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.
The main document to use for Bayesian inference is runStanv2.R which will call the model in Stan : ODE_plasmid_v2.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.
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
- 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
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)
Citation for this repository CITATION
This project is licensed under the terms of the MIT License.