Mixed-Effect Models, with or without Spatial Random Effects

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Documentation for package ‘spaMM’ version 4.5.0

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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 X 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 ANOVA tables, and likelihood ratio tests of fixed and random effects.
anova.HLfit ANOVA tables, and likelihood ratio tests of fixed and random effects.
anova.LMLT ANOVA tables, and likelihood ratio tests of fixed and random effects.
antisym Random-effect structures for diallel experiments and other dyadic interactions
AR1 Fitting autoregressive models
arabidopsis Arabidopsis genetic and climatic data
ARMA Random effect with AR(p) (autoregressive of order p) or ARMA(p,q) structure.
ARp Random effect with AR(p) (autoregressive of order p) or ARMA(p,q) structure.
as_LMLT Conversion to input for procedures from lmerTest package
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
betabin Beta-binomial family object
beta_resp Beta-response family object
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:LMLTslots Conversion to input for procedures from lmerTest package
class:missingOrNULL S4 classes for structured matrices
class:ZAXlist S4 classes for structured matrices
clinics Toy dataset for binomial response
coef.corMatern Matern Correlation Structure as a corSpatial object
coef<-.corMatern Matern Correlation Structure as a corSpatial object
combinepar Interface for parallel computations
COMPoisson Conway-Maxwell-Poisson (COM-Poisson) GLM family
composite-ranef Composite random effects
confint Confidence intervals
confint.HLfit Confidence intervals
control.HLfit Control parameters of the HLfit fitting algorithm
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 Using corrFamily constructors and descriptors.
corrFamily-definition corrFamily definition
corrFamily-design Designing new corrFamily descriptors for 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.
df.residual Functions to extract various components of a fit.
df.residual.HLfit Functions to extract various components of a fit.
DHARMa Applying post-fit procedures on spaMM results
diagnose_conv Information about numerical problems
diallel Random-effect structures for diallel experiments and other dyadic interactions
dim.Kronfacto S4 classes for structured matrices
div_info Information about numerical problems
DoF Degrees of freedom extractor
dofuture Interface for parallel computations
dopar Interface for parallel computations
drop1 Drop all possible single fixed-effect terms from a model
drop1.HLfit Drop all possible single fixed-effect terms from a model
drop1.LMLT Drop all possible single fixed-effect terms from a model

-- 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 and prior weights
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_fittedPars Operations on lists of parameters
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 and prior weights
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
hyper Interpolated Markov Random Field models

-- 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 --

keepInREML Fixing some parameters
Kronfacto S4 classes for structured matrices
Kronfacto-class S4 classes for structured matrices

-- L --

landMask Masks of seas or lands
Leuca Leucadendron data
lev2bool Conversion of factor to 0/1 variable
LevenbergM spaMM options settings
LL-family Link-linear regression models (LLMs)
llm.fit Link-linear regression models (LLMs)
lmerTest Applying post-fit procedures on spaMM results
LMLTslots Conversion to input for procedures from lmerTest package
LMLTslots-class Conversion to input for procedures from lmerTest package
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
LR2R2 Pseudo R-squared
LRT ANOVA tables, and likelihood ratio tests of fixed and random 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.
MaternIMRFa corrFamily constructor for Interpolated Markov Random Field (IMRF) covariance structure approximating a 2D Matern correlation model.
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.
model.matrix.LMLTslots Conversion to input for procedures from lmerTest package
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 negative binomial "2" response (including truncated variant).
negbin1 Alternative negative-binomial family
negbin2 Family function for negative binomial "2" response (including truncated variant).
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.
numInfo Information matrix

-- O --

obsInfo Fitting methods (objective functions maximized)
oceanmask Masks of seas or lands

-- P --

pdep_effects Partial-dependence effects and plots
pedigree Fit mixed-effects models incorporating pedigrees
phi-resid.model Residual dispersion model for gaussian and Gamma response
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.
print.singeigs Information matrix
prior.weights Fit mixed models with given correlation matrix
pseudoR2 Pseudo R-squared

-- 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
ranGCA Random-effect structures for diallel experiments and other dyadic interactions
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
register_cF Declare corrFamily constructor for use in formula
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 Structured dispersion models
residuals Extract model residuals
residuals.HLfit Extract model residuals
residVar Residual variance extractor
respName Updates a fit
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.
setNbThreads Parallel computations in fits
simulate Simulate realizations of a fitted model.
simulate.HLfit Simulate realizations of a fitted model.
simulate.HLfitlist Simulate realizations of a fitted model.
simulate4boot Simulate realizations of a fitted model.
simulate_ranef 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
spaMM2boot Parametric bootstrap
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 negative binomial "2" response (including truncated variant).
Tpoisson Family function for GLMs and mixed models with Poisson and zero-truncated Poisson response.

-- U --

unregister_cF Declare corrFamily constructor for use in formula
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
verbose Tracking progress of fits

-- W --

wafers Data from a resistivity experiment for semiconductor materials.
weights Functions to extract various components of a fit.
weights.HLfit Functions to extract various components of a fit.
welding Welding data set
WinterWheat Example of yield stability analysis
worldcountries Masks of seas or lands
wrap_parallel Selecting interfaces for parallelisation

-- X --

X.antisym Fixed-effect terms for dyadic interactions
X.GCA Fixed-effect terms for dyadic interactions
X2X Fitting multivariate responses

-- 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
`DHARMa-on-HLfit` Model checking plots for mixed models