https://github.com/csgillespie/hybrid-pmcmc
https://github.com/csgillespie/hybrid-pmcmc
Last synced: 2 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/csgillespie/hybrid-pmcmc
- Owner: csgillespie
- Created: 2013-11-06T15:01:47.000Z (over 11 years ago)
- Default Branch: master
- Last Pushed: 2014-07-13T15:17:03.000Z (almost 11 years ago)
- Last Synced: 2025-02-08T08:47:08.515Z (4 months ago)
- Language: FORTRAN
- Size: 459 KB
- Stars: 2
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
Bayesian Inference for Hybrid Discrete-Continuous Systems Biology Models
------------------------------------------------------------------------
This repository contains the source code for the paper
[Sherlock, C.](http://www.maths.lancs.ac.uk/~sherlocc/), [Golightly, A.](http://www.mas.ncl.ac.uk/~nag48/), [Gillespie, C.S.](http://www.mas.ncl.ac.uk/~ncsg3/) (2013) *Bayesian Inference for Hybrid Discrete-Continuous Systems Biology Models*
([arXiv](http://arxiv.org/abs/1402.6602))
To download the code, either clone this repository or download the [zip](https://github.com/csgillespie/hybrid-pmcmc/archive/master.zip) file and unpack.
1. Change to the `src` directory
```
cd src
```
2. Type
```
make
```
should build the code with no errors and create an executable called `pmcmc`.
Note the `gsl` math library is needed.
3. The `pmcmc` executable has a number of options:
* `-s` the simulator used - either `gillespie`, `hybridLNA`, `hybridSDE`
* `-n` the number of iterations
* `-d` the input directory. This directory should contain a sub-directory with the name of the simulator used.
* `-b` the burnin - default 0
* `-t` thin - default 1
For example
```
./pmcmc -s gillespie -n 1000 -d ../input/inference/run1/ -t 2
```
4. Running the `pmcmc` executable will create two files:
* `name_of_simulator.csv` - mcmc output;
* `timing.csv` - run time (in seconds)