diff --git a/.github/workflows/onlabel_Fedora_setup.yml b/.github/workflows/Fedora_setup.yml
similarity index 55%
rename from .github/workflows/onlabel_Fedora_setup.yml
rename to .github/workflows/Fedora_setup.yml
index 56047282a..1dfba6136 100644
--- a/.github/workflows/onlabel_Fedora_setup.yml
+++ b/.github/workflows/Fedora_setup.yml
@@ -44,13 +44,12 @@ jobs:
- name: install config and build dependencies
run: |
- dnf -y install pkg-config
- dnf -y install cmake
- dnf -y install R-devtools
+ dnf -y install libcurl-devel # needed for pak
- - name: install GSL
+ - name: install pak
run: |
- dnf -y install gsl-devel
+ install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
+ shell: Rscript {0}
- name: install JAGS
run: |
@@ -73,38 +72,16 @@ jobs:
library("rjags")
shell: Rscript {0}
- - name: install INLA dependencies
- run: |
- dnf -y install udunits2-devel
- dnf -y install libcurl-devel # rCurls package (for INLA)
- dnf -y install openssl-devel # s2 package
- dnf -y install libjpeg-devel # jpeg package
- dnf -y install proj-devel # sf package
- dnf -y install geos-devel # sf package
- dnf -y install gdal-devel # terra package
-
- - name: install INLA
- run: |
- install.packages("INLA", repos = c(CRAN = "https://cran.r-project.org", INLA = "https://inla.r-inla-download.org/R/stable"), dep = TRUE)
- shell: Rscript {0}
-
- - name: installing dependencies from BiocManager
- run: |
- if (!requireNamespace("BiocManager", quietly = TRUE))
- install.packages("BiocManager", repos=c(CRAN="https://cran.r-project.org"))
- BiocManager::install("Rgraphviz")
- BiocManager::install("graph")
- shell: Rscript {0}
-
- - name: install from CRAN
- run: |
- install.packages('abn', repos=c(CRAN="https://cran.r-project.org"))
- library('abn')
- shell: Rscript {0}
+ # - name: install from CRAN with pak
+ # run: |
+ # pak::pkg_install('abn', dependencies=TRUE)
+ # library('abn')
+ # shell: Rscript {0}
- - name: install from GitHub
+ - name: pak install from GitHub
run: |
- devtools::install_github("furrer-lab/abn", ref="${{ env.BRANCH }}", dependencies=c("Depends", "Imports", "LinkingTo"), local=FALSE)
+ pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/")
+ pak::pkg_install("furrer-lab/abn@${{ env.BRANCH }}", dependencies=TRUE)
library('abn')
shell: Rscript {0}
@@ -118,7 +95,5 @@ jobs:
- name: install from source
run: |
- devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade='never', repos=c(CRAN="https://cran.r-project.org"))
- devtools::build(pkg = '.', path = '${{ env.BUILD_LOC }}/abn.tar.gz', vignettes = FALSE)
- install.packages('${{ env.BUILD_LOC }}/abn.tar.gz', repos=NULL, type="source")
+ pak::local_install(dependencies=TRUE)
shell: Rscript {0}
diff --git a/.github/workflows/onlabel_Macos_setup.yml b/.github/workflows/Macos_setup.yml
similarity index 60%
rename from .github/workflows/onlabel_Macos_setup.yml
rename to .github/workflows/Macos_setup.yml
index 1b7027d9d..e8e0dd8d7 100644
--- a/.github/workflows/onlabel_Macos_setup.yml
+++ b/.github/workflows/Macos_setup.yml
@@ -39,11 +39,11 @@ jobs:
run: |
brew install jags
- - name: install rjags
- run: |
- install.packages("rjags", type="source", repos=c(CRAN="https://cran.r-project.org"))
- library("rjags")
- shell: Rscript {0}
+ # - name: install rjags
+ # run: |
+ # install.packages("rjags", type="source", repos=c(CRAN="https://cran.r-project.org"))
+ # library("rjags")
+ # shell: Rscript {0}
- name: install INLA dependencies
run: |
@@ -58,23 +58,21 @@ jobs:
