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......@@ -37,7 +37,7 @@ The performance of likelihood ratio tests based on `spaMM` fits, and the impact
Rousset F., Ferdy J.-B. (2014) [Testing environmental and genetic effects in the presence of spatial autocorrelation](http://onlinelibrary.wiley.com/doi/10.1111/ecog.00566/abstract). Ecography, 37: 781-790.
Also available here is the [Supplementary Appendix G](http://kimura.univ-montp2.fr/%7Erousset/spaMM/RoussetF14AppendixG.pdf) from that paper, including comparisons with a trick that has been uncritically used to constrain the functions `lmer` and `glmmPQL` to analyse spatial models.
For some substantial use of various features of `spaMM`, see e.g. the [IsoriX project](https://github.com/courtiol/IsoriX), or a story about [social dominance in hyaenas](https://doi.org/10.1038/s41559-018-0718-9), or [yet another depressing story about climate change](https://doi.org/10.1038/s41467-019-10924-4), or [the life-history of mothers of twins](https://doi.org/10.1038/s41467-022-30366-9), or a comparison of prediction by LMMs and by random-forest methods (in supplementary material of [a paper on protected area personnel](https://doi.org/10.1038/s41893-022-00970-0)), or [analyses of dyadic interactions in mandrills](https://doi.org/10.7554/eLife.79417).
For some substantial use of various features of `spaMM`, see e.g. the [IsoriX project](https://github.com/courtiol/IsoriX), or a story about [social dominance in hyaenas](https://doi.org/10.1038/s41559-018-0718-9), or [yet another depressing story about climate change](https://doi.org/10.1038/s41467-019-10924-4), or [the life-history of mothers of twins](https://doi.org/10.1038/s41467-022-30366-9), or a comparison of prediction by LMMs and by random-forest methods (in supplementary material of [a paper on protected area personnel](https://doi.org/10.1038/s41893-022-00970-0)), or [analyses of dyadic interactions in mandrills](https://doi.org/10.7554/eLife.79417), or [comparative analyses by heteroscedastic models with phylogenetic autocorrelation](https://doi.org/10.1038/s42003-024-06165-x).
Initial development drew inspiration from work by Lee and Nelder on _h_-likelihood and more elaborate approximations of likelihood (e.g. [Lee, Nelder & Pawitan](https://doi.org/10.1201/9781420011340), 2006; [Lee & Lee](http://dx.doi.org/10.1007/s11222-011-9265-9) 2012; see also [Molas and Lesaffre](http://dx.doi.org/10.1002/sim.3852), 2010). The latter two references, and `spaMM` itself, may actually be more widely understood as applications of Laplace approximations of likelihood than as applications of a distinctive _h_-likelihood concept. `spaMM` retains from Lee & Nelder's work several distinctive features, such as a concept of restricted likelihood applicable beyond LMMs, specific methods to fit models with non-gaussian random effects, structured dispersion models with random effects, and implementation of several variants of Laplace and PQL approximations. However, it has departed from their work in various ways. Notably, the default likelihood and restricted likelihood approximations now go beyond those discussed in these works. For ML fits, it is the same Laplace approximation as in `TMB` ([Kristensen et al., 2016](https://doi.org/10.18637/jss.v070.i05)) and packages based on `TMB`, because `TMB` and `spaMM` (with default arguments) use the observed Hessian matrix of ``joint likelihood'' where the _h_-likelihood literature only considers the expected Hessian matrix. This makes a difference for GLM families with non-canonical link, or for response families not of the GLM class.
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