https://github.com/poissonconsulting/jmbr

An R package to facilitate analyses using JAGS
https://github.com/poissonconsulting/jmbr

jags mbr rstats

Last synced: about 1 month ago
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An R package to facilitate analyses using JAGS

• Host: GitHub
• URL: https://github.com/poissonconsulting/jmbr
• Owner: poissonconsulting
• License: other
• Created: 2017-01-03T00:26:30.000Z (about 8 years ago)
• Default Branch: main
• Last Pushed: 2024-11-24T07:44:39.000Z (about 2 months ago)
• Last Synced: 2024-11-24T08:25:48.666Z (about 2 months ago)
• Topics: jags, mbr, rstats
• Language: R
• Homepage: https://poissonconsulting.github.io/jmbr/
• Size: 54.4 MB
• Stars: 3
• Watchers: 4
• Forks: 0
• Open Issues: 5
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: .github/CODE_OF_CONDUCT.md
  • Support: .github/SUPPORT.md

Awesome Lists containing this project

README

        
---

output: github_document

---

```{r, echo = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "tools/README-"

)

```

[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)

[![R-CMD-check](https://github.com/poissonconsulting/jmbr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/poissonconsulting/jmbr/actions/workflows/R-CMD-check.yaml)

[![Codecov test coverage](https://codecov.io/gh/poissonconsulting/jmbr/branch/master/graph/badge.svg)](https://codecov.io/gh/poissonconsulting/jmbr?branch=master)

[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/license/mit/)

# jmbr

## Introduction

`jmbr` (pronounced jimber) is an R package to facilitate analyses using Just Another Gibbs Sampler ([`JAGS`](http://mcmc-jags.sourceforge.net)).

It is part of the [mbr](https://github.com/poissonconsulting/mbr) family of packages.

## Demonstration

```{r, message = FALSE}

library(jmbr)

library(mbr)

```

```{r}

# define model in JAGS language

model <- model("model {

  alpha ~ dnorm(0, 10^-2)

  beta1 ~ dnorm(0, 10^-2)

  beta2 ~ dnorm(0, 10^-2)

  beta3 ~ dnorm(0, 10^-2)

  log_sAnnual ~ dnorm(0, 10^-2)

  log(sAnnual) <- log_sAnnual

  for(i in 1:nAnnual) {

    bAnnual[i] ~ dnorm(0, sAnnual^-2)

  }

  for (i in 1:length(Pairs)) {

    log(ePairs[i]) <- alpha + beta1 * Year[i] + beta2 * Year[i]^2 + beta3 * Year[i]^3 + bAnnual[Annual[i]]

    Pairs[i] ~ dpois(ePairs[i])

  }

}")

# add R code to calculate derived parameters

model <- update_model(model, new_expr = "

for (i in 1:length(Pairs)) {

  log(prediction[i]) <- alpha + beta1 * Year[i] + beta2 * Year[i]^2 + beta3 * Year[i]^3 + bAnnual[Annual[i]]

}")

# define data types and center year

model <- update_model(model,

  select_data = list("Pairs" = integer(), "Year*" = integer(), Annual = factor()),

  derived = "sAnnual",

  random_effects = list(bAnnual = "Annual")

)

data <- bauw::peregrine

data$Annual <- factor(data$Year)

set_analysis_mode("report")

# analyse

analysis <- analyse(model, data = data)

analysis <- reanalyse(analysis)

coef(analysis, simplify = TRUE)

plot(analysis)

```

```{r, message = FALSE}

# make predictions by varying year with other predictors including the random effect of Annual held constant

year <- predict(analysis, new_data = "Year")

# plot those predictions

library(ggplot2)

ggplot(data = year, aes(x = Year, y = estimate)) +

  geom_point(data = bauw::peregrine, aes(y = Pairs)) +

  geom_line() +

  geom_line(aes(y = lower), linetype = "dotted") +

  geom_line(aes(y = upper), linetype = "dotted") +

  expand_limits(y = 0)

```

## Installation

To install from GitHub

```

install.packages("devtools")

devtools::install_github("poissonconsulting/jmbr")

```

## Citation

```{r, comment="", echo=FALSE}

citation(package = "jmbr")

```

## Contribution

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

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

## Code of Conduct

Please note that the jmbr 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.

## Inspiration

- [jaggernaut](https://github.com/poissonconsulting/jaggernaut)