ecomix is a package to implement model based species level (Species Archetype Models) or site level (Regions of Common Profile) grouping of community data.
[x] Starting values for Poisson Point Process mixture model.
[x] Fit GLMs to all species.
[x] Cluster the coefficients across species.
[x] refit with $\tau$ ?
[x] For SAMs add in back ground points to species and carry weights through to loglikelihood estimation. e.g. rowSums(dpois(y, means[[k]], log = TRUE)*ppm_wts)
[x] Write out Poisson loglikelihood
[x] Write out Poisson derivatives.
[x] Test out loglike and gradient using numDeriv::grad.
[ ] Write out loglike in C++, so vmin can handle pars, function, gradient and data.
[ ] Write out partial derivs in C++
[ ] Add noise, look at RCP papers how they add noise - needs add variation within a constrained domain.
[ ] Create a species_mix_multifit via plapply for parallalisation, this should help improve convergence.
rowSums(dpois(y, means[[k]], log = TRUE)*ppm_wts)