Run model + order folder

ottiP · Nov 10, 2021 · 4867415 · 4867415
1 parent cb559ce
commit 4867415
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Showing 19 changed files with 8 additions and 8 deletions.
diff --git a/HH_transmission_model_project.Rmd b/HH_transmission_model_project.Rmd
@@ -16,11 +16,11 @@ library(ggplot2)
 library(msm)
 library(doParallel)
 library(reshape2)
-source('./compute_CI.R')
-source('./sim_functions/generate_delay_dist.R')
-source('./sim_functions/simulation_analysis_gamma.R')
-source("./chain_bin_lik.R")
-source("./sim_functions/parRead.R")
+source('./R/compute_CI.R')
+source('./R/generate_delay_dist.R')
+source('./R/simulation_analysis_gamma.R')
+source("./R/chain_bin_lik.R")
+source("./R/parRead.R")
 
 N.delay.draw <- 10
 ```
@@ -36,13 +36,13 @@ cl1 <-makeCluster(nCores)
 clusterExport(cl1, c('sim.hh.func.fixed'), environment())
 
 
-  sim.ds.ls3 <- parLapply(cl=cl1, 1:100000,sim.hh.func.fixed, hh.size=3) #650K HH=~2m ppl
+  sim.ds.ls3 <- parLapply(cl=cl1, 1:100000,sim.hh.func.fixed, hh.size=3) #100K HH=~300K ppl
 sim.ds3 <- bind_rows(sim.ds.ls3)
 
-  sim.ds.ls2 <- parLapply(cl=cl1, 1:100000,sim.hh.func.fixed, hh.size=2) #650K HH=~2m ppl
+  sim.ds.ls2 <- parLapply(cl=cl1, 1:100000,sim.hh.func.fixed, hh.size=2) #100K HH=~200K ppl
 sim.ds2 <- bind_rows(sim.ds.ls2)
 
-  sim.ds.ls1 <- parLapply(cl=cl1, 1:100000,sim.hh.func.fixed, hh.size=1) #650K HH=~2m ppl
+  sim.ds.ls1 <- parLapply(cl=cl1, 1:100000,sim.hh.func.fixed, hh.size=1) #100K HH=~100K ppl
 sim.ds1 <- bind_rows(sim.ds.ls1)
 
 stopCluster(cl1)

diff --git a/chain_bin_lik.R → R/chain_bin_lik.R b/chain_bin_lik.R → R/chain_bin_lik.R
diff --git a/compute_CI.R → R/compute_CI.R b/compute_CI.R → R/compute_CI.R
diff --git a/sim_functions/generate_delay_dist.R → R/generate_delay_dist.R b/sim_functions/generate_delay_dist.R → R/generate_delay_dist.R
diff --git a/...nctions/generate_delay_dist_exponential.R → R/generate_delay_dist_exponential.R b/...nctions/generate_delay_dist_exponential.R → R/generate_delay_dist_exponential.R
diff --git a/sim_functions/parRead.R → R/parRead.R b/sim_functions/parRead.R → R/parRead.R
diff --git a/sim_functions/simulation_analysis_gamma.R → R/simulation_analysis_gamma.R b/sim_functions/simulation_analysis_gamma.R → R/simulation_analysis_gamma.R
diff --git a/intermediate_data/sim_ds_fix_gamma.rds b/intermediate_data/sim_ds_fix_gamma.rds
diff --git a/intermediate_data/summary_table_ 1 iter_SIM.rds b/intermediate_data/summary_table_ 1 iter_SIM.rds
diff --git a/intermediate_data/summary_table_ 10 iter_SIM.rds b/intermediate_data/summary_table_ 10 iter_SIM.rds
diff --git a/intermediate_data/summary_table_ 2 iter_SIM.rds b/intermediate_data/summary_table_ 2 iter_SIM.rds
diff --git a/intermediate_data/summary_table_ 3 iter_SIM.rds b/intermediate_data/summary_table_ 3 iter_SIM.rds
diff --git a/intermediate_data/summary_table_ 4 iter_SIM.rds b/intermediate_data/summary_table_ 4 iter_SIM.rds
diff --git a/intermediate_data/summary_table_ 5 iter_SIM.rds b/intermediate_data/summary_table_ 5 iter_SIM.rds
diff --git a/intermediate_data/summary_table_ 6 iter_SIM.rds b/intermediate_data/summary_table_ 6 iter_SIM.rds
diff --git a/intermediate_data/summary_table_ 7 iter_SIM.rds b/intermediate_data/summary_table_ 7 iter_SIM.rds
diff --git a/intermediate_data/summary_table_ 8 iter_SIM.rds b/intermediate_data/summary_table_ 8 iter_SIM.rds
diff --git a/intermediate_data/summary_table_ 9 iter_SIM.rds b/intermediate_data/summary_table_ 9 iter_SIM.rds
diff --git a/results/mod_result.rds b/results/mod_result.rds