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VGAM (version 0.9-2)

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

42,087

Version

0.9-2

License

GPL-2

Maintainer

Last Published

September 20th, 2013

Functions in VGAM (0.9-2)

Bivariate Probit Model

Bradley Terry Model

Beta-geometric Distribution Family Function

Computes Model Coefficients and Quantities

Coef.rrvglm-class

Class ``Coef.rrvglm''

The AB-Ab-aB-ab Blood Group System

Redirects the user to rrvglm

The AA-Aa-aa Blood Group System

Bivariate normal distribution family function

Bayesian Information Criterion

Vector Generalized Linear and Additive Models

The G1G2G3 Blood Group System

Asymmetric Least Squares Quantile Regression

Exponential Distribution

Hormone Assay Data

Clayton Copula (Bivariate) Family Function

Cardioid Distribution

Bivariate Gamma: McKay's Distribution

The Beta-Normal Distribution

calibrate.qrrvglm.control

Control function for CQO/UQO/CAO calibration

The Two-parameter Beta Distribution Family Function

Censored Gumbel Distribution

Fitting Constrained Additive Ordination (CAO)

Ordinal Regression with Adjacent Categories Probabilities

Chinese Population in New Zealand 1867--2001 Data

Negative binomial canonical link function

Fitted Values of a VLM object

Binomial Logistic Regression by Asymmetric Maximum Likelihood Estimation

Borel-Tanner Distribution Family Function

Exponential Logarithmic Distribution Family Function

Cardioid Distribution Family Function

The Poisson Lognormal Distribution

Gamma-Ordinal Link Function

Binomial Family Function

double.cennormal

Univariate Normal Distribution with Double Censoring

The Beta-Prime Distribution

Complementary Log-log Link Function

The Positive-Normal Distribution

invparalogistic

Inverse Paralogistic Distribution Family Function

Ordinal Regression with Continuation Ratios

The Exponential Integral and Variants

Dagum Distribution Family Function

The Exponential Poisson Distribution

Fisk Distribution family function

Farlie-Gumbel-Morgenstern's Bivariate Distribution Family Function

The Two-parameter Beta Distribution Family Function

Corbet's Butterfly Data

Returns Important Matrices etc. of a RR-VGLM Object

Bivariate Logistic Distribution

Gompertz Distribution Family Function

Logarithmic Distribution

Logit Link Function

The Birnbaum-Saunders Distribution

The Borel-Tanner Distribution

The Inverse Gaussian Distribution

Quasi-variances Preprocessing Function

The Beta-Binomial Distribution

Response variable extracted

Asymmetric Laplace Distribution Family Functions

Inverse Lomax Distribution Family Function

Bivariate Student-t distribution cumulative distribution function

Extract Model Constrained/Canonical Coefficients

Simplex Distribution Family Function

Skew-Normal Distribution

calibrate.qrrvglm

Calibration for CQO, UQO and CAO models

Bivariate normal distribution cumulative distribution function

The ABO Blood Group System

Gumbel's Type I Bivariate Distribution Family Function

Residual Degrees-of-Freedom

Generalized Beta Distribution of the Second Kind

Frank's Bivariate Distribution Family Function

Poisson Regression by Asymmetric Maximum Likelihood Estimation

Seemingly Unrelated Regressions

Exponential Geometric Distribution Family Function

Gaussian Copula (Bivariate) Family Function

Beta-binomial Distribution Family Function

Loglinear Model for Two Binary Responses

Bradley Terry Model With Ties

Test For a Smart Object

Censored Normal Distribution

Chest Pain in NZ Adults Data

Body Mass Index of New Zealand Adults Data

The Laplace Distribution

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

Lomax Distribution Family Function

Generalized Poisson distribution

Breathlessness and Wheeze Amongst Coalminers Data

Mixture of Two Univariate Normal Distributions

double.expbinomial

Double Exponential Binomial Distribution Family Function

Haight's Zeta Distribution

The Paralogistic Distribution

Felix Distribution Family Function

Leipnik Distribution Family Function

Gumbel-II Distribution Family Function

Nakagami Distribution

Fitting Unconstrained Quadratic Ordination (UQO)

