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paciorek merged 5 commits into from
Aug 14, 2025
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Add derived quantities info to manual #1567

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93d1cfa
Add deriv quants info to manual.
paciorek Jul 3, 2025
69a7345
Make minor addition to deriv quant manual text.
paciorek Jul 7, 2025
e6951b5
fix typo in derived output
danielturek Jul 28, 2025
9512b55
Fine tune deriv quantities manual info based on Daniel comments.
paciorek Jul 31, 2025
571bfc8
Merge branch 'deriv_quant_manual' of github.com:nimble-dev/nimble int…
paciorek Jul 31, 2025
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2 changes: 2 additions & 0 deletions UserManual/src/chapter_LightningIntroduction.Rmd
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Expand Up @@ -166,6 +166,8 @@ the point of this example.
Once you learn the MCMC system, you can write your own samplers and
include them. The entire system is written in nimbleFunctions.

In addition to customizing samplers, you can also choose additional quantities (e.g., model log-probabilities) to generate in the MCMC output, using the MCMC derived quantities functionality (Section \@ref(sec:derived-quantities), introduced in NIMBLE version 1.4.0.

## Running MCEM {#sec:running-mcem}

NIMBLE is a system for working with algorithms, not just an MCMC engine. So let's try maximizing the marginal likelihood for `alpha` and `beta` using Monte Carlo Expectation Maximization^[Note that for this model, one could analytically integrate over `theta` and then numerically maximize the resulting marginal likelihood.].
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