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bnaiar

Bayesian Network Analysis of Intracranial Aneurysm

https://github.com/matteodelucchi/bnaiar

Science Score: 57.0%

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Repository

Bayesian Network Analysis of Intracranial Aneurysm

Basic Info
  • Host: GitHub
  • Owner: matteodelucchi
  • License: cc-by-4.0
  • Language: R
  • Default Branch: main
  • Size: 102 MB
Statistics
  • Stars: 3
  • Watchers: 3
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 4 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Citation

README.md

bnaiaR

Bayesian Network Analysis of Intracranial Aneurysm. Data preparation and analysis of risk factors for intracranial aneurysms.

Installation

You can install the released version of bnaiaR from Github with:

r devtools::install_github("matteodelucchi/bnaiaR")

In case of installation issues caused by the package igraph, check this post: github.com/igraph

To ensure smooth compatibility and to remain your local setup untouched, I recommend to use this package within a virtual environment from renv. A local installation of mcmcabn was used,which can be installed withrenv` following this guide.

Description

Data

There are different data sets attached to the package. For example, the preprocessed raw data can be accessed with this command.

r data(adb)

The data sets description can be accessed in the respective help page.

r help(adb)

To follow the data preparation and more details consider the vignettes in this order:

  1. rawdataharmonization: Querying the raw data from a private data base resulting in the adb.raw data set.
  2. data_preprocessing: From raw data to the preprocessed adb data set.
  3. datapreparationfor_experiments: Implementation of prior knowledge (blacklist, banned-matrix), specification of variable distributions and variable selection for each analysis scenario.
  4. correlation_analysis: Descriptive statistics.
  5. regression_analysis: Multivariable logistic regression models.
  6. Discrete BN structure learning: Structure learning for discrete BNs.
  7. DBN validation: Classification error estimation and inference.

  8. ABN analysis: Structure learning was performed on a high-performance computing cluster followed by local postprocessing Details from additive BNs.

  9. For the publication additional figures and tables were produced.

Citations

If you make use of this R package or one of its data sets in your research we would appreciate a citation of the following article:

Matteo Delucchi, Georg R. Spinner, Marco Scutari, Philippe Bijlenga, Sandrine Morel, Christoph M. Friedrich, Reinhard Furrer and Sven Hirsch. 2022. Bayesian network analysis reveals the interplay of intracranial aneurysm rupture risk factors. Computers in Biology and Medicine. 10.1016/j.compbiomed.2022.105740.

you can get it as BibTeX entry with

r citation("bnaiaR")

Owner

  • Name: Matteo Delucchi
  • Login: matteodelucchi
  • Kind: user
  • Location: Switzerland
  • Company: Zurich University of Applied Sciences ZHAW @hirsch-lab

I like espresso. README: linkedin.com/in/matteodelucchi/

Citation (CITATION.cff) 

