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VGAM (version 0.9-5)

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). 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

31,223

Version

0.9-5

License

GPL-2

Maintainer

Thomas Yee

Last Published

November 6th, 2014

Functions in VGAM (0.9-5)

Bivariate normal distribution cumulative distribution function

The Fisk Distribution

The Exponential Logarithmic Distribution

Create a Survival Object

Clayton Copula (Bivariate) Distribution

Negative Binomial-Ordinal Link Function

Exponential Regression by Asymmetric Maximum Likelihood Estimation

Ordinal Regression with Cumulative Probabilities

Bivariate Gamma: McKay's Distribution

Bayesian Information Criterion

Borel-Tanner Distribution Family Function

Chest Pain in NZ Adults Data

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

Returns Important Matrices etc. of a RR-VGLM Object

The A1A2A3 Blood Group System

Cauchy Distribution Family Function

Extract Model Coefficients

Captures of Peromyscus maniculatus, also known as deer mice.

The Borel-Tanner Distribution

Extract Model Coefficients for VLM Objects

Chinese Population in New Zealand 1867--2001 Data

F Distribution Family Function

Bivariate Probit Model (Family Function)

double.expbinomial

Double Exponential Binomial Distribution Family Function

Ordinal Poisson Family Function

The AB-Ab-aB-ab Blood Group System

The Inverse Gaussian Distribution

The Pareto Distribution

Kumaraswamy Distribution Family Function

Computes Model Coefficients and Quantities

calibrate.qrrvglm

Calibration for CQO and CAO models

Plackett's Bivariate Copula

Cardioid Distribution Family Function

Bivariate Student-t distribution cumulative distribution function

Fitting a Dirichlet-Multinomial Distribution

The Benini Distribution

Mark the Baseline of Row and Column on a Matrix data

Positive-Poisson Distribution

The Beta-Prime Distribution

Fitting Constrained Quadratic Ordination (CQO)

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

Exponential Logarithmic Distribution Family Function

Inputting Data to fit a Bradley Terry Model

The MNSs Blood Group System

Coef.rrvglm-class

Class ``Coef.rrvglm''

Bivariate Binary Regression with an Odds Ratio (Family Function)

Gaussian Copula (Bivariate) Family Function

The Exponential Integral and Variants

The Frechet Distribution

Censored Normal Distribution

calibrate.qrrvglm.control

Control function for CQO/CAO calibration

Exponential Geometric Distribution Family Function

Redirects the user to cqo

Cystic Fibrosis Data

Makeham Distribution Family Function

Lomax Distribution Family Function

Expectiles-Uniform

Expectiles of the Uniform Distribution

Auckland University Undergraduate Counts Data

Expectiles-Normal

Expectiles of the Normal Distribution

Coef.qrrvglm-class

Class ``Coef.qrrvglm''

Generalized Extreme Value Distribution Family Function

Gamma-Ordinal Link Function

Seemingly Unrelated Regressions

Plackett's Bivariate Copula Family Function

Crashes on New Zealand Roads in 2009

Breathlessness and Wheeze Amongst Coalminers Data

Latent Variables

Gumbel's Type I Bivariate Distribution Family Function

The Felix Distribution

Link functions for VGLM/VGAM/etc. families

Fitted Values of a VLM object

plotqtplot.lmscreg

Quantile Plot for LMS Quantile Regression

Ali-Mikhail-Haq Distribution Family Function

The Exponential Geometric Distribution

Binomial Logistic Regression by Asymmetric Maximum Likelihood Estimation

CommonVGAMffArguments

Common VGAM family function Arguments

The Log-Laplace Distribution

Farlie-Gumbel-Morgenstern's Bivariate Distribution

Hyperbolic Secant Distribution Family Function

get.smart.prediction

Retrieves ``.smart.prediction''

