Revert to calling Rcolgem within class function to address #9

rcolgem.py

@@ -2,17 +2,13 @@
 
 class Rcolgem ():
     def __init__ (self, ncores, nreps, t0=0, fgy_resolution=500., integration_method='rk4'):
-        # load Rcolgem
-        robjects.r("require(rcolgem, quietly=TRUE)")
-
         # default settings
         robjects.globalenv['n.cores'] = ncores
         robjects.globalenv['nreps'] = nreps
         robjects.globalenv['fgyResolution'] = fgy_resolution
         robjects.globalenv['integrationMethod'] = integration_method
         robjects.globalenv['t0'] = t0
 
-
     def init_SI_model (self, N=1000, beta=0.01, gamma=1/520., mu=1/3640.):
         """
         Defines a susceptible-infected-recovered model in rcolgem.
@@ -129,6 +125,9 @@ def simulate_SI2_trees(self, params, tip_heights):
         robjects.r("m <- nrow(births)")
         robjects.r("maxSampleTime <- max(sampleTimes)")
 
+        # load Rcolgem package
+        robjects.r("require(rcolgem, quietly=TRUE)")
+
         # solve first ODE
         robjects.r("tfgy.1 <- make.fgy( t0, times[fgyRes.1], births, deaths, nonDemeDynamics, x0,"
                    "migrations=migrations, parms=parms, fgyResolution = fgyRes.1, "