Mixed-Effect Models, Particularly Spatial Models

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Documentation for package ‘spaMM’ version 2.4.8

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A B C D E F G H I L M N O P R S T U V W

spaMM-package Inference in mixed models, in particular spatial GLMMs

-- A --

adjacency Fitting autoregressive models
AIC Functions to extract various components of a fit
AIC.HLfit Functions to extract various components of a fit
anova Likelihood ratio test of fixed effects.
anova.HLfit Likelihood ratio test of fixed effects.
AR1 Fitting autoregressive models
arabidopsis Arabidopsis genetic and climatic data
autoregressive Fitting autoregressive models

-- B --

Beta-distribution-random-effects Fit mixed models with given correlation matrix
binomialize Analyzing multinomial data
blackcap Genetic polymorphism in relation to migration in the blackcap

-- C --

CAR Fitting autoregressive models
Cauchy Cauchy correlation function and Cauchy formula term
CauchyCorr Cauchy correlation function and Cauchy formula term
coef.corMatern Matern Correlation Structure as a corSpatial object
coef<-.corMatern Matern Correlation Structure as a corSpatial object
COMPoisson Conway-Maxwell-Poisson (COM-Poisson) GLM family
confint Confidence intervals for fixed-effect parameters
confint.HLfit Confidence intervals for fixed-effect parameters
corFactor.corMatern Matern Correlation Structure as a corSpatial object
corMatern Matern Correlation Structure as a corSpatial object
corMatrix.corMatern Matern Correlation Structure as a corSpatial object
Corr Functions to extract various components of a fit
corrHLfit Fits a mixed model, typically a spatial GLMM.
corrMatrix Using a corrMatrix argument
covStruct Specifying correlation structures

-- D --

designL.from.Corr Computation of "square root" of correlation matrix
deviance Functions to extract various components of a fit
deviance.HLfit Functions to extract various components of a fit
dev_resids Functions to extract various components of a fit

-- E --

Earth Scaled distances between unique locations
etaFix Fixing some parameters
extractors Functions to extract various components of a fit

-- F --

filled.mapMM Colorful plots of predicted responses in two-dimensional space.
fitme Fitting function for fixed- and mixed-effect models with GLM response.
fitted Functions to extract various components of a fit
fitted.HLfit Functions to extract various components of a fit
fitted.HLfitlist Analyzing multinomial data
fixed Fixing some parameters
fixedLRT Likelihood ratio test of fixed effects.
fixef Functions to extract various components of a fit
fixef.HLfit Functions to extract various components of a fit
freight Freight dataset

-- G --

Gamma Distribution families for Gamma and inverse Gamma-distributed random effects
geometric Conway-Maxwell-Poisson (COM-Poisson) GLM family
getCovariate.corMatern Matern Correlation Structure as a corSpatial object
getDistMat Functions to extract various components of a fit
get_any_IC Functions to extract various components of a fit
get_boot_response Functions to extract various components of a fit
get_fixefVar Prediction from a model fit.
get_intervals Prediction from a model fit.
get_predCov_var_fix Prediction from a model fit.
get_predVar Prediction from a model fit.
get_rankinfo Checking the rank of the fixed-effects design matrix
get_residVar Prediction from a model fit.
get_respVar Prediction from a model fit.
get_RLRTSim_args Functions to extract various components of a fit
get_ZALMatrix Functions to extract various components of a fit
good-practice Clear and trustworthy formulas

-- H --

HLCor Fits a (spatially) correlated mixed model, for given correlation parameters
HLfit Fit mixed models with given correlation matrix

-- I --

Initialize.corMatern Matern Correlation Structure as a corSpatial object
intervals Prediction from a model fit.
inverse.Gamma Distribution families for Gamma and inverse Gamma-distributed random effects

-- L --

landMask Masks of seas or lands
LevenbergM spaMM options settings
Loaloa Loa loa prevalence in North Cameroon, 1991-2001
logDet.corMatern Matern Correlation Structure as a corSpatial object
logLik Functions to extract various components of a fit
logLik.HLfit Functions to extract various components of a fit
logLik.HLfitlist Analyzing multinomial data
LRT Likelihood ratio test of fixed effects.

