| adjlg | Simulated data set for testing sparse-precision code |
| AIC | Extractors for information criteria such as AIC |
| algebra | Control of matrix-algebraic methods |
| aliases | Variable aliases for multivariate-response fits |
| anova.HLfit | ANOVA tables (and likelihood ratio tests). |
| arabidopsis | Arabidopsis genetic and climatic data |
| ARp | Random effect with AR(p) (autoregressive of order p) or... |
| as_LMLT | Conversion to input for procedures from lmerTest package |
| autoregressive | Fitting autoregressive models |
| betabin | Beta-binomial family object |
| beta_resp | Beta-distribution family object |
| blackcap | Genetic polymorphism in relation to migration in the blackcap |
| CauchyCorr | Cauchy correlation function and Cauchy formula term |
| clinics | Toy dataset for binomial response |
| COMPoisson | Conway-Maxwell-Poisson (COM-Poisson) GLM family |
| composite_ranef | Composite random effects |
| confint | Confidence intervals |
| control.HLfit | Control parameters of the HLfit fitting algorithm |
| convergence | Assessing convergence for fitted models |
| corMatern | Matern Correlation Structure as a corSpatial object |
| corr_family | 'corr_family' objects |
| corrFamily | Using corrFamily constructors and descriptors. |
| corrFamily-definition | corrFamily definition |
| corrFamily-design | Designing new corrFamily descriptors for parametric... |
| corrHLfit | Fits a mixed model, typically a spatial GLMM. |
| corrMatrix | Using the 'corrMatrix' and 'distmatrix' arguments |
| covStruct | Specifying correlation structures |
| diallel | Random-effect structures for symmetric or antisymmetric... |
| diallel_fixed | Fixed-effect terms for dyadic interactions |
| div_info | Information about numerical problems |
| DoF | Degrees of freedom extractor |
| dofuture | Interface for parallel computations |
| dopar | Interface for parallel computations |
| drop1.HLfit | Drop all possible single fixed-effect terms from a model |
| eval_replicate | Evaluating bootstrap replicates |
| extractors | Functions to extract various components of a fit. |
| extreme_eig | Utilities for regularization of a matrix |
| fitme | Fitting function for fixed- and mixed-effect models with GLM... |
| fitmv | Fitting multivariate responses |
| fixed | Fixing some parameters |
| fixed.LRT | Likelihood ratio test of fixed effects. |
| fix_predVar | Prediction from models with nearly-singular covariance... |
| freight | Freight dataset |
| genX2X | Fitting fixed-effects coefficients shared between submodels |
| get_cPredVar | Estimation of prediction variance with bootstrap correction |
| get_fittedPars | Operations on lists of parameters |
| get_inits_from_fit | Initiate a fit from another fit |
| get_matrix | Extract matrices from a fit |
| get_RLRSim_args | Extractors of arguments for functions from package RLRsim |
| GLM.fit | Fitting generalized linear models without initial-value or... |
| gof | Goodness of fit test |
| good-practice | Clear and trustworthy formulas and prior weights |
| Gryphon | Gryphon data |
| hatvalues.HLfit | Hat values and leverages extractor |
| HLCor | Fits a (spatially) correlated mixed model, for given... |
| HLfit | Fit mixed models with given correlation matrix |
| how | Extract information about how an object was obtained |
| IMRF | Interpolated Markov Random Field models |
| inits | Controlling optimization strategy through initial values |
| inner-vs-outer | Inner iterations versus outer optimization |
| inverse.Gamma | Distribution families for Gamma and inverse Gamma-distributed... |
| is_separated | Checking for (quasi-)separation in binomial-response model. |
| Leuca | Leucadendron data |
| lev2bool | Conversion of factor to 0/1 variable |
| llm.fit | Link-linear regression models (LLMs) |
| Loaloa | Loa loa prevalence in North Cameroon, 1991-2001 |
| LRT | Likelihood ratio tests of fixed and random effects. |
| make.scaled.dist | Scaled distances between unique locations, and Earth... |
| mapMM | Colorful plots of predictions in two-dimensional space. |
| MaternCorr | Matern correlation function and Matern formula term. |
| MaternIMRF | corrFamily constructor for Interpolated Markov Random Field... |
| mat_sqrt | Computation of "square root" of symmetric positive definite... |
| method | Fitting methods (objective functions maximized) |
| MSFDR | Multiple-Stage False Discovery Rate procedure |
| multinomial | Analyzing multinomial data |
| mv | Virtual factor for multivariate responses |
| negbin | Family function for negative binomial "2" response (including... |
| negbin1 | Alternative negative-binomial family |
| numInfo | Information matrix |
| optimBounds | Optimization bounds |
| options | spaMM options settings |
| PAIRfn | Correlated random effects in dyadic interactions |
| pedigree | Fit mixed-effects models incorporating pedigrees |
| phi-resid.model | Residual dispersion model for gaussian and Gamma response |
| plot_effect | Partial-dependence effects and plots |
| plot.HL | Model checking plots for mixed models |
| PLS-internals | Internal functions for procedure using the ((I,0),(Z,X))... |
| pois4mlogit | Fit multinomial logit models |
| poisson | Family function for GLMs and mixed models with Poisson and... |
| post-fit | Applying post-fit procedures from other packages on spaMM... |
| predict | Prediction from a model fit |
| predVar | Prediction and response variances |
| R2 | Pseudo R-squared |
| random-effects | Structure of random effects |
| rankinfo | Checking the rank of the fixed-effects design matrix |
| register_cF | Declare corrFamily constructor for use in formula |
| remove_fixef | Remove specified fixed-effect terms from a model formula |
| resid.model | Structured dispersion models |
| residuals.HLfit | Extract model residuals |
| residVar | Residual variance extractor |
| salamander | Salamander mating data |
| scotlip | Lip cancer in Scotland 1975 - 1980 |
| seaMask | Masks of seas or lands |
| seeds | Seed germination data |
| setNbThreads | Parallel computations in fits |
| simulate | Simulate realizations of a fitted model. |
| spaMM | Inference in mixed models, in particular spatial GLMMs |
| spaMM_boot | Parametric bootstrap |
| spaMMcolors | A flashy color palette. |
| spaMM-conventions | spaMM conventions and differences from related fitting... |
| spaMM.filled.contour | Level (Contour) Plots with better aspect ratio control (for... |
| spaMM-internal | Internal spaMM Functions |
| spaMM-S3 | S3 methods of generics defined in other packages |
| stripHLfit | Reduce the size of fitted objects |
| summary.HL | Summary and print methods for fit and test results. |
| transffit | Transformation of the data. |
| tweedie | Tweedie (compound Poisson Gamma) family |
| update | Updates a fit |
| vcov | Extract covariance or correlation components from a fitted... |
| verbose | Details of the 'verbose' argument of various functions |
| wafers | Data from a resistivity experiment for semiconductor... |
| welding | Welding data set |
| WinterWheat | Example of yield stability analysis |
| wrap_parallel | Selecting interfaces for parallelisation |
| ZAXlist | S4 classes for structured matrices |
