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VGAM (version 0.7-2)

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

42,195

Version

0.7-2

License

GPL version 2

Maintainer

Thomas Yee

Last Published

February 12th, 2025

Functions in VGAM (0.7-2)

AB.Ab.aB.ab

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

Beta-binomial Distribution Family Function
Coef.rrvglm

Returns Important Matrices etc. of a RR-VGLM Object
Opt

Maxima
betabin.ab

Beta-binomial Distribution Family Function
Sinmad

The Singh-Maddala Distribution
auuc

Auckland University Undergraduate Counts
ABO

The ABO Blood Group System
Lomax

The Lomax Distribution
AB.Ab.aB.ab2

The AB-Ab-aB-ab2 Blood Group System
brat

Bradley Terry Model
Coef.qrrvglm-class

Class ``Coef.qrrvglm''
betaff

The Two-parameter Beta Distribution Family Function
Betabin

The Beta-Binomial Distribution
cgumbel

Censored Gumbel Distribution
acat

Ordinal Regression with Adjacent Categories Probabilities
G1G2G3

The G1G2G3 Blood Group System
calibrate

Model Calibrations
genpoisson

Generalized Poisson distribution
ParetoIV

The Pareto(IV/III/II) Distributions
Tol

Tolerances
benini

Benini Distribution Family Function
gamma2.ab

2-parameter Gamma Distribution
cauchit

Cauchit Link Function
Coef

Computes Model Coefficients and Quantities
dcnormal1

Univariate Normal Distribution with Double Censoring
chisq

Chi-squared Distribution
biplot-methods

Biplot of Constrained Regression Models
cnormal1

Censored Normal Distribution
binomialff

Binomial Family Function
bilogis4

Bivariate Logistic Distribution
Links

Link functions for VGLM/VGAM/etc. families
fsqrt

Folded Square Root Link Function
betaII

Beta Distribution of the Second Kind
Rayleigh

The Rayleigh Distribution
calibrate-methods

Calibration for Constrained Regression Models
calibrate.qrrvglm.control

Control function for CQO/UQO/CAO calibration
Coef.vlm

Extract Model Coefficients for VLM Objects
Pareto

The Pareto Distribution
bminz

Body Mass Index of New Zealand Adults
cauchy1

Cauchy Distribution Family Function
Fisk

The Fisk Distribution
constraints

Constraint Matrices
AA.Aa.aa

The AA-Aa-aa Blood Group System
dagum

Dagum Distribution Family Function
gammahyp

Gamma Hyperbola Bivariate Distribution
binom2.rho

Bivariate Probit Model
cumulative

Ordinal Regression with Cumulative Probabilities
fisherz

Fisher's Z Link Function
Zeta

The Zeta Distribution
iam

Index from Array to Matrix
fgm

Farlie-Gumbel-Morgenstern's Bivariate Distribution Family Function
gamma1

1-parameter Gamma Distribution
fitted.vlm

Fitted Values of a VLM object
lgammaff

Log-gamma Distribution Family Function
Invlomax

The Inverse Lomax Distribution
Frechet

The Frechet Distribution
ccoef

Extract Model Constrained/Canonical Coefficients
dirmul.old

Fitting a Dirichlet-Multinomial Distribution
guplot

Gumbel Plot
leipnik

Leipnik Distribution Family Function
genbetaII

Generalized Beta Distribution of the Second Kind
invparalogistic

Inverse Paralogistic Distribution Family Function
cgo

Redirects the user to cqo
binom2.or

Bivariate Logistic Regression
betaprime

The Beta-Prime Distribution
Coef.rrvglm-class

Class ``Coef.rrvglm''
Maxwell

The Maxwell Distribution
Paralogistic

The Paralogistic Distribution
Max

Maxima
Coef.qrrvglm

Returns Important Matrices etc. of a QO Object
bratt

Bradley Terry Model With Ties
Inv.gaussian

The Inverse Gaussian Distribution
cao

Fitting Constrained Additive Ordination (CAO)
bilogistic4

Bivariate Logistic Distribution Family Function
cao.control

Control Function for RR-VGAMs (CAO)
Betageom

The Beta-Geometric Distribution
clo

Redirects the user to rrvglm
betageometric

Beta-geometric Distribution Family Function
chest

Chest Pain in NZ Adults
ccoef-methods

Constrained (Canonical) Coefficients
erlang

Erlang Distribution
cratio

Ordinal Regression with Continuation Ratios
coalminers

Breathlessness and Wheeze Amongst Coalminers
fff

F Distribution Family Function
