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j-i-l committed Jul 14, 2024
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Expand Up @@ -35,7 +35,7 @@ Officially supported is R version >= 4.4
## Prerequisites

<details>
<summary><b>Ubuntu</b></summary>
<summary><b><i>Ubuntu</i></b></summary>


Most likely you have R installed already but if not run:
Expand Down Expand Up @@ -64,7 +64,7 @@ Officially supported is R version >= 4.4
</details>

<details>
<summary><b>Fedora</b></summary>
<summary><b><i>Fedora</i></b></summary>

You will need C/C++ and Fortran compilers and various libraries:

Expand Down Expand Up @@ -101,7 +101,7 @@ Officially supported is R version >= 4.4
</details>

<details>
<summary><b>MacOS</b></summary>
<summary><b><i>MacOS</i></b></summary>

The installation process on MacOS relies on [Homebrew](https://brew.sh/), head over to their site to see the installation process or simply open a terminal and run:

Expand Down Expand Up @@ -138,16 +138,16 @@ Some are C/C++ libraries and some are R packages that are not hosted on CRAN.

Below is a list of these dependencies with details on how to install and configure them:

<details>
<summary><b>GSL</b></summary>

[GSL](https://www.gnu.org/software/gsl/), the _GNU Scientific Library_, is a numerical library for C/C++.
It is required to compile `abn`'s C/C++ code.
#### Installation
- <details>
<summary><b>Ubuntu</b></summary>
<summary><b>GSL</b></summary>

[GSL](https://www.gnu.org/software/gsl/), the _GNU Scientific Library_, is a numerical library for C/C++.
It is required to compile `abn`'s C/C++ code.
#### Installation
<details>
<summary><b><i>Ubuntu</i></b></summary>
`GSL` is available through the Advanced Package Tool, `APT`, simply type:
Expand All @@ -156,8 +156,8 @@ It is required to compile `abn`'s C/C++ code.
```
</details>
- <details>
<summary><b>Fedora</b></summary>
<details>
<summary><b><i>Fedora</i></b></summary>
`GSL` is available through Fedoras standard package manager, `DNF`, simply type:
Expand All @@ -166,17 +166,17 @@ It is required to compile `abn`'s C/C++ code.
```
</details>
- <details>
<summary><b>MacOS</b></summary>
<details>
<summary><b><i>MacOS</i></b></summary>
With Homebrew you can install the `GSL` binaries directly:
```
brew install gsl
```
</details>
- <details>
<summary><b>Windows</b></summary>
<details>
<summary><b><i>Windows</i></b></summary>
In Windows `GSL` is available a.o. through [cygwin](https://cygwin.com/index.html), which has a straight forward installation process.
Either head over to the website, download and install the setup-x86_64.exe file, or use PowerShell:
Expand All @@ -188,38 +188,38 @@ It is required to compile `abn`'s C/C++ code.
Start-Process -Wait -FilePath "C:\Program Files\cygwin\setup-x86_64.exe" -ArgumentList "/S" -PassThru
```
</details>
</details>
<details><summary><b>JAGS & rjags</b></summary>
[JAGS](https://mcmc-jags.sourceforge.io/), _Just Another Gibbs Sampler_, is a program for analyzing Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. [rjags](https://cran.r-project.org/web/packages/rjags/index.html) is R's interface to the `JAGS` library.
`JAGS` is required in some simulations `abn` can perform.

#### Installation

In principle, we could only install `JAGS` and have `rjags` be installed automatically as dependency when installing `abn`, however, there are situations where `rjags` cannot find the `JAGS` libraries or `jags` at runtime, and therefore we recommend installing `rjags` directly after `JAGS` so to make sure that everything works as expected:

- <details>
<summary><b>Ubuntu</b></summary>

</details>
- <details><summary><b>JAGS & rjags</b></summary>
[JAGS](https://mcmc-jags.sourceforge.io/), _Just Another Gibbs Sampler_, is a program for analyzing Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. [rjags](https://cran.r-project.org/web/packages/rjags/index.html) is R's interface to the `JAGS` library.
`JAGS` is required in some simulations `abn` can perform.
#### Installation
In principle, we could only install `JAGS` and have `rjags` be installed automatically as dependency when installing `abn`, however, there are situations where `rjags` cannot find the `JAGS` libraries or `jags` at runtime, and therefore we recommend installing `rjags` directly after `JAGS` so to make sure that everything works as expected:
<details>
<summary><b><i>Ubuntu</i></b></summary>
`JAGS` is available through the Advanced Package Tool, `APT`, simply type:

```bash
sudo apt-get install jags
```
And to install `rjags` open an R session and type:

```R
install.packages("rjags", configure.args="--enable-rpath", repos=c(CRAN="https://cran.r-project.org"))
library("rjags")
```

</details>
- <details>
<summary><b>Fedora</b></summary>

<details>
<summary><b><i>Fedora</i></b></summary>
`JAGS` must be installed from source.
Below are the steps to install `JAGS 4.3.2`.

