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring. This is done via the vector generalized linear and additive model (VGLM/VGAM) classes and associated models (reduced-rank VGLMs, quadratic RR-VGLMs, reduced-rank VGAMs, row-column interaction models). These are abbreviated RR-VGLMs, QRR-VGLMs, RR-VGAMs and RCIMs. These include constrained and unconstrained quadratic ordination (CQO/UQO) models in ecology as well as constrained additive ordination (CAO).

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Version

Install

install.packages('VGAM')

Monthly Downloads

53,958

Version

0.9-4

License

GPL-2

Maintainer

Thomas Yee

Last Published

May 28th, 2014

Functions in VGAM (0.9-4)

Machinists Accidents

Latent Variable Plot for RR-VGLMs

pgamma.deriv.unscaled

Derivatives of the Incomplete Gamma Integral (Unscaled Version)

Predict Method for a CQO fit

Weibull Distribution Family Function

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

Reciprocal Inverse Gaussian distribution

Slash Distribution

Trajectory Plot

Log-Laplace and Logit-Laplace Distribution Family Functions

Positive Bernoulli Family Function with Time Effects

Vector cubic smoothing spline

Logit Link Function

Mixture of Two Poisson Distributions

Pneumoconiosis in Coalminers Data

Loglinear Model for Two Binary Responses

Quasi-Poisson Family Function

Lognormal Distribution

The Pareto(IV/III/II) Distributions

Zero-Inflated Geometric Distribution

Zero-Altered Geometric Distribution

qrrvglm.control

Control function for QRR-VGLMs (CQO)

Poisson Family Function

Smart Prediction

Short-tailed Symmetric Distribution Family Function

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

Class ``rrvglm''

Plackett's Bivariate Distribution Family Function

The Log-Laplace Distribution

matched.binomial

The Matched Binomial Distribution Family Function

The Dirichlet distribution

Log-log Link Function

Log link function, and variants

The Perks Distribution

Probability Plots for Categorical Data Analysis

Log link function with an offset

Logistic Distribution Family Function

Zero-Inflated Geometric Distribution Family Function

Latent Variable Plot

Mean Excess Plot

The Rayleigh Distribution

The Two-stage Sequential Binomial Distribution Family Function

Trajectory plot for QRR-VGLMs

The Paralogistic Distribution

Lomax Distribution Family Function

Positive Bernoulli Family Function with Behavioural Effects

The Triangle Distribution

Proportional Odds Model for Ordinal Regression

Constrained Quadratic Ordination

Quasi-variances Extraction Function

Upper Record Values from a 1-parameter Exponential Distribution

Riemann's Zeta Function

Prentice (1974) Log-gamma Distribution

Student t Distribution

Upper Record Values from a Univariate Normal Distribution

Control function for vgam

Positive-geometric Distribution

Reciprocal link function

The Poisson Lognormal Distribution

The Skellam Distribution

The Positive-Normal Distribution

Univariate Skew-Normal Distribution Family Function

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

The zero Argument in VGAM Family Functions

Minimizing the L-q norm Family Function

Power Link Function

The Truncated Pareto Distribution

Control function for vglm

Simplex Distribution Family Function

Positive Negative Binomial Distribution Family Function

posbernoulli.tb

Positive Bernoulli Family Function with Time and Behavioural Effects

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

Return Level Plot for GEV Fits

Zero-Altered Negative Binomial Distribution

Prior and Working Weights of a VGLM fit

Predict Method for a VGLM fit

rrvglm.optim.control

Control function for rrvglm() calling optim()