Bivariate Logistic Distribution Family Function

The Gumbel-II Distribution

Latent Variable Plot for RR-VGLMs

Quasi-variances Preprocessing Function

McCullagh (1989) Distribution Family Function

The Generalized Extreme Value Distribution

Ordinal Regression with Continuation Ratios

The Lindley Distribution

The Folded-Normal Distribution

Birnbaum-Saunders Distribution Family Function

Exponential Distribution

Control Function for RR-VGAMs (CAO)

Folded Square Root Link Function

Bacon and Eggs Data

Expectiles-Exponential

Expectiles of the Exponential Distribution

Cauchit Link Function

Logarithmic Distribution

Zero-Altered Binomial Distribution

Ordinal Regression with Adjacent Categories Probabilities

2-parameter Gamma Distribution

Derivatives of the Incomplete Gamma Integral

log F Distribution

Redirects the user to rrvglm

Mixture of Two Exponential Distributions

The Exponential Poisson Distribution

Asymmetric Laplace Distribution Family Functions

Pareto and Truncated Pareto Distribution Family Functions

The Maxwell Distribution

LMS Quantile Regression with a Box-Cox Transformation to Normality

Density Plot for LMS Quantile Regression

2-parameter Gamma Distribution

model.matrixvlm

Construct the Design Matrix of a VLM Object

Huber's least favourable distribution

Cumulative Distribution Function for LMS Quantile Regression

The Generalized Pareto Distribution

melbmaxtemp daily maximum temperatures

Bitterness in Wine Data

concoef-methods

Constrained (Canonical) Coefficients

The Inverse Lomax Distribution

Residual Degrees-of-Freedom

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

Short-tailed Symmetric Distribution Family Function

Positive Binomial Distribution Family Function

undocumented-methods

Undocumented Methods Functions

Student t Distribution

aux.posbernoulli.t

Auxiliary Function for the Positive Bernoulli Family Function with Time Effects

Fitting Constrained Additive Ordination (CAO)

Bivariate normal distribution family function

Akaike's Information Criterion

Fitting a Dirichlet-Multinomial Distribution

2008 and 2012 Summer Olympic Final Medal Count Data

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

Complementary-log Link Function

Dagum Distribution Family Function

Gaussian (normal) Family Function

Levy Distribution Family Function

The Rice Distribution

The Lambert W function

Data on Back Pain Prognosis, from Anderson (1984)

Negative binomial canonical link function

Geometric (Truncated and Untruncated) Distributions

Bradley Terry Model With Ties

Positive Normal Distribution Family Function

Parallelism Constraint Matrices

Gamma Hyperbola Bivariate Distribution

Generalized Beta Distribution Family Function

Machinists Accidents

V1 Flying-Bombs Hits in London

Logit Link Function

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

LMS Quantile Regression with a Yeo-Johnson Transformation to Normality

Grain Prices Data in USA

Generalized Poisson distribution

Bivariate Farlie-Gumbel-Morgenstern Exponential Distribution Family Function

Rice Distribution Family Function

Exponential Poisson Distribution Family Function

Trajectory plot for QRR-VGLMs

Proportional Odds Model for Ordinal Regression

Smart Prediction Setup

Beta-geometric Distribution Family Function

Vector cubic smoothing spline

Zero-Altered Poisson Distribution

Toxicity trial for insects

Upper Record Values from a Univariate Normal Distribution

Quantile Plot for LMS Quantile Regression

Erlang Distribution

Chi-squared Distribution

Mixture of Two Poisson Distributions

Gumbel-II Distribution Family Function

Inv.paralogistic

The Inverse Paralogistic Distribution

The Two-parameter Beta Distribution Family Function

Body Mass Index of New Zealand Adults Data

Censored Poisson Family Function

plotvgam.control

Control Function for plotvgam()

Hunting Spider Data

Slash Distribution Family Function

Pneumoconiosis in Coalminers Data

Nested reduced-rank autoregressive models for multiple time series

Vector Generalized Linear and Additive Models

Lerch Phi Function

Pareto(IV/III/II) Distribution Family Functions

Log link function with an offset

Trajectory Plot

Gaussian Copula (Bivariate) Distribution

The Singh-Maddala Distribution

The Zeta Distribution

Hunua Ranges Data

pgamma.deriv.unscaled

Derivatives of the Incomplete Gamma Integral (Unscaled Version)

