Mixed-Effect Models, with or without Spatial Random Effects
corr_family objects
Extractors for information criteria such as AIC
corrFamily definition
Drop all possible single fixed-effect terms from a model
Evaluating bootstrap replicates
Fixing some parameters
Estimation of prediction variance with bootstrap correction
Operations on lists of parameters
Checking for (quasi-)separation in binomial-response model.
Alternative negative-binomial family
Information matrix
spaMM options settings
Fit mixed-effects models incorporating pedigrees
Residual dispersion model for gaussian and Gamma response
Model checking plots for mixed models
Simulate realizations of a fitted model.
Beta-binomial family object
Control of matrix-algebraic methods
ANOVA tables, and likelihood ratio tests of fixed and random effects.
Random effect with AR(p) (autoregressive of order p) or ARMA(p,q) stru...
Conversion to input for procedures from lmerTest package
Fitting autoregressive models
Beta-response family object
Cauchy correlation function and Cauchy formula term
Conway-Maxwell-Poisson (COM-Poisson) GLM family
Composite random effects
Confidence intervals
Control parameters of the HLfit fitting algorithm
Assessing convergence for fitted models
Matern Correlation Structure as a corSpatial object
Designing new corrFamily descriptors for parametric correlation famili...
Using corrFamily constructors and descriptors.
Fits a mixed model, typically a spatial GLMM.
Using a corrMatrix argument
Specifying correlation structures
Interface for parallel computations
Random-effect structures for diallel experiments and other dyadic inte...
Fixed-effect terms for dyadic interactions
Information about numerical problems
Degrees of freedom extractor
Interface for parallel computations
Functions to extract various components of a fit.
Utilities for regularization of a matrix
Fitting function for fixed- and mixed-effect models with GLM response.
Fitting multivariate responses
Prediction from models with nearly-singular covariance matrices
Likelihood ratio test of fixed effects.
Initiate a fit from another fit
Extract matrices from a fit
Extractors of arguments for functions from package RLRsim
Fitting generalized linear models without initial-value or divergence ...
Clear and trustworthy formulas and prior weights
Leverage extractor for HLfit objects
Fits a (spatially) correlated mixed model, for given correlation param...
Computation of square root of symmetric positive definite matrix
Fit mixed models with given correlation matrix
Extract information about how an object was obtained
Interpolated Markov Random Field models
Controlling optimization strategy through initial values
Distribution families for Gamma and inverse Gamma-distributed random e...
Conversion of factor to 0/1 variable
Installing external libraries
Link-linear regression models (LLMs)
Scaled distances between unique locations
Colorful plots of predictions in two-dimensional space.
Matern correlation function and Matern formula term.
corrFamily constructor for Interpolated Markov Random Field (IMRF) cov...
Fitting methods (objective functions maximized)
Multiple-Stage False Discovery Rate procedure
Analyzing multinomial data
Virtual factor for multivariate responses
Family function for negative binomial 2 response (including truncated ...
Partial-dependence effects and plots
Internal functions for procedure using the ((I,0),(Z,X)) block-order
Family function for GLMs and mixed models with Poisson and zero-trunca...
Applying post-fit procedures on spaMM results
Prediction from a model fit
Prediction and response variances
Pseudo R-squared
Parallel computations in fits
Structure of random effects
Checking the rank of the fixed-effects design matrix
Declare corrFamily constructor for use in formula
Structured dispersion models
Extract model residuals
Residual variance extractor
spaMM conventions and differences from related fitting procedures
Internal spaMM Functions
S3 methods of generics defined in other packages
Level (Contour) Plots with better aspect ratio control (for geographic...
Inference in mixed models, in particular spatial GLMMs
Parametric bootstrap
A flashy color palette.
Example of yield stability analysis
Reduce the size of fitted objects
Summary and print methods for fit and test results.
Updates a fit
Extract covariance or correlation components from a fitted model objec...
Tracking progress of fits
Selecting interfaces for parallelisation
S4 classes for structured matrices
Inference based on models with or without spatially-correlated random effects, multivariate responses, or non-Gaussian random effects (e.g., Beta). Variation in residual variance (heteroscedasticity) can itself be represented by a mixed-effect model. Both classical geostatistical models (Rousset and Ferdy 2014 <doi:10.1111/ecog.00566>), and Markov random field models on irregular grids (as considered in the 'INLA' package, <https://www.r-inla.org>), can be fitted, with distinct computational procedures exploiting the sparse matrix representations for the latter case and other autoregressive models. Laplace approximations are used for likelihood or restricted likelihood. Penalized quasi-likelihood and other variants discussed in the h-likelihood literature (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) are also implemented.