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VGAM (version 1.0-2)

Vector Generalized Linear and Additive Models

Description

An implementation of about 6 major classes of statistical regression models. At the heart of it are the vector generalized linear and additive model (VGLM/VGAM) classes, and the book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) gives details of the statistical framework and VGAM package. Currently only fixed-effects models are implemented, i.e., no random-effects models. Many (150+) models and distributions are estimated by maximum likelihood estimation (MLE) or penalized MLE, using Fisher scoring. VGLMs can be loosely thought of as multivariate GLMs. VGAMs are data-driven VGLMs (i.e., with smoothing). The other classes are RR-VGLMs (reduced-rank VGLMs), quadratic RR-VGLMs, reduced-rank VGAMs, RCIMs (row-column interaction models)---these classes perform 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; see the NEWS and ChangeLog files for latest changes.

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Version

Install

install.packages('VGAM')

Monthly Downloads

31,077

Version

1.0-2

License

GPL-2 | GPL-3

Maintainer

Thomas Yee

Last Published

May 27th, 2016

Functions in VGAM (1.0-2)

beggs

Bacon and Eggs Data
backPain

Data on Back Pain Prognosis, from Anderson (1984)
betabinomialff

Beta-binomial Distribution Family Function
betaff

The Two-parameter Beta Distribution Family Function
binom2.rho

Bivariate Probit Model (Family Function)
alaplace

Asymmetric Laplace Distribution Family Functions
alaplaceUC

The Laplace Distribution
biplot-methods

Biplot of Constrained Regression Models
bisa

The Birnbaum-Saunders Distribution
calibrate.qrrvglm

Calibration for CQO and CAO models
acat

Ordinal Regression with Adjacent Categories Probabilities
AICvlm

Akaike's Information Criterion
AA.Aa.aa

The AA-Aa-aa Blood Group System
A1A2A3

The A1A2A3 Blood Group System
AR1EIM

Computation of the Exact EIM of an Order-1 Autoregressive Process
cao.control

Control Function for RR-VGAMs (CAO)
AR1

Autoregressive Process with Order-1 Family Function
chinese.nz

Chinese Population in New Zealand 1867--2001 Data
chisq

Chi-squared Distribution
cratio

Ordinal Regression with Continuation Ratios
Coef.rrvglm

Returns Important Matrices etc. of a RR-VGLM Object
Coef.rrvglm-class

Class ``Coef.rrvglm''
cumulative

Ordinal Regression with Cumulative Probabilities
double.cens.normal

Univariate Normal Distribution with Double Censoring
exppoisson

Exponential Poisson Distribution Family Function
double.expbinomial

Double Exponential Binomial Distribution Family Function
amlnormal

Asymmetric Least Squares Quantile Regression
amlpoisson

Poisson Regression by Asymmetric Maximum Likelihood Estimation
Betanorm

The Beta-Normal Distribution
betaprime

The Beta-Prime Distribution
BICvlm

Bayesian Information Criterion
bifgmcop

Farlie-Gumbel-Morgenstern's Bivariate Distribution Family Function
exppois

The Exponential Poisson Distribution
frechet

Frechet Distribution Family Function
formulavlm

Model Formulae and Term Names for VGLMs
gammahyperbola

Gamma Hyperbola Bivariate Distribution
gammaR

2-parameter Gamma Distribution
gengammaUC

The Generalized Gamma Distribution
genpoisson

Generalized Poisson distribution
grain.us

Grain Prices Data in USA
gpdUC

The Generalized Pareto Distribution
hunua

Hunua Ranges Data
betaR

The Two-parameter Beta Distribution Family Function
biamhcop

Ali-Mikhail-Haq Distribution Family Function
bifgmexp

Bivariate Farlie-Gumbel-Morgenstern Exponential Distribution Family Function
Binormcop

Gaussian Copula (Bivariate) Distribution
binormalcop

Gaussian Copula (Bivariate) Family Function
bmi.nz

Body Mass Index of New Zealand Adults Data
borel.tanner

Borel-Tanner Distribution Family Function
AB.Ab.aB.ab

The AB-Ab-aB-ab Blood Group System
ABO

The ABO Blood Group System
Benini

The Benini Distribution
betabinomial

Beta-binomial Distribution Family Function
bigumbelIexp

Gumbel's Type I Bivariate Distribution Family Function
bigamma.mckay

Bivariate Gamma: McKay's Distribution
binom2.or

Bivariate Binary Regression with an Odds Ratio
biplackettcop

Plackett's Bivariate Copula Family Function
Biplackett

Plackett's Bivariate Copula
cens.gumbel

Censored Gumbel Distribution
cauchit

Cauchit Link Function
Card

Cardioid Distribution
cens.normal

Censored Normal Distribution
Coef.vlm

Extract Model Coefficients for VLM Objects
coefvgam

Extract Model Coefficients of a vgam() Object
amlexponential

Exponential Regression by Asymmetric Maximum Likelihood Estimation
amlbinomial

Binomial Logistic Regression by Asymmetric Maximum Likelihood Estimation
concoef-methods