gumbelUC

The Gumbel Distribution
expexp1

Exponentiated Exponential Distribution
hspider

Hunting Spider Data
cqo

Fitting Constrained Quadratic Ordination (CQO)
erf

Error Function
ggamma

Generalized Gamma distribution family function
lms.yjn

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

The Generalized Extreme Value Distribution
Log

Logarithmic Distribution
model.matrixvlm

Construct the Design Matrix of a VLM Object
fill

Creates a Matrix of Appropriate Dimension
logff

Logarithmic Distribution
frank

Frank's Bivariate Distribution Family Function
hzeta

Haight's Zeta Family Function
logoff

Log link function with an offset
negbinomial

Negative Binomial Distribution Family Function
get.smart

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

Complementary-log Link Function
lgammaUC

The Log-Gamma Distribution
golf

Gamma-Ordinal Link Function
pareto1

Pareto and Truncated Pareto Distribution Family Functions
gaussianff

Gaussian (normal) Family Function
ggammaUC

The Generalized Gamma Distribution
gumbelIbiv

Gumbel's Type I Bivariate Distribution Family Function
gamma2

2-parameter Gamma Distribution
meplot

Mean Excess Plot
gew

General Electric and Westinghouse Data
cloglog

Complementary Log-log Link Function
grc

Fitting Goodman's RC Association Model
model.framevlm

Construct the Model Frame of a VLM Object
freund61

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

Latent Variable Plot
Posbinom

Positive-Binomial Distribution
Polono

The Poisson Lognormal Distribution
normal1

Univariate normal distribution
plotdeplot.lmscreg

Density Plot for LMS Quantile Regression
mix2normal1

Mixture of Two Univariate Normal Distributions
gev

Generalized Extreme Value Distribution Family Function
qrrvglm.control

Control function for QRR-VGLMs (CQO)
gumbel

Gumbel Distribution Family Function
deplot.lmscreg

Density Plot for LMS Quantile Regression
gpdUC

The Generalized Pareto Distribution
rcqo

Constrained Quadratic Ordination
posnegbinomial

Positive Negative Binomial Distribution Family Function
cdf.lmscreg

Cumulative Distribution Function for LMS Quantile Regression
Bisa

The Birnbaum-Saunders Distribution
is.smart

Test For a Smart Object
identity

Identity Link Function
enzyme

Enzyme data
Pospois

Positive-Poisson Distribution
recnormal1

Upper Record Values from a Univariate Normal Distribution
rig

Reciprocal Inverse Gaussian distribution
geometric

Geometric Distribution
rrvglm.optim.control

Control function for rrvglm() calling optim()
poissonff

Poisson Family Function
plotqtplot.lmscreg

Quantile Plot for LMS Quantile Regression
morgenstern

Morgenstern's Bivariate Distribution Family Function
exponential

Exponential Distribution
levy

Levy Distribution Family Function
gpd

Generalized Pareto Distribution Family Function
rrvglm.control

Control function for rrvglm
nakagami

Nakagami Distribution Family Function
sratio

Ordinal Regression with Stopping Ratios
loglinb3

Loglinear Model for Three Binary Responses
hypersecant

Hyperbolic Secant Distribution Family Function
hyperg

Hypergeometric Family Function
laplaceUC

The Laplace Distribution
mix2poisson

Mixture of Two Poisson Distributions
notdocumentedyet

Undocumented and Internally Used Functions and Classes
nbolf

Negative Binomial-Ordinal Link Function
lms.bcg

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

Log link function
lino

Generalized Beta Distribution Family Function
loglog

Log-log Link Function
inv.gaussianff

Inverse Gaussian Distribution Family Function
loglinb2

Loglinear Model for Two Binary Responses
logit

Logit Link Function
lvplot.qrrvglm

Latent Variable Plot for QO models
mccullagh89

McCullagh (1989) Distribution Family Function
Tikuv

A Short-tailed Symmetric Distribution
quasibinomialff

Quasi-Binomial Family Function
logistic

Logistic Distribution Family Function
ordpoisson

Ordinal Poisson Family Function
plotvgam

Default VGAM Plotting
Posnorm

The Positive-Normal Distribution
