recipe r-hemdag

a collection of Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs (DAGs).

Homepage:

https://CRAN.R-project.org/package=HEMDAG

Documentation:

https://hemdag.readthedocs.io

Developer docs:

https://github.com/marconotaro/hemdag

License:

GPL3 / GPL-3.0-or-later

Recipe:

/r-hemdag/meta.yaml

[](https://hemdag.readthedocs.io/en/latest/?badge=latest)

HEMDAG library: * implements several Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs (DAGs); * reconciles flat predictions with the topology of the ontology; * can enhance predictions of virtually any flat learning methods by taking into account the hierarchical relationships between ontology classes; * provides biologically meaningful predictions that always obey the true-path-rule, the biological and logical rule that governs the internal coherence of biomedical ontologies; * is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but can be safely applied to tree-structured taxonomies as well (e.g. FunCat), since trees are DAGs; * scales nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples; * provides several utility functions to process and analyze graphs; * provides several performance metrics to evaluate HEMs algorithms.

package r-hemdag

versions:

2.7.4-8,  2.7.4-7,  2.7.4-6,  2.7.4-5,  2.7.4-4,  2.7.4-3,  2.7.4-2,  2.7.4-1,  2.7.4-0, 

2.7.4-8,  2.7.4-7,  2.7.4-6,  2.7.4-5,  2.7.4-4,  2.7.4-3,  2.7.4-2,  2.7.4-1,  2.7.4-0,  2.7.3-2,  2.7.3-0,  2.6.1-1,  2.6.1-0,  2.6.0-0,  2.5.9-0,  2.4.8-0,  2.4.7-1,  2.4.7-0,  2.2.5-1,  2.2.5-0,  2.1.3-0,  2.1.2-0,  2.0.1-0

depends bioconductor-graph:

>=1.84.0,<1.85.0a0

depends bioconductor-preprocesscore:

>=1.68.0,<1.69.0a0

depends bioconductor-rbgl:

>=1.82.0,<1.83.0a0

depends libgcc:

>=13

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-doparallel:

depends r-foreach:

depends r-plyr:

depends r-precrec:

requirements:

additional platforms:

linux-aarch64

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install r-hemdag

and update with::

   mamba update r-hemdag

To create a new environment, run:

mamba create --name myenvname r-hemdag

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

(see `r-hemdag/tags`_ for valid values for ``<tag>``)

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