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VGAM (version 0.9-1)

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

0.9-1

License

GPL-2

Maintainer

Last Published

April 27th, 2013

Functions in VGAM (0.9-1)

calibrate.qrrvglm.control

Control function for CQO/UQO/CAO calibration

Constrained (Canonical) Coefficients

Extract Model Constrained/Canonical Coefficients

Constraint Matrices

Frank's Bivariate Distribution

Hypergeometric Family Function

Hunua Ranges Data

CommonVGAMffArguments

Common VGAM family function Arguments

Returns Important Matrices etc. of a RR-VGLM Object

Captures of peromyscus maniculatus

Exponential Regression by Asymmetric Maximum Likelihood Estimation

Binomial Logistic Regression by Asymmetric Maximum Likelihood Estimation

Extract Model Coefficients for VLM Objects

Asymmetric Least Squares Quantile Regression

Hormone Assay Data

Minimizing the L-q norm Family Function

Poisson Family Function

Fitting Constrained Additive Ordination (CAO)

Fitting a Dirichlet Distribution

Quasi-variances Preprocessing Function

posbernoulli.tb

Positive Bernoulli Family Function with Time and Behavioural Effects (experimental)

The AA-Aa-aa Blood Group System

Quantile Plot for LMS Quantile Regression

Beta-geometric Distribution Family Function

Create a Survival Object

Double Exponential Binomial Distribution Family Function

Computes Model Coefficients and Quantities

Farlie-Gumbel-Morgenstern's Bivariate Distribution Family Function

Binomial Family Function

The Beta-Binomial Distribution

The MNSs Blood Group System

The AB-Ab-aB-ab2 Blood Group System

Fitting Constrained Quadratic Ordination (CQO)

Borel-Tanner Distribution Family Function

Erlang Distribution

The Birnbaum-Saunders Distribution

The Beta-Normal Distribution

Logarithmic Distribution

Control Function for RR-VGAMs (CAO)

Cumulative Distribution Function for LMS Quantile Regression

The AB-Ab-aB-ab Blood Group System

Poisson Regression by Asymmetric Maximum Likelihood Estimation

Mark the Baseline of Row and Column on a Matrix data

The ABO Blood Group System

Complementary-log Link Function

The Pareto Distribution

Expectiles-Uniform

Expectiles of the Uniform Distribution

Bivariate normal distribution family function

Model Calibrations

The Frechet Distribution

Benford's Distribution

The Beta-Geometric Distribution

Beta Distribution of the Second Kind

Acute Myelogenous Leukemia Survival Data

Akaike's Information Criterion

Censored Poisson Family Function

Inverse Lomax Distribution Family Function

Bivariate Binary Regression with an Odds Ratio

Bivariate Probit Model (Family Function)

Univariate Skew-Normal Distribution Family Function

Fitted Values of a VLM object

Fisher's Z Link Function

Chest Pain in NZ Adults Data

Returns Important Matrices etc. of a QO Object

The Tobit Distribution

Complementary Log-log Link Function

Crashes on New Zealand Roads in 2009

Fitting Vector Generalized Linear Models

Table 1 of Huggins (1989)

The Exponential Geometric Distribution

1-parameter Gamma Distribution

GARMA (Generalized Autoregressive Moving-Average) Models

Folded Normal Distribution Family Function

Exponential Geometric Distribution Family Function

Auckland University Undergraduate Counts Data

LMS Quantile Regression with a Box-Cox Transformation to Normality

Expectiles-Exponential

Expectiles of the Exponential Distribution

Bradley Terry Model

Ali-Mikhail-Haq Distribution's Bivariate Distribution

Gumbel-II Distribution Family Function

Bradley Terry Model With Ties

The Two-parameter Beta Distribution Family Function

2-parameter Gamma Distribution

Fisk Distribution family function

2-parameter Gamma Distribution

Bivariate Logistic Distribution Family Function

Generalized Gamma distribution family function

Fitting a Dirichlet-Multinomial Distribution

The Laplace Distribution

Chi-squared Distribution

Control function for rrvglm

Exponentiated Exponential Distribution

The Exponential Poisson Distribution

Breathlessness and Wheeze Amongst Coalminers Data

Data on Back Pain Prognosis, from Anderson (1984)

calibrate.qrrvglm

Calibration for CQO, UQO and CAO models

Gaussian (normal) Family Function

Bivariate Logistic Distribution

Coef.qrrvglm-class

Class ``Coef.qrrvglm''

Dagum Distribution Family Function

Felix Distribution Family Function

Univariate Normal Distribution with Double Censoring

Skew-Normal Distribution

Proportional Odds Model for Ordinal Regression

Generalized Poisson distribution

Toxicity trial for insects

The Borel-Tanner Distribution

Cardioid Distribution

Low-iron Rat Teratology Data

Redirects the user to cqo

Exponential Link Function

Coef.rrvglm-class

Class ``Coef.rrvglm''

