From 7bf0d787f8ffd9c53433488c38c2dc2a70956951 Mon Sep 17 00:00:00 2001
From: Matthew L Fidler <matthew.fidler@gmail.com>
Date: Thu, 24 Oct 2024 00:40:01 -0500
Subject: [PATCH 1/5] PopED + babelmixr2 for windows

---
 R/Doptim.R                     |  2 +-
 R/LEDoptim.R                   |  1 +
 R/LinMatrixH.R                 |  5 ++++-
 R/LinMatrixL.R                 |  2 +-
 R/LinMatrixLH.R                |  3 +++
 R/LinMatrixL_occ.R             |  1 +
 R/RS_opt.R                     |  2 +-
 R/a_line_search.R              |  1 +
 R/blockexp.R                   |  5 ++++-
 R/blockfinal.R                 |  1 +
 R/blockheader.R                |  1 +
 R/blockopt.R                   |  5 +++--
 R/blockother.R                 |  1 +
 R/calc_ofv_and_fim.R           |  6 ++++--
 R/convert_variables.R          |  1 +
 R/create_ofv.R                 |  2 +-
 R/d2fimdalpha2.R               |  1 +
 R/dfimdalpha.R                 |  3 ++-
 R/downsizing_general_design.R  |  1 +
 R/ed_laplace_ofv.R             |  1 +
 R/ed_mftot.R                   |  1 +
 R/evaluate.e.ofv.fim.R         |  2 +-
 R/evaluate.fim.R               |  2 +-
 R/evaluate_design.R            |  3 ++-
 R/evaluate_fim_map.R           |  4 ++--
 R/evaluate_power.R             |  3 ++-
 R/get_all_params.R             |  1 +
 R/get_cv.R                     |  3 ++-
 R/get_fim_size.R               |  1 +
 R/get_unfixed_params.R         |  2 +-
 R/grad_bpop.R                  |  5 +++--
 R/graddetmf.R                  |  1 +
 R/graddetmf_ext.R              |  2 +-
 R/gradff.R                     |  1 +
 R/gradfg.R                     |  1 +
 R/gradfg_occ.R                 |  1 +
 R/gradofv_a.R                  |  2 +-
 R/gradofv_xt.R                 |  2 +-
 R/gradtrmf.R                   |  2 +-
 R/helper.R                     |  3 ++-
 R/hessian_eta_complex.R        |  2 +-
 R/hesskalpha2.R                |  1 +
 R/ind_estimates.R              |  3 ++-
 R/ind_likelihood.R             |  1 +
 R/m1.R                         |  1 +
 R/m2.R                         |  1 +
 R/m3.R                         |  2 +-
 R/mf3.R                        |  2 +-
 R/mf7.R                        |  2 +-
 R/mf_all.R                     |  2 +-
 R/mfea.R                       |  2 +-
 R/mftot.R                      |  1 +
 R/ofv_fim.R                    |  2 +-
 R/optimize_n.R                 |  8 +++++---
 R/par_and_space_tbl.R          |  4 +++-
 R/pargen.R                     |  2 +-
 R/plot_efficiency_of_windows.R |  4 ++--
 R/plot_model_prediction.R      |  1 +
 R/poped_optim.R                |  2 +-
 R/poped_optim_1.R              |  2 +-
 R/poped_optim_2.R              |  2 +-
 R/poped_optim_3.R              |  2 +-
 R/poped_optimize.R             |  2 +-
 R/shrinkage.R                  |  4 ++--
 R/start_parallel.R             | 11 ++++++++++-
 R/v.R                          |  2 +-
 R/write_iterationfile.R        |  2 +-
 67 files changed, 106 insertions(+), 51 deletions(-)

diff --git a/R/Doptim.R b/R/Doptim.R
index 85183879..7122e603 100644
--- a/R/Doptim.R
+++ b/R/Doptim.R
@@ -73,7 +73,7 @@ Doptim <- function(poped.db,ni, xt, model_switch, x, a, bpopdescr,
                    iter_tot=poped.db$settings$iNumSearchIterationsIfNotLineSearch,
                    iter_max=10,
                    ...){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   
   ## update poped.db with options supplied in function
   called_args <- match.call()
diff --git a/R/LEDoptim.R b/R/LEDoptim.R
index c7c23f6c..0e1fc9d2 100644
--- a/R/LEDoptim.R
+++ b/R/LEDoptim.R
@@ -52,6 +52,7 @@ LEDoptim <- function(poped.db,
                      laplace.fim=FALSE, 
                      use_RS=poped.db$settings$bUseRandomSearch,
                      ...){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   #+++++++++++++++++++++  D CONTINUOUS VARIABLE OPTIMIZATION FUNCTION
   
   # ------------- downsizing of general design
diff --git a/R/LinMatrixH.R b/R/LinMatrixH.R
index 3b241b84..b533a61b 100644
--- a/R/LinMatrixH.R
+++ b/R/LinMatrixH.R
@@ -23,13 +23,15 @@
 ## Function translated automatically using 'matlab.to.r()'
 ## Author: Andrew Hooker
 
-LinMatrixH <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,poped.db){
+LinMatrixH <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,
+poped.db){
   #----------Model linearization with respect to epsilon.
   #
   # size of return is (samples per individual x number of epsilons) 
   #
   # derivative of model w$r.t. eps eval at e=0
   #
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   NumEPS = size(poped.db$parameters$sigma,1)
   if((NumEPS==0)){
     y=0
@@ -61,6 +63,7 @@ LinMatrixH <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,poped.db){
 #' @keywords internal
 #' 
 gradf_eps <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,num_eps,poped.db){
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   #----------Model linearization with respect to epsilon.
   #
   # size of return is (samples per individual x number of epsilons)
diff --git a/R/LinMatrixL.R b/R/LinMatrixL.R
index 29eba463..361294cc 100644
--- a/R/LinMatrixL.R
+++ b/R/LinMatrixL.R
@@ -22,7 +22,7 @@
 ## Author: Andrew Hooker
 
 LinMatrixL <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,poped.db){
-  
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   if((poped.db$parameters$NumRanEff==0)){
     y=0
   } else {
diff --git a/R/LinMatrixLH.R b/R/LinMatrixLH.R
index 27e4e1a5..6bed8d01 100644
--- a/R/LinMatrixLH.R
+++ b/R/LinMatrixLH.R
@@ -20,6 +20,7 @@
 ## Author: Andrew Hooker
 
 LinMatrixLH <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,NumEPS,poped.db){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   #----------Model linearization with respect to epsilon.
   #
   # size of return is (samples per individual x (number of sigma x number of omega)) 
@@ -56,6 +57,8 @@ LinMatrixLH <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,NumEPS,poped
 