Exponential Poisson Distribution Family Function

Koenker's Distribution Family Function

Marginal effects for the multinomial logit and cumulative models

Beta Distribution of the Second Kind

Venice Maximum Sea Levels Data

Quasi-Poisson Family Function

Generalized Gamma distribution family function

Negative Binomial-Ordinal Link Function

Identity Link Function

The Kumaraswamy Distribution

Frechet Distribution Family Function

Control function for rrvglm

betabinomial.ab

Beta-binomial Distribution Family Function

The Pareto(IV/III/II) Distributions

Positive-Binomial Distribution

Grain Prices Data in USA

Frank's Bivariate Distribution

CommonVGAMffArguments

Common VGAM family function Arguments

Chi-squared Distribution

The MNSs Blood Group System

Coef.qrrvglm-class

Class ``Coef.qrrvglm''

Hyperbolic Secant Distribution Family Function

Predict Method for a CQO fit

Link functions for VGLM/VGAM/etc. families

Kendall's Tau Statistic

2-parameter Gamma Distribution

The Pareto Distribution

LMS Quantile Regression with a Yeo-Johnson Transformation to Normality

Create a Survival Object

Captures of Peromyscus maniculatus, also known as deer mice.

Mark the Baseline of Row and Column on a Matrix data

The Laplace Distribution

Logarithmic Distribution

Hat Values and Regression Deletion Diagnostics

The Benini Distribution

Bivariate Binary Regression with an Odds Ratio (Family Function)

Ali-Mikhail-Haq Distribution Distribution Family Function

Constrained Quadratic Ordination

Bacon and Eggs Data

notdocumentedyet

Undocumented and Internally Used Functions and Classes

Predict Method for a VGLM fit

Gamma Hyperbola Bivariate Distribution

Biplot of Constrained Regression Models

Constraint Matrices

The AB-Ab-aB-ab2 Blood Group System

aux.posbernoulli.t

Auxiliary Function for the Positive Bernoulli Family Function with Time Effects

Probability Plots for Categorical Data Analysis

The Gumbel-II Distribution

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

Expectiles-Uniform

Expectiles of the Uniform Distribution

The Dirichlet distribution

The Exponential Logarithmic Distribution

Slash Distribution Family Function

Row-Column Interaction Models including Goodman's RC Association Model

Folded Square Root Link Function

Upper Record Values from a Univariate Normal Distribution

Generalized Rayleigh Distribution Family Function

Cumulative Distribution Function for LMS Quantile Regression

pgamma.deriv.unscaled

Derivatives of the Incomplete Gamma Integral (Unscaled Version)

Generalized Extreme Value Distribution Family Function

Gumbel Distribution Family Function

Redirects the user to cqo

Cauchy Distribution Family Function

The Tobit Distribution

Inverse Binomial Distribution Family Function

Density Plot for LMS Quantile Regression

Latent Variables

Log-gamma Distribution Family Function

Poisson-Ordinal Link Function

Parallelism Constraint Matrices

Upper Record Values from a 1-parameter Exponential Distribution

The Folded-Normal Distribution

The Lindley Distribution

Gaussian (normal) Family Function

Akaike's Information Criterion

Generalized Beta Distribution Family Function

Fitting Vector Generalized Additive Models

Pareto and Truncated Pareto Distribution Family Functions

Zero-Altered Binomial Distribution

The Perks Distribution

V1 Flying-Bombs Hits in London

Huber's least favourable distribution

Inverse Gaussian Distribution Family Function

Complementary-log Link Function

Weibull Distribution Family Function

Lerch Phi Function

Quantile Plot for Gumbel Regression

qrrvglm.control

Control function for QRR-VGLMs (CQO)

