Mixed-Effect Models, Particularly Spatial Models

[Up] [Top]

Documentation for package ‘spaMM’ version 2.7.1

Help Pages

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

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

-- A --

adjacency Fitting autoregressive models
adjlg Simulated data set for testing sparse-precision code
adjlgMat Simulated data set for testing sparse-precision code
AIC Extractors for informations criteria such as AIC
AIC.HLfit Extractors for informations criteria such as AIC
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
as_precision Specifying correlation structures
autoregressive Fitting autoregressive models

-- B --

Beta Fit mixed models with given correlation matrix
Beta-distribution-random-effects Fit mixed models with given correlation matrix
beta_table Extract covariance or correlation matrices from a fitted model object
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
class:missingOrNULL ZAXlist class and (cross) products for ZAL matrix
class:ZAXlist ZAXlist class and (cross) products for ZAL matrix
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 Extract covariance or correlation matrices from a fitted model object
corrHLfit Fits a mixed model, typically a spatial GLMM.
corrMatrix Using a corrMatrix argument
corr_family 'corr_family' objects
covStruct Specifying correlation structures
crossprod-method ZAXlist class and (cross) products for ZAL matrix
crossprod-methods ZAXlist class and (cross) products for ZAL matrix

-- 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
EarthChord Scaled distances between unique locations
etaFix Fixing some parameters
extractAIC Extractors for informations criteria such as AIC
extractAIC.HLfit Extractors for informations criteria such as AIC
extractors Functions to extract various components of a fit

-- F --

family Functions to extract various components of a fit
family.HLfit Functions to extract various components of a fit
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
formula Functions to extract various components of a fit
formula.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 Extractors for informations criteria such as AIC
get_fixefVar Prediction from a model fit.
get_intervals Prediction from a model fit.
get_matrix Extract matrices from a 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_ranPars Operations on lists of parameters
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 Extract matrices from 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
how Extract information about how an object was obtained
how.default Extract information about how an object was obtained
how.HLfit Extract information about how an object was obtained

-- I --

IMRF Interpolated Markov Random Field models
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
is_separated Checking for (quasi-)separation in binomial-response model.

-- 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.
mat_sqrt Computation of "square root" of symmetric positive definite matrix
missingOrNULL ZAXlist class and (cross) products for ZAL matrix
missingOrNULL-class ZAXlist class and (cross) products for ZAL matrix
model.frame.HLfit Functions to extract various components of a fit
model.matrix.HLfit Functions to extract various components of a fit
MSFDR Multiple-Stage False Discovery Rate procedure
multi Analyzing multinomial data
multIMRF Interpolated Markov Random Field models
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
nobs Functions to extract various components of a fit
nobs.HLfit Functions to extract various components of a fit

-- O --

oceanmask Masks of seas or lands

-- P --

pdep_effects Partial-dependence effects and plots
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
plot_effects Partial-dependence effects and plots
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 Specifying correlation structures
preprocess_fix_corr Prediction from a model fit.
print Summary and print methods for fit and test results.
print.corr_family 'corr_family' objects
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
refit Updates a fit
remove_from_parlist Operations on lists of parameters
residuals Functions to extract various components of a fit
residuals.HLfit Functions to extract various components of a fit
response Functions to extract various components of a fit
rho.mapping Scaled distances between unique locations

-- S --

salamander Salamander mating data
SAR_WWt 'corr_family' objects
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.
small_spde Interpolated Markov Random Field models
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
str.inla.spde2 Interpolated Markov Random Field models
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 --

tcrossprod-method ZAXlist class and (cross) products for ZAL matrix
tcrossprod-methods ZAXlist class and (cross) products for ZAL matrix
terms Functions to extract various components of a fit
terms.HLfit Functions to extract various components of a fit
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 a fit
update.HLfit Updates a fit
update_resp Updates a fit

-- V --

Variogram.corMatern Matern Correlation Structure as a corSpatial object
vcov Extract covariance or correlation matrices from a fitted model object
vcov.HLfit Extract covariance or correlation matrices from a fitted model object

-- W --

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

-- Z --

ZAXlist ZAXlist class and (cross) products for ZAL matrix
ZAXlist-class ZAXlist class and (cross) products for ZAL matrix

-- misc --

%*%-method ZAXlist class and (cross) products for ZAL matrix
%*%-methods ZAXlist class and (cross) products for ZAL matrix