 #Helper function to get the hessian for the AD derivative
 new_ferror_file <- function(model_switch,deriv_vec,xt_ind,x,a,bpop,bocc_ind,poped.db){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
+
   fg0=feval(poped.db$model$fg_pointer,x,a,bpop,deriv_vec(1:poped.db$parameters$NumRanEff),bocc_ind) #Interaction
   returnArgs <- feval(poped.db$model$ferror_pointer,model_switch,xt_ind,fg0,deriv_vec(poped.db$parameters$NumRanEff+1:length(deriv_vec)),poped.db) 
   f_error <- returnArgs[[1]]
diff --git a/R/LinMatrixL_occ.R b/R/LinMatrixL_occ.R
index 722ff497..f4df5ed2 100644
--- a/R/LinMatrixL_occ.R
+++ b/R/LinMatrixL_occ.R
@@ -18,6 +18,7 @@
 ## Author: Andrew Hooker
 
 LinMatrixL_occ <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,iCurrentOcc,poped.db){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   #
   # size: (samples per individual x number of iovs)
   #
diff --git a/R/RS_opt.R b/R/RS_opt.R
index 703bb182..570de71e 100644
--- a/R/RS_opt.R
+++ b/R/RS_opt.R
@@ -73,7 +73,7 @@ RS_opt <- function(poped.db,
                        out_file=NULL,
                        compute_inv=TRUE,
                        ...){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2    
   
   # Only get inputs that are needed, not double inputs
   # needed inputs to function: get first then run function
diff --git a/R/a_line_search.R b/R/a_line_search.R
index c7a37ce6..37411b3f 100644
--- a/R/a_line_search.R
+++ b/R/a_line_search.R
@@ -48,6 +48,7 @@ a_line_search <- function(poped.db,
                           opt_samps=poped.db$settings$optsw[1],
                           opt_inds=poped.db$settings$optsw[5],
                           ls_step_size=poped.db$settings$ls_step_size){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   
   optsw <- cbind(opt_samps,opt_xt,opt_x,opt_a,opt_inds)
   # 
diff --git a/R/blockexp.R b/R/blockexp.R
index 4bb6a248..d98174b8 100644
--- a/R/blockexp.R
+++ b/R/blockexp.R
@@ -25,7 +25,8 @@
 blockexp <- function(fn,poped.db,e_flag=FALSE,
                      opt_xt=poped.db$settings$optsw[2],opt_a=poped.db$settings$optsw[4],opt_x=poped.db$settings$optsw[4],
                      opt_samps=poped.db$settings$optsw[1],opt_inds=poped.db$settings$optsw[5]){
-  
+
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   fprintf(fn,'==============================================================================\n')
   fprintf(fn,'Model description : %s \n',poped.db$settings$modtit)
   fprintf(fn,'\n')
@@ -155,6 +156,8 @@ blockexp <- function(fn,poped.db,e_flag=FALSE,
 }
 
 print_params <- function (params,name_str, fn, poped.db, param_sqrt=FALSE,head_txt=NULL,matrix_elements=F,e_flag=FALSE) {
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
+      
   if(is.null(head_txt)) head_txt <- "Parameter Values"
   uncer_txt <- ""
   if(e_flag) uncer_txt <- " (Uncertainty Distribution)"
diff --git a/R/blockfinal.R b/R/blockfinal.R
index 5e67eb65..ee0cbac4 100644
--- a/R/blockfinal.R
+++ b/R/blockfinal.R
@@ -31,6 +31,7 @@ blockfinal <- function(fn,fmf,dmf,groupsize,ni,xt,x,a,model_switch,bpop,d,docc,s
                        compute_inv=TRUE,out_file=NULL,trflag=TRUE,footer_flag=TRUE,
                        run_time = NULL,
                        ...){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   time_value <- NULL
   
   if(!trflag) return(invisible() ) 
diff --git a/R/blockheader.R b/R/blockheader.R
index b06d473d..80f4f2b5 100644
--- a/R/blockheader.R
+++ b/R/blockheader.R
@@ -37,6 +37,7 @@ blockheader <- function(poped.db,name="Default",iter=NULL,
                           header_flag=TRUE,
                           ...)
 {
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   # BLOCKHEADER_2
   #   filename to write to is 
   #   poped.db$settings$strOutputFilePath,poped.db$settings$strOutputFileName,NAME,iter,poped.db$settings$strOutputFileExtension
diff --git a/R/blockopt.R b/R/blockopt.R
index 79338488..a6a7ff46 100644
--- a/R/blockopt.R
+++ b/R/blockopt.R
@@ -20,7 +20,8 @@
 ## Author: Andrew Hooker
 
 blockopt <- function(fn,poped.db,opt_method=""){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
+
   if(any(opt_method==c("RS","SG","DO"))){
     fprintf(fn,'==============================================================================\n')
     fprintf(fn,'Optimization Settings\n\n')
@@ -50,4 +51,4 @@ blockopt <- function(fn,poped.db,opt_method=""){
     fprintf(fn,"\n")
   }
   return( ) 
-}
\ No newline at end of file
+}
diff --git a/R/blockother.R b/R/blockother.R
index 4d07b831..2fde0ac1 100644
--- a/R/blockother.R
+++ b/R/blockother.R
@@ -2,6 +2,7 @@
 ## Author: Andrew Hooker
 
 blockother <- function(fn,poped.db,d_switch=poped.db$settings$d_switch){
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   fprintf(fn,'==============================================================================\n')
   fprintf(fn,'Criterion Specification\n\n')
   
diff --git a/R/calc_ofv_and_fim.R b/R/calc_ofv_and_fim.R
index 47f2be76..b2ae8ede 100644
--- a/R/calc_ofv_and_fim.R
+++ b/R/calc_ofv_and_fim.R
@@ -47,7 +47,9 @@ calc_ofv_and_fim <- function (poped.db,
                               ofv_fun = poped.db$settings$ofv_fun,
                               evaluate_fim = TRUE,
                               ...) {
-  
+
+
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   ## compute the OFV
   if((ofv==0)){
     if(d_switch){ 
@@ -177,4 +179,4 @@ calc_ofv_and_fim <- function (poped.db,
     fim <- fmf
   }
   return(list(ofv=ofv,fim=fim)) 
-}
\ No newline at end of file
+}
diff --git a/R/convert_variables.R b/R/convert_variables.R
index b5f83e93..8d79fdbe 100644
--- a/R/convert_variables.R
+++ b/R/convert_variables.R
@@ -16,6 +16,7 @@
 ## Author: Andrew Hooker
 