install.packages("INLA", repos = c(CRAN = "https://cran.r-project.org", INLA = "https://inla.r-inla-download.org/R/stable"), dep = TRUE)
shell: Rscript {0}
- - name: installing dependencies from BiocManager
+ - name: install pak
run: |
- if (!requireNamespace("BiocManager", quietly = TRUE))
- install.packages("BiocManager", repos=c(CRAN="https://cran.r-project.org"))
- BiocManager::install("Rgraphviz")
- BiocManager::install("graph")
+ install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
shell: Rscript {0}
- - name: install from CRAN
- run: |
- install.packages('abn', repos=c(CRAN="https://cran.r-project.org"))
- library('abn')
- shell: Rscript {0}
+ # - name: install from CRAN with pak
+ # run: |
+ # pak::pkg_install('abn', dependencies=TRUE)
+ # library('abn')
+ # shell: Rscript {0}
- - name: install from GitHub
+ - name: pak install from GitHub
run: |
- devtools::install_github("furrer-lab/abn", ref="${{ env.BRANCH }}", dependencies=c("Depends", "Imports", "LinkingTo"), local=FALSE)
+ pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/")
+ pak::pkg_install("furrer-lab/abn@${{ env.BRANCH }}", dependencies=TRUE)
library('abn')
shell: Rscript {0}
@@ -88,7 +86,5 @@ jobs:
- name: install from source
run: |
- devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade='never', repos=c(CRAN="https://cran.r-project.org"))
- devtools::build(pkg = '.', path = '${{ env.BUILD_LOC }}/abn.tar.gz', vignettes = FALSE)
- install.packages('${{ env.BUILD_LOC }}/abn.tar.gz', repos=NULL, type="source")
+ pak::local_install(dependencies=TRUE)
shell: Rscript {0}
diff --git a/.github/workflows/Ubuntu_setup.yml b/.github/workflows/Ubuntu_setup.yml
new file mode 100644
index 000000000..08596207c
--- /dev/null
+++ b/.github/workflows/Ubuntu_setup.yml
@@ -0,0 +1,77 @@
+# Workflow is triggered on label and check installation on various operating systems
+# This action is adapted from https://github.com/t4d-gmbh/stubbed_versioning
+name: Ubuntu Install
+
+on:
+ push:
+ branches:
+ - "main"
+
+env:
+ BRANCH: ${{ github.head_ref || github.ref_name }}
+
+permissions:
+ packages: read
+ contents: write
+ pull-requests: write
+ repository-projects: write
+
+jobs:
+ setup-and-install:
+ runs-on: ubuntu-latest
+ name: ubuntu-latest R release
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ R_KEEP_PKG_SOURCE: yes
+
+ steps:
+
+ - name: Update and upgrade
+ run: |
+ sudo apt-get update && sudo apt-get upgrade
+
+ - name: install R
+ run: |
+ sudo apt-get -y install r-base
+
+ - name: fixing folder perms for local lib
+ run: |
+ sudo chown root:adm -R /usr/lib/R
+ sudo chmod g+w -R /usr/lib/R
+ sudo chown root:adm -R /usr/local/lib/R
+ sudo chmod g+w -R /usr/local/lib/R
+
+ - name: install config and build dependencies
+ run: |
+ sudo apt-get -y install libcurl4-openssl-dev # needed for pak
+
+ - name: install pak
+ run: |
+ install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
+ shell: Rscript {0}
+
+ # - name: install from CRAN with pak
+ # run: |
+ # pak::pkg_install('abn', dependencies=TRUE)
+ # library('abn')
+ # shell: Rscript {0}
+
+ - name: pak install from GitHub
+ run: |
+ pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/")
+ pak::pkg_install("furrer-lab/abn@${{ env.BRANCH }}", dependencies=TRUE)
+ library('abn')
+ shell: Rscript {0}
+
+ - name: fetch the repository from GitHub
+ uses: actions/checkout@v4
+
+ - name: deactivate the renv
+ run: |
+ renv::deactivate()
+ shell: Rscript {0}
+
+ - name: install from source
+ run: |
+ pak::local_install(dependencies=TRUE)
+ shell: Rscript {0}