```bash
wget -O /tmp/jags.tar.gz https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.3.2.tar.gz/download
cd /tmp
Expand All @@ -229,89 +229,89 @@ In principle, we could only install `JAGS` and have `rjags` be installed automat
make
sudo make install
```

**Note:**

_If you are on a 64bit system (you likely are) mind the `--libdir=/usr/local/lib64` argument when launching `./configure`._
_Omitting this argument will lead to `rjags` "not seeing" `jags`._


On Fedora `rjags` might need some special configuration for it to link properly to the `JAGS` library.
Also, it might be needed to add the path to the `JAGS` library to the linker path (see [rjags INSTALL file](https://github.com/cran/rjags/blob/master/INSTALL) for further details).

In order to add the `JAGS` library to the linker path, run the following commands:

```bash
sudo echo "/usr/local/lib64" > /etc/ld.so.conf.d/jags.conf
sudo /sbin/ldconfig
```
**Note:**
_These commands might not be needed, you might first try to install `rjags` (see below) and only run them if you encounter a `configure: error: Runtime link error`._

To install `rjags` open an R session and type:

```R
install.packages("rjags", configure.args="--enable-rpath", repos=c(CRAN="https://cran.r-project.org"))
```

</details>
- <details>
<summary><b>MacOS</b></summary>

<details>
<summary><b><i>MacOS</i></b></summary>
With Homebrew you can install the `JAGS` binaries directly:

```
brew install jags
```

And now to install `rjags`, open an R session and type:

```R
install.packages("rjags", type="source", repos=c(CRAN="https://cran.r-project.org"))
library("rjags")
```

</details>
- <details>
<summary><b>Windows</b></summary>

<details>
<summary><b><i>Windows</i></b></summary>
You can either head over to the [JAGS download page](https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/), download and execute the installable, or use PowerShell.
The following instructions will download and install `JAGS 4.3.1` in PowerShell:

```
Import-Module bitstransfer
New-Item -ItemType Directory -Force -Path "C:\Program Files\JAGS\JAGS-4.3.1"
start-bitstransfer -source https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Windows/JAGS-4.3.1.exe/download "C:\Program Files\JAGS\JAGS-4.3.1\JAGS-4.3.1.exe"
Start-Process -Wait -FilePath "C:\Program Files\JAGS\JAGS-4.3.1\JAGS-4.3.1.exe" -ArgumentList "/S" -PassThru
```

In order to make sure `rjags` finds `JAGS` we set the environment variable `JAGS_HOME` before installing `rjags`.
To do so, open your R session and type:

```R
Sys.setenv(JAGS_HOME="C:/Program Files/JAGS/JAGS-4.3.1")
install.packages("rjags", repos=c(CRAN="https://cran.r-project.org"))
library("rjags")
```


</details>
</details>
</details>
<details>
<summary><b>INLA</b></summary>

[INLA](https://www.r-inla.org/) is an R package that is not hosted on CRAN and thus needs to be installed separately.
`anb` uses `INLA` to fit some models.

#### Dependencies

`INLA` relies on various other R packages and C/C++ libraries.
It thus needs some additional installation steps:

- <details>
<summary><b>Ubuntu</b></summary>
<summary><b>INLA</b></summary>

[INLA](https://www.r-inla.org/) is an R package that is not hosted on CRAN and thus needs to be installed separately.
`anb` uses `INLA` to fit some models.

#### Dependencies

`INLA` relies on various other R packages and C/C++ libraries.
It thus needs some additional installation steps:

<details>
<summary><b><i>Ubuntu</i></b></summary>

Install with:

```bash
apt-get install --no-install-recommends libudunits2-dev
apt-get install libjpeg-dev
Expand All @@ -320,62 +320,62 @@ It thus needs some additional installation steps:
apt-get install libproj-dev
```
</details>
- <details>
<summary><b>Fedora</b></summary>
<details>
<summary><b><i>Fedora</i></b></summary>

Install with:

```bash
dnf install udunits2-devel
dnf install libjpeg-devel
dnf install gdal-devel
dnf install geos-devel
dnf install proj-devel
```

</details>
- <details>
<summary><b>MacOS</b></summary>
<details>
<summary><b><i>MacOS</i></b></summary>

Install with:

```bash
brew install udunits
brew install gdal # installs also geos as dependency
brew install proj
```


</details>

#### Installation

The installation is straight forward on common platforms, simply start an R session and run:

```R
install.packages("INLA", repos = c(getOption("repos"), INLA = "https://inla.r-inla-download.org/R/stable"), dep = TRUE)
```

If you run into trouble, please see also [INLA's installation instructions](https://www.r-inla.org/download-install) for further details.
</details>
- <details>
<summary><b>Dependencies from BiocManager</b></summary>
[Rgraphviz](https://www.bioconductor.org/packages/release/bioc/html/Rgraphviz.html) and [graph](https://bioconductor.org/packages/3.19/bioc/html/graph.html) are used to produce plots of network graphs.
Both packages are hosted on [Bioconductor](https://www.bioconductor.org/) and thus need to be installed with `BiocManager`:
#### Installation
The installation is straight forward on most common platforms, simply start an R session and run:
```R
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Rgraphviz")
BiocManager::install("graph")
```
</details>

#### Installation

The installation is straight forward on common platforms, simply start an R session and run:

```R
install.packages("INLA", repos = c(getOption("repos"), INLA = "https://inla.r-inla-download.org/R/stable"), dep = TRUE)
```

If you run into trouble, please see also [INLA's installation instructions](https://www.r-inla.org/download-install) for further details.
</details>
<details>
<summary><b>Dependencies from BiocManager</b></summary>
[Rgraphviz](https://www.bioconductor.org/packages/release/bioc/html/Rgraphviz.html) and [graph](https://bioconductor.org/packages/3.19/bioc/html/graph.html) are used to produce plots of network graphs.
Both packages are hosted on [Bioconductor](https://www.bioconductor.org/) and thus need to be installed with `BiocManager`:
#### Installation
The installation is straight forward on most common platforms, simply start an R session and run:
```R
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Rgraphviz")
BiocManager::install("graph")
```
</details>
_Click on each dependency to see the specific installation instructions_
Expand Down

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