 convert_variables <- function(poped.db){
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
     design = poped.db$design
     design_space = poped.db$design_space
 
diff --git a/R/create_ofv.R b/R/create_ofv.R
index 03c2cf5b..f49e2f02 100644
--- a/R/create_ofv.R
+++ b/R/create_ofv.R
@@ -15,7 +15,7 @@ create_ofv <- function(poped.db,
                        ofv_fun = poped.db$settings$ofv_fun,
                        transform_parameters=T,
                        ...){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   #------------ update poped.db with options supplied in function
   called_args <- match.call()
   default_args <- formals()
diff --git a/R/d2fimdalpha2.R b/R/d2fimdalpha2.R
index 765bb5c0..ba9b7abb 100644
--- a/R/d2fimdalpha2.R
+++ b/R/d2fimdalpha2.R
@@ -1,4 +1,5 @@
 d2fimdalpha2 <- function(alpha, model_switch,groupsize,ni,xtoptn,xoptn,aoptn,bpopdescr,ddescr,covd,sigma,docc,poped.db,ha){  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   bpop=bpopdescr[,2,drop=F]
   bpop[bpopdescr[,1,drop=F]!=0]=alpha[1:sum(bpopdescr[,1,drop=F]!=0)]
   d=ddescr[,2,drop=F]
diff --git a/R/dfimdalpha.R b/R/dfimdalpha.R
index ee072bfc..b574ec11 100644
--- a/R/dfimdalpha.R
+++ b/R/dfimdalpha.R
@@ -1,5 +1,6 @@
 
 dfimdalpha <- function(alpha, model_switch,groupsize,ni,xtoptn,xoptn,aoptn,bpopdescr,ddescr,covd,sigma,docc,poped.db,ha){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   bpop=bpopdescr[,2,drop=F]
   bpop[bpopdescr[,1,drop=F]!=0]=alpha[1:sum(bpopdescr[,1,drop=F]!=0)]
   d=ddescr[,2,drop=F]
@@ -33,4 +34,4 @@ dfimdalpha <- function(alpha, model_switch,groupsize,ni,xtoptn,xoptn,aoptn,bpopd
   }
   return(list( grad= grad,fim =fim )) 
 }
-  
\ No newline at end of file
+  
diff --git a/R/downsizing_general_design.R b/R/downsizing_general_design.R
index 0bd92d95..a790965f 100644
--- a/R/downsizing_general_design.R
+++ b/R/downsizing_general_design.R
@@ -24,6 +24,7 @@
 
 
 downsizing_general_design <- function(poped.db){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   # ------------- downsizing of general design
   
   ni=poped.db$design$ni[1:poped.db$design$m,,drop=F]
diff --git a/R/ed_laplace_ofv.R b/R/ed_laplace_ofv.R
index c5171701..031c8c84 100644
--- a/R/ed_laplace_ofv.R
+++ b/R/ed_laplace_ofv.R
@@ -492,6 +492,7 @@ calc_k <- function(alpha, model_switch,groupsize,ni,xtoptn,xoptn,aoptn,bpopdescr
   if(return_gradient){
     
     comp_grad_1 <- function(alpha, model_switch, groupsize, ni, xtoptn, xoptn, aoptn, bpopdescr, ddescr, covd, sigma, docc, poped.db, grad_p) {
+      start_parallel_env$babelmixr2 <- poped.db$babelmixr2
       returnArgs <- dfimdalpha(alpha,model_switch,groupsize,ni,xtoptn,xoptn,aoptn,bpopdescr,ddescr,covd,sigma,docc,poped.db,1e-6) 
       d_fim <- returnArgs[[1]]
       fim <- returnArgs[[2]]
diff --git a/R/ed_mftot.R b/R/ed_mftot.R
index 6f32fa66..49d8faf6 100644
--- a/R/ed_mftot.R
+++ b/R/ed_mftot.R
@@ -27,6 +27,7 @@
 
 ed_mftot <- function(model_switch,groupsize,ni,xtoptn,xoptn,aoptn,bpopdescr,ddescr,covd,sigma,docc,poped.db,
                      calc_fim=TRUE,...){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   #+++++++++++++++++++++++ ED OFV(MF) VALUE
   s=0
   s1=0
diff --git a/R/evaluate.e.ofv.fim.R b/R/evaluate.e.ofv.fim.R
index 705ddb39..0eab613d 100644
--- a/R/evaluate.e.ofv.fim.R
+++ b/R/evaluate.e.ofv.fim.R
@@ -45,7 +45,7 @@ evaluate.e.ofv.fim <- function(poped.db,
                                use_laplace=poped.db$settings$iEDCalculationType, 
                                laplace.fim=FALSE, 
                                ...){
-
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   ## update poped.db with options supplied in function
   called_args <- match.call()
   default_args <- formals()
diff --git a/R/evaluate.fim.R b/R/evaluate.fim.R
index 4b871fde..e2ade131 100644
--- a/R/evaluate.fim.R
+++ b/R/evaluate.fim.R
@@ -71,7 +71,7 @@ evaluate.fim <- function(poped.db,
                          groupsize=NULL,
                          deriv.type = NULL,
                          ...){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   
   if(is.null(bpop.val)) bpop.val <- poped.db$parameters$param.pt.val$bpop
   if(is.null(d_full)) d_full <- poped.db$parameters$param.pt.val$d
diff --git a/R/evaluate_design.R b/R/evaluate_design.R
index da0826b5..d30fcf17 100644
--- a/R/evaluate_design.R
+++ b/R/evaluate_design.R
@@ -12,6 +12,7 @@
 #' @family evaluate_design
 
 evaluate_design <- function(poped.db, ...) {
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   out <- calc_ofv_and_fim(poped.db,...)
   if(is.null(out$fim)){
     out$rse <- NULL
@@ -23,4 +24,4 @@ evaluate_design <- function(poped.db, ...) {
     colnames(out$fim) <- names(out$rse)
   }
   return(out)
-}
\ No newline at end of file
+}
diff --git a/R/evaluate_fim_map.R b/R/evaluate_fim_map.R
index 4bbdc13f..2f1bbc95 100644
--- a/R/evaluate_fim_map.R
+++ b/R/evaluate_fim_map.R
@@ -37,7 +37,7 @@ evaluate_fim_map <- function(poped.db,
                       num_sim_ids = 1000,
                       use_purrr = FALSE,
                       shrink_mat=F){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   # if (poped.db$design$m > 1) {
   #   warning("Shrinkage should only be computed for a single arm, please adjust your script accordingly.")
   # }
@@ -176,4 +176,4 @@ evaluate_fim_map <- function(poped.db,
   return(out_df)
   
