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VGAM (version 0.9-3)

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

0.9-3

License

GPL-2

Maintainer

Last Published

November 11th, 2013

Functions in VGAM (0.9-3)

Link functions for VGLM/VGAM/etc. families

Coef.rrvglm-class

Class ``Coef.rrvglm''

Akaike's Information Criterion

Bayesian Information Criterion

The Laplace Distribution

Bivariate Binary Regression with an Odds Ratio

Ali-Mikhail-Haq Bivariate Distribution

aux.posbernoulli.t

Auxiliary Function for the Positive Bernoulli Family Function with Time Effects

The G1G2G3 Blood Group System

The AB-Ab-aB-ab Blood Group System

V1 Flying-Bombs Hits in London

Benini Distribution Family Function

The AB-Ab-aB-ab2 Blood Group System

calibrate.qrrvglm.control

Control function for CQO/CAO calibration

Beta-binomial Distribution Family Function

The Beta-Geometric Distribution

The Pareto Distribution

Table 1 of Huggins (1989)

Chest Pain in NZ Adults Data

Asymmetric Least Squares Quantile Regression

Ordinal Regression with Adjacent Categories Probabilities

Asymmetric Laplace Distribution Family Functions

Computes Model Coefficients and Quantities

CommonVGAMffArguments

Common VGAM family function Arguments

The Beta-Prime Distribution

The MNSs Blood Group System

The ABO Blood Group System

Birnbaum-Saunders Distribution Family Function

Quasi-variances Preprocessing Function

The Beta-Normal Distribution

Model Calibrations

calibrate.qrrvglm

Calibration for CQO and CAO models

Bradley Terry Model

Bivariate Logistic Distribution

Binomial Logistic Regression by Asymmetric Maximum Likelihood Estimation

Control Function for RR-VGAMs (CAO)

Vector Generalized Linear and Additive Models

Cauchy Distribution Family Function

Extract Model Coefficients for VLM Objects

double.expbinomial

Double Exponential Binomial Distribution Family Function

Bivariate Logistic Distribution Family Function

Frank's Bivariate Distribution

Gaussian Copula (Bivariate) Distribution

Clayton Copula (Bivariate) Distribution

Coef.qrrvglm-class

Class ``Coef.qrrvglm''

The Borel-Tanner Distribution

Binomial Family Function

The Exponential Geometric Distribution

Seemingly Unrelated Regressions

Bivariate normal distribution family function

Residual Degrees-of-Freedom

Fitting Constrained Additive Ordination (CAO)

Censored Normal Distribution

Response variable extracted

Mark the Baseline of Row and Column on a Matrix data

Gaussian Copula (Bivariate) Family Function

2-parameter Gamma Distribution

Bacon and Eggs Data

Exponential Logarithmic Distribution Family Function

Data on Back Pain Prognosis, from Anderson (1984)

