Add support for AD

This release adds support for automatic differentiation (AD) including:

• Confirmation that all existing distributions except dNmixture are AD-compatible;
• new dNmixtureAD distributions that are compatible with AD;
• Documentation for each distribution and in the package vignette discussing the use of nimbleEcology functions with AD

Add 3 N-mixture variations, fix *HMM C++/R rounding error

In nimbleEcology 0.4.0, we add three variations of the N-mixture model. The standard version of the N-mixture model is a two-level hierarchical model where a latent state N, representing the true abundance at a site, is a Poisson random variable, and the observed count y is a binomial random variable with size N and probability p. We provide distributions for the cases where the Poisson is substituted for a negative binomial (dNmixture_BNB), the binomial is substituted for a beta binomial (dNmixture_BBP), or both (dNmixture_BBNB). These are sometimes used to represent overdispersion in the abundance or detection processes.

We implement these using an algorithm that's considerably faster than the straightforward loop over values of N, which we hope will make it feasible to use beta binomial and negative binomial N-mixtures in large data contexts.

The 0.4.0 update also addresses an issue where rounding errors in C++ compiled code caused the hidden Markov models to fail the condition that the sum of the initial state probabilities was one.

Improve dNmixture efficient algorithm

This release updated the efficient N-mixture algorithm to catch rounding errors in cases where len is large.

nimbleEcology 0.3.0

This release includes substantial bug fixes for the HMM distribution as well as improvements to documentation and package vignette.

nimbleEcology 0.2.1

Fixed typos in examples.

nimbleEcology 0.2.0

Match CRAN release 0.2.0. Introduced dNmixture.

nimbleEcology 0.1.0

Version 0.1.0 on CRAN.