Gompertz Distribution Family Function

The Generalized Pareto Distribution

Bivariate Gamma: McKay's Distribution

Logit Link Function

Ordinal Regression with Cumulative Probabilities

Censored Normal Distribution

University California Berkeley Graduate Admissions

Parallelism Constraint Matrices

The G1G2G3 Blood Group System

Zero-Inflated Binomial Distribution Family Function

Trajectory Plot

Cauchy Distribution Family Function

Redirects the user to rrvglm

Generalized Extreme Value Distribution Family Function

Invparalogistic

The Inverse Paralogistic Distribution

The Kumaraswamy Distribution

Exponentiated Exponential Distribution

The Beta-Prime Distribution

Exponential Distribution

Density Plot for LMS Quantile Regression

General Electric and Westinghouse Data

Censored Gumbel Distribution

Zero Constraint Matrices

Student t Distribution

Folded Square Root Link Function

Body Mass Index of New Zealand Adults Data

Beta-binomial Distribution Family Function

Generalized Pareto Distribution Family Function

Log link function

The Gumbel Distribution

The Generalized Gamma Distribution

Multinomial Logit Model

LMS Quantile Regression with a Yeo-Johnson Transformation to Normality

Logarithmic Distribution

Gumbel Distribution Family Function

Gamma-Ordinal Link Function

Cardioid Distribution Family Function

Ordinal Regression with Continuation Ratios

model.matrixvlm

Construct the Design Matrix of a VLM Object

F Distribution Family Function

Latent Variable Plot for RR-VGLMs

Log link function with an offset

DeLury's Method for Population Size Estimation

The Inverse Gaussian Distribution

Plackett's Bivariate Distribution Family Function

Mixture of Two Univariate Normal Distributions

Pareto and Truncated Pareto Distribution Family Functions

Makeham Distribution Family Function

Prentice (1974) Log-gamma Distribution

Chinese Population in New Zealand 1867--2001 Data

Expectiles-Normal

Expectiles of the Normal Distribution

The Two-parameter Beta Distribution Family Function

Poisson-Ordinal Link Function

Creates a Matrix of Appropriate Dimension

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

Levy Distribution Family Function

The Laplace Distribution

Seemingly Unrelated Regressions

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

The Generalized Beta Distribution (Libby and Novick, 1982)

Lerch Phi Function

Grain Prices Data in USA

Ordinal Regression with Adjacent Categories Probabilities

Hat Values and Regression Deletion Diagnostics

Exponential Poisson Distribution Family Function

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

Leipnik Distribution Family Function

The Folded-Normal Distribution

betabinomial.ab

Beta-binomial Distribution Family Function

Latent Variable Plot for QO models

Positive Binomial Distribution Family Function

Nakagami Distribution

Log-log Link Function

Lomax Distribution Family Function

Identity Link Function

McCullagh (1989) Distribution Family Function

The Exponential Logarithmic Distribution

The Generalized Extreme Value Distribution

Link functions for VGLM/VGAM/etc. families

The Perks Distribution

Biplot of Constrained Regression Models

Maxwell Distribution Family Function

Constrained Quadratic Ordination

Loglinear Model for Three Binary Responses

Asymmetric Laplace Distribution Family Functions

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

Vector Generalized Linear and Additive Models

Benini Distribution Family Function

New Zealand Marital Data.

Morgenstern's Bivariate Distribution Family Function

Log-Laplace and Logit-Laplace Distribution Family Functions

Residual Degrees-of-Freedom

Upper Record Values from a 1-parameter Exponential Distribution

Cauchit Link Function

Positive Poisson Distribution Family Function

Inverse Binomial Distribution Family Function

The Poisson Lognormal Distribution

Exponential Logarithmic Distribution Family Function

The Lindley Distribution

Ordinal Poisson Family Function

Negative Binomial-Ordinal Link Function

Gamma Hyperbola Bivariate Distribution

Perspective plot for QRR-VGLMs

Test For a Smart Object

notdocumentedyet

Undocumented and Internally Used Functions and Classes

The Log-Laplace Distribution

Negative binomial canonical link function

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

Generalized Rayleigh Distribution Family Function

Negative Binomial Distribution Family Function

Expectiles-Koenker

Expectiles/Quantiles of the Koenker Distribution

The Rayleigh Distribution

Defining smooths in VGAM formulae

The Pareto(IV/III/II) Distributions

Gumbel's Type I Bivariate Distribution Family Function

The Triangle Distribution

Short-tailed Symmetric Distribution Family Function

Return Level Plot for GEV Fits

Positive Normal Distribution Family Function

Log-gamma Distribution Family Function

Hunting Spider Data

calibrate-methods

Calibration for Constrained Regression Models

Reciprocal link function

The Truncated Pareto Distribution

Derivatives of the Incomplete Gamma Integral

The Gumbel-II Distribution

Response variable extracted

Class ``rrvglm''