Nakagami Distribution Family Function

Haight's Zeta Distribution

Benford's Distribution

Beta-binomial Distribution Family Function

Binomial Family Function

negbinomial.size

Negative Binomial Distribution Family Function With Known Size

Model Calibrations

Frank's Bivariate Distribution Family Function

The Positive-Normal Distribution

Multinomial Logit Model

Ordinal Regression with Stopping Ratios

The Skellam Distribution

Extract Log-likelihood for VGLMs/VGAMs/etc.

Simplex Distribution

Minimizing the L-q norm Family Function

Negative Binomial Distribution Family Function

Rhobit Link Function

Positive Bernoulli Sequence Model

Truncated Weibull Distribution Family Function

Generalized Pareto Distribution Family Function

Marginal effects for the multinomial logit and cumulative models

The Rayleigh Distribution

Triangle Distribution Family Function

Error Function, and variants

Latent Variable Plot for QO models

Mean Excess Plot

Loglinear Model for Two Binary Responses

The Beta-Normal Distribution

Toxoplasmosis Data

Generalized Beta Distribution of the Second Kind

Hormone Assay Data

Extract Model Constrained/Canonical Coefficients

Generalized Gamma distribution family function

The Dirichlet distribution

Hat Values and Regression Deletion Diagnostics

Gumbel Distribution Family Function

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

Response variable extracted

Pregnant Rats Toxological Experiment Data

Test For a Smart Object

Model Diagnostic Plots for QRR-VGLMs

Loglinear Model for Three Binary Responses

The Truncated Pareto Distribution

Log-log Link Function

The Gompertz Distribution

Fitting Vector Generalized Linear Models

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

Cardioid Distribution

Prentice (1974) Log-gamma Distribution

Censored Gumbel Distribution

The Perks Distribution

Multi-logit Link Function

Zero-Inflated Geometric Distribution Family Function

double.cens.normal

Univariate Normal Distribution with Double Censoring

Univariate Skew-Normal Distribution Family Function

Returns Important Matrices etc. of a QO Object

rrvglm.optim.control

Control function for rrvglm() calling optim()

Paralogistic Distribution Family Function

Index from Array to Matrix

Scaled Student t Distribution with 2 df Family Function

Wald Distribution Family Function

Natural Exponential Family Generalized Hyperbolic Secant Distribution Family Function

