Package Recipe 'r-grbase'

recipe r-grbase

The 'gRbase' package provides graphical modelling features used by e.g. the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' implements graph algorithms including (i) maximum cardinality search (for marked and unmarked graphs). (ii) moralization, (iii) triangulation, (iv) creation of junction tree. 'gRbase' facilitates array operations, 'gRbase' implements functions for testing for conditional independence. 'gRbase' illustrates how hierarchical log-linear models may be implemented and describes concept of graphical meta data. The facilities of the package are documented in the book by Højsgaard, Edwards and Lauritzen (2012, <doi:10.1007/978-1-4614-2299-0>) and in the paper by Dethlefsen and Højsgaard, (2005, <doi:10.18637/jss.v014.i17>). Please see 'citation("gRbase")' for citation details. NOTICE 'gRbase' requires that the packages graph, 'Rgraphviz' and 'RBGL' are installed from 'bioconductor'; for installation instructions please refer to the web page given below.

Homepage:: http://people.math.aau.dk/~sorenh/software/gR/
License:: GPL2 / GPL-2.0-or-later
Recipe:: /r-grbase/meta.yaml

package r-grbase¶

Versions:

2.0.3-2, 2.0.3-1, 2.0.3-0, 2.0.2-0, 2.0.1-1, 2.0.1-0, 2.0.0-0, 1.9.0-0, 1.8.9-3,

2.0.3-2, 2.0.3-1, 2.0.3-0, 2.0.2-0, 2.0.1-1, 2.0.1-0, 2.0.0-0, 1.9.0-0, 1.8.9-3, 1.8.9-2, 1.8.9-1, 1.8.9-0, 1.8.8-1, 1.8.8-0, 1.8.7-1, 1.8.7-0, 1.8_6.7-2, 1.8_6.7-1, 1.8_6.7-0, 1.8_3.4-6, 1.8_3.4-5, 1.8_3.4-4, 1.8_3.4-3, 1.8_3.4-2, 1.8_3.4-1, 1.8_3.4-0

Depends:

on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on libstdcxx >=14
on r-base >=4.5,<4.6.0a0
on r-igraph
on r-magrittr
on r-matrix
on r-rcpp >=0.11.1
on r-rcpparmadillo
on r-rcppeigen

Additional platforms:

linux-aarch64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install r-grbase

to add into an existing workspace instead, run:

pixi add r-grbase

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install r-grbase

Alternatively, to install into a new environment, run:

conda create -n envname r-grbase

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/r-grbase:<tag>

(see r-grbase/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

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