Constrained (Canonical) Coefficients
concoef

Extract Model Constrained/Canonical Coefficients
deplot.lmscreg

Density Plot for LMS Quantile Regression
deermice

Captures of Peromyscus maniculatus, also known as deer mice.
erf

Error Function, and variants
erlang

Erlang Distribution
Fisk

Fisk Distribution family function
fittedvlm

Fitted Values of a VLM object
gamma2

2-parameter Gamma Distribution
gamma1

1-parameter Gamma Distribution
corbet

Corbet's Butterfly Data
expint

The Exponential Integral and Variants
expgeom

The Exponential Geometric Distribution
crashes

Crashes on New Zealand Roads in 2009
fff

F Distribution Family Function
felix

Felix Distribution Family Function
flourbeetle

Mortality of Flour Beetles from Carbon Disulphide
foldnormal

Folded Normal Distribution Family Function
garma

GARMA (Generalized Autoregressive Moving-Average) Models
aux.posbernoulli.t

Auxiliary Function for the Positive Bernoulli Family Function with Time Effects
auuc

Auckland University Undergraduate Counts Data
get.smart.prediction

Retrieves ``.smart.prediction''
gev

Generalized Extreme Value Distribution Family Function
inv.lomax

The Inverse Lomax Distribution
inv.gaussianff

Inverse Gaussian Distribution Family Function
Huggins89.t1

Table 1 of Huggins (1989)
dhuber

Huber's Least Favourable Distribution
leukemia

Acute Myelogenous Leukemia Survival Data
lerch

Lerch Phi Function
lakeO

Annual catches on Lake Otamangakau from October 1974 to October 1989
lambertW

The Lambert W function
benini1

Benini Distribution Family Function
Benford

Benford's Distribution
hyperg

Hypergeometric Family Function
hypersecant

Hyperbolic Secant Distribution Family Function
laplace

Laplace Distribution
is.zero

Zero Constraint Matrices
hzeta

Haight's Zeta Family Function
kendall.tau

Kendall's Tau Statistic
loglinb2

Loglinear Model for Two Binary Responses
logLik.vlm

Extract Log-likelihood for VGLMs/VGAMs/etc.
laplaceUC

The Laplace Distribution
bistudentt

Bivariate Student-t Family Function
lomax

The Lomax Distribution
cardioid

Cardioid Distribution Family Function
cao

Fitting Constrained Additive Ordination (CAO)
clo

Redirects the User to rrvglm()
cloglog

Complementary Log-log Link Function
cdf.lmscreg

Cumulative Distribution Function for LMS Quantile Regression
cauchy

Cauchy Distribution Family Function
confintvglm

Confidence Intervals for VGLM Parameters
betageometric

Beta-geometric Distribution Family Function
dirichlet

Fitting a Dirichlet Distribution
constraints

Constraint Matrices
betaII

Beta Distribution of the Second Kind
biclaytoncop

Clayton Copula (Bivariate) Family Function
bilogistic

Bivariate Logistic Distribution Family Function
bilogis

Bivariate Logistic Distribution
bratt

Bradley Terry Model With Ties
brat

Inputting Data to fit a Bradley Terry Model
mix2poisson

Mixture of Two Poisson Distributions
mix2normal

Mixture of Two Univariate Normal Distributions
machinists

Machinists Accidents
lvplot.rrvglm

Latent Variable Plot for RR-VGLMs
nbcanlink

Negative Binomial Canonical Link Function
oipospoisson

One-inflated Positive Poisson Distribution Family Function
nbolf

Negative Binomial-Ordinal Link Function
Oipospois

One-Inflated Positive Poisson Distribution
ParetoIV

Pareto(IV/III/II) Distribution Family Functions
posnegbinomial

Positive Negative Binomial Distribution Family Function
rrvglm.control

Control Function for rrvglm()
rrvglm-class

Class ``rrvglm''
Posnegbin

Positive-Negative Binomial Distribution
undocumented-methods

Undocumented Methods Functions
ucberk

University California Berkeley Graduate Admissions
trplot.qrrvglm

Trajectory plot for QRR-VGLMs
trplot

Trajectory Plot
vsmooth.spline

Vector cubic smoothing spline
calibrate

Model Calibrations
cgo

Redirects the user to cqo
chest.nz

Chest Pain in NZ Adults Data
calibrate.qrrvglm.control

Control Function for CQO/CAO Calibration
coefvlm

Extract Model Coefficients
CommonVGAMffArguments

