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Updated readme
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Cole-Monnahan-NOAA committed Feb 19, 2021
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Expand Up @@ -27,12 +27,13 @@ assessments. ICES Journal of Marine Science. http://dx.doi.org/10.1093/icesjms/f


## Usage
The 'sample_admb' function draws posterior samples from an ADMB model using
an MCMC algorithm (NUTS by default). The returned fitted object contains
samples and other information. The function 'extract_samples' can be used
to get posterior samples (post warmup and thinning) into a data frame for
inference, while 'launch_shinyadmb' can be used for interactive diagnostics
based on 'ShinyStan'.
The 'sample_rwm' and 'sample_nuts' functions draw posterior samples
from an ADMB model using an MCMC algorithm (random walk Metropolis or
no-U-turn sampler). The returned fitted object contains samples and
other information. The function 'extract_samples' can be used to get
posterior samples (post warmup and thinning) into a data frame for
inference, while 'launch_shinyadmb' can be used for interactive
diagnostics based on 'ShinyStan'.

A brief [demonstration file](https://github.com/Cole-Monnahan-NOAA/adnuts/blob/master/inst/demo.R) is
provided to help get you started, and there is also a user guide:
Expand All @@ -44,10 +45,15 @@ To use the ADMB functionality you need to build your model with version
12.0 (released December 2017) or later, otherwise this functionality is not
available. See [the ADMB installation
instructions](http://www.admb-project.org/docs/install/) for more
information.
information. ADMB 12.2 is highly recommended for it provides better
console output, and fixes bugs and adds improved capabilities as
compared to 12.0.

The adnuts R package version 1.0.1 can be installed from CRAN:
`install.packages('adnuts')`.
`install.packages('adnuts')`. I recommend version 1.1.1 (released
2021-02-19) which can be installed with
`devtools::install_github('Cole-Monnahan-NOAA/adnuts')`


The development version of 'adnuts' can be installed with
`devtools::install_github('Cole-Monnahan-NOAA/adnuts', ref='dev')`

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