diff --git a/.github/workflows/onlabel_Windows_setup.yml b/.github/workflows/Windows_setup.yml
similarity index 65%
rename from .github/workflows/onlabel_Windows_setup.yml
rename to .github/workflows/Windows_setup.yml
index d5ebad6c3..b3f6a30bd 100644
--- a/.github/workflows/onlabel_Windows_setup.yml
+++ b/.github/workflows/Windows_setup.yml
@@ -29,9 +29,9 @@ jobs:
R_KEEP_PKG_SOURCE: yes
steps:
- - name: prepare windows
+ - name: install pak
run: |
- install.packages("devtools", repos=c(CRAN="https://cran.r-project.org"))
+ install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
shell: Rscript {0}
- name: install GSL
@@ -55,28 +55,16 @@ jobs:
library("rjags")
shell: Rscript {0}
- - name: install INLA
- run: |
- install.packages("INLA", repos = c(CRAN = "https://cran.r-project.org", INLA = "https://inla.r-inla-download.org/R/stable"), dep = TRUE)
- shell: Rscript {0}
-
- - name: installing dependencies from BiocManager
- run: |
- if (!requireNamespace("BiocManager", quietly = TRUE))
- install.packages("BiocManager", repos=c(CRAN="https://cran.r-project.org"))
- BiocManager::install("Rgraphviz")
- BiocManager::install("graph")
- shell: Rscript {0}
-
- - name: install from CRAN
- run: |
- install.packages('abn', repos=c(CRAN="https://cran.r-project.org"))
- library('abn')
- shell: Rscript {0}
+ # - name: install from CRAN with pak
+ # run: |
+ # pak::pkg_install('abn', dependencies=TRUE)
+ # library('abn')
+ # shell: Rscript {0}
- - name: install from GitHub
+ - name: pak install from GitHub
run: |
- devtools::install_github("furrer-lab/abn", ref="${{ env.BRANCH }}", dependencies=c("Depends", "Imports", "LinkingTo"), local=FALSE)
+ pak::repo_add(INLA = "https://inla.r-inla-download.org/R/stable/")
+ pak::pkg_install("furrer-lab/abn@${{ env.BRANCH }}", dependencies=TRUE)
library('abn')
shell: Rscript {0}
@@ -90,7 +78,12 @@ jobs:
- name: install from source
run: |
- devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade='never', repos=c(CRAN="https://cran.r-project.org"))
- devtools::build(pkg = '.', path = '${{ env.BUILD_LOC }}/abn.tar.gz', vignettes = FALSE)
- install.packages('${{ env.BUILD_LOC }}/abn.tar.gz', repos=NULL, type="source")
+ pak::local_install(dependencies=TRUE)
+ shell: Rscript {0}
+
+ - name: run the tests
+ run: |
+ pak::pak('r-lib/testthat')
+ library("abn")
+ testthat::test_local(path='tests', load_package='none')
shell: Rscript {0}
diff --git a/.github/workflows/onlabel_Ubuntu_setup.yml b/.github/workflows/onlabel_Ubuntu_setup.yml
deleted file mode 100644
index c0f3fe5bb..000000000
--- a/.github/workflows/onlabel_Ubuntu_setup.yml
+++ /dev/null
@@ -1,113 +0,0 @@
-# Workflow is triggered on label and check installation on various operating systems
-# This action is adapted from https://github.com/t4d-gmbh/stubbed_versioning
-name: Ubuntu Install
-
-on:
- push:
- branches:
- - "main"
-
-env:
- JAGS: '4.3.2'
- BUILD_LOC: "./build"
- BRANCH: ${{ github.head_ref || github.ref_name }}
-
-permissions:
- packages: read
- contents: write
- pull-requests: write
- repository-projects: write
-
-jobs:
- setup-and-install:
- runs-on: ubuntu-latest
- name: ubuntu-latest R release
- env:
- GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
- R_KEEP_PKG_SOURCE: yes
- steps:
-
- - name: install R
- run: |
- sudo apt-get -y install r-base
-
- - name: install config and build dependencies
- run: |
- sudo apt-get -y install pkg-config
- sudo apt-get -y install cmake
- sudo apt-get -y install r-cran-devtools
-
- - name: fixing folder perms for local lib
- run: |