   
-}
\ No newline at end of file
+}
diff --git a/R/evaluate_power.R b/R/evaluate_power.R
index 2925f0d9..0dabd120 100644
--- a/R/evaluate_power.R
+++ b/R/evaluate_power.R
@@ -38,6 +38,7 @@
 evaluate_power <- function(poped.db, bpop_idx, h0=0, alpha=0.05, power=0.80, twoSided=TRUE, 
                            find_min_n=TRUE,
                            fim=NULL, out=NULL,...) {
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   # If two-sided then halve the alpha
   if (twoSided == TRUE) alpha = alpha/2
   
@@ -85,4 +86,4 @@ evaluate_power <- function(poped.db, bpop_idx, h0=0, alpha=0.05, power=0.80, two
   }
   
   return(out)
-}
\ No newline at end of file
+}
diff --git a/R/get_all_params.R b/R/get_all_params.R
index 6880ba2c..e7ce86e4 100644
--- a/R/get_all_params.R
+++ b/R/get_all_params.R
@@ -20,6 +20,7 @@
 ## Author: Andrew Hooker
 
 get_all_params <- function(poped.db){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   #Return all params (in a vector all) with the specified order above
   
   #bpop = poped.db$parameters$bpop[,2,drop=F] 
diff --git a/R/get_cv.R b/R/get_cv.R
index 13e0162c..3e6c344a 100644
--- a/R/get_cv.R
+++ b/R/get_cv.R
@@ -1,4 +1,5 @@
 get_cv <- function(param_vars,poped.db){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   #Return the RSE,CV of parameters
   ## Author: Andrew Hooker
   params_all <-  get_all_params(poped.db)[[8]] 
@@ -62,7 +63,7 @@ get_rse <- function (fim, poped.db,
                      prior_fim = poped.db$settings$prior_fim,
                      #pseudo_on_fail = FALSE,
                      ...) {
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   ## update poped.db with options supplied in function
   called_args <- match.call()
   default_args <- formals()
diff --git a/R/get_fim_size.R b/R/get_fim_size.R
index 856b7e56..1f6c856e 100644
--- a/R/get_fim_size.R
+++ b/R/get_fim_size.R
@@ -2,6 +2,7 @@
 ## Author: Andrew Hooker
 
 get_fim_size <- function(poped.db){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   #Returns the size of FIM, i$e. col or row size
   numnotfixed_bpop = sum(poped.db$parameters$notfixed_bpop)
   numnotfixed_d    = sum(poped.db$parameters$notfixed_d)
diff --git a/R/get_unfixed_params.R b/R/get_unfixed_params.R
index 813b40df..a914450b 100644
--- a/R/get_unfixed_params.R
+++ b/R/get_unfixed_params.R
@@ -15,7 +15,7 @@
 #' @export
 #' @keywords internal
 get_unfixed_params <- function(poped.db,params=NULL){
-  
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   if(is.null(params)){
     bpop = poped.db$parameters$bpop[,2,drop=F]
     d = poped.db$parameters$d[,2,drop=F]
diff --git a/R/grad_bpop.R b/R/grad_bpop.R
index 7999b340..61ba636f 100644
--- a/R/grad_bpop.R
+++ b/R/grad_bpop.R
@@ -2,6 +2,7 @@
 ## Author: Andrew Hooker
 
 grad_bpop <- function(func,select_par,nout,model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,d,sigma,docc,poped.db,subset=poped.db$parameters$notfixed_bpop, offdiag = FALSE){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   #----------Model linearization with respect to pop parameters
   #
   # use helper function to check for/include EBEs
@@ -13,7 +14,7 @@ grad_bpop <- function(func,select_par,nout,model_switch,xt_ind,x,a,bpop,b_ind,bo
 
 # helper for m2
 helper_v_EBE <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,d,sigma,docc,poped.db) {
-  
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   if((poped.db$settings$bCalculateEBE)){
     #zeros(size(b_ind)[1],size(b_ind)[2])
     b_ind_x = ind_estimates(poped.db$mean_data,bpop,d,sigma,t(b_ind),(poped.db$settings$iApproximationMethod==2),FALSE,model_switch,xt_ind,x,a,b_ind,bocc_ind,poped.db)
@@ -28,7 +29,7 @@ helper_v_EBE <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,d,sigma,doc
 
 # helper for m1
 helper_LinMatrix <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,d,sigma,docc,poped.db) {
-  
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   epsi0 = zeros(1,length(poped.db$parameters$notfixed_sigma))
   
   # create linearized model
diff --git a/R/graddetmf.R b/R/graddetmf.R
index ee1fe9e6..fcca6b78 100644
--- a/R/graddetmf.R
+++ b/R/graddetmf.R
@@ -3,6 +3,7 @@
 
 graddetmf <- function(model_switch,aX,groupsize,ni,xt,x,a,bpop,d,sigma,docc,poped.db,lndet=FALSE,gradxt=FALSE){
   
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   n = get_fim_size(poped.db)
   m=size(ni,1)
   if (gradxt == FALSE) {
diff --git a/R/graddetmf_ext.R b/R/graddetmf_ext.R
index b8e8190e..76abdaba 100644
--- a/R/graddetmf_ext.R
+++ b/R/graddetmf_ext.R
@@ -2,7 +2,7 @@
 ## Author: Andrew Hooker
 
 graddetmf_ext <- function(model_switch,aX,groupsize,ni,xt,x,a,bpop,d,sigma,docc,poped.db,lndet=FALSE,gradxt=FALSE){
-  
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   n = get_fim_size(poped.db)
   m=size(ni,1)
   if (gradxt==FALSE) {
diff --git a/R/gradff.R b/R/gradff.R
index 18952a28..260f80be 100644
--- a/R/gradff.R
+++ b/R/gradff.R
@@ -9,6 +9,7 @@ gradff <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,poped.db){
   # derivative of model w.r.t. g eval at b=b_ind
   #
   #
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   fg0 = feval(poped.db$model$fg_pointer,x,a,bpop,b_ind,bocc_ind)
   epsi0 = zeros(1,length(poped.db$parameters$notfixed_sigma))
 
diff --git a/R/gradfg.R b/R/gradfg.R
index da5b693c..865d9414 100644
--- a/R/gradfg.R
+++ b/R/gradfg.R
@@ -2,6 +2,7 @@
 ## Author: Andrew Hooker
 