Common VGAM Family Function Arguments
dagum

Dagum Distribution Family Function
depvar

Response Variable Extracted
df.residual

Residual Degrees-of-Freedom
Expectiles-Uniform

Expectiles of the Uniform Distribution
Foldnorm

The Folded-Normal Distribution
finney44

Toxicity trial for insects
fill

Creates a Matrix of Appropriate Dimension
expexpff

Exponentiated Exponential Distribution
foldsqrt

Folded Square Root Link Function
freund61

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

Gaussian (Normal) Family Function
genrayleigh

Generalized Rayleigh Distribution Family Function
golf

Gamma-Ordinal Link Function
genray

The Generalized Rayleigh Distribution
guplot

Gumbel Plot
gompertz

Gompertz Distribution Family Function
identitylink

Identity Link Function
has.interceptvlm

Has a Fitted VGLM Got an Intercept Term?
inv.binomial

Inverse Binomial Distribution Family Function
leipnik

Leipnik Distribution Family Function
latvar

Latent Variables
log1mexp

Logarithms with an Unit Offset and Exponential Term
logit

Logit Link Function
logc

Complementary-log Link Function
normal.vcm

Univariate Normal Distribution as a Varying-Coefficient Model
lrtest

Likelihood Ratio Test of Nested Models
logitoffsetlink

Logit-with-an-Offset Link Function
lqnorm

Minimizing the L-q norm Family Function
notdocumentedyet

Undocumented and Internally Used Functions and Classes
gevUC

The Generalized Extreme Value Distribution
Pareto

The Pareto Distribution
gew

General Electric and Westinghouse Data
huber2

Huber's Least Favourable Distribution Family Function
hspider

Hunting Spider Data
gpd

Generalized Pareto Distribution Family Function
inv.paralogistic

Inverse Paralogistic Distribution Family Function
is.buggy

Does the fitted object suffer from a known bug?
waitakere

Waitakere Ranges Data
yulesimon

Yule-Simon Family Function
Zibinom

Zero-Inflated Binomial Distribution
zibinomial

Zero-Inflated Binomial Distribution Family Function
zabinomial

Zero-Altered Binomial Distribution
Frank

Frank's Bivariate Distribution
bifrankcop

Frank's Bivariate Distribution Family Function
binomialff

Binomial Family Function
binormal

Bivariate Normal Distribution Family Function
calibrate-methods

Calibration for Constrained Regression Models
lino

Generalized Beta Distribution Family Function
Max

Maximums
maxwell

The Maxwell Distribution
model.matrixvlm

Construct the Design Matrix of a VLM Object
moffset

Matrix Offset
negbinomial

Negative Binomial Distribution Family Function
negbinomial.size

Negative Binomial Distribution Family Function With Known Size
Opt

Optimums
plotdeplot.lmscreg

Density Plot for LMS Quantile Regression
ordpoisson

Ordinal Poisson Family Function
plotqrrvglm

Model Diagnostic Plots for QRR-VGLMs
poissonff

Poisson Family Function
polf

Poisson-Ordinal Link Function
powerlink

Power Link Function
prats

Pregnant Rats Toxological Experiment Data
Rayleigh

Rayleigh Distribution Family Function
rhobit

Rhobit Link Function
cfibrosis

Cystic Fibrosis Data
cens.poisson

Censored Poisson Family Function
coalminers

Breathlessness and Wheeze Amongst Coalminers Data
Coef

Computes Model Coefficients and Quantities
Expectiles-Exponential

Expectiles of the Exponential Distribution
ducklings

Relative Frequencies of Serum Proteins in White Pekin Ducklings
Expectiles-Normal

Expectiles of the Normal Distribution
enzyme

Enzyme Data
explog

The Exponential Logarithmic Distribution
exponential

Exponential Distribution
fisherz

Fisher's Z Link Function
genbetaII

Generalized Beta Distribution of the Second Kind
gengamma.stacy

Generalized Gamma distribution family function
gumbel

Gumbel Distribution Family Function
gumbelII

Gumbel-II Distribution Family Function
kumar

The Kumaraswamy Distribution
levy

Levy Distribution Family Function
lms.bcn

LMS Quantile Regression with a Box-Cox Transformation to Normality
lms.yjn

LMS Quantile Regression with a Yeo-Johnson Transformation to Normality
loglaplace