Lognormal Distribution

Model Diagnostic Plots for QRR-VGLMs

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

Riemann's Zeta Function

Cauchit Link Function

Rayleigh Distribution Family Function

Zipf Distribution Family Function

Exponential Link Function

The Log-Laplace Distribution

Truncated Weibull Distribution Family Function

The Skellam Distribution

Zero-Inflated Binomial Distribution

The Generalized Extreme Value Distribution

Expectiles-Exponential

Expectiles of the Exponential Distribution

quasibinomialff

Quasi-Binomial Family Function

Expectiles-Normal

Expectiles of the Normal Distribution

Zeta Distribution Family Function

Crashes on New Zealand Roads in 2009

2-parameter Gamma Distribution

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

The Generalized Rayleigh Distribution

Reciprocal link function

The Gumbel Distribution

LMS Quantile Regression with a Box-Cox Transformation to Normality

New Zealand Marital Data.

Hypergeometric Family Function

Index from Array to Matrix

Makeham Distribution Family Function

Univariate Normal Distribution as a Varying-Coefficient Model

Class ``vglmff''

Data on Back Pain Prognosis, from Anderson (1984)

calibrate-methods

Calibration for Constrained Regression Models

Control function for vgam

The Generalized Pareto Distribution

The Generalized Gamma Distribution

Derivatives of the Incomplete Gamma Integral

log F Distribution

The Lambert W function

The Log-Gamma Distribution

plotvgam.control

Control Function for plotvgam()

get.smart.prediction

Retrieves ``.smart.prediction''

Bivariate Logistic Distribution Family Function

Fitting a Dirichlet-Multinomial Distribution

Log-Laplace and Logit-Laplace Distribution Family Functions

Model Calibrations

matched.binomial

The Matched Binomial Distribution Family Function

Machinists Accidents

Huber's least favourable distribution family function

Oxford Temperature Data

Generalized Pareto Distribution Family Function

posbernoulli.tb

Positive Bernoulli Family Function with Time and Behavioural Effects

Probit Link Function

Nested reduced-rank autoregressive models for multiple time series

Poisson Family Function

Quantile Plot for LMS Quantile Regression

Reciprocal Inverse Gaussian distribution

rrvglm.optim.control

Control function for rrvglm() calling optim()

Folded Normal Distribution Family Function

Positive-geometric Distribution

concoef-methods

Constrained (Canonical) Coefficients

Censored Poisson Family Function

GARMA (Generalized Autoregressive Moving-Average) Models

Univariate Skew-Normal Distribution Family Function

The Singh-Maddala Distribution

Ordinal Regression with Cumulative Probabilities

General Electric and Westinghouse Data

Cleans Up After Smart Prediction

Fitting a Dirichlet-Multinomial Distribution

Maxwell Distribution Family Function

Prior and Working Weights of a VGLM fit

Exponentiated Exponential Distribution

Morgenstern's Bivariate Distribution Family Function

Hunua Ranges Data

Natural Exponential Family Generalized Hyperbolic Secant Distribution Family Function

McCullagh (1989) Distribution Family Function

Latent Variable Plot for RR-VGLMs

Ordinal Regression with Stopping Ratios

Pneumoconiosis in Coalminers Data

Negative Binomial Distribution Family Function

Positive Negative Binomial Distribution Family Function

Acute Myelogenous Leukemia Survival Data

Fitting a Dirichlet Distribution

Vector cubic smoothing spline

The zero Argument in VGAM Family Functions

Levy Distribution Family Function

Construct the Model Frame of a VLM Object

Erlang Distribution

Log link function, and variants

Zero-Altered Negative Binomial Distribution

Prentice (1974) Log-gamma Distribution

Proportional Odds Model for Ordinal Regression

Power Link Function

Smart Prediction

Zero-Inflated Geometric Distribution

Expectiles-Koenker

Expectiles/Quantiles of the Koenker Distribution

1-parameter Gamma Distribution

Fisher's Z Link Function

Low-iron Rat Teratology Data

Rice Distribution Family Function

model.matrixvlm

Construct the Design Matrix of a VLM Object

Logistic Distribution Family Function

Default VGAM Plotting

Rhobit Link Function

Rutherford-Geiger Polonium Data

The Triangle Distribution

Poisson Points Distribution

Log link function with an offset

Control function for vglm

Loglinear Model for Three Binary Responses

Class ``rrvglm''

