Index: AA.Aa.aa The AA-Aa-aa Blood Group System AB.Ab.aB.ab The AB-Ab-aB-ab Blood Group System AB.Ab.aB.ab2 The AB-Ab-aB-ab2 Blood Group System ABO The ABO Blood Group System Benini The Benini Distribution Betabin The Beta-Binomial Distribution Betageom The Beta-Geometric Distribution Betanorm The Beta-Normal Distribution Bisa The Birnbaum-Saunders Distribution Brat Inputting Data to fit a Bradley Terry Model Coef Computes Model Coefficients and Quantities Coef.qrrvglm Returns Important Matrices etc. of a QO Object Coef.qrrvglm-class Class "Coef.qrrvglm" Coef.rrvglm Returns Important Matrices etc. of a RR-VGLM Object Coef.rrvglm-class Class "Coef.rrvglm" Coef.vlm Extract Model Coefficients for VLM Objects Dagum The Dagum Distribution Fisk The Fisk Distribution Frank Frank's Bivariate Distribution Frechet The Frechet Distribution G1G2G3 The G1G2G3 Blood Group System Hzeta Haight's Zeta Function Inv.gaussian The Inverse Gaussian Distribution Invlomax The Inverse Lomax Distribution Invparalogistic The Inverse Paralogistic Distribution Links Link functions for VGLM/VGAM/etc. families Lino The Generalized Beta Distribution (Libby and Novick, 1982) Log Logarithmic Distribution Lomax The Lomax Distribution MNSs The MNSs Blood Group System Max Maxima Maxwell The Maxwell Distribution Nakagami Nakagami Distribution Opt Maxima Paralogistic The Paralogistic Distribution Pareto The Pareto Distribution ParetoIV The Pareto(IV/III/II) Distributions Polono The Poisson Lognormal Distribution Posbinom Positive-Binomial Distribution Posnorm The Positive-Normal Distribution Pospois Positive-Poisson Distribution Rayleigh The Rayleigh Distribution Sinmad The Singh-Maddala Distribution Tikuv A Short-tailed Symmetric Distribution Tol Tolerances Tpareto The Truncated Pareto Distribution Zeta The Zeta Distribution Zibinom Zero-Inflated Binomial Distribution Zipf The Zipf Distribution Zipois Zero-Inflated Poisson Distribution acat Ordinal Regression with Adjacent Categories Probabilities auuc Auckland University Undergraduate Counts benini Benini Distribution Family Function betaII Beta Distribution of the Second Kind betabin.ab Beta-binomial Distribution Family Function betabinomial Beta-binomial Distribution Family Function betaff The Two-parameter Beta Distribution Family Function betageometric Beta-geometric Distribution Family Function betaprime The Beta-Prime Distribution bilogis4 Bivariate Logistic Distribution bilogistic4 Bivariate Logistic Distribution Family Function binom2.or Bivariate Logistic Regression binom2.rho Bivariate Probit Model binomialff Binomial Family Function bisa Birnbaum-Saunders Distribution Family Function bminz Body Mass Index of New Zealand Adults brat Bradley Terry Model bratt Bradley Terry Model With Ties calibrate Model Calibrations calibrate.qrrvglm Calibration for CQO, UQO and CAO models calibrate.qrrvglm.control Control function for CQO/UQO/CAO calibration cao Fitting Constrained Additive Ordination (CAO) cao.control Control Function for RR-VGAMs (CAO) cauchit Cauchit Link Function cauchy1 Cauchy Distribution Family Function ccoef Extract Model Constrained/Canonical Coefficients cdf.lmscreg Cumulative Distribution Function for LMS Quantile Regression cexpon Censored Exponential Distribution cgo Redirects the user to cqo cgumbel Censored Gumbel Distribution chest Chest Pain in NZ Adults chisq Chi-squared Distribution clo Redirects the user to rrvglm cloglog Complementary Log-log Link Function cnormal1 Censored Normal Distribution coalminers Breathlessness and Wheeze Amongst Coalminers constraints Constraint Matrices cqo Fitting Constrained Quadratic Ordination (CQO) cratio Ordinal Regression with Continuation Ratios cumulative Ordinal Regression with Cumulative Probabilities dagum Dagum Distribution Family Function dcnormal1 Univariate Normal Distribution with Double Censoring deplot.lmscreg Density Plot for LMS Quantile Regression dgumbel The Gumbel Distribution dirichlet Fitting a Dirichlet Distribution