- sudo chown root:adm -R /usr/lib/R
- sudo chmod g+w -R /usr/lib/R
- sudo chown root:adm -R /usr/local/lib/R
- sudo chmod g+w -R /usr/local/lib/R
-
- - name: update R packages
- run: |
- update.packages(ask = FALSE, checkBuilt = TRUE)
- shell: Rscript {0}
-
- - name: install GSL
- run: |
- sudo apt-get -y install libgsl-dev
-
- - name: install JAGS
- run: |
- sudo apt-get -y install jags
-
- - name: install rjags
- run: |
- install.packages("rjags", configure.args="--enable-rpath", repos=c(CRAN="https://cran.r-project.org"))
- library("rjags")
- shell: Rscript {0}
-
- - name: install INLA dependencies
- run: |
- sudo apt-get install -y --no-install-recommends libudunits2-dev
- sudo apt -y install libcurl4-openssl-dev # rCurl for (for INLA)
- sudo apt-get -y install libssl-dev # s2 package
- sudo apt-get -y install libproj-dev # sf package
- sudo apt-get -y install libgeos-dev # terra package
- sudo apt-get -y install libgdal-dev # terra package
-
- - name: install INLA
- run: |
- install.packages("INLA", repos = c(CRAN = "https://cran.r-project.org", INLA = "https://inla.r-inla-download.org/R/stable"), dep = TRUE)
- shell: Rscript {0}
-
- - name: installing dependencies from BiocManager
- run: |
- if (!requireNamespace("BiocManager", quietly = TRUE))
- install.packages("BiocManager", repos=c(CRAN="https://cran.r-project.org"))
- BiocManager::install("Rgraphviz")
- BiocManager::install("graph")
- shell: Rscript {0}
-
- - name: install from CRAN
- run: |
- install.packages('abn', repos=c(CRAN="https://cran.r-project.org"))
- library('abn')
- shell: Rscript {0}
-
- - name: install from GitHub
- run: |
- devtools::install_github("furrer-lab/abn", ref="${{ env.BRANCH }}", dependencies=c("Depends", "Imports", "LinkingTo"), local=FALSE)
- library('abn')
- shell: Rscript {0}
-
- - name: fetch the repository from GitHub
- uses: actions/checkout@v4
-
- - name: deactivate the renv
- run: |
- renv::deactivate()
- shell: Rscript {0}
-
- - name: install from source
- run: |
- devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade='never', repos=c(CRAN="https://cran.r-project.org"))
- devtools::build(pkg = '.', path = '${{ env.BUILD_LOC }}/abn.tar.gz', vignettes = FALSE)
- install.packages('${{ env.BUILD_LOC }}/abn.tar.gz', repos=NULL, type="source")
- shell: Rscript {0}
diff --git a/DESCRIPTION b/DESCRIPTION
index 7e924332b..b7cd02393 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -51,8 +51,6 @@ Imports:
Rgraphviz,
rjags,
stringi,
- entropy,
- moments
Suggests:
bookdown,
boot,
@@ -62,13 +60,16 @@ Suggests:
gridExtra,
INLA,
knitr,
- Matrix (>= 1.6.3),
+ Matrix,
MatrixModels (>= 0.5.3),
microbenchmark,
R.rsp,
RhpcBLASctl,
rmarkdown,
- testthat (>= 3.0.0)
+ testthat (>= 3.0.0),
+ entropy,
+ moments,
+ R6
LinkingTo:
Rcpp,
RcppArmadillo
@@ -77,7 +78,7 @@ VignetteBuilder:
Additional_repositories: https://inla.r-inla-download.org/R/stable/
Config/testthat/edition: 3
Encoding: UTF-8
-LazyData: true
+LazyData: TRUE
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
-SystemRequirements: Gnu Scientific Library version >= 1.12, jpeg, gdal, geos, proj
+SystemRequirements: pkg-config, cmake, gsl, jpeg, gdal, geos, proj, udunits-2, openssl, libcurl, jags
diff --git a/README.md b/README.md
index 667eaae18..d526d51e6 100644
--- a/README.md
+++ b/README.md
@@ -18,175 +18,80 @@ It derives a directed acyclic graph (DAG) from empirical data that describes the
The package provides routines for structure learning and parameter estimation of additive Bayesian network models.
