# spaMM v2.2.0

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## Mixed-Effect Models, Particularly Spatial Models

Inference in mixed-effect models, including generalized linear mixed models with spatial
correlations and models with non-Gaussian random effects (e.g., Beta Binomial,
or negative-binomial mixed models). Variation in residual variance is handled and can be modelled
as a linear model. Various approximations
of likelihood or restricted likelihood are implement, in particular h-likelihood and Laplace approximation.

## Functions in spaMM

Name | Description | |

LRT | Likelihood ratio test of fixed effects. | |

arabidopsis | Arabidopsis genetic and climatic data | |

HLCor | Fits a (spatially) correlated mixed model, for given correlation parameters | |

HLfit | Fit mixed models with given correlation matrix | |

Loaloa | Loa loa prevalence in North Cameroon, 1991-2001 | |

MaternCorr | Matern correlation function and Matern formula term. | |

PLS-internals | Internal, Experimental Functions for procedure using the ((I,0),(Z,X)) block-order | |

Predictor | Interface for model formulas | |

COMPoisson | Conway-Maxwell-Poisson (COM-Poisson) GLM family | |

spaMM_glm.fit | Fitting generalized linear models without initial-value or divergence headaches | |

corrHLfit | Fits a mixed model, typically a spatial GLMM. | |

corrMatrix | Using a corrMatrix argument | |

extractors | Functions to extract various components of a fit | |

fitme | Fitting function for fixed- and mixed-effect models with GLM response. | |

confint.HLfit | Confidence intervals for fixed-effect parameters | |

corMatern | Matern Correlation Structure as a corSpatial object | |

make_scaled_dist | Scaled distances between unique locations | |

mapMM | Colorful plots of predicted responses in two-dimensional space. | |

good-practice | Clear and trustworthy formulas | |

inverse.Gamma | Distribution families for Gamma and inverse Gamma-distributed random effects | |

seeds | Seed germination data | |

scotlip | Lip cancer in Scotland 1975 - 1980 | |

seaMask | Masks of seas or lands | |

spaMM-internal | Internal spaMM Functions | |

adjacency | Fitting autoregressive models | |

blackcap | Genetic polymorphism in relation to migration in the blackcap | |

pedigree | Fit mixed-effects models incorporating pedigrees | |

multinomial | Analyzing multinomial data | |

negbin | Family function for negative binomial GLMs and mixed models. | |

predict | Prediction from a model fit. | |

salamander | Salamander mating data | |

spaMM-conventions | spaMM conventions and differences from related fitting procedures | |

spaMM-Rcpp-internal | Internal spaMM Functions using Rcpp/RcppEigen | |

update.HLfit | Updates an HLCor or HLfit fit | |

wafers | Data from a resistivity experiment for semiconductor materials. | |

options | spaMM options settings | |

separation | Checking separation in binomial-response models | |

spaMM.filled.contour | Level (Contour) Plots with better aspect ratio control (for geographical maps, at least) | |

spaMM.colors | A flashy color palette. | |

spaMM | Inference in mixed models, in particular spatial GLMMs | |

covStruct | Specifying correlation structures | |

designL.from.Corr | Computation of “square root” of correlation matrix | |

fixedLRT | Likelihood ratio test of fixed effects. | |

freight | Freight dataset | |

phiHGLM | Fitting random effects in the residual dispersion model | |

plot.HLfit | Model checking plots for mixed models | |

sparse_precision | Sparse_precision algorithm | |

stripHLfit | Reduce the size of fitted objects | |

welding | Welding data set | |

simulate.HLfit | Simulate realizations of a fitted model. | |

spaMM-S3 | S3 methods of generics defined in other packages | |

summary.HLfit | Summary and print methods for fit and test results. | |

sym_eigen | Singular Value Decomposition of a Symmetric Matrix | |

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## Last month downloads

## Details

Type | Package |

Encoding | UTF-8 |

Date | 2017-10-03 |

LinkingTo | Rcpp, RcppEigen |

NeedsCompilation | yes |

License | CeCILL-2 |

URL | https://www.r-project.org, http://kimura.univ-montp2.fr/~rousset/spaMM.htm |

RoxygenNote | 5.0.1 |

Packaged | 2017-10-03 11:59:23 UTC; Francois.rousset |

Repository | CRAN |

Date/Publication | 2017-10-03 20:00:13 UTC |

suggests | e1071 , ff , foreach , lme4 , maps , pedigreemm , rcdd , rsae , testthat |

imports | graphics , MASS , Matrix , methods , nlme , nloptr , proxy , Rcpp (>= 0.11.0) , stats |

depends | R (>= 3.2.0) |

linkingto | RcppEigen |

Contributors | Jean-Baptiste Ferdy, Alexandre Courtiol, GSL authors |

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