Log-Laplace and Logit-Laplace Distribution Family Functions
lvplot

Latent Variable Plot
loglapUC

The Log-Laplace Distribution
lvplot.qrrvglm

Latent Variable Plot for QO models
melbmaxtemp

Melbourne Daily Maximum Temperatures
mccullagh89

McCullagh (1989) Distribution Family Function
riceff

Rice Distribution Family Function
ruge

Rutherford-Geiger Polonium Data
seq2binomial

The Two-stage Sequential Binomial Distribution Family Function
s

Defining Smooths in VGAM Formulas
setup.smart

Smart Prediction Setup
tikuv

A Short-tailed Symmetric Distribution
triangle

Triangle Distribution Family Function
VGAM-package

Vector Generalized Linear and Additive Models
vgam.control

Control Function for vgam()
vglm

Fitting Vector Generalized Linear Models
vglm.control

Control Function for vglm()
zetaff

Zeta Distribution Family Function
zigeometric

Zero-Inflated Geometric Distribution Family Function
Zeta

The Zeta Distribution
Zigeom

Zero-Inflated Geometric Distribution
lgamma1

Log-gamma Distribution Family Function
lirat

Low-iron Rat Teratology Data
logff

Logarithmic Distribution
lms.bcg

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

Log Link Function with an Offset
logistic

Logistic Distribution Family Function
lognormal

Lognormal Distribution
Makeham

Makeham Distribution Family Function
meplot

Mean Excess Plot
micmen

Michaelis-Menten Model
oxtemp

Oxford Temperature Data
paralogistic

The Paralogistic Distribution
plotqtplot.lmscreg

Quantile Plot for LMS Quantile Regression
plotrcim0

Main Effects Plot for a Row-Column Interaction Model (RCIM)
Posgeom

Positive-Geometric Distribution
Posbinom

Positive-Binomial Distribution
prentice74

Prentice (1974) Log-gamma Distribution
prinia

Yellow-bellied Prinia
quasibinomialff

Quasi-Binomial Family Function
plotvgam.control

Control Function for plotvgam()
perks

The Perks Distribution
plotvgam

Default VGAM Plotting
predictqrrvglm

Predict Method for a CQO fit
posbernoulli.tb

Positive Bernoulli Family Function with Time and Behavioural Effects
posbinomial

Positive Binomial Distribution Family Function
predictvglm

Predict Method for a VGLM fit
qtplot.gumbel

Quantile Plot for Gumbel Regression
qtplot.lmscreg

Quantile Plot for LMS Quantile Regression
dirmul.old

Fitting a Dirichlet-Multinomial Distribution
expexpff1

Exponentiated Exponential Distribution
expgeometric

Exponential Geometric Distribution Family Function
explogff

Exponential Logarithmic Distribution Family Function
explink

Exponential Link Function
get.smart

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

Geometric (Truncated and Untruncated) Distributions
gumbelUC

The Gumbel Distribution
Gumbel-II

The Gumbel-II Distribution
hatvalues

Hat Values and Regression Deletion Diagnostics
hormone

Hormone Assay Data
is.parallel

Parallelism Constraint Matrices
iam

Index from Array to Matrix
lgammaUC

The Log-Gamma Distribution
is.smart

Test For a Smart Object
linkfun

Link Functions
lindley

1-parameter Gamma Distribution
linkfun.vglm

Link Functions for VGLMs
mix2exp

Mixture of Two Exponential Distributions
multilogit

Multi-logit Link Function
multinomial

Multinomial Logit Model
paretoff

Pareto and Truncated Pareto Distribution Family Functions
posbernoulli.b

Positive Bernoulli Family Function with Behavioural Effects
posbernoulli.t

Positive Bernoulli Family Function with Time Effects
perspqrrvglm

Perspective plot for QRR-VGLMs
rdiric

The Dirichlet distribution
rec.exp1

Upper Record Values from a 1-parameter Exponential Distribution
rrvglm

Fitting Reduced-Rank Vector Generalized Linear Models (RR-VGLMs)
rrvglm.optim.control