Positive Normal Distribution Family Function

The Maxwell Distribution

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

Quantile Plot for Gumbel Regression

Univariate Normal Distribution

Yule-Simon Family Function

Toxoplasmosis Data

Zero-Inflated Binomial Distribution

Zeta Distribution Family Function

Poisson-Ordinal Link Function

Zero-Altered Poisson Distribution

Ordinal Regression with Stopping Ratios

plotdeplot.lmscreg

Density Plot for LMS Quantile Regression

Determine What Mode the Smart Prediction is In

Skew-Normal Distribution

Zipf Distribution Family Function

smart.expression

S Expression for Smart Functions

Rutherford-Geiger Polonium Data

The Rice Distribution

Perspective plot for QRR-VGLMs

Zero-Altered Geometric Distribution

Positive Binomial Distribution Family Function

Zero-Inflated Binomial Distribution Family Function

Singh-Maddala Distribution Family Function

Zero-Inflated Poisson Distribution Family Function

Zero-Altered Negative Binomial Distribution

von Mises Distribution Family Function

Wald Distribution Family Function

Truncated Weibull Distribution Family Function

Plots for VGLMs

Zero-Altered Binomial Distribution

Positive-Binomial Distribution

Zero-Inflated Negative Binomial Distribution

Pregnant Rats Toxological Experiment Data

Fitting Vector Generalized Linear Models

Positive-Negative Binomial Distribution

Default VGAM Plotting

Bitterness in Wine Data

Positive-Poisson Distribution

Smart Prediction Setup

Zero-Inflated Poisson Distribution

Derivatives of the Incomplete Gamma Integral

Model Diagnostic Plots for QRR-VGLMs

The AB-Ab-aB-ab2 Blood Group System

Class ``vglmff''

Defining smooths in VGAM formulae

Zero-Altered Binomial Distribution

Quantile Plot for LMS Quantile Regression

Yeo-Johnson Transformation

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

Cardioid Distribution

Positive Bernoulli Sequence Model

Positive Poisson Distribution Family Function

Zero-Inflated Negative Binomial Distribution Family Function

Model Calibrations

Extract Model Coefficients

Bivariate Probit Model (Family Function)

The ABO Blood Group System

plotvgam.control

Control Function for plotvgam()

Biplot of Constrained Regression Models

University California Berkeley Graduate Admissions

Inverse Gaussian Distribution Family Function

The Inverse Gaussian Distribution

undocumented-methods

Undocumented Methods Functions

Rice Distribution Family Function

Fitting Vector Generalized Additive Models

Probit Link Function

Cumulative Distribution Function for LMS Quantile Regression

F Distribution Family Function

Complementary Log-log Link Function

Control Function for RR-VGAMs (CAO)

Cauchy Distribution Family Function

Create a Survival Object

Venice Maximum Sea Levels Data

Binomial Logistic Regression by Asymmetric Maximum Likelihood Estimation

The Birnbaum-Saunders Distribution

Bradley Terry Model

The Frechet Distribution

Returns Important Matrices etc. of a QO Object

Ali-Mikhail-Haq Distribution Family Function

Chinese Population in New Zealand 1867--2001 Data

Gaussian Copula (Bivariate) Family Function

Asymmetric Least Squares Quantile Regression

Index from Array to Matrix

2-parameter Gamma Distribution

Body Mass Index of New Zealand Adults Data

Generalized Gamma distribution family function

Crashes on New Zealand Roads in 2009

Beta Distribution of the Second Kind

The Borel-Tanner Distribution

Leipnik Distribution Family Function

Exponentiated Exponential Distribution

GARMA (Generalized Autoregressive Moving-Average) Models

Loglinear Model for Three Binary Responses

Poisson Regression by Asymmetric Maximum Likelihood Estimation

The Beta-Geometric Distribution

Akaike's Information Criterion

Gumbel Distribution Family Function

Binomial Family Function

Haight's Zeta Family Function

1-parameter Gamma Distribution

Corbet's Butterfly Data

LMS Quantile Regression with a Yeo-Johnson Transformation to Normality

Mark the Baseline of Row and Column on a Matrix data

Multinomial Logit Model

The Folded-Normal Distribution

The MNSs Blood Group System

Fisk Distribution family function

Breathlessness and Wheeze Amongst Coalminers Data

Bivariate normal distribution family function

Residual Degrees-of-Freedom

The Laplace Distribution

The Exponential Logarithmic Distribution

The Pareto Distribution

Huber's least favourable distribution family function

calibrate.qrrvglm

Calibration for CQO and CAO models

General Electric and Westinghouse Data

Fitting Constrained Additive Ordination (CAO)