 gradfg <- function(x,a,bpop,b_ind,bocc_ind,poped.db){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
 #
 #
 # size: (number of g's x number of random effects)
diff --git a/R/gradfg_occ.R b/R/gradfg_occ.R
index d57891be..7d2a7a79 100644
--- a/R/gradfg_occ.R
+++ b/R/gradfg_occ.R
@@ -5,6 +5,7 @@ gradfg_occ <- function(x,a,bpop,b_ind,bocc_ind,currentOcc,poped.db){
 #
 # deriv of g's w$r.t. bocc's eval at b_ind, bocc_ind at occ currentOcc
 #
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   dfg_db0 = grad_all(poped.db$model$fg_pointer,5,poped.db$parameters$ng,x,a,bpop,b_ind,bocc_ind,poped.db,currentOcc = currentOcc,noPopED = TRUE)
   return(dfg_db0) 
 }
diff --git a/R/gradofv_a.R b/R/gradofv_a.R
index 42d7ae1a..d7353d88 100644
--- a/R/gradofv_a.R
+++ b/R/gradofv_a.R
@@ -2,7 +2,7 @@
 ## Author: Andrew Hooker
 
 gradofv_a <- function(model_switch,aa,groupsize,ni,xt,x,a,bpop,d,sigma,docc,poped.db){
-  
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   #Input: the prior FIM or (empty) and all the other things to calculate the
   #grad with for a
   #Return a vector that is the gradient
diff --git a/R/gradofv_xt.R b/R/gradofv_xt.R
index 2b3f603e..4821a063 100644
--- a/R/gradofv_xt.R
+++ b/R/gradofv_xt.R
@@ -2,7 +2,7 @@
 ## Author: Andrew Hooker
 
 gradofv_xt <- function(model_switch,axt,groupsize,ni,xt,x,a,bpop,d,sigma,docc,poped.db){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   #Input: the prior FIM or (empty) and all the other things to calculate the
   #grad with
   #Return a vector that is the gradient and the global structure
diff --git a/R/gradtrmf.R b/R/gradtrmf.R
index 53db2470..6568d72c 100644
--- a/R/gradtrmf.R
+++ b/R/gradtrmf.R
@@ -3,7 +3,7 @@ gradtrmf <- function(model_switch,aX,groupsize,ni,xt,x,a,bpop,d,sigma,docc,poped
   #  Looks at the gradient of tr(FIM^-1) with respect to time (xt) or covariate (a).
   #  problems can arise when a or xt goes negative. So only do forward
   #  differencing. 
-  
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   m=size(ni,1)
   if (gradxt == FALSE) {
     gdmf=matrix(1,m,size(a,2))
diff --git a/R/helper.R b/R/helper.R
index e8aa2c01..280a6a1c 100644
--- a/R/helper.R
+++ b/R/helper.R
@@ -96,6 +96,7 @@ tryCatch.W.E <- function(expr){
 
 
 get_fim_size <- function(poped.db) {
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   numnotfixed_bpop = sum(poped.db$parameters$notfixed_bpop)
   numnotfixed_d    = sum(poped.db$parameters$notfixed_d)
   numnotfixed_covd = sum(poped.db$parameters$notfixed_covd)
@@ -109,4 +110,4 @@ get_fim_size <- function(poped.db) {
     numnotfixed_covdocc+numnotfixed_sigma+numnotfixed_covsigma
   fim_size <- n_fixed_eff+n_rand_eff
   return(fim_size)
-}
\ No newline at end of file
+}
diff --git a/R/hessian_eta_complex.R b/R/hessian_eta_complex.R
index abd98194..629f54fc 100644
--- a/R/hessian_eta_complex.R
+++ b/R/hessian_eta_complex.R
@@ -1,6 +1,6 @@
 #Hessian over eta, evaluated at eta_hat => laplace approximation possible
 hessian_eta_complex <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,poped.db,return_gradient=F){
-  
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   bAutomatic = FALSE
   epsi0 = zeros(1,length(poped.db$parameters$notfixed_sigma))
   n=length(b_ind)
diff --git a/R/hesskalpha2.R b/R/hesskalpha2.R
index 7df387e2..c4cd1719 100644
--- a/R/hesskalpha2.R
+++ b/R/hesskalpha2.R
@@ -1,5 +1,6 @@
 
 hesskalpha2 <- function(alpha, model_switch,groupsize,ni,xtoptn,xoptn,aoptn,bpopdescr,ddescr,covd,sigma,docc,poped.db,ha,Engine){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   #D2KALPHA2 calculates the hessian of k with respect to alpha
   #   Detailed explanation goes here
   returnArgs <- log_prior_pdf(alpha,bpopdescr,ddescr,return_gradient=T,return_hessian=T) 
diff --git a/R/ind_estimates.R b/R/ind_estimates.R
index 3e85e20d..49b84cdf 100644
--- a/R/ind_estimates.R
+++ b/R/ind_estimates.R
@@ -1,7 +1,7 @@
 #Get the emperical bayes estimates for one individual
 #Written for PopED by JN
 ind_estimates <- function(data,bpop,d,sigma,start_bind,bInter,bUDDLike,model_switch,xt_ind,x,a,b_ind,bocc_ind,poped.db){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   b_i = t(start_bind)
   c1 = length(t(start_bind))/2*log(2*pi)
   c2 = 1/2*log(det(d))
@@ -33,6 +33,7 @@ ind_estimates <- function(data,bpop,d,sigma,start_bind,bInter,bUDDLike,model_swi
 
 #This is the function that should be minimized, w$r.t eta
 min_function <- function(data,bpop,d,sigma,bInter,bUDDLike,model_switch,xt_ind,x,a,bocc_ind,poped.db,c1,c2,c3,lC,det_res_var,b_ind,return_deriv=F){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   bAnalytic = FALSE
   li = ind_likelihood(data,bpop,d,sigma,bInter,bUDDLike,model_switch,xt_ind,x,a,bocc_ind,poped.db,lC,det_res_var,b_ind) #Individual log likelihood
   ret =c1+c2+1/2*t(b_ind)*c3*b_ind-li
diff --git a/R/ind_likelihood.R b/R/ind_likelihood.R
index 036f72e8..b2d1bae7 100644
--- a/R/ind_likelihood.R
+++ b/R/ind_likelihood.R
@@ -23,6 +23,7 @@
 #        log(det(RR))+ (res'/RR)*res;        
 
 ind_likelihood <- function(data,bpop,d,sigma,bInter,bUDDLike,model_switch,xt_ind,x,a,bocc_ind,poped.db,lC,det_res_var,b_ind){
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   # % from davidian and giltinan p 173 
   if((!bUDDLike)){
     #browser()
diff --git a/R/m1.R b/R/m1.R
index 80c1e588..35437b9a 100644
--- a/R/m1.R
+++ b/R/m1.R
@@ -2,6 +2,7 @@
 ## Author: Andrew Hooker
 
