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mcmcderive

Calculate derived parameters from MCMC samples

https://github.com/poissonconsulting/mcmcderive

Science Score: 26.0%

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    CITATION.cff file
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    Low similarity (17.6%) to scientific vocabulary

Keywords

cran derived-parameters mcmc mcmcr

Keywords from Contributors

chk assertion checkr fish kootenay-lake species-sensitivity-distribution ssd water-quality-guideline
Last synced: 9 months ago · JSON representation

Repository

Calculate derived parameters from MCMC samples

Basic Info
Statistics
  • Stars: 0
  • Watchers: 4
  • Forks: 0
  • Open Issues: 6
  • Releases: 1
Topics
cran derived-parameters mcmc mcmcr
Created over 8 years ago · Last pushed 12 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Support

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# mcmcderive 


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![CRAN downloads](https://cranlogs.r-pkg.org/badges/mcmcderive)


## Why `mcmcderive`?

`mcmcderive` is an R package to generate derived parameter(s) from Monte Carlo Markov Chain (MCMC) samples using R code.

This is useful because it means Bayesian models can be fitted without the inclusion of derived parameters which add unnecessary clutter and slows model fitting.
For more information on MCMC samples see Brooks et al. (2011).

## Demonstration

```{r}
library(mcmcderive)

mcmcr::mcmcr_example

expr <- "
  log(alpha2) <- alpha
  gamma <- sum(alpha) * sigma
"

mcmc_derive(mcmcr::mcmcr_example, expr, silent = TRUE)
```

### Parallel Chains

If the MCMC object has multiple chains the run time can be substantially reduced by generating the derived parameters for each chain in parallel.
In order for this to work it is necessary to:

1) Ensure plyr and doParallel are installed using `install.packages(c("plyr", "doParallel"))`.
2) Register a parallel backend using `doParallel::registerDoParallel(4)`.
3) Set `parallel = TRUE` in the call to `mcmc_derive()`.

### Extras

To facilitate the translation of model code into R code the `extras` package provides the R equivalent to common model functions such as `pow()`, `phi()` and `log() <- `.

## Installation

### Release

To install the release version from [CRAN](https://CRAN.R-project.org/package=mcmcderive).
```r
install.packages("mcmcderive")
```

The website for the release version is at .

### Development

To install the development version from [GitHub](https://github.com/poissonconsulting/mcmcderive)
```r
# install.packages("remotes")
remotes::install_github("poissonconsulting/mcmcderive")
```

or from [r-universe](https://poissonconsulting.r-universe.dev/mcmcderive).
```r
install.packages("mcmcderive", repos = c("https://poissonconsulting.r-universe.dev", "https://cloud.r-project.org"))
```

## Contribution

Please report any [issues](https://github.com/poissonconsulting/mcmcderive/issues).

[Pull requests](https://github.com/poissonconsulting/mcmcderive/pulls) are always welcome.

## Code of Conduct

Please note that the mcmcderive project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). 
By contributing to this project, you agree to abide by its terms.

## References

Brooks, S., Gelman, A., Jones, G.L., and Meng, X.-L. (Editors). 2011. Handbook for Markov Chain Monte Carlo. Taylor & Francis, Boca Raton.

Owner

  • Name: Poisson Consulting Ltd.
  • Login: poissonconsulting
  • Kind: organization
  • Email: software@poissonconsulting.ca
  • Location: Nelson, BC, Canada

Computational Biology and Statistical Ecology

GitHub Events

Total
  • Push event: 15
  • Pull request event: 2
  • Create event: 2
Last Year
  • Push event: 15
  • Pull request event: 2
  • Create event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 172
  • Total Committers: 7
  • Avg Commits per committer: 24.571
  • Development Distribution Score (DDS): 0.273
Past Year
  • Commits: 42
  • Committers: 4
  • Avg Commits per committer: 10.5
  • Development Distribution Score (DDS): 0.476
Top Committers
Name Email Commits
joethorley j****e@p****a 125
Ayla Pearson a****a@p****a 22
Kirill Müller k****r@m****g 16
Ayla Pearson a****3@g****m 4
Nadine Hussein n****3@g****m 3
Kirill Müller k****l@c****m 1
Mowahid Latif m****f@M****l 1
Committer Domains (Top 20 + Academic)
poissonconsulting.ca: 2 cynkra.com: 1 mailbox.org: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 12
  • Total pull requests: 13
  • Average time to close issues: 5 months
  • Average time to close pull requests: 1 day
  • Total issue authors: 2
  • Total pull request authors: 6
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.15
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 3
  • Average time to close issues: N/A
  • Average time to close pull requests: about 21 hours
  • Issue authors: 0
  • Pull request authors: 2
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • joethorley (11)
Pull Request Authors
  • dunkenwg (5)
  • aylapear (4)
  • krlmlr (3)
  • joethorley (1)
  • nadinehussein (1)
  • MowahidLatif (1)
Top Labels
Issue Labels
Type: Refactor (1) Difficulty: Intermediate (1) Effort: Small (1) Importance: Medium (1) Timeline: Soon (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 164 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 3
  • Total versions: 4
  • Total maintainers: 1
cran.r-project.org: mcmcderive

Derive MCMC Parameters

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 164 Last month
Rankings
Dependent repos count: 16.5%
Forks count: 27.8%
Dependent packages count: 28.8%
Average: 32.5%
Stargazers count: 34.6%
Downloads: 54.9%
Maintainers (1)
joe@poissonconsulting.ca
Last synced: 9 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5 depends
  • abind * imports
  • chk * imports
  • extras * imports
  • mcmcr * imports
  • nlist * imports
  • purrr * imports
  • universals * imports
  • coda * suggests
  • covr * suggests
  • doParallel * suggests
  • plyr * suggests
  • testthat * suggests