lognormal

Lognormal Distribution
plotqrrvglm

Model Diagnostic Plots for QRR-VGLMs
rdiric

The Dirichlet distribution
smart.expression

S Expression for Smart Functions
micmen

Michaelis-Menten Model
quasipoissonff

Quasi-Poisson Family Function
vglm

Fitting Vector Generalized Linear Models
wald

Wald Distribution Family Function
qtplot.gumbel

Quantile Plot for Gumbel Regression
polf

Poisson-Ordinal Link Function
prentice74

Prentice (1974) Log-gamma Distribution
rrvglm

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

Return Level Plot for GEV Fits
posbinomial

Positive Binomial Distribution Family Function
vglm-class

Class ``vglm''
posnormal1

Positive Normal Distribution Family Function
vgam-class

Class ``vgam''
persp.qrrvglm

Perspective plot for QRR-VGLMs
pospoisson

Positive Poisson Distribution Family Function
vglm.control

Control function for vglm
vglmff-class

Class ``vglmff''
lerch

Lerch Phi Function
vgam.control

Control function for vgam
rrvglm-class

Class ``rrvglm''
Tpareto

The Truncated Pareto Distribution
weibull

Weibull Distribution Family Function
trplot.qrrvglm

Trajectory plot for QRR-VGLMs
recexp1

Upper Record Values from a 1-parameter Exponential Distribution
put.smart

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

Smart Prediction Setup
venice

Venice Maximum Sea Levels
snorm

Skew-Normal Distribution
multinomial

Multinomial Logit Model
lvplot.rrvglm

Latent Variable Plot for RR-VGLMs
nzc

Chinese Population in New Zealand 1867--2001
plotvgam.control

Control Function for plotvgam()
vsmooth.spline

Vector cubic smoothing spline
qtplot.lmscreg

Quantile Plot for LMS Quantile Regression
zipoisson

Zero-Inflated Poisson Distribution Family Function
trplot

Trajectory Plot
weightsvglm

Prior and Working Weights of a VGLM fit
rrar

Nested reduced-rank autoregressive models for multiple time series
mckaygamma2

McKay's Bivariate Gamma Distribution
vonmises

von Mises Distribution Family Function
rposnegbin

Positive-negative binomial distribution random variates
smart.mode.is

Determine What Mode the Smart Prediction is In
skewnormal1

Univariate Skew-Normal Distribution Family Function
oxtemp

Oxford Temperature Data
zetaff

Zeta Distribution Family Function
probit

Probit Link Function
studentt

Student t Distribution
Zibinom

Zero-Inflated Binomial Distribution
simplex

Simplex distribution
tobit

Tobit Model
smartpred

Smart Prediction
zapoisson

Zero-Altered Poisson Distribution
zibinomial

Zero-Inflated Binomial Distribution Family Function
vgam

Fitting Vector Generalized Additive Models
yip88

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

Fitting Unconstrained Quadratic Ordination (UQO)
zero

The zero Argument in VGAM Family Functions
uqo.control

Control Function for UQO models
undocumented-methods

Undocumented Methods Functions
zanegbinomial

Zero-Altered Negative Binomial Distribution
Zipois

Zero-Inflated Poisson Distribution
wrapup.smart

Cleans Up After Smart Prediction
yeo.johnson

Yeo-Johnson Transformation
MNSs

The MNSs Blood Group System
Betanorm

The Beta-Normal Distribution
calibrate.qrrvglm

Calibration for CQO, UQO and CAO models
cexpon

Censored Exponential Distribution
dirichlet

Fitting a Dirichlet Distribution
dirmultinomial

Fitting a Dirichlet-Multinomial Distribution
expexp

Exponentiated Exponential Distribution
garma

GARMA (Generalized Autoregressive Moving-Average) Models
get.smart.prediction

Retrieves ``.smart.prediction''
lms.bcn

LMS Quantile Regression with a Box-Cox Transformation to Normality
lirat

Low-iron Rat Teratology Data
lv

Latent Variables
predict.vglm

Predict Method for a VGLM fit
powl

Power Link Function
reciprocal

Reciprocal link function
rhobit

Rhobit Link Function
s

Defining smooths in VGAM formulae
Zipf

The Zipf Distribution
pneumo

Pneumoconiosis amongst a group of coalminers
hunua

Hunua Ranges data
usagrain

USA grain prices
ruge

Rutherford-Geiger polonium data
waitakere

Waitakere Ranges data