 m1 <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,d,sigma,poped.db){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   #
   # function computes the derivative of the
   # linerarized model function w$r.t. bpop
diff --git a/R/m2.R b/R/m2.R
index d4c4e478..cf95b9f4 100644
--- a/R/m2.R
+++ b/R/m2.R
@@ -2,6 +2,7 @@
 ## Author: Andrew Hooker
 
 m2 <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,d,sigma,docc,poped.db){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
 # M2 derivative of the vectorized variance w$r.t. bpops
 # 
 # the output is a matrix with dimensions (ind_samps^2 X nbpop)
diff --git a/R/m3.R b/R/m3.R
index 989da56b..4291969d 100644
--- a/R/m3.R
+++ b/R/m3.R
@@ -4,7 +4,7 @@
 m3 <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,d,sigma,docc,bUseVarSigmaDerivative,poped.db){
   #
   # size: (samps per subject^2 x (number of random effects + number of occasion variances + number of sigmas))
-
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   dv_dd = NULL
   dv_covd = NULL
   dv_ddocc = NULL
diff --git a/R/mf3.R b/R/mf3.R
index cc589cca..992643ed 100644
--- a/R/mf3.R
+++ b/R/mf3.R
@@ -22,7 +22,7 @@
 ## Author: Andrew Hooker
 
 mf3 <- function(model_switch,xt,x,a,bpop,d,sigma,docc,poped.db){
-
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   numnotfixed_bpop = sum(poped.db$parameters$notfixed_bpop)
   numnotfixed_d    = sum(poped.db$parameters$notfixed_d)
   numnotfixed_covd = sum(poped.db$parameters$notfixed_covd)
diff --git a/R/mf7.R b/R/mf7.R
index e7aaa6d5..d49a47ce 100644
--- a/R/mf7.R
+++ b/R/mf7.R
@@ -19,7 +19,7 @@
 ## Author: Andrew Hooker
 
 mf7 <- function(model_switch,xt_ind,x,a,bpop,d,sigma,docc,poped.db){
-  
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   #This calculation of FIM divides the calculation up into one calculation
   #per model switch
   
diff --git a/R/mf_all.R b/R/mf_all.R
index 369b6c7d..f0007adf 100644
--- a/R/mf_all.R
+++ b/R/mf_all.R
@@ -3,7 +3,7 @@
 ## Author: Andrew Hooker
 
 mf_all <- function(model_switch,xt_ind,x,a,bpop,d,sigma,docc,poped.db){
-
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
     returnArgs <- switch(poped.db$settings$iFIMCalculationType+1,
                          mf3(model_switch,xt_ind,x,a,bpop,d,sigma,docc,poped.db), #Default (with no assumption that bpop and b are uncorrelated)
                          mf3(model_switch,xt_ind,x,a,bpop,d,sigma,docc,poped.db), #Reduced FIM
diff --git a/R/mfea.R b/R/mfea.R
index d019f424..dedda2b8 100644
--- a/R/mfea.R
+++ b/R/mfea.R
@@ -36,7 +36,7 @@ mfea <- function(poped.db,model_switch,ni,xt,x,a,bpopdescr,ddescr,maxxt,minxt,ma
                  #opt_inds=poped.db$settings$optsw[5],
                  trflag=T,
                  ...){
-  
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   if((poped.db$settings$EACriteria!=1)){
     stop(sprintf('The criteria that can be used is Modified Fedorov Exchange Algorithm (EACriteria = 1)'))
   }
diff --git a/R/mftot.R b/R/mftot.R
index 0f63c73b..1da3690f 100644
--- a/R/mftot.R
+++ b/R/mftot.R
@@ -30,6 +30,7 @@
 ## Author: Andrew Hooker
 
 mftot <- function(model_switch,groupsize,ni,xt,x,a,bpop,d,sigma,docc,poped.db,...){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   m=size(ni,1)
   s=0
   for(i in 1:m){
diff --git a/R/ofv_fim.R b/R/ofv_fim.R
index 5e27d4e7..9b31e7c0 100644
--- a/R/ofv_fim.R
+++ b/R/ofv_fim.R
@@ -37,7 +37,7 @@ ofv_fim <- function(fmf,poped.db,
                     ds_index=poped.db$parameters$ds_index,
                     use_log = TRUE,
                     ...){
-  
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   #Input: the FIM
   #Return the single value that should be maximized
   
diff --git a/R/optimize_n.R b/R/optimize_n.R
index 403b0bcf..bb8ae53a 100644
--- a/R/optimize_n.R
+++ b/R/optimize_n.R
@@ -9,6 +9,7 @@
 #' @keywords internal
 #'
 extract_norm_group_fim <- function (poped.db,...) {
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
   num_groups <- poped.db$design$m
   fim_group <- list()
   for(i in 1:num_groups){
@@ -62,7 +63,7 @@ optimize_groupsize <-
            props = c(poped.db$design$groupsize/sum(poped.db$design$groupsize)),
            trace=1,
            ...){
-    
+      start_parallel_env$babelmixr2 <- poped.db$babelmixr2
     # need to fix:
     # limits on the proportions to account for max and min values of N in each group
     # return actual values.
@@ -115,6 +116,7 @@ optimize_groupsize <-
   norm_group_fim <- extract_norm_group_fim(poped.db)
   
   ofv_fun <- function(props,norm_group_fim,n_tot, poped.db, ...){
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2
     fim_tmp <- combine_norm_group_fim(norm_group_fim,props*n_tot)
     ofv_fim(fim_tmp,poped.db,...)
   }
@@ -231,7 +233,7 @@ optimize_n_rse <- function(poped.db,
                            allowed_values = seq(poped.db$design$m,
                                                 sum(poped.db$design$groupsize)*5,
                                                 by=poped.db$design$m)){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   n_per_group = poped.db$design$groupsize
   n_tot <- sum(n_per_group)
   props = c(n_per_group/n_tot)
@@ -275,7 +277,7 @@ optimize_n_eff <- function(poped.db,
                            ofv_ref,
                            norm_group_fim = NULL,  
                            ...){
-  
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   n_per_group = poped.db$design$groupsize
   n_tot <- sum(n_per_group)
   props = c(n_per_group/n_tot)
diff --git a/R/par_and_space_tbl.R b/R/par_and_space_tbl.R
index d529ddc6..fa609c64 100644
--- a/R/par_and_space_tbl.R
+++ b/R/par_and_space_tbl.R
@@ -1,4 +1,5 @@
 par_and_space_tbl <- function(poped.db) {
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   df <- NULL
   allowed_values <- allowed_values_2 <- cont <- lower <- upper <- par <- NULL
   
