modelsir_cpp =function(t,x){
S = x[1]
I1 = x[2]
I2 = x[3]
N=S+I1+I2
with(as.list(parm), {
   dS=B*I1-mu*S-beta*(S*(I1+I2)/N)
   dI1=beta*(S*(I1+I2)/N)-B*I1-lambda12*I1
   dI2=lambda12*I1
   res=c(dS,dI1,dI2)
   return(res)
 })
}

times = seq(0, 10, by = 1/52)
parm=c(B=0.01,mu=0.008,beta=10,lambda12=1)
xstart=c(S=900,I1=100,I2=0)
out = as.data.frame(lsoda(xstart, times, modelsir, parm))

#include <Rcpp.h>
#include <boost/array.hpp>

// include Boost's odeint
#include <boost/numeric/odeint.hpp>

// [[Rcpp::depends(BH)]]

using namespace Rcpp;
using namespace std;
using namespace boost::numeric::odeint;

typedef boost::array< double ,3 > state_type;

void eqsir(const state_type &x, state_type &dxdt, const double t){
  Rcpp::NumericVector nvec=boost_array_to_nvec(x);
  Rcpp::NumericVector nvec2(3);
  nvec2=my_fun2(nvec,t);
  dxdt=nvec_to_boost_array(nvec2);
}

void write_cout_2( const state_type &x , const double t ) {
  // use Rcpp's stream
  Rcpp::Rcout << t << 't' << x[0] << 't' << x[1] << 't' << x[2] <<  endl;
}
typedef runge_kutta_dopri5< state_type > stepper_type;

// [[Rcpp::export]]
bool my_fun10_solver() {
  state_type x = { 900 , 100, 0 }; // initial conditions
  integrate_adaptive(make_controlled( 1E-12 , 1E-12 , stepper_type () ) ,
                     eqsir , x , 1.0 , 2 , 1/52 , write_cout_2 );
  return true;
}

#include <Rcpp.h>
#include <boost/array.hpp>

// include Boost's odeint
#include <boost/numeric/odeint.hpp>

// [[Rcpp::depends(BH)]]

using namespace Rcpp;
using namespace std;
using namespace boost::numeric::odeint;


typedef boost::array< double ,3 > state_type;

void rhs( const state_type &x , state_type &dxdt , const double t ) {

  dxdt[0] = 3.0/(2.0*t*t) + x[0]/(2.0*t);
  dxdt[1] = 3.0/(2.0*t*t) + x[1]/(2.0*t);
  dxdt[2] = 3.0/(2.0*t*t) + x[1]/(2.0*t);
}

void write_cout( const state_type &x , const double t ) {
  // use Rcpp's stream
  Rcpp::Rcout << t << 't' << x[0] << 't' << x[1] << 't' << x[2] <<  endl;
}

 typedef runge_kutta_dopri5< state_type > stepper_type;

// [[Rcpp::export]]
bool boostExample() {
  state_type x = { 1.0 , 1.0, 1.0 }; // initial conditions
  integrate_adaptive(make_controlled( 1E-12 , 1E-12 , stepper_type () ) ,
                     rhs , x , 1.0 , 10.0 , 0.1 , write_cout );
  return true;
}