nimbleEcology
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`nimbleOccu` use of `nimbleHMC` via `suggests`
We're currently planning to include a wrapper function, nimbleOccu
, to provide lme4-like interface for setting up occupancy models using macros and (optionally) running MCMC.
If we try to use nimbleHMC
via suggests
, sampler_NUTS
is not found when invoking configureHMC
.
@kenkellner I think a work-around is to do this (avoiding configureHMC
, which is just a convenience wrapper):
conf <- configureMCMC(mod, nodes = NULL, print = FALSE)
conf$addSampler(nimbleHMC::sampler_NUTS, target = 'mu',
control = list(warmupMode = "iterations", warmup=100))
That way sampler_NUTS
is found via namespace resolution within nimbleOccu
and passed in, so that we're not trying to find it from within nimble's MCMC configuration code, which does not know about nimbleHMC
namespace objects.
I'm going to file an issue on nimbleHMC
to consider the more general issue that this reveals.