-- M --

make_scaled_dist Scaled distances between unique locations
mapMM Colorful plots of predicted responses in two-dimensional space.
Matern Matern correlation function and Matern formula term.
MaternCorr Matern correlation function and Matern formula term.
MaternCorr.default Matern correlation function and Matern formula term.
multi Analyzing multinomial data
multinomial Analyzing multinomial data

-- N --

negbin Family function for GLMs and mixed models with negative binomial and zero-truncated negative binomial response.
Nmatrix Lip cancer in Scotland 1975 - 1980

-- O --

oceanmask Masks of seas or lands

-- P --

pedigree Fit mixed-effects models incorporating pedigrees
phiHGLM Fitting random effects in the residual dispersion model
plot Model checking plots for mixed models
plot.HLfit Model checking plots for mixed models
Poisson Family function for GLMs and mixed models with Poisson and zero-truncated Poisson response.
predict Prediction from a model fit.
predict.HLfit Prediction from a model fit.
Predictor Interface for model formulas
preprocess_fix_corr Prediction from a model fit.
print Summary and print methods for fit and test results.
print.fixedLRT Summary and print methods for fit and test results.
print.HLfit Summary and print methods for fit and test results.
print.HLfitlist Summary and print methods for fit and test results.
print.ranef Functions to extract various components of a fit

-- R --

ranCoefs Fixing some parameters
ranef Functions to extract various components of a fit
ranef.HLfit Functions to extract various components of a fit
ranFix Fixing some parameters
rankinfo Checking the rank of the fixed-effects design matrix
ranPars Fixing some parameters
recalc.corMatern Matern Correlation Structure as a corSpatial object
residuals Functions to extract various components of a fit
residuals.HLfit Functions to extract various components of a fit
rho.mapping Scaled distances between unique locations

-- S --

salamander Salamander mating data
scotlip Lip cancer in Scotland 1975 - 1980
seaMask Masks of seas or lands
seeds Seed germination data
separation Checking separation in binomial-response models
simulate Simulate realizations of a fitted model.
simulate.HLfit Simulate realizations of a fitted model.
simulate.HLfitlist Simulate realizations of a fitted model.
spaMM Inference in mixed models, in particular spatial GLMMs
spaMM-conventions spaMM conventions and differences from related fitting procedures
spaMM.colors A flashy color palette.
spaMM.filled.contour Level (Contour) Plots with better aspect ratio control (for geographical maps, at least)
spaMM.getOption spaMM options settings
spaMM.options spaMM options settings
spaMMplot2D Colorful plots of predicted responses in two-dimensional space.
spaMM_boot Parametric bootstrap
spaMM_glm Fitting generalized linear models without initial-value or divergence headaches
spaMM_glm.fit Fitting generalized linear models without initial-value or divergence headaches
sparse_precision Sparse_precision algorithm
stripHLfit Reduce the size of fitted objects
summary Summary and print methods for fit and test results.
summary.fixedLRT Summary and print methods for fit and test results.
summary.HLfit Summary and print methods for fit and test results.
summary.HLfitlist Summary and print methods for fit and test results.
sym_eigen Singular Value Decomposition of a Symmetric Matrix

-- T --

Tnegbin Family function for GLMs and mixed models with negative binomial and zero-truncated negative binomial response.
Tpoisson Family function for GLMs and mixed models with Poisson and zero-truncated Poisson response.

-- U --

update Updates an HLCor or HLfit fit
update.HLfit Updates an HLCor or HLfit fit

-- V --

Variogram.corMatern Matern Correlation Structure as a corSpatial object
vcov Functions to extract various components of a fit
vcov.HLfit Functions to extract various components of a fit

-- W --

wafers Data from a resistivity experiment for semiconductor materials.
welding Welding data set
worldcountries Masks of seas or lands