Huber's least favourable distribution family function

Zero-Altered Binomial Distribution

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

Haight's Zeta Function

Fitting a Dirichlet-Multinomial Distribution

quasibinomialff

Quasi-Binomial Family Function

Smart Prediction Setup

Singh-Maddala Distribution Family Function

pgamma.deriv.unscaled

Derivatives of the Incomplete Gamma Integral (Unscaled Version)

Venice Maximum Sea Levels Data

Positive Bernoulli Sequence Model

Quantile Plot for Gumbel Regression

Waitakere Ranges Data

Logistic Distribution Family Function

Fitting Unconstrained Quadratic Ordination (UQO)

Nested reduced-rank autoregressive models for multiple time series

Slash Distribution

Michaelis-Menten Model

Fitting Vector Generalized Additive Models

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

plotqtplot.lmscreg

Quantile Plot for LMS Quantile Regression

Mean Excess Plot

Zero-Altered Poisson Distribution

Zero-Altered Negative Binomial Distribution

Quasi-Poisson Family Function

The Matched Binomial Distribution Family Function

The Dirichlet distribution

Riemann's Zeta Function

Inverse Gaussian Distribution Family Function

Mixture of Two Exponential Distributions

Truncated Weibull Distribution Family Function

Generalized Beta Distribution of the Second Kind

Laplace Distribution

Positive Bernoulli Family Function with Time Effects

Skellam Distribution Family Function

Mixture of Two Poisson Distributions

The Log-Gamma Distribution

Positive Bernoulli Family Function with Behavioural Effects

Probit Link Function

Positive-geometric Distribution

2008 and 2012 Summer Olympic Final Medal Count Data

The Generalized Rayleigh Distribution

2008 World Fly Fishing Championships (Team results) Data

Zero-Altered Poisson Distribution

Paralogistic Distribution Family Function

Positive-Poisson Distribution

The Lambert W function

Positive-Binomial Distribution

smart.expression

S Expression for Smart Functions

Control Function for UQO models

Pneumoconiosis in Coalminers Data

Cleans Up After Smart Prediction

get.smart.prediction

Retrieves ``.smart.prediction''

Likelihood Ratio Test of Nested Models

plotdeplot.lmscreg

Density Plot for LMS Quantile Regression

Latent Variables

Hyperbolic Secant Distribution Family Function

Oxford Temperature Data

Probability Plots for Categorical Data Analysis

Wald Distribution Family Function

Zero-Altered Geometric Distribution

Zero-Inflated Negative Binomial Distribution

The Positive-Normal Distribution

Zero-Inflated Geometric Distribution

Positive Negative Binomial Distribution Family Function

Zero-Altered Geometric Distribution

Huber's least favourable distribution

Lognormal Distribution

Control function for vgam

qrrvglm.control

Control function for QRR-VGLMs (CQO)

Zero-Inflated Negative Binomial Distribution Family Function

Univariate Normal Distribution

Index from Array to Matrix

Yeo-Johnson Transformation

Bivariate normal distribution cumulative distribution function

The Two-stage Sequential Binomial Distribution Family Function

Marginal effects for the multinomial logit and cumulative models

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

Simplex Distribution

Latent Variable Plot

Control function for vglm

undocumented-methods

Undocumented Methods Functions

Reciprocal Inverse Gaussian distribution

Loglinear Model for Two Binary Responses

von Mises Distribution Family Function

Determine What Mode the Smart Prediction is In

Weibull Distribution Family Function

Zero-Altered Negative Binomial Distribution

Zero-Inflated Binomial Distribution

Rutherford-Geiger Polonium Data

Multinomial Logit Link Function

Geometric (Truncated and Untruncated) Distributions

Construct the Model Frame of a VLM Object

2008 World Fly Fishing Championships Data

Toxoplasmosis Data

Koenker's Distribution Family Function

Predict Method for a CQO fit

Vector cubic smoothing spline

Default VGAM Plotting

Rice Distribution Family Function

rrvglm.optim.control

Control function for rrvglm() calling optim()

negbinomial.size

Negative Binomial Distribution Family Function With Known Size

Trajectory plot for QRR-VGLMs

Model Diagnostic Plots for QRR-VGLMs

Zero-Inflated Poisson Distribution

Predict Method for a VGLM fit

Zero-Inflated Poisson Distribution Family Function

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

Zipf Distribution Family Function

The zero Argument in VGAM Family Functions

Ordinal Regression with Stopping Ratios

Class ``vglmff''

Yule-Simon Family Function

2008 World Fly Fishing Championships (Individual results) Data

Power Link Function

Smart Prediction

Positive-Negative Binomial Distribution

Prior and Working Weights of a VGLM fit

plotvgam.control

Control Function for plotvgam()

Upper Record Values from a Univariate Normal Distribution

Rhobit Link Function

The Rice Distribution

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

2008 World Fly Fishing Championships (Number of captures) Data

Yule-Simon Distribution

Point System for the 2008 World Fly Fishing Championships

Zero-Altered Binomial Distribution

Zero-Inflated Geometric Distribution Family Function

Zeta Distribution Family Function