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https://github.com/salleuska/nimble-ness-2022
Materials for NIMBLE (hybrid) short course at the NESS 2022 conference.
https://github.com/salleuska/nimble-ness-2022
Last synced: about 2 months ago
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Materials for NIMBLE (hybrid) short course at the NESS 2022 conference.
- Host: GitHub
- URL: https://github.com/salleuska/nimble-ness-2022
- Owner: salleuska
- Created: 2022-05-04T09:49:30.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-03-25T13:40:38.000Z (10 months ago)
- Last Synced: 2024-03-25T15:27:31.225Z (10 months ago)
- Language: HTML
- Size: 171 MB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# nimble-ness-2022
Materials for the NIMBLE short course at the NESS 2022 conference, May 23, 2022.
To prepare for the workshop:
- Install NIMBLE (see below)
- Install additional packages (see below)
- Download these materials (and check back before the workshop on Monday May 23 for updates)
All materials for the workshop will be in this GitHub repository. If you're familiar with Git/GitHub, you already know how to get all the materials on your computer. If you're not, simply click [here](https://github.com/salleuska/nimble-ness-2022/archive/main.zip).
## More resources (especially for new users)
- Lighting introduction in the user manual [https://r-nimble.org/html_manual/cha-lightning-intro.html](https://r-nimble.org/html_manual/cha-lightning-intro.html)
- Examples on nimble websites [https://r-nimble.org/examples](https://r-nimble.org/examples)
- Other workshops material [nimble-training](https://github.com/nimble-training)
## Credits
The material for this workshop is based on othe workshops material available at [nimble-training](https://github.com/nimble-training) by the Nimble Development Team
## Tentative Schedule
Monday, May 22, 2022
Location: AUST 108
Click [here](https://raw.githack.com/salleuska/nimble-ness-2022/main/overview.html) for an overview of the material
Morning: 9am - 12pm
- Introduction to NIMBLE: basic concepts and workflows
- 1_introduction_to_nimble
- 2_nimble_models
- Customizing an MCMC
- 3_customizing_mcmc
Afternoon: 1pm - 5pm
- Programming in NIMBLE
- 4_writing_user_distributions
- 5_writing_user_samplers
- Highlights of special features in NIMBLE
- 6_nimble_highlights
## Help with NIMBLE
Our user manual is [here](https://r-nimble.org/html_manual/cha-welcome-nimble.html).
We have a cheatsheet on nimble models and distributions [here](https://r-nimble.org/documentation).
For those of you who are not already familiar with writing models in WinBUGS, JAGS, or NIMBLE, you may want to look at Section 5.2 of our user manual in advance.
## Installing NIMBLE
NIMBLE is an R package on CRAN, so in general it will be straightforward to install as with any R package, but you do need a compiler and related tools on your system.
In summary, here are the steps.
1. Install compiler tools on your system. [https://r-nimble.org/download](https://r-nimble.org/download) has more details on how to install *Rtools* on Windows and how to install the command line tools of *Xcode* on a Mac. Note that if you have packages requiring a compiler (e.g., *Rcpp*) on your computer, you should already have the compiler tools installed.
2. Install the *nimble* package from CRAN in the usual fashion for an R package. More details (including troubleshooting tips) can also be found in Section 4 of the [NIMBLE manual](https://r-nimble.org/html_manual/cha-installing-nimble.html).
3) To test that things are working please run the following code in R:
```
library(nimble)
code <- nimbleCode({
y ~ dnorm(0,1)
})
model <- nimbleModel(code)
cModel <- compileNimble(model)
```
If that runs without error, you're all set. If not, please see the [troubleshooting tips](https://r-nimble.org/html_manual/cha-installing-nimble.html#troubleshooting-installation-problems) and email me in case you can't get things going.
In general we encourage you to update to the most recent version of NIMBLE, 0.12.2.
## Installing additional packages
Some of the packages we will use (beyond those automatically installed with `nimble`) can be installed as follows:
```
install.packages(c("mcmcplots", "classInt", "coda"))
```
`compareMCMCs` is a package in development that is not yet on CRAN:
```
library(remotes)
install_github("nimble-dev/compareMCMCs", subdir = "compareMCMCs")
```
Windows users will probably need to use this invocation:
```
library(remotes)
install_github("nimble-dev/compareMCMCs", subdir = "compareMCMCs", INSTALL_opts = "--no-multiarch")
```