# Installation
-[](https://github.com/furrer-lab/abn/actions/workflows/onlabel_Ubuntu_setup.yml)
-[](https://github.com/furrer-lab/abn/actions/workflows/onlabel_Fedora_setup.yml)
-[](https://github.com/furrer-lab/abn/actions/workflows/onlabel_Macos_setup.yml)
-[](https://github.com/furrer-lab/abn/actions/workflows/onlabel_Windows_setup.yml)
+[](https://github.com/furrer-lab/abn/actions/workflows/Ubuntu_setup.yml)
+[](https://github.com/furrer-lab/abn/actions/workflows/Fedora_setup.yml)
+[](https://github.com/furrer-lab/abn/actions/workflows/Macos_setup.yml)
+[](https://github.com/furrer-lab/abn/actions/workflows/Windows_setup.yml)
`abn` and its installation process relies on various software that might, or might not, be present in your system.
## Prior to installing
-In order for `abn` to work correctly on your system some dependencies need to be installed first.
-The required steps to achieve this are specific to the operating system you are using and the following drop-down sections detail these steps for the most common ones:
+In order for `abn` to work correctly on your system some dependencies need to be installed.
+If you are on a Linux based system (most of) these dependencies are installed automatically for you when following the [pak](https://pak.r-lib.org/)-based installation procedure described in the [Installing from GitHub](#installing-from-github-recommended) section.
+For MacOS and Windows based system some more preparatory steps are required.
+
+The following paragraphs provide detailed instructions for the most common operating systems on the steps that need to be carried out prior to installing `abn`.
Ubuntu
-#### Prerequisites
-
-Most likely you have R installed already but if not run:
+You presumably have R installed already, if not, open a terminal and type:
```bash
apt-get install r-base
```
-To configure and build `abn` correctly we need `cmake` and `pkg-config`, as well as, the R `devtools` package:
-
-```bash
-apt-get install pkg-config
-apt-get install cmake
-apt-get install r-cran-devtools
-```
-
-Finally, we will use `wget` to download `JAGS` later, as well as, the development headers of `curl` and `openssl`:
-
-```bash
-apt-get install wget
-apt-get install libcurl4-openssl-dev
-apt-get install libssl-dev
-
-```
-
-#### Dependencies
+_**Note:** You might need to prepend `sudo ` to this command._
-- **GSL**
+All you need for the installation is to have the R-package [pak](https://pak.r-lib.org/) installed.
+`pak` is installed like any other R-package, however, it relies on `curl` being present on your system, so we make sure it is there:
- [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.
-
- `GSL` is available through the Advanced Package Tool, `APT`, simply type:
-
```bash
- sudo apt-get install libgsl-dev
+ apt-get install libcurl4-openssl-dev
```
+ Now, to install `pak` we start an R session and write:
-- **JAGS & rjags**
-
- [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.
-
- `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")
+ install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
```
-- **INLA**
-
- [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.
-
- `INLA` relies on various other R packages and C/C++ libraries.
- It thus needs some additional installation steps:
-
- ```bash
- apt-get install --no-install-recommends libudunits2-dev
- apt-get install libjpeg-dev
- apt-get install libgdal-dev
- apt-get install libgeos-dev # might not be needed
- apt-get install libproj-dev
- ```
-
- Now, to install `INLA` itself, 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.
-
-- **Dependencies from BiocManager**
-
- [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`:
-
- 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")
- ```
+ With that you should be ready to [install `abn` from GitHub](#installing-from-github-recommended).