dirmul.old Fitting a Dirichlet-Multinomial Distribution dirmultinomial Fitting a Dirichlet-Multinomial Distribution dlaplace The Laplace Distribution enzyme Enzyme data erf Error Function erlang Erlang Distribution expexp Exponentiated Exponential Distribution expexp1 Exponentiated Exponential Distribution exponential Exponential Distribution fff F Distribution Family Function fill Creates a Matrix of Appropriate Dimension fisherz Fisher's Z Link Function fisk Fisk Distribution family function fitted.vlm Fitted Values of a VLM object frank Frank's Bivariate Distribution Family Function frechet2 Frechet Distribution Family Function freund61 Freund's (1961) Bivariate Extension of the Exponential Distribution gamma1 1-parameter Gamma Distribution gamma2 2-parameter Gamma Distribution gamma2.ab 2-parameter Gamma Distribution gammahyp Gamma Hyperbola Bivariate Distribution garma GARMA (Generalized Autoregressive Moving-Average) Models gaussianff Gaussian (normal) Family Function genbetaII Generalized Beta Distribution of the Second Kind genpoisson Generalized Poisson distribution geometric Geometric Distribution get.smart Retrieve One Component of ".smart.prediction" get.smart.prediction Retrieves ".smart.prediction" gev Generalized Extreme Value Distribution Family Function gevUC The Generalized Extreme Value Distribution gew General Electric and Westinghouse Data ggamma Generalized Gamma distribution family function ggammaUC The Generalized Gamma Distribution golf Gamma-Ordinal Link Function gpd Generalized Pareto Distribution Family Function gpdUC The Generalized Pareto Distribution grc Fitting Goodman's RC Association Model gumbel Gumbel Distribution Family Function guplot Gumbel Plot hspider Hunting Spider Data hunua Hunua Ranges data hyper Hypergeometric Family Function hzeta Haight's Zeta Family Function iam Index from Array to Matrix identity Identity Link Function inv.gaussianff Inverse Gaussian Distribution Family Function invlomax Inverse Lomax Distribution Family Function invparalogistic Inverse Paralogistic Distribution Family Function is.smart Test For a Smart Object leipnik Leipnik Distribution Family Function lerch Lerch Phi Function levy Levy Distribution Family Function lgammaUC The Log-Gamma Distribution lgammaff Log-gamma Distribution Family Function lino Generalized Beta Distribution Family Function lirat Low-iron Rat Teratology Data lms.bcg LMS Quantile Regression with a Box-Cox transformation to a Gamma Distribution lms.bcn LMS Quantile Regression with a Box-Cox Transformation to Normality lms.yjn LMS Quantile Regression with a Yeo-Johnson Transformation to Normality logc Complementary-log Link Function loge Log link function logff Logarithmic Distribution logistic Logistic Distribution Family Function logit Logit Link Function loglinb2 Loglinear Model for Two Binary Responses loglinb3 Loglinear Model for Three Binary Responses loglog Log-log Link Function lognormal Lognormal Distribution logoff Log link function with an offset lomax Lomax Distribution Family Function lv Latent Variables lvplot Latent Variable Plot lvplot.qrrvglm Latent Variable Plot for QO models lvplot.rrvglm Latent Variable Plot for RR-VGLMs maxwell Maxwell Distribution Family Function mccullagh89 McCullagh (1989) Distribution Family Function mckaygamma2 McKay's Bivariate Gamma Distribution meplot Mean Excess Plot micmen Michaelis-Menten Model mix2normal1 Mixture of Two Univariate Normal Distributions mix2poisson Mixture of Two Poisson Distributions model.framevlm Construct the Model Frame of a VLM Object model.matrixvlm Construct the Design Matrix of a VLM Object multinomial Multinomial Logit Model nakagami Nakagami Distribution Family Function nbolf Negative Binomial-Ordinal Link Function negbinomial Negative Binomial Distribution Family Function normal1 Univariate normal distribution notdocumentedyet Undocumented and Internally Used Functions and Classes nzc Chinese Population in New Zealand 1867-2001 oxtemp Oxford Temperature Data