library(DNAr)
#
# Examples
#
run_ApBeC <- function() {
behavior <- react(
species = c('A', 'B', 'C'),
ci = c(1e3, 1e3, 0),
reactions = c('A + B -> C'),
ki = c(1e-7),
t = seq(0, 72000, 10)
)
return(behavior)
}
run_lotka <- function() {
behavior <- react(
species = c('A', 'B'),
ci = c(2, 1),
reactions = c('A + B -> 2B',
'A -> 2A',
'B -> 0'),
ki = c(1.5,
1,
1),
t = seq(0, 45, 0.1)
)
return(behavior)
}
run_lotka_scaled <- function() {
behavior <- react(
species = c('A', 'B'),
ci = c(20e-9, 10e-9),
reactions = c('A + B -> 2B',
'A -> 2A',
'B -> 0'),
ki = c(5e5,
1/300,
1/300),
t = seq(0, 12600, 1)
)
return(behavior)
}
run_ApBeC_4domain <- function() {
behavior <- react(
species = c('A', 'B', 'C', 'L', 'H', 'W', 'O', 'T'),
ci = c(1e3, 1e3, 0.0, 1e5, 0.0, 1e5, 0.0, 1e5),
reactions = c('A + L -> H + W',
'H + W -> A + L',
'B + H -> O',
'O + T -> C'),
ki = c(1e-7,
1e-3,
1e-3,
1e-3),
t = seq(0, 72000, 1)
)
return(behavior)
}
run_origonator <- function() {
# It is not working properly yet
behavior <- react(
species = c('A', 'B', 'C'),
ci = c(0.8e-9, 4.5e-9, 0.8e-9),
reactions = c('B -> A',
'B + A -> 0',
'A -> 2A + C',
'2A -> 0',
'C -> B',
'C -> 0'),
ki = c(3.889e-7,
5e5,
0.00232,
12500,
0.00198,
1.195e-5),
t = seq(0, 360000, 1)
)
return(behavior)
}
run_rossler <- function() {
# It is not working properly yet
behavior <- react(
species = c('A', 'B', 'C'),
ci = c(1.8e-9, 1.8e-9, 1.8e-9),
reactions = c('A -> 2A',
'2A -> A',
'B + A -> 2B',
'B -> 0',
'A + C -> 0',
'C -> 2C',
'2C -> C'),
ki = c(0.002,
200000,
400000,
0.000667,
400000,
0.001,
200000),
t = seq(0, 144000, 1)
)
return(behavior)
}
run_consensus <- function() {
behavior <- react(
species = c('X', 'Y', 'B'),
ci = c(0.7 * 80e-9, 0.3 * 80e-9, 0.0),
reactions = c('X + Y -> 2B',
'B + X -> 2X',
'B + Y -> 2Y'),
ki = c(2e3, 2e3, 2e3),
t = seq(0, 54000, 5)
)
}
#behavior <- run_ApBeC()
#behavior <- run_lotka()
#behavior <- run_lotka_scaled()
#behavior <- run_ApBeC_4domain()
#behavior <- run_origonator()
#behavior <- run_rossler()
behavior <- run_consensus()
plot_behavior(behavior)
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