Fedora
-#### Prerequisites
-
- You will need C/C++ and Fortran compilers and various libraries:
-
- ```bash
- dnf install gcc
- dnf install gcc-c++
- dnf install gfortran
- dnf install lapack* # is needed on fedora server
- dnf install blas*
- dnf install atlas*
- ```
-
- Most likely you have R installed already but if not run:
+ You presumably have R installed already, if not, open a terminal and type:
```bash
dnf install R
```
-
- To configure and build `abn` correctly we need `cmake` and `pkg-config`, as well as, the R `devtools` package:
-
- ```bash
- dnf install pkg-config
- dnf install cmake
- dnf install R-devtools
- ```
-
- Finally, we will use `wget` to download `JAGS` later, as well as, the development headers of `curl` and `openssl`:
-
+
+ _**Note:** You might need to prepend `sudo ` to this command._
+
+ For the installation you need to have the R-package [pak](https://pak.r-lib.org/) installed.
+ `pak` is installed like any other R-package, however, it relies on `curl` being installed on your system, so we make sure it is there:
+
```bash
- dnf install wget
dnf install libcurl-devel
- dnf install openssl-devel
```
+ Now, to install `pak` we start an R session and write:
-#### Dependencies
-
-- **GSL**
+ ```R
+ install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
+ ```
- [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.
+ There is one more thing we need to do before we can install `abn`:
- `GSL` is available through Fedoras standard package manager, `DNF`, simply type:
-
- ```bash
- sudo dnf install gsl-devel
- ```
+ **Install JAGS from source**
-- **JAGS & rjags**
-
[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.
- `JAGS` must be installed from source.
- Below are the steps to install `JAGS 4.3.2`.
+ The steps needed to install `JAGS 4.3.2` are:
```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
@@ -198,10 +103,9 @@ apt-get install libssl-dev
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`.
-
+ _**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).
@@ -213,68 +117,37 @@ apt-get install libssl-dev
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:
+ _**Note:**_
+ _These commands might not be needed, you might first try to install the R-package `rjags` and only run them if you encounter a `configure: error: Runtime link error`._
+
+ With that you should be ready to [install `abn` from GitHub](#installing-from-github-recommended).
- ```R
- install.packages("rjags", configure.args="--enable-rpath", repos=c(CRAN="https://cran.r-project.org"))
- ```
+
-- **INLA**
+
+MacOS
- [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.
-
- `INLA` relies on various other R packages and C/C++ libraries.
- It thus needs some additional installation steps:
-
+ Most likely you have R installed already but if not run:
+
```bash
- dnf install udunits2-devel
- dnf install libjpeg-devel
- dnf install gdal-devel
- dnf install geos-devel
- dnf install proj-devel
- ```
-
- Now, to install `INLA` itself, 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)
+ brew install R
```
-
- If you run into trouble, please see also [INLA's installation instructions](https://www.r-inla.org/download-install) for further details.
-- **Dependencies from BiocManager**
+ For the installation you need to have the R-package [pak](https://pak.r-lib.org/) installed.
+ `pak` is installed like any other R-package, we start an R session and write:
- [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`:
-
- 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")
+ install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
```
-
-
-
-MacOS
-
-#### Prerequisites
-
-
- 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:
+ We will install the system dependencies with [Homebrew](https://brew.sh/).
+ Head over to their site to see the installation process or simply open a terminal and run:
```bash
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
```
- To configure and build `abn` correctly we need `cmake` and `pkg-config`:
+ To correctly link to installed libraries and to build them, we need `pkg-config` and `automake`:
```bash
brew install pkg-config
@@ -288,154 +161,133 @@ apt-get install libssl-dev
brew install openssl@1.1
```
- Most likely you have R installed already but if not run:
-
- ```bash
- brew install R
- ```
-
-
-#### Dependencies
-
-- **GSL**
-
- [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.
-
- With Homebrew you can install the `GSL` binaries directly:
-
- ```
- brew install gsl
- ```
-
-- **JAGS & rjags**
-
- [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.
-
- 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")
- ```
-
-- **INLA**
-
- [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.
-
- `INLA` relies on various other R packages and C/C++ libraries.