Poisson Points Distribution

Makeham Distribution Family Function

The Two-parameter Beta Distribution Family Function

Asymmetric Laplace Distribution Family Functions

Frank's Bivariate Distribution

Frank's Bivariate Distribution Family Function

betabinomial.ab

Beta-binomial Distribution Family Function

Response variable extracted

Fitting a Dirichlet-Multinomial Distribution

Creates a Matrix of Appropriate Dimension

Borel-Tanner Distribution Family Function

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

Extract Log-likelihood for VGLMs/VGAMs/etc.

calibrate-methods

Calibration for Constrained Regression Models

plotqtplot.lmscreg

Quantile Plot for LMS Quantile Regression

Exponential Distribution

The G1G2G3 Blood Group System

The Benini Distribution

The Lindley Distribution

The Two-parameter Beta Distribution Family Function

Complementary-log Link Function

Lerch Phi Function

Clayton Copula (Bivariate) Family Function

Captures of Peromyscus maniculatus, also known as deer mice.

The Kumaraswamy Distribution

Hyperbolic Secant Distribution Family Function

negbinomial.size

Negative Binomial Distribution Family Function With Known Size

Auckland University Undergraduate Counts Data

Coef.rrvglm-class

Class ``Coef.rrvglm''

The Beta-Normal Distribution

Cystic Fibrosis Data

Inverse Binomial Distribution Family Function

aux.posbernoulli.t

Auxiliary Function for the Positive Bernoulli Family Function with Time Effects

Kendall's Tau Statistic

Univariate Normal Distribution as a Varying-Coefficient Model

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

Erlang Distribution

Generalized Beta Distribution of the Second Kind

Exponential Geometric Distribution Family Function

The Generalized Rayleigh Distribution

Fitting Constrained Quadratic Ordination (CQO)

Expectiles-Exponential

Expectiles of the Exponential Distribution

Extract Model Constrained/Canonical Coefficients

Data on Back Pain Prognosis, from Anderson (1984)

Coef.qrrvglm-class

Class ``Coef.qrrvglm''

Returns Important Matrices etc. of a RR-VGLM Object

Chi-squared Distribution

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

Yellow-bellied Prinia

Extract Model Coefficients for VLM Objects

Nakagami Distribution Family Function

Rhobit Link Function

Mixture of Two Exponential Distributions

Exponential Logarithmic Distribution Family Function

Generalized Beta Distribution Family Function

get.smart.prediction

Retrieves ``.smart.prediction''

Chest Pain in NZ Adults Data

Expectiles-Normal

Expectiles of the Normal Distribution

Gumbel's Type I Bivariate Distribution Family Function

Fitting a Dirichlet Distribution

Exponential Regression by Asymmetric Maximum Likelihood Estimation

quasibinomialff

Quasi-Binomial Family Function

Morgenstern's Bivariate Distribution Family Function

double.expbinomial

Double Exponential Binomial Distribution Family Function

Zero Constraint Matrices

Gamma-Ordinal Link Function

The Generalized Gamma Distribution

Control function for rrvglm

Waitakere Ranges Data

Grain Prices Data in USA

Ordinal Poisson Family Function

Yule-Simon Distribution

Ordinal Regression with Adjacent Categories Probabilities

Bivariate Student-t Family Function

2008 and 2012 Summer Olympic Final Medal Count Data

The Exponential Geometric Distribution

Table 1 of Huggins (1989)

Negative Binomial-Ordinal Link Function

Censored Normal Distribution

Link functions for VGLM/VGAM/etc. families

Log-gamma Distribution Family Function

Bradley Terry Model With Ties

Bivariate Logistic Distribution Family Function

Construct the Model Frame of a VLM Object

Felix Distribution Family Function

Folded Square Root Link Function

Fisher's Z Link Function

Computes Model Coefficients and Quantities

Zero-Altered Poisson Distribution

Bivariate normal distribution cumulative distribution function

The Gumbel Distribution

Pareto and Truncated Pareto Distribution Family Functions

Generalized Poisson distribution

Oxford Temperature Data

Gompertz Distribution Family Function

Laplace Distribution

The AB-Ab-aB-ab Blood Group System

Bivariate Logistic Distribution

Cauchit Link Function

Geometric (Truncated and Untruncated) Distributions

Bivariate Binary Regression with an Odds Ratio (Family Function)