paralogistic Paralogistic Distribution Family Function pareto1 Pareto and Truncated Pareto Distribution Family Functions paretoIV Pareto(IV/III/II) Distribution Family Functions persp.qrrvglm Perspective plot for QRR-VGLMs plotdeplot.lmscreg Density Plot for LMS Quantile Regression plotqrrvglm Model Diagnostic Plots for QRR-VGLMs plotqtplot.lmscreg Quantile Plot for LMS Quantile Regression plotvgam Default VGAM Plotting plotvgam.control Control Function for plotvgam() pneumo Pneumoconiosis amongst a group of coalminers poissonff Poisson Family Function polf Poisson-Ordinal Link Function posbinomial Positive Binomial Distribution Family Function posnegbinomial Positive Negative Binomial Distribution Family Function posnormal1 Positive Normal Distribution Family Function pospoisson Positive Poisson Distribution Family Function predict.vglm Predict Method for a VGLM fit prentice74 Prentice (1974) Log-gamma Distribution probit Probit Link Function put.smart Adds a List to the End of the List ".smart.prediction" qrrvglm.control Control function for QRR-VGLMs (CQO) qtplot.gumbel Quantile Plot for Gumbel Regression qtplot.lmscreg Quantile Plot for LMS Quantile Regression quasibinomialff Quasi-Binomial Family Function quasipoissonff Quasi-Poisson Family Function rayleigh Rayleigh Distribution Family Function rcqo Constrained Quadratic Ordination rdiric The Dirichlet distribution recexp1 Upper Record Values from a 1-parameter Exponential Distribution reciprocal Reciprocal link function recnormal1 Upper Record Values from a Univariate Normal Distribution rhobit Rhobit Link Function rig Reciprocal Inverse Gaussian distribution rlplot.egev Return Level Plot for GEV Fits rposnegbin Positive-negative binomial distribution random variates rrar Nested reduced-rank autoregressive models for multiple time series rrvglm Fitting Reduced-Rank Vector Generalized Linear Models (RR-VGLMs) rrvglm-class Class "rrvglm" rrvglm.control Control function for rrvglm rrvglm.optim.control Control function for rrvglm() calling optim() s Defining smooths in VGAM formulae setup.smart Smart Prediction Setup simplex Simplex distribution sinmad Singh-Maddala Distribution Family Function skewnormal1 Univariate Skew-Normal Distribution Family Function smart.expression S Expression for Smart Functions smart.mode.is Determine What Mode the Smart Prediction is In smartpred Smart Prediction snorm Skew-Normal Distribution sratio Ordinal Regression with Stopping Ratios studentt Student t Distribution tikuv Short-tailed Symmetric Distribution Family Function tobit Tobit Model trplot Trajectory Plot trplot.qrrvglm Trajectory plot for QRR-VGLMs uqo Fitting Unconstrained Quadratic Ordination (UQO) uqo.control Control Function for UQO models usagrain USA grain prices venice Venice Maximum Sea Levels vgam Fitting Vector Generalized Additive Models vgam-class Class "vgam" vgam.control Control function for vgam vglm Fitting Vector Generalized Linear Models vglm-class Class "vglm" vglm.control Control function for vglm vglmff-class Class "vglmff" vonmises von Mises Distribution Family Function vsmooth.spline Vector cubic smoothing spline waitakere Waitakere Ranges data wald Wald Distribution Family Function weibull Weibull Distribution Family Function weightsvglm Prior and Working Weights of a VGLM fit wrapup.smart Cleans Up After Smart Prediction yeo.johnson Yeo-Johnson Transformation yip88 Zero-Inflated Poisson Distribution (Yip (1988) algorithm) zanegbinomial Zero-Altered Negative Binomial Distribution zapoisson Zero-Altered Poisson Distribution zero The zero Argument in VGAM Family Functions zeta Riemann's Zeta Function zetaff Zeta Distribution Family Function zibinomial Zero-Inflated Binomial Distribution Family Function zipf Zipf Distribution Family Function zipoisson Zero-Inflated Poisson Distribution Family Function
Yee, T. W. and Wild, C. J. (1996) Vector generalized additive models. Journal of the Royal Statistical Society, Series B, Methodological, 58, 481--493.