- It thus needs some additional installation steps:
-
- ```bash
- brew install udunits
- brew install gdal # installs also geos as dependency
- brew install proj
- ```
-
- Now, to install `INLA` itself, 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.
-
-- **Dependencies from BiocManager**
-
- [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`:
-
- 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")
- ```
+ #### Dependencies
+
+ On MacOS we need to install some system dependencies separately:
+
+
+ - **GSL**
+
+ [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.
+
+ With Homebrew you can install the `GSL` binaries directly:
+
+ ```
+ brew install gsl
+ ```
+
+ - **JAGS & rjags**
+
+ [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.
+
+ 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")
+ ```
+
+ - **INLA**
+
+ [INLA](https://www.r-inla.org/) is an R package that is not hosted on CRAN and thus needs to be installed separately.
+ `abn` uses `INLA` to fit some models.
+
+ `INLA` relies on various other R packages and C/C++ libraries.
+ It thus needs some additional installation steps:
+
+ ```bash
+ brew install udunits
+ brew install gdal # installs also geos as dependency
+ brew install proj
+ ```
+
+ Now, to install `INLA` itself, 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.
Windows
-#### Dependencies
-
-- **GSL**
-
- [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.
-
- 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:
-
- ```
- Import-Module bitstransfer
- New-Item -ItemType Directory -Force -Path "C:\Program Files\cygwin"
- start-bitstransfer -source https://cygwin.com/setup-x86_64.exe "C:\Program Files\cygwin\setup-x86_64.exe"
- Start-Process -Wait -FilePath "C:\Program Files\cygwin\setup-x86_64.exe" -ArgumentList "/S" -PassThru
- ```
+ For the installation you need to have the R-package [pak](https://pak.r-lib.org/) installed.
+ `pak` is installed like any other R-package, we start an R session and write:
-- **JAGS & rjags**
-
- [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.
-
-
- 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")
- ```
-
-- **INLA**
-
- [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.
-
- The installation is straight forward, 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.
-
-- **Dependencies from BiocManager**
-
- [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`:
-
- The installation is straight forward on most common platforms, simply start an R session and run:
+ install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
+ ```
+
+
+ #### Dependencies
+
+ On Windows we need to install some system dependencies separately:
+
+
+ - **GSL**
+
+ [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.
+
+ 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:
+
+ ```
+ Import-Module bitstransfer
+ New-Item -ItemType Directory -Force -Path "C:\Program Files\cygwin"
+ start-bitstransfer -source https://cygwin.com/setup-x86_64.exe "C:\Program Files\cygwin\setup-x86_64.exe"
+ Start-Process -Wait -FilePath "C:\Program Files\cygwin\setup-x86_64.exe" -ArgumentList "/S" -PassThru
+ ```
+
+ - **JAGS & rjags**
+
+ [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.
+
+
+ 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")
+ ```
+
+ - **INLA**
+
+ [INLA](https://www.r-inla.org/) is an R package that is not hosted on CRAN and thus needs to be installed separately.
+ `abn` uses `INLA` to fit some models.
+
+ The installation is straight forward, 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.
- ```R
- if (!requireNamespace("BiocManager", quietly = TRUE))
- install.packages("BiocManager")
- BiocManager::install("Rgraphviz")
- BiocManager::install("graph")
- ```
-
_Click on your operating system to see the specific installation instructions_
@@ -451,34 +303,37 @@ We recommend to not directly install `main`, but to a specific version.
Head over to our [version list](https://github.com/furrer-lab/abn/releases) to see which one is the latest version.
Here we assume the version is `3.1.1`.
-We use [devtools](https://github.com/r-lib/devtools) to install from GitHub.
-At this point `devtools` should already be installed in your system.
-if not, install it first.
Open an R session and type:
+We use [pak](https://pak.r-lib.org/) for the installation process.
+If you followed the [Prior to installing](#prior-to-installing) section `pak` should already be installed.
+If not, install it first.
Open an R session and type:
```R
-install.packages("devtools", repos=c(CRAN="https://cran.r-project.org"))
+install.packages('pak', repos=c(CRAN="https://cran.r-project.org"))
```