---
title: "Decaying-Dimerization Reaction Set (Gillespie, 2001)"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{Decaying-Dimerization Reaction Set (Gillespie, 2001)}
%\VignetteEncoding{UTF-8}
%\VignetteEngine{knitr::rmarkdown}
editor_options:
chunk_output_type: console
---
```{r, setseed, echo=FALSE}
set.seed(1)
knitr::opts_chunk$set(fig.width = 8, fig.height = 6)
```
The Decaying-Dimerization Reaction Set consists of three species and four reaction channels.
```
S1 --c1--> 0
S1 + S1 --c2--> S2
S2 --c3--> S1 + S1
S2 --c4--> S3
```
Load package
```{r}
library(GillespieSSA)
```
Define parameters
```{r}
parms <- c(c1=1.0, c2=0.002, c3=0.5, c4=0.04)
tf <- 10 # Final time
simName <- "Decaying-Dimerizing Reaction Set" # Name
```
Define initial state vector
```{r}
x0 <- c(s1=10000, s2=0, s3=0)
```
Define state-change matrix
```{r}
nu <- matrix(c(-1, -2, +2, 0,
0, +1, -1, -1,
0, 0, 0, +1),
nrow=3,byrow=TRUE)
```
Define propensity functions
```{r}
a <- c("c1*s1", "c2*s1*s1", "c3*s2", "c4*s2")
```
Run simulations with the Direct method
```{r direct}
set.seed(1)
out <- ssa(
x0 = x0,
a = a,
nu = nu,
parms = parms,
tf = tf,
method = ssa.d(),
simName = simName,
verbose = FALSE,
consoleInterval = 1
)
ssa.plot(out, show.title = TRUE, show.legend = FALSE)
```
Run simulations with the Explict tau-leap method
```{r etl}
set.seed(1)
out <- ssa(
x0 = x0,
a = a,
nu = nu,
parms = parms,
tf = tf,
method = ssa.etl(tau = 0.003),
simName = simName,
verbose = FALSE,
consoleInterval = 1
)
ssa.plot(out, show.title = TRUE, show.legend = FALSE)
```
Run simulations with the Binomial tau-leap method
```{r btl}
set.seed(1)
out <- ssa(
x0 = x0,
a = a,
nu = nu,
parms = parms,
tf = tf,
method = ssa.btl(),
simName = simName,
verbose = FALSE,
consoleInterval = 1
)
ssa.plot(out, show.title = TRUE, show.legend = FALSE)
```
Run simulations with the Optimized tau-leap method
```{r otl}
set.seed(1)
out <- ssa(
x0 = x0,
a = a,
nu = nu,
parms = parms,
tf = tf,
method = ssa.otl(),
simName = simName,
verbose = FALSE,
consoleInterval = 1
)
ssa.plot(out, show.title = TRUE, show.legend = FALSE)
```