last version

exploration/NEA_sensitivity_analysis/tryFromJava.R

@@ -5,14 +5,14 @@ library(tidyverse)
 library(jdx)
 library(tictoc)
 
-rm(list = ls())
 
+rm(list = ls())
 
 ## to have the same working directory as GR3D
 #setwd("~/Documents/workspace/GR3D/exploration/NEA_sensitivity_analysis")
 setwd("../..")
 
-
+source("exploration/GR3D_Rdescription/GR3Dmetapopulation.R")
 # ====================================== LOCAL FUNCTIONS =====================================
 convertFromSALtoR = function(java_out){
   require(jdx)
@@ -81,7 +81,10 @@ exploreEasyRun = function(){
     mutate(year =0) %>% rename(originBasin = natalBasin) %>% 
     identyMetapopulation(., threshold = .95, verbose = FALSE)
   
-  nbMetapopulation = metapopulations$metapopulation %>% distinct(metapop) %>% summarise(n = n())
+  nbMetapopulation = metapopulations$metapopulation %>% 
+    distinct(metapop) %>% 
+    summarise(n = n()) %>% 
+    unlist(use.names = FALSE)
   
   return(tibble(northern_basin_id = range$northern_basin_id, 
                 effective_centroid_latitude = range$effective_centroid_latitude,
@@ -95,36 +98,37 @@ exploreEasyRun = function(){
 
 
 # GR3D arguments -----------------------------------------
-jarfile = "target/GR3D-3.2-SNAPSHOT.jar"
-simDuration = 150
-simBegin = 1
-timeStepDuration = 1
-
-seed = 1
-#'-q',
-arguments = c('-simDuration', simDuration, '-simBegin',simBegin,
-              '-timeStepDuration', timeStepDuration, 
-              '-RNGStatusIndex', format(seed,scientific = FALSE),
-