Yee, T. W. (2004) A new technique for maximum-likelihood canonical Gaussian ordination. Ecological Monographs, 74, 685--701.
Yee, T. W. (2006) Constrained additive ordination. Ecology, 87, 203--213.
# Fit the proportional odds model, p.179, in McCullagh and Nelder (1989)
data(pneumo)
pneumo = transform(pneumo, let=log(exposure.time))
(fit = vglm(cbind(normal, mild, severe) ~ let,
cumulative(parallel=TRUE, reverse=TRUE), pneumo))
fit@y # Sample proportions
weights(fit, type="prior") # Number of observations
coef(fit, matrix=TRUE)
constraints(fit) # Constraint matrices
# Fit a two species GAM simultaneously
data(hunua)
fit2 = vgam(cbind(agaaus, kniexc) ~ s(altitude),
fam = binomialff(mv=TRUE), hunua)
coef(fit2, mat=TRUE) # Not really interpretable
plot(fit2, se=TRUE, overlay=TRUE, lcol=1:2, scol=1:2)
attach(hunua)
o = order(altitude)
matplot(altitude[o], fitted(fit2)[o,], type="l", lwd=2, las=1,
xlab="Altitude (m)", ylab="Probability of presence",
main="Two plant species' response curves", ylim=c(0,.8))
rug(altitude)
detach(hunua)
# LMS quantile regression
data(bminz)
fit = vgam(BMI ~ s(age, df=c(4,2)), fam=lms.bcn(zero=1), data=bminz, tr=TRUE)
predict(fit)[1:3,]
fitted(fit)[1:3,]
bminz[1:3,]
# Person 1 is near the lower quartile of BMI amongst people his age
cdf(fit)[1:3]
# Quantile plot
par(bty="l", mar=c(5,4,4,3)+0.1, xpd=TRUE)
qtplot(fit, percentiles=c(5,50,90,99), main="Quantiles",
xlim=c(15,90), las=1, ylab="BMI", lwd=2, lcol=4)
# Density plot
ygrid = seq(15, 43, len=100) # BMI ranges
par(mfrow=c(1,1), lwd=2)
a = deplot(fit, x0=20, y=ygrid, xlab="BMI", col="black",
main="Density functions at Age = 20 (black), 42 (red) and 55 (blue)")
a
a = deplot(fit, x0=42, y=ygrid, add=TRUE, llty=2, col="red")
a = deplot(fit, x0=55, y=ygrid, add=TRUE, llty=4, col="blue", Attach=TRUE)
a@post$deplot # Contains density function values
# GEV distribution for extremes
data(oxtemp)
(fit = vglm(maxtemp ~ 1, egev, data=oxtemp, trace=TRUE))
fitted(fit)[1:3,]
coef(fit, mat=TRUE)
Coef(fit)
vcov(fit)
vcov(fit, untransform=TRUE)
sqrt(diag(vcov(fit))) # Approximate standard errors
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