@@ -264,7 +265,8 @@ get_par_and_space_optim <- function(poped.db,
                                     cont_cat = "both",
                                     warn_when_none=TRUE) 
 {
-    
+
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   type <- index <- fixed <- cont <- par <- lower <- upper <- NULL
   
   #----------- checks
diff --git a/R/pargen.R b/R/pargen.R
index bde9b221..2e7d8f6f 100644
--- a/R/pargen.R
+++ b/R/pargen.R
@@ -29,7 +29,7 @@
 ## Author: Andrew Hooker
 
 pargen <- function(par,user_dist_pointer,sample_size,bLHS,sample_number,poped.db){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   nvar=size(par,1)
   ret=zeros(sample_size,nvar)
   
diff --git a/R/plot_efficiency_of_windows.R b/R/plot_efficiency_of_windows.R
index 64dc21fd..9e91d39c 100644
--- a/R/plot_efficiency_of_windows.R
+++ b/R/plot_efficiency_of_windows.R
@@ -69,7 +69,7 @@ plot_efficiency_of_windows <- function(poped.db,
                                        #mrgsolve_model=NULL,
                                        seed=round(runif(1,0,10000000)),
                                        ...){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   if(!is.null(seed)) set.seed(seed)
   
   design = poped.db$design
@@ -394,4 +394,4 @@ plot_efficiency_of_windows <- function(poped.db,
   p <- p+ylab("Value in %")+xlab("Simulation number of design sampled from defined windows")
   #p <- p + stat_summary(fun.y = "mean", geom="hline")
   return(p)
-}
\ No newline at end of file
+}
diff --git a/R/plot_model_prediction.R b/R/plot_model_prediction.R
index 68c0c589..8a89f90a 100644
--- a/R/plot_model_prediction.R
+++ b/R/plot_model_prediction.R
@@ -93,6 +93,7 @@ plot_model_prediction <- function(poped.db,
                                   PI_alpha=0.3,
                                   #PI_fill="blue",
                                   ...){
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   PI_u <- PI_l <- NULL
   df <-  model_prediction(poped.db,
                           #models_to_use,
diff --git a/R/poped_optim.R b/R/poped_optim.R
index d6e15aff..6fe3eee0 100644
--- a/R/poped_optim.R
+++ b/R/poped_optim.R
@@ -105,7 +105,7 @@ poped_optim <- function(poped.db,
                         allow_replicates_xt=TRUE,
                         allow_replicates_a=TRUE,
                         ...){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   
  
   #------------ update argument list with called arguments
diff --git a/R/poped_optim_1.R b/R/poped_optim_1.R
index 217bd877..f42a555d 100644
--- a/R/poped_optim_1.R
+++ b/R/poped_optim_1.R
@@ -92,7 +92,7 @@ poped_optim_1 <- function(poped.db,
                         ofv_fun = poped.db$settings$ofv_fun,
                         maximize=T,
                         ...){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2    
   #------------ update poped.db with options supplied in function
   called_args <- match.call()
   default_args <- formals()
diff --git a/R/poped_optim_2.R b/R/poped_optim_2.R
index e77a8422..62361965 100644
--- a/R/poped_optim_2.R
+++ b/R/poped_optim_2.R
@@ -94,7 +94,7 @@ poped_optim_2 <- function(poped.db,
                           maximize=T,
                           transform_parameters = F,
                           ...){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   #------------ update poped.db with options supplied in function
   called_args <- match.call()
   default_args <- formals()
diff --git a/R/poped_optim_3.R b/R/poped_optim_3.R
index 3dee7851..eff507fc 100644
--- a/R/poped_optim_3.R
+++ b/R/poped_optim_3.R
@@ -96,7 +96,7 @@ poped_optim_3 <- function(poped.db,
                           allow_replicates_xt=TRUE,
                           allow_replicates_a=TRUE,
                           ...){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2    
   #------------ update poped.db with options supplied in function
   called_args <- match.call()
   default_args <- formals()
diff --git a/R/poped_optimize.R b/R/poped_optimize.R
index 7399eef7..e93517af 100644
--- a/R/poped_optimize.R
+++ b/R/poped_optimize.R
@@ -67,7 +67,7 @@ poped_optimize <- function(poped.db,
                            bLHS=poped.db$settings$bLHS,
                            use_laplace=poped.db$settings$iEDCalculationType,
                            ...){
-  
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   ## update poped.db with options supplied in function
   called_args <- match.call()
   default_args <- formals()
diff --git a/R/shrinkage.R b/R/shrinkage.R
index 0eb4e86b..e3b447bd 100644
--- a/R/shrinkage.R
+++ b/R/shrinkage.R
@@ -31,7 +31,7 @@ shrinkage <- function(poped.db,
                       use_mc = FALSE,
                       num_sim_ids = 1000,
                       use_purrr = FALSE){
-  
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   # if (poped.db$design$m > 1) {
   #   warning("Shrinkage should only be computed for a single arm, please adjust your script accordingly.")
   # }
@@ -200,4 +200,4 @@ shrinkage <- function(poped.db,
   return(out_df)
   
   
-}
\ No newline at end of file
+}
diff --git a/R/start_parallel.R b/R/start_parallel.R
index ca7e5d73..884068de 100644
--- a/R/start_parallel.R
+++ b/R/start_parallel.R
@@ -1,3 +1,5 @@
+start_parallel_env <- new.env(parent=emptyenv())
+start_parallel_env$babelmixr2 <- NULL
 #' Start parallel computational processes
 #' 
 #' This tool chooses the type of parallelization process to use based on the
@@ -87,6 +89,13 @@ start_parallel <- function(parallel=TRUE,
         }
         parallel::clusterCall(cl, mrgsolve::loadso, x=mrgsolve_model)
       }
+      if (!is.null(start_parallel_env$babelmixr2)) {
+        if (!requireNamespace("babelmixr2", quietly=TRUE)) {
+          stop("babelmixr2 package needed for this function to work. Please install it.",
+               call.=FALSE)
+        }
+        parallel::clusterCall(cl, babelmixr2::.popedCluster, start_parallel_env$babelmixr2)
+      }
       # if(!is.null(cpp_files)){
       #   for(i in cpp_files){
       #     parallel::clusterCall(cl, 
@@ -108,4 +117,4 @@ start_parallel <- function(parallel=TRUE,
   }
   
