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plasmid_loss_bayesian

https://github.com/egilfischer/plasmid_loss_bayesian

Science Score: 44.0%

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  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
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    Academic publication links
  • ○
    Committers with academic emails
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.8%) to scientific vocabulary
Last synced: 8 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: EgilFischer
  • License: mit
  • Language: R
  • Default Branch: main
  • Size: 11.6 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme License Citation

README.md

Plasmid loss and conjugation estimation with Bayesian methods

This project contains files to estimate the loss of plasmids from bacterial population is conjection with uptake by conjugation. Two main parameters can be estimated "\rho" = loss parameter and "\gamma" = conjugation parameter.

Usage

The main document to use for Bayesian inference is runStanv2.R which will call the model in Stan : ODEplasmidv2.stan. This latter includes the code with the model and prior distributions. This model is thus run from runStanv2.R. The script in ABC_modelfit.R fits the same model as in the stan file but then with an ABC-SMC approach.

Installation

The project is written in R and Stan.

The version of R [4.4.1]

More information about Stan: https://mc-stan.org

Install Rstan: https://cran.r-project.org/web/packages/rstan/index.html

Dependencies

  • deSolve [* -> 1.40]
  • EasyABC [* -> 1.5.2]
  • ggplot2 [* -> 3.5.1]
  • MASS [* -> 7.3-60.2]
  • Rcpp [* -> 1.0.12]
  • rstan [* -> 2.32.6]
  • rstanarm [* -> 2.32.1]
  • rstantools [* -> 2.4.0]

Link to dependencies

Project Structure

The project structure distinguishes three kinds of folders: - read-only (RO): not edited by either code or researcher - human-writeable (HW): edited by the researcher only. - project-generated (PG): folders generated when running the code; these folders can be deleted or emptied and will be completely reconstituted as the project is run.

``` . ├── .gitignore ├── CITATION.cff ├── LICENSE ├── README.md ├── requirements.txt ├── data <- All project data, ignored by git (RO) | ├── docs <- Documentation notebook for users (HW) │ ├── manuscript <- Manuscript source, e.g., LaTeX, Markdown, etc. (HW) │ └── reports <- Other project reports and notebooks (e.g. Jupyter, .Rmd) (HW) ├── results │ ├── figures <- Figures for the manuscript or reports (PG) │ └── output <- Other output for the manuscript or reports (PG) └── src <- Source code for this project (HW) ├── R <- R-codes (HW) └── Stan <- Stan code (HW)

```

Add a citation file

Citation for this repository CITATION

License

This project is licensed under the terms of the MIT License.

Owner

  • Name: Dr ir Egil A.J. Fischer
  • Login: EgilFischer
  • Kind: user
  • Location: Utrecht, The Netherlands
  • Company: Universiteit Utrecht

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Plasmid loss and conjugation estimation
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: 'Egil A.J. '
    family-names: Fischer
    email: e.a.j.fischer@uu.nl
    name-particle: Egil
    orcid: 'https://orcid.org/0000-0002-0599-701X'
abstract: >-
  Estimate the plasmid loss and conjugation from growth 
  rates and conjugation experiments using Bayesian methods. 
keywords:
  - conjugation
  - plasmid
  - ordinary differential equation
license: MIT

GitHub Events

Total
  • Issues event: 1
  • Push event: 2
  • Public event: 1
  • Fork event: 1
Last Year
  • Issues event: 1
  • Push event: 2
  • Public event: 1
  • Fork event: 1

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 29
  • Total Committers: 1
  • Avg Commits per committer: 29.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 29
  • Committers: 1
  • Avg Commits per committer: 29.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Dr ir Egil A.J. Fischer 3****r 29

Issues and Pull Requests

Last synced: 8 months ago

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  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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