The Inverse Gaussian Distribution

Poisson Regression by Asymmetric Maximum Likelihood Estimation

Crashes on New Zealand Roads in 2009

Hunting Spider Data

Cardioid Distribution

Returns Important Matrices etc. of a RR-VGLM Object

Fitting a Dirichlet-Multinomial Distribution

The Two-parameter Beta Distribution Family Function

betabinomial.ab

Beta-binomial Distribution Family Function

Bivariate Student-t Family Function

Exponential Regression by Asymmetric Maximum Likelihood Estimation

Auckland University Undergraduate Counts Data

Censored Gumbel Distribution

calibrate-methods

Calibration for Constrained Regression Models

Bivariate Gamma: McKay's Distribution

Borel-Tanner Distribution Family Function

Bivariate Probit Model

Cauchit Link Function

The Beta-Binomial Distribution

Beta Distribution of the Second Kind

Returns Important Matrices etc. of a QO Object

The Two-parameter Beta Distribution Family Function

The Dagum Distribution

Fitting a Dirichlet Distribution

Generalized Pareto Distribution Family Function

Hormone Assay Data

Expectiles-Normal

Expectiles of the Normal Distribution

The AA-Aa-aa Blood Group System

Gamma-Ordinal Link Function

Create a Survival Object

Bradley Terry Model With Ties

Benford's Distribution

Chinese Population in New Zealand 1867--2001 Data

Extract Model Constrained/Canonical Coefficients

Chi-squared Distribution

Exponentiated Exponential Distribution

Bivariate normal distribution cumulative distribution function

Complementary Log-log Link Function

The Felix Distribution

Generalized Poisson distribution

Fitting a Dirichlet-Multinomial Distribution

Marginal effects for the multinomial logit and cumulative models

Exponentiated Exponential Distribution

Generalized Rayleigh Distribution Family Function

Generalized Extreme Value Distribution Family Function

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

log F Distribution

The Exponential Integral and Variants

Redirects the user to rrvglm

Beta-geometric Distribution Family Function

Exponential Poisson Distribution Family Function

concoef-methods

Constrained (Canonical) Coefficients

The Generalized Extreme Value Distribution

The Lambert W function

Gumbel's Type I Bivariate Distribution Family Function

Latent Variable Plot for RR-VGLMs

Toxicity trial for insects

Geometric (Truncated and Untruncated) Distributions

Grain Prices Data in USA

Index from Array to Matrix

Gamma Hyperbola Bivariate Distribution

Cumulative Distribution Function for LMS Quantile Regression

F Distribution Family Function

Redirects the user to cqo

The Maxwell Distribution

Logarithmic Distribution

Frank's Bivariate Distribution Family Function

Exponential Geometric Distribution Family Function

Nakagami Distribution Family Function

Body Mass Index of New Zealand Adults Data

Log-gamma Distribution Family Function

Lognormal Distribution

Creates a Matrix of Appropriate Dimension

Logit Link Function

The Fisk Distribution

Huber's least favourable distribution family function

The Kumaraswamy Distribution

double.cennormal

Univariate Normal Distribution with Double Censoring

get.smart.prediction

Retrieves ``.smart.prediction''

McCullagh (1989) Distribution Family Function

The Lindley Distribution

Logarithms with an Unit Offset and Exponential Term

Leipnik Distribution Family Function

Lerch Phi Function

Inverse Binomial Distribution Family Function

Erlang Distribution

Latent Variable Plot

Folded Square Root Link Function

Mean Excess Plot

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

model.matrixvlm

Construct the Design Matrix of a VLM Object

The Generalized Beta Distribution (Libby and Novick, 1982)

Plackett's Bivariate Distribution

Michaelis-Menten Model

Poisson Family Function

Cardioid Distribution Family Function

Positive Poisson Distribution Family Function

Quasi-Poisson Family Function

Biplot of Constrained Regression Models

The Frechet Distribution

The Generalized Gamma Distribution

Exponential Link Function

Haight's Zeta Distribution

Constraint Matrices

Farlie-Gumbel-Morgenstern's Bivariate Distribution

Hypergeometric Family Function

Breathlessness and Wheeze Amongst Coalminers Data

Logistic Distribution Family Function

Censored Poisson Family Function

Gompertz Distribution Family Function

Latent Variables

pgamma.deriv.unscaled

Derivatives of the Incomplete Gamma Integral (Unscaled Version)

Exponential Distribution

The Log-Gamma Distribution

Loglinear Model for Two Binary Responses

Log-log Link Function

The Generalized Pareto Distribution

Ordinal Regression with Cumulative Probabilities

The Paralogistic Distribution

Captures of Peromyscus maniculatus, also known as deer mice.

Fisher's Z Link Function

GARMA (Generalized Autoregressive Moving-Average) Models

Likelihood Ratio Test of Nested Models

Corbet's Butterfly Data

Fitting Constrained Quadratic Ordination (CQO)

Log link function with an offset

Pareto(IV/III/II) Distribution Family Functions

Fitted Values of a VLM object

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

The Lomax Distribution

Folded Normal Distribution Family Function

Gaussian (normal) Family Function

1-parameter Gamma Distribution

Inverse Gaussian Distribution Family Function

posbernoulli.tb

Positive Bernoulli Family Function with Time and Behavioural Effects

Latent Variable Plot for QO models

Hat Values and Regression Deletion Diagnostics

Expectiles-Uniform

Expectiles of the Uniform Distribution

Negative Binomial Distribution Family Function

The Exponential Poisson Distribution

Derivatives of the Incomplete Gamma Integral

quasibinomialff

Quasi-Binomial Family Function

Mixture of Two Poisson Distributions

Invparalogistic

The Inverse Paralogistic Distribution

The Truncated Pareto Distribution

Poisson-Ordinal Link Function

Control function for vgam

2-parameter Gamma Distribution

General Electric and Westinghouse Data

The Poisson Lognormal Distribution

Positive Negative Binomial Distribution Family Function

Ordinal Regression with Continuation Ratios

Construct the Model Frame of a VLM Object

Low-iron Rat Teratology Data

Generalized Beta Distribution of the Second Kind

Minimizing the L-q norm Family Function

Positive-Binomial Distribution

Gumbel-II Distribution Family Function

Parallelism Constraint Matrices

Density Plot for LMS Quantile Regression

Perks Distribution Family Function

Loglinear Model for Three Binary Responses

Generalized Gamma distribution family function

Positive Binomial Distribution Family Function

Prentice (1974) Log-gamma Distribution

The Generalized Rayleigh Distribution

qrrvglm.control

Control function for QRR-VGLMs (CQO)