Pregnant Rats Toxological Experiment Data

Extract Model Coefficients for VLM Objects

Hunting Spider Data

Smart Prediction Setup

Control Function for UQO models

smart.expression

S Expression for Smart Functions

Zero-Altered Negative Binomial Distribution

von Mises Distribution Family Function

Positive-Poisson Distribution

Short-tailed Symmetric Distribution Family Function

Univariate Normal Distribution

Exponentiated Exponential Distribution

Plackett's Bivariate Distribution

Zero-Inflated Poisson Distribution

Multi-logit Link Function

Table 1 of Huggins (1989)

Return Level Plot for GEV Fits

Latent Variable Plot for QO models

Likelihood Ratio Test of Nested Models

Latent Variable Plot

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

negbinomial.size

Negative Binomial Distribution Family Function With Known Size

Michaelis-Menten Model

Mean Excess Plot

Log-log Link Function

Positive Binomial Distribution Family Function

Zero-Inflated Geometric Distribution Family Function

Gaussian Copula (Bivariate) Distribution

Determine What Mode the Smart Prediction is In

Zero-Altered Binomial Distribution

Trajectory Plot

Control Function for RR-VGAMs (CAO)

Positive Bernoulli Sequence Model

Ordinal Poisson Family Function

Zero-Altered Poisson Distribution

Minimizing the L-q norm Family Function

The Truncated Pareto Distribution

Mixture of Two Poisson Distributions

Multinomial Logit Model

Zero-Altered Poisson Distribution

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

Yeo-Johnson Transformation

Student t Distribution

plotdeplot.lmscreg

Density Plot for LMS Quantile Regression

2008 and 2012 Summer Olympic Final Medal Count Data

University California Berkeley Graduate Admissions

Wald Distribution Family Function

plotqtplot.lmscreg

Quantile Plot for LMS Quantile Regression

Zero-Inflated Binomial Distribution Family Function

Positive Bernoulli Family Function with Time Effects

Plots for VGLMs

undocumented-methods

Undocumented Methods Functions

Waitakere Ranges Data

Positive Normal Distribution Family Function

The Exponential Geometric Distribution

Returns Important Matrices etc. of a QO Object

Toxicity trial for insects

Zero-Altered Geometric Distribution

Defining smooths in VGAM formulae

Exponential Regression by Asymmetric Maximum Likelihood Estimation

Benford's Distribution

Fitting Vector Generalized Linear Models

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

Logarithms with an Unit Offset and Exponential Term

Yule-Simon Distribution

Zero-Altered Geometric Distribution

The Beta-Geometric Distribution

Mixture of Two Exponential Distributions

Zero-Inflated Negative Binomial Distribution

Perspective plot for QRR-VGLMs

Positive Bernoulli Family Function with Behavioural Effects

Positive-Negative Binomial Distribution

The Rice Distribution

Auckland University Undergraduate Counts Data

Fitting Constrained Quadratic Ordination (CQO)

F Distribution Family Function

Creates a Matrix of Appropriate Dimension

Geometric (Truncated and Untruncated) Distributions

Yule-Simon Family Function

Zero Constraint Matrices

Toxoplasmosis Data

Laplace Distribution

Positive Poisson Distribution Family Function

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

The Two-stage Sequential Binomial Distribution Family Function

Zero-Inflated Poisson Distribution Family Function

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

Trajectory plot for QRR-VGLMs

Zero-Inflated Negative Binomial Distribution Family Function