Fitting a Dirichlet-Multinomial Distribution

Bacon and Eggs Data

Michaelis-Menten Model

Parallelism Constraint Matrices

Negative Binomial Distribution Family Function

concoef-methods

Constrained (Canonical) Coefficients

Hat Values and Regression Deletion Diagnostics

Seemingly Unrelated Regressions

Beta-binomial Distribution Family Function

Censored Gumbel Distribution

Redirects the user to cqo

The AA-Aa-aa Blood Group System

model.matrixvlm

Construct the Design Matrix of a VLM Object

The Dagum Distribution

Koenker's Distribution Family Function

Likelihood Ratio Test of Nested Models

invparalogistic

Inverse Paralogistic Distribution Family Function

The Exponential Integral and Variants

The Exponential Poisson Distribution

V1 Flying-Bombs Hits in London

Vector Generalized Linear and Additive Models

Identity Link Function

Generalized Rayleigh Distribution Family Function

Inverse Lomax Distribution Family Function

The Beta-Binomial Distribution

Gamma Hyperbola Bivariate Distribution

Cleans Up After Smart Prediction

Hormone Assay Data

double.cennormal

Univariate Normal Distribution with Double Censoring

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

Ordinal Regression with Continuation Ratios

mmt daily maximum temperatures

Censored Poisson Family Function

Gumbel-II Distribution Family Function

Latent Variables

The Laplace Distribution

Density Plot for LMS Quantile Regression

Farlie-Gumbel-Morgenstern's Bivariate Distribution Family Function

Exponentiated Exponential Distribution

Logarithmic Distribution

Bivariate Gamma: McKay's Distribution

Logarithms with an Unit Offset and Exponential Term

Hunua Ranges Data

Test For a Smart Object

Mixture of Two Univariate Normal Distributions

Beta-geometric Distribution Family Function

Gaussian Copula (Bivariate) Distribution

The Log-Gamma Distribution

Ordinal Regression with Cumulative Probabilities

The Lambert W function

calibrate.qrrvglm.control

Control function for CQO/CAO calibration

Gaussian (normal) Family Function

Generalized Pareto Distribution Family Function

Fitted Values of a VLM object

Hypergeometric Family Function

The Beta-Prime Distribution

Expectiles-Koenker

Expectiles/Quantiles of the Koenker Distribution

Levy Distribution Family Function

Latent Variable Plot for QO models

Cardioid Distribution Family Function

Exponential Link Function

Marginal effects for the multinomial logit and cumulative models

Expectiles-Uniform

Expectiles of the Uniform Distribution

notdocumentedyet

Undocumented and Internally Used Functions and Classes

McCullagh (1989) Distribution Family Function

New Zealand Marital Data.

Acute Myelogenous Leukemia Survival Data

Generalized Extreme Value Distribution Family Function

Folded Normal Distribution Family Function

Low-iron Rat Teratology Data

Natural Exponential Family Generalized Hyperbolic Secant Distribution Family Function

Hunting Spider Data

The Generalized Pareto Distribution

Constraint Matrices

Negative binomial canonical link function

LMS Quantile Regression with a Box-Cox Transformation to Normality

Toxicity trial for insects

The Gumbel-II Distribution

Nested reduced-rank autoregressive models for multiple time series

Huber's least favourable distribution

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

Exponential Poisson Distribution Family Function

log F Distribution

Logarithmic Distribution

The Generalized Extreme Value Distribution

Bayesian Information Criterion

Benford's Distribution

2-parameter Gamma Distribution

Redirects the user to rrvglm

CommonVGAMffArguments

Common VGAM family function Arguments

Annual catches on Lake Otamangakau from October 1974 to October 1989

Multi-logit Link Function

Simulate Responses for VGLMs and VGAMs