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.2.2
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "bnaiaR" in publications use:'
type: software
license: CC-BY-4.0
title: 'bnaiaR: Bayesian Network Analysis of Intracranial Aneurysm'
version: 1.0.0.0000
abstract: Data preparation and analysis of risk factors for intracranial aneurysms.
authors:
- family-names: Delucchi
  given-names: Matteo
  email: matteo.delucchi@zhaw.ch
  orcid: https://orcid.org/0000-0002-9327-1496
preferred-citation:
  type: article
  title: Bayesian network analysis reveals the interplay of intracranial aneurysm
    rupture risk factors
  authors:
  - family-names: Delucchi
    given-names: Matteo
    email: matteo.delucchi@zhaw.ch
    orcid: https://orcid.org/0000-0002-9327-1496
  - family-names: Spinner
    given-names: Georg R.
  - family-names: Scutari
    given-names: Marco
  - family-names: Bijlenga
    given-names: Philippe
  - family-names: Morel
    given-names: Sandrine
  - family-names: Friedrich
    given-names: Christoph M.
  - family-names: Furrer
    given-names: Reinhard
  - family-names: Hirsch
    given-names: Sven
  journal: Computers in Biology and Medicine
  year: '2022'
  volume: '105740'
  url: https://doi.org/10.1016/j.compbiomed.2022.105740
repository-code: https://github.com/hirsch-lab/bnaiaR/releases/tag/v1.0
url: https://github.com/hirsch-lab/bnaiaR/releases/tag/v1.0
date-released: '2022-06-21'
contact:
- family-names: Delucchi
  given-names: Matteo
  email: matteo.delucchi@zhaw.ch
  orcid: https://orcid.org/0000-0002-9327-1496
references:
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  notes: Suggests
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  notes: Suggests
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  notes: Suggests
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- type: software
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  abstract: 'sjPlot: Data Visualization for Statistics in Social Science'
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  url: https://CRAN.R-project.org/package=sjPlot
- type: software
  title: survminer
  abstract: 'survminer: Drawing Survival Curves using ''ggplot2'''
  notes: Suggests
  authors:
  - family-names: Kassambara
    given-names: Alboukadel
    email: alboukadel.kassambara@gmail.com
  - family-names: Kosinski
    given-names: Marcin
  - family-names: Biecek
    given-names: Przemyslaw
    email: przemyslaw.biecek@gmail.com
  year: '2022'
  url: https://CRAN.R-project.org/package=survminer
- type: software
  title: survAUC
  abstract: 'survAUC: Estimators of prediction accuracy for time-to-event data.'
  notes: Suggests
  authors:
  - family-names: Potapov
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  year: '2022'
  url: https://CRAN.R-project.org/package=survAUC
- type: software
  title: survival
  abstract: 'survival: Survival Analysis'
  notes: Suggests
  authors:
  - family-names: Therneau
    given-names: Terry M
    email: therneau.terry@mayo.edu
  year: '2022'
  url: https://CRAN.R-project.org/package=survival
- type: software
  title: Rgraphviz
  abstract: 'Rgraphviz: Provides plotting capabilities for R graph objects'
  notes: Suggests
  authors:
  - family-names: Hansen
    given-names: Kasper Daniel
    email: kasperdanielhansen@gmail.com
  - family-names: Gentry
    given-names: Jeff
  - family-names: Long
    given-names: Li
  - family-names: Gentleman
    given-names: Robert
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    given-names: Seth
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    given-names: Florian
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    given-names: Deepayan
  year: '2022'
- type: software
  title: BiocManager
  abstract: 'BiocManager: Access the Bioconductor Project Package Repository'
  notes: Suggests
  authors:
  - family-names: Morgan
    given-names: Martin
    email: martin.morgan@roswellpark.org
    orcid: https://orcid.org/0000-0002-5874-8148
  year: '2022'
  url: https://CRAN.R-project.org/package=BiocManager
- type: software
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  abstract: 'cowplot: Streamlined Plot Theme and Plot Annotations for ''ggplot2'''
  notes: Suggests
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  - family-names: Wilke
    given-names: Claus O.
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    orcid: https://orcid.org/0000-0002-7470-9261
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- type: software
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  abstract: 'correlationfunnel: Speed Up Exploratory Data Analysis (EDA) with the
    Correlation Funnel'
  notes: Suggests
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    given-names: Matt
    email: mdancho@business-science.io
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  abstract: 'tidyr: Tidy Messy Data'
  notes: Imports
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    given-names: Hadley
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    given-names: Maximilian
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  year: '2022'
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  abstract: 'purrr: Functional Programming Tools'
  notes: Imports
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    email: hadley@rstudio.com
    orcid: https://orcid.org/0000-0003-4757-117X
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  notes: Imports
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  notes: Imports
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    email: krlmlr+r@mailbox.org
    orcid: https://orcid.org/0000-0002-1416-3412
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    orcid: https://orcid.org/0000-0002-4035-0289
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  year: '2022'
  url: https://CRAN.R-project.org/package=RMariaDB
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  notes: Imports
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    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=stringr
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  title: dplyr
  abstract: 'dplyr: A Grammar of Data Manipulation'
  notes: Imports
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
    orcid: https://orcid.org/0000-0003-4757-117X
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    orcid: https://orcid.org/0000-0002-2444-4226
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    orcid: https://orcid.org/0000-0002-1416-3412
  year: '2022'
  url: https://CRAN.R-project.org/package=dplyr
- type: software
  title: tidyselect
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  notes: Imports
  authors:
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    given-names: Lionel
    email: lionel@rstudio.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=tidyselect
- type: software
  title: abn
  abstract: 'abn: Modelling Multivariate Data with Additive Bayesian Networks'
  notes: Imports
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  - family-names: Furrer
    given-names: Reinhard
    email: reinhard.furrer@math.uzh.ch
    orcid: https://orcid.org/0000-0002-6319-2332
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    given-names: Gilles
    email: gilles.kratzer@gmail.com
    orcid: https://orcid.org/0000-0002-5929-8935
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    given-names: Fraser Iain
    email: fraser.iain.lewis@gmail.com
    orcid: https://orcid.org/0000-0003-4580-2712
  year: '2022'
  url: https://CRAN.R-project.org/package=abn
- type: software
  title: bnlearn
  abstract: 'bnlearn: Bayesian Network Structure Learning, Parameter Learning and
    Inference'
  notes: Imports
  authors:
  - family-names: Scutari
    given-names: Marco
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    given-names: Robert
  year: '2022'
  url: https://CRAN.R-project.org/package=bnlearn
- type: software
  title: data.table
  abstract: 'data.table: Extension of `data.frame`'
  notes: Imports
  authors:
  - family-names: Dowle
    given-names: Matt
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  - family-names: Srinivasan
    given-names: Arun
    email: asrini@pm.me
  year: '2022'
  url: https://CRAN.R-project.org/package=data.table
- type: software
  title: caret
  abstract: 'caret: Classification and Regression Training'
  notes: Imports
  authors:
  - family-names: Kuhn
    given-names: Max
    email: mxkuhn@gmail.com
    orcid: https://orcid.org/0000-0003-2402-136X
  year: '2022'
  url: https://CRAN.R-project.org/package=caret
- type: software
  title: magrittr
  abstract: 'magrittr: A Forward-Pipe Operator for R'
  notes: Imports
  authors:
  - family-names: Bache
    given-names: Stefan Milton
    email: stefan@stefanbache.dk
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  year: '2022'
  url: https://CRAN.R-project.org/package=magrittr
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2022'
  url: https://www.R-project.org/
  institution:
    name: R Foundation for Statistical Computing
  version: '>= 3.5.0'

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