Control Function for rrvglm() Calling optim()
simplex

Simplex Distribution
tobit

The Tobit Distribution
SURff

Seemingly Unrelated Regressions Family Function
venice

Venice Maximum Sea Levels Data
vgam-class

Class ``vgam''
wine

Bitterness in Wine Data
Zageom

Zero-Altered Geometric Distribution
wrapup.smart

Cleans Up After Smart Prediction
zanegbinomial

Zero-Altered Negative Binomial Distribution
zoabetaR

Zero- and One-Inflated Beta Distribution Family Function
Zoabeta

The Zero/One-Inflated Beta Distribution
loge

Log Link Function, and Variants
logF

Natural Exponential Family Generalized Hyperbolic Secant Distribution Family Function
loglinb3

Loglinear Model for Three Binary Responses
loglog

Log-log Link Function
margeff

Marginal effects for several categorical response models
MNSs

The MNSs Blood Group System
marital.nz

New Zealand Marital Data
model.framevlm

Construct the Model Frame of a VLM Object
nakagami

Nakagami Distribution
SurvS4

Create a Survival Object
Pospois

Positive-Poisson Distribution
pospoisson

Positive Poisson Distribution Family Function
ps

Defining Penalized Spline Smooths in VGAM Formulas
put.smart

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

Number of Parameters
Oiposbinom

One-Inflated Positive Binomial Distribution
pgamma.deriv

Derivatives of the Incomplete Gamma Integral
pgamma.deriv.unscaled

Derivatives of the Incomplete Gamma Integral (Unscaled Version)
poisson.points

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

Probability Plots for Categorical Data Analysis
posnormal

Positive Normal Distribution Family Function
pneumo

Pneumoconiosis in Coalminers Data
Posnorm

The Positive-Normal Distribution
probit

Probit Link Function
propodds

Proportional Odds Model for Ordinal Regression
Rcim

Mark the Baseline of Row and Column on a Matrix data
qvar

Quasi-variances Preprocessing Function
rlplot.gevff

Return Level Plot for GEV Fits
rcqo

Constrained Quadratic Ordination
rrar

Nested reduced-rank autoregressive models for multiple time series
sinmad

The Singh-Maddala Distribution
studentt

Student t Distribution
Truncpareto

The Truncated Pareto Distribution
truncweibull

Truncated Weibull Distribution Family Function
V1

V1 Flying-Bombs Hits in London
vcovvlm

Calculate Variance-Covariance Matrix for a Fitted VLM or RR-VGLM Object
waldff

Wald Distribution Family Function
weibull.mean

Weibull Distribution Family Function, Parameterized by the Mean
summaryvglm

Summarizing Vector Generalized Linear Model Fits
quasipoissonff

Quasi-Poisson Family Function
rigff

Reciprocal Inverse Gaussian distribution
Rice

The Rice Distribution
sc.studentt2

Scaled Student t Distribution with 2 df Family Function
Expectiles-sc.t2

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

Control Function for QRR-VGLMs (CQO)
rec.normal

Upper Record Values from a Univariate Normal Distribution
reciprocal

Reciprocal Link Function
skellam

Skellam Distribution Family Function
skewnormal

Univariate Skew-Normal Distribution Family Function
smart.expression

S Expression for Smart Functions
weightsvglm

Prior and Working Weights of a VGLM fit
weibullR

Weibull Distribution Family Function
zinegbinomial

Zero-Inflated Negative Binomial Distribution Family Function
Zinegbin

Zero-Inflated Negative Binomial Distribution
slash

Slash Distribution
sratio

Ordinal Regression with Stopping Ratios
smartpred

Smart Prediction
toxop

Toxoplasmosis Data
UtilitiesVGAM

Utility Functions for the VGAM Package
Tol

Tolerances
smart.mode.is

Determine What Mode the Smart Prediction is In
vonmises

von Mises Distribution Family Function
vglmff-class

Class ``vglmff''
yeo.johnson

Yeo-Johnson Transformation
yip88

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

Zero-Altered Poisson Distribution
uninormal

Univariate Normal Distribution
zero

The zero Argument in VGAM Family Functions
zipoisson

Zero-Inflated Poisson Distribution Family Function
Zipois

Zero-Inflated Poisson Distribution
vgam

Fitting Vector Generalized Additive Models
zageometric

Zero-Altered Geometric Distribution
Zabinom

Zero-Altered Binomial Distribution
vglm-class

Class ``vglm''
Zanegbin

Zero-Altered Negative Binomial Distribution
zapoisson

Zero-Altered Poisson Distribution
zipf

Zipf Distribution Family Function
zipebcom

Exchangeable Bivariate cloglog Odds-ratio Model From a Zero-inflated Poisson Distribution