Positive-Negative Binomial Distribution

Yule-Simon Distribution

Quantile Plot for Gumbel Regression

Reciprocal Inverse Gaussian distribution

Huber's least favourable distribution family function

Poisson Regression by Asymmetric Maximum Likelihood Estimation

Fitting a Dirichlet Distribution

Control function for rrvglm

notdocumentedyet

Undocumented and Internally Used Functions and Classes

Skew-Normal Distribution

Zero-Inflated Binomial Distribution Family Function

plotdeplot.lmscreg

Density Plot for LMS Quantile Regression

Mixture of Two Univariate Normal Distributions

The Poisson Lognormal Distribution

The Generalized Gamma Distribution

Positive-geometric Distribution

Reciprocal link function

Fisher's Z Link Function

Poisson Family Function

Fitting Vector Generalized Additive Models

Identity Link Function

Smart Prediction

Frank's Bivariate Distribution

Bivariate Logistic Distribution

Predict Method for a VGLM fit

Determine What Mode the Smart Prediction is In

Kendall's Tau Statistic

Annual catches on Lake Otamangakau from October 1974 to October 1989

Log-Laplace and Logit-Laplace Distribution Family Functions

Quasi-Poisson Family Function

Mortality of Flour Beetles from Carbon Disulphide

The AA-Aa-aa Blood Group System

Exponentiated Exponential Distribution

Constrained Quadratic Ordination

Zero-Inflated Binomial Distribution

smart.expression

S Expression for Smart Functions

The Two-stage Sequential Binomial Distribution Family Function

Likelihood Ratio Test of Nested Models

posbernoulli.tb

Positive Bernoulli Family Function with Time and Behavioural Effects

Power Link Function

Poisson-Ordinal Link Function

quasibinomialff

Quasi-Binomial Family Function

Lognormal Distribution

Upper Record Values from a 1-parameter Exponential Distribution

The Laplace Distribution

Univariate Normal Distribution as a Varying-Coefficient Model

Leipnik Distribution Family Function

Weibull Distribution Family Function

Positive Bernoulli Family Function with Behavioural Effects

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

Predict Method for a CQO fit

calibrate-methods

Calibration for Constrained Regression Models

Zero Constraint Matrices

Zero-Altered Negative Binomial Distribution

Michaelis-Menten Model

Zero-Inflated Negative Binomial Distribution

Zipf Distribution Family Function

Zero-Inflated Negative Binomial Distribution Family Function

Plots for VGLMs

Rutherford-Geiger Polonium Data

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

Inverse Binomial Distribution Family Function

Positive Poisson Distribution Family Function

New Zealand Marital Data.

The zero Argument in VGAM Family Functions

Zero-Inflated Geometric Distribution

GARMA (Generalized Autoregressive Moving-Average) Models

Creates a Matrix of Appropriate Dimension

Generalized Rayleigh Distribution Family Function

Probability Plots for Categorical Data Analysis

Prior and Working Weights of a VGLM fit

Zeta Distribution Family Function

Control function for vglm

Latent Variable Plot

Univariate Normal Distribution

Log-gamma Distribution Family Function

The Beta-Binomial Distribution

University California Berkeley Graduate Admissions

Zero-Altered Geometric Distribution

Construct the Model Frame of a VLM Object

Perspective plot for QRR-VGLMs

Waitakere Ranges Data

Acute Myelogenous Leukemia Survival Data

Zero-Altered Binomial Distribution

Class ``vglmff''

1-parameter Gamma Distribution

Zero-Altered Poisson Distribution

Hypergeometric Family Function

Poisson Points Distribution

Benini Distribution Family Function

Biplot of Constrained Regression Models

Expectiles-sc.t2

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

Logarithms with an Unit Offset and Exponential Term

Log link function, and variants

Folded Normal Distribution Family Function

Laplace Distribution

Inverse Gaussian Distribution Family Function

Zero-Inflated Poisson Distribution

Corbet's Butterfly Data

The Beta-Geometric Distribution

Constraint Matrices

Zero-Altered Geometric Distribution

von Mises Distribution Family Function

Oxford Temperature Data

qrrvglm.control

Control function for QRR-VGLMs (CQO)

The ABO Blood Group System

Beta-binomial Distribution Family Function

Asymmetric Least Squares Quantile Regression

Return Level Plot for GEV Fits

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

Positive Bernoulli Family Function with Time Effects

The Laplace Distribution

The Two-parameter Beta Distribution Family Function

Class ``rrvglm''

Complementary Log-log Link Function

Positive-Binomial Distribution

The Gumbel Distribution

Zero-Altered Negative Binomial Distribution

Probit Link Function

The Log-Gamma Distribution

General Electric and Westinghouse Data

Logarithmic Distribution

Cleans Up After Smart Prediction

Table 1 of Huggins (1989)

Default VGAM Plotting

Control function for vgam

The Generalized Rayleigh Distribution

Exponential Link Function

Beta Distribution of the Second Kind

Low-iron Rat Teratology Data

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

Positive Negative Binomial Distribution Family Function

Defining smooths in VGAM formulae

Exponentiated Exponential Distribution

Yeo-Johnson Transformation

Venice Maximum Sea Levels Data

Zero-Inflated Poisson Distribution Family Function

Logistic Distribution Family Function

Yellow-bellied Prinia

Yule-Simon Family Function

Simulate Responses for VGLMs and VGAMs