Short-tailed Symmetric Distribution Family Function

Triangle Distribution Family Function

matched.binomial

The Matched Binomial Distribution Family Function

Power Link Function

Trajectory plot for QRR-VGLMs

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

Complementary-log Link Function

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

Proportional Odds Model for Ordinal Regression

Logarithmic Distribution

Truncated Weibull Distribution Family Function

Venice Maximum Sea Levels Data

Default VGAM Plotting

Control function for vglm

Univariate Skew-Normal Distribution Family Function

Univariate Normal Distribution

Identity Link Function

Expectiles-Exponential

Expectiles of the Exponential Distribution

negbinomial.size

Negative Binomial Distribution Family Function With Known Size

Positive Bernoulli Family Function with Behavioural Effects

Wald Distribution Family Function

Cleans Up After Smart Prediction

Yeo-Johnson Transformation

The Laplace Distribution

Predict Method for a CQO fit

Yellow-bellied Prinia

Univariate Normal Distribution as a Varying-Coefficient Model

Zero-Inflated Poisson Distribution Family Function

Zero-Inflated Poisson Distribution

The Gumbel-II Distribution

Log-Laplace and Logit-Laplace Distribution Family Functions

The Inverse Lomax Distribution

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

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

Singh-Maddala Distribution Family Function

Zero-Altered Geometric Distribution

plotdeplot.lmscreg

Density Plot for LMS Quantile Regression

mmt daily maximum temperatures

Pneumoconiosis in Coalminers Data

Levy Distribution Family Function

Predict Method for a VGLM fit

Gumbel Distribution Family Function

Rhobit Link Function

Positive-geometric Distribution

Zero Constraint Matrices

The Dirichlet distribution

Mixture of Two Exponential Distributions

Simplex Distribution Family Function

rrvglm.optim.control

Control function for rrvglm() calling optim()

Koenker's Distribution Family Function

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

Pareto and Truncated Pareto Distribution Family Functions

Poisson Points Distribution

The Rayleigh Distribution

Machinists Accidents

The Skellam Distribution

The zero Argument in VGAM Family Functions

Positive-Negative Binomial Distribution

The Folded-Normal Distribution

Pregnant Rats Toxological Experiment Data

The Gumbel Distribution

Ordinal Poisson Family Function

Expectiles-Koenker

Expectiles/Quantiles of the Koenker Distribution

Skew-Normal Distribution

Huber's least favourable distribution

LMS Quantile Regression with a Box-Cox Transformation to Normality

Hunua Ranges Data

Negative Binomial-Ordinal Link Function

Trajectory Plot

2008 and 2012 Summer Olympic Final Medal Count Data

Plots for VGLMs

Zero-Altered Binomial Distribution

Zero-Altered Negative Binomial Distribution

Positive Bernoulli Sequence Model

Laplace Distribution

Positive Normal Distribution Family Function

Mixture of Two Univariate Normal Distributions

Zero-Inflated Negative Binomial Distribution

Positive-Poisson Distribution

Test For a Smart Object

The Zipf Distribution

The Log-Laplace Distribution

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

Reciprocal link function

Natural Exponential Family Generalized Hyperbolic Secant Distribution Family Function

Determine What Mode the Smart Prediction is In

Hyperbolic Secant Distribution Family Function

Class ``rrvglm''

Toxoplasmosis Data

Acute Myelogenous Leukemia Survival Data

Morgenstern's Bivariate Distribution Family Function

Constrained Quadratic Ordination

Perspective plot for QRR-VGLMs

Kendall's Tau Statistic

Nested reduced-rank autoregressive models for multiple time series

The Two-stage Sequential Binomial Distribution Family Function

Slash Distribution Family Function

Makeham Distribution Family Function

von Mises Distribution Family Function

Vector cubic smoothing spline

Class ``vglmff''

Model Diagnostic Plots for QRR-VGLMs

Fitting Vector Generalized Additive Models

Waitakere Ranges Data

Weibull Distribution Family Function

Zero-Altered Binomial Distribution

Rutherford-Geiger Polonium Data

The Zeta Distribution

Zeta Distribution Family Function

Oxford Temperature Data

New Zealand Marital Data.

Yule-Simon Family Function

Zero-Inflated Negative Binomial Distribution Family Function

Yule-Simon Distribution

LMS Quantile Regression with a Yeo-Johnson Transformation to Normality

notdocumentedyet

Undocumented and Internally Used Functions and Classes

Log link function, and variants

Zero-Altered Negative Binomial Distribution

Smart Prediction

University California Berkeley Graduate Admissions

Zero-Inflated Geometric Distribution

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

Zero-Inflated Binomial Distribution Family Function

Positive Bernoulli Family Function with Time Effects

Negative binomial canonical link function

undocumented-methods

Undocumented Methods Functions

Probability Plots for Categorical Data Analysis

Multinomial Logit Model

Prior and Working Weights of a VGLM fit

Zero-Altered Poisson Distribution

Quantile Plot for Gumbel Regression

Multi-logit Link Function

plotqtplot.lmscreg

Quantile Plot for LMS Quantile Regression

Upper Record Values from a Univariate Normal Distribution

Zero-Altered Geometric Distribution

Control function for rrvglm

Return Level Plot for GEV Fits

Upper Record Values from a 1-parameter Exponential Distribution

The Positive-Normal Distribution

Rice Distribution Family Function

Probit Link Function

Student t Distribution

Ordinal Regression with Stopping Ratios

plotvgam.control

Control Function for plotvgam()

Zero-Inflated Geometric Distribution Family Function

The Rice Distribution

Reciprocal Inverse Gaussian distribution

Zero-Altered Poisson Distribution

Defining smooths in VGAM formulae

The Exponential Logarithmic Distribution

Smart Prediction Setup

Quantile Plot for LMS Quantile Regression

smart.expression

S Expression for Smart Functions

Fitting Vector Generalized Linear Models

Zero-Inflated Binomial Distribution