   return(parallel)
-}
\ No newline at end of file
+}
diff --git a/R/v.R b/R/v.R
index 7b0b89b0..f399085d 100644
--- a/R/v.R
+++ b/R/v.R
@@ -3,7 +3,7 @@
 
 v <- function(model_switch,xt_ind,x,a,bpop,b_ind,bocc_ind,d,sigma,docc,poped.db){
   # number of samples X number of samples (per individual)
-  
+    start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
   bUseAutoCorrelation = !isempty(poped.db$model$auto_pointer)
   
   bUseFullSigmaCorrelation = FALSE
diff --git a/R/write_iterationfile.R b/R/write_iterationfile.R
index acbc3196..ad879cee 100644
--- a/R/write_iterationfile.R
+++ b/R/write_iterationfile.R
@@ -3,7 +3,7 @@
 ## Author: Andrew Hooker
 
 write_iterationfile <- function(strSearch,iteration,xt,a,x,ni,groupsize,fim,ofv,poped.db){
-
+  start_parallel_env$babelmixr2 <- poped.db$babelmixr2  
 ## #Make sure that this doesn't crash the search
 ## try 
 ##     fn = file(poped.db$settings$strIterationFileName, 'w')

From c8be2997883894977805673611a7ce74888a84df Mon Sep 17 00:00:00 2001
From: Matthew L Fidler <matthew.fidler@gmail.com>
Date: Thu, 24 Oct 2024 00:54:03 -0500
Subject: [PATCH 2/5] Add babelmixr2 to suggests

---
 DESCRIPTION | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f0f30702..8a1fb581 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -32,7 +32,8 @@ Suggests:
     gridExtra,
     covr,
     devtools,
-    mrgsolve
+    mrgsolve,
+    babelmixr2
 Authors@R: c(
     person("Andrew C.","Hooker", email="andrew.hooker@farmaci.uu.se", 
       role=c("aut","cre","trl","cph"),

From bf0584cf440832a37cdaf10437ca94efc8865e33 Mon Sep 17 00:00:00 2001
From: Matthew L Fidler <matthew.fidler@gmail.com>
Date: Thu, 24 Oct 2024 00:56:31 -0500
Subject: [PATCH 3/5] Add to news

---
 NEWS.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 7a1b6557..36e0cc2d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# PopED development verson
+
+* Make parallelization work with `babelmixr2` models on windows (#79)
+
 # PopED 0.7.0
 
 * `create.poped.database()` now uses a better method of identifying the total number of parameters of each type (bpop, d, sigma, etc.) in a user defined model parameter function (the `ff_fun` argument in `create.poped.database()`) (#73).

From 4b136a024736ed46cdd34c1da82bd503473bfcb0 Mon Sep 17 00:00:00 2001
From: Matthew L Fidler <matthew.fidler@gmail.com>
Date: Thu, 24 Oct 2024 01:02:40 -0500
Subject: [PATCH 4/5] add babelmixr2 dev for check

---
 .github/workflows/R-CMD-check.yaml   | 18 +++++++++++++++++-
 .github/workflows/test-coverage.yaml | 19 ++++++++++++++++++-
 2 files changed, 35 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index d46a6175..93515f18 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -43,7 +43,23 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: |
+            any::rcmdcheck
+            nlmixr2/n1qn1c
+            nlmixr2/lbfgsb3c
+            nlmixr2/PreciseSums
+            nlmixr2/dparser-R
+            nlmixr2/lotri
+            nlmixr2/rxode2ll
+            nlmixr2/rxode2
+            nlmixr2/nlmixr2est
+            nlmixr2/nlmixr2extra
+            nlmixr2/nlmixr2plot
+            nlmixr2/nlmixr2
+            nlmixr2/nonmem2rx
+            nlmixr2/monolix2rx
+            nlmixr2/babelmixr2
+            lixoftConnectors=?ignore
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 98822609..77b45620 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -25,7 +25,24 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr, any::xml2
+          extra-packages:  |
+            any::covr
+            any::xml2
+            nlmixr2/n1qn1c
+            nlmixr2/lbfgsb3c
+            nlmixr2/PreciseSums
+            nlmixr2/dparser-R
+            nlmixr2/lotri
+            nlmixr2/rxode2ll
+            nlmixr2/rxode2
+            nlmixr2/nlmixr2est
+            nlmixr2/nlmixr2extra
+            nlmixr2/nlmixr2plot
+            nlmixr2/nlmixr2
+            nlmixr2/nonmem2rx
+            nlmixr2/monolix2rx
+            nlmixr2/babelmixr2
+            lixoftConnectors=?ignore
           needs: coverage
 
       - name: Test coverage

From 63f3442e6d08f177923a3d0bb48f068d3d8bb2d6 Mon Sep 17 00:00:00 2001
From: Matthew Fidler <matthew.fidler@gmail.com>
Date: Thu, 7 Nov 2024 15:36:20 -0600
Subject: [PATCH 5/5] Revert "add babelmixr2 dev for check"

This reverts commit 4b136a024736ed46cdd34c1da82bd503473bfcb0.
---
 .github/workflows/R-CMD-check.yaml   | 18 +-----------------
 .github/workflows/test-coverage.yaml | 19 +------------------
 2 files changed, 2 insertions(+), 35 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 93515f18..d46a6175 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -43,23 +43,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: |
-            any::rcmdcheck
-            nlmixr2/n1qn1c
-            nlmixr2/lbfgsb3c
-            nlmixr2/PreciseSums
-            nlmixr2/dparser-R
-            nlmixr2/lotri
-            nlmixr2/rxode2ll
-            nlmixr2/rxode2
-            nlmixr2/nlmixr2est
-            nlmixr2/nlmixr2extra
-            nlmixr2/nlmixr2plot
-            nlmixr2/nlmixr2
-            nlmixr2/nonmem2rx
-            nlmixr2/monolix2rx
-            nlmixr2/babelmixr2
-            lixoftConnectors=?ignore
+          extra-packages: any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 77b45620..98822609 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -25,24 +25,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages:  |
-            any::covr
-            any::xml2
-            nlmixr2/n1qn1c
-            nlmixr2/lbfgsb3c
-            nlmixr2/PreciseSums
-            nlmixr2/dparser-R
-            nlmixr2/lotri
-            nlmixr2/rxode2ll
-            nlmixr2/rxode2
-            nlmixr2/nlmixr2est
-            nlmixr2/nlmixr2extra
-            nlmixr2/nlmixr2plot
-            nlmixr2/nlmixr2
-            nlmixr2/nonmem2rx
-            nlmixr2/monolix2rx
-            nlmixr2/babelmixr2
-            lixoftConnectors=?ignore
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage