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skiptoniam / ecomix

ecomix is a package to implement model based species level (Species Archetype Models) or site level (Regions of Common Profile) grouping of community data.
https://skiptoniam.github.io/ecomix/
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Need to harmonise the statistical distribution names in function calls #3

Closed skiptoniam closed 7 years ago

skiptoniam commented 7 years ago

Currently species mix uses:

bernoulli (presence absence data; default), negbin (abundance data with negative binomial) or tweedie (biomass data with tweedie distribution).

While RCPmod uses: Bernoulli (for binary data), Poisson and NegBin (for count data), Tweedie (for biomass, non-negative, data), and Normal (for quantity data).

I suggest we use lower case: bernoulli poisson - this will be essentially negative_binomal with dispersion parameter set to 1 (phi). negative_binomial tweedie gaussian - appears to be missing from species mix - we might need to fix this or create an error message.

skiptoniam commented 7 years ago

Create a poisson likelihood function for SAMs

skiptoniam commented 7 years ago

It might be possible to create a Poisson distribution using a fixed dispersion parameter.

skiptoniam commented 7 years ago

finally went with ipp,poisson,negative_binomial,bernoulli,tweedie,gaussian