Mixed-Effect Models, with or without Spatial Random Effects

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Documentation for package ‘spaMM’ version 3.10.0

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A B C D E F G H I K 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 information criteria such as AIC
AIC.HLfit Extractors for information criteria such as AIC
algebra Control of matrix-algebraic methods
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 --

barstyle spaMM options settings
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 components 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
CauchyCorr.default Cauchy correlation function and Cauchy formula term
CauchyCorr.dgCMatrix Cauchy correlation function and Cauchy formula term
CauchyCorr.dsCMatrix Cauchy correlation function and Cauchy formula term
class:Kronfacto S4 classes for structured matrices
class:missingOrNULL S4 classes for structured matrices
class:ZAXlist S4 classes for structured matrices
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
composite-ranef Composite random effects
confint Confidence intervals
confint.HLfit Confidence intervals
convergence Assessing convergence for fitted models
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 components from a fitted model object
corrFamily Defining parametric correlation families
corrHLfit Fits a mixed model, typically a spatial GLMM.
corrMatrix Using a corrMatrix argument
corrPars Fixing some parameters
corr_family 'corr_family' objects
covStruct Specifying correlation structures
crossprod-method S4 classes for structured matrices
crossprod-methods S4 classes for structured matrices

-- D --

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
DHARMa Applying post-fit procedures on spaMM results
dim.Kronfacto S4 classes for structured matrices
div_info Information about numerical problems
dofuture Interface for parallel computations
dopar Interface for parallel computations

-- E --

Earth Scaled distances between unique locations
EarthChord Scaled distances between unique locations
etaFix Fixing some parameters
eval_replicate Evaluating bootstrap replicates
external-libraries Installing external libraries
extractAIC Extractors for information criteria such as AIC
extractAIC.HLfit Extractors for information criteria such as AIC
extractors Functions to extract various components of a fit
extreme_eig Utilities for regularization of a matrix

-- 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 predictions in two-dimensional space.
fitme Fitting function for fixed- and mixed-effect models with GLM response.
fitmv Fitting multivariate responses
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
fix_predVar Prediction from models with nearly-singular covariance matrices
formula Functions to extract various components of a fit
formula.HLfit Functions to extract various components of a fit
formula_env Clear and trustworthy formulas
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 information criteria such as AIC
get_cPredVar Estimation of prediction variance with bootstrap correction
get_fixefVar Prediction from a model fit
get_inits_from_fit Initiate a fit from another 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_RLRsim_args Extractors of arguments for functions from package RLRsim
get_RLRTSim_args Extractors of arguments for functions from package RLRsim
get_ZALMatrix Extract matrices from a fit
glht Applying post-fit procedures on spaMM results
good-practice Clear and trustworthy formulas
Gryphon Gryphon data
Gryphon_A Gryphon data
Gryphon_df Gryphon data
Gryphon_pedigree Gryphon data
GxE Example of yield stability analysis

-- H --

hatvalues Leverage extractor for HLfit objects
hatvalues.HLfit Leverage extractor for HLfit objects
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
how.HLfitlist Extract information about how an object was obtained

-- I --

IMRF Interpolated Markov Random Field models
Initialize.corMatern Matern Correlation Structure as a corSpatial object
inits Controlling optimization strategy through initial values
inla.spde2.matern Interpolated Markov Random Field models
inla.spde2.pcmatern Interpolated Markov Random Field models
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.
is_separated.formula Checking for (quasi-)separation in binomial-response model.

-- K --

Kronfacto S4 classes for structured matrices
Kronfacto-class S4 classes for structured matrices

-- 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 predictions in two-dimensional space.
map_ranef Colorful plots of predictions 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.
MaternCorr.dgCMatrix Matern correlation function and Matern formula term.
MaternCorr.dsCMatrix Matern correlation function and Matern formula term.
mat_sqrt Computation of "square root" of symmetric positive definite matrix
method Fitting methods (objective functions maximized)
missingOrNULL S4 classes for structured matrices
missingOrNULL-class S4 classes for structured matrices
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
multcomp Applying post-fit procedures on spaMM results
multi Analyzing multinomial data
multIMRF Interpolated Markov Random Field models
multinomial Analyzing multinomial data
mv Virtual factor for multivariate responses

-- 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.
post-fit Applying post-fit procedures on spaMM results
predict Prediction from a model fit
predict.HLfit Prediction from a model fit
Predictor Specifying correlation structures
predVar Prediction and response variances
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
random-effects Structure of random effects
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
regularize Utilities for regularization of a matrix
REMLformula Fit mixed models with given correlation matrix
remove_from_parlist Operations on lists of parameters
resid.model Fitting random effects in the residual dispersion model
residuals Extract model residuals
residuals.HLfit Extract model residuals
residVar Residual variance extractor
response Functions to extract various components of a fit
rho.mapping Scaled distances between unique locations
RLRsim Applying post-fit procedures on spaMM results

-- 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 for (quasi-)separation in binomial-response model.
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 predictions 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 Control of matrix-algebraic methods
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.

-- T --

t.ZAXlist S4 classes for structured matrices
tcrossprod-method S4 classes for structured matrices
tcrossprod-methods S4 classes for structured matrices
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.formula Updates a fit
update.HLfit Updates a fit
update_formulas Updates a fit
update_resp Updates a fit

-- V --

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

-- W --

wafers Data from a resistivity experiment for semiconductor materials.
welding Welding data set
WinterWheat Example of yield stability analysis
worldcountries Masks of seas or lands
wrap_parallel Selecting interfaces for parallelisation

-- Z --

ZAXlist S4 classes for structured matrices
ZAXlist-class S4 classes for structured matrices

-- misc --

%*%-method S4 classes for structured matrices
%*%-methods S4 classes for structured matrices
.eval_replicate2 Evaluating bootstrap replicates