mparseRcpp | R Documentation |
SimInf
style markupParse custom model using SimInf
style markup.
Does not have full functionality of mparse
. Currently only supports
simulations on a single node.
mparseRcpp(
transitions = NULL,
compartments = NULL,
pars = NULL,
obsProcess = NULL,
addVars = NULL,
stopCrit = NULL,
tspan = FALSE,
incidence = FALSE,
afterTstar = NULL,
PF = FALSE,
runFromR = TRUE
)
transitions |
character vector containing transitions on the form |
compartments |
contains the names of the involved compartments, for
example, |
pars |
a |
obsProcess |
|
addVars |
a |
stopCrit |
A |
tspan |
A |
incidence |
A |
afterTstar |
A |
PF |
A |
runFromR |
|
Uses a SimInf
style markup to create compartmental state-space
written using Rcpp
. A helper run
function exists to compile
and run the model. Another helper function, compileRcpp
,
can compile the model to produce a function that can be run directly from R,
or compiled into an external pointer (using the RcppXPtrUtils
package).
An object of class SimBIID_model
, which is essentially a list
containing elements:
code: |
parsed code to compile; |
transitions: |
copy of |
compartments: |
copy of |
pars: |
copy of |
obsProcess: |
copy of |
stopCrit: |
copy of |
addVars: |
copy of |
tspan: |
copy of |
incidence: |
copy of |
afterTstar: |
copy of |
PF: |
copy of |
runFromR: |
copy of |
This can be compiled into an XPtr
or function
object
using compileRcpp()
.
run
, compileRcpp
, print.SimBIID_model
## set up SIR simulation model
transitions <- c(
"S -> beta * S * I -> I",
"I -> gamma * I -> R"
)
compartments <- c("S", "I", "R")
pars <- c("beta", "gamma")
model <- mparseRcpp(
transitions = transitions,
compartments = compartments,
pars = pars
)
## compile and run model
sims <- run(
model = model,
pars = c(beta = 0.001, gamma = 0.1),
tstart = 0,
tstop = 100,
u = c(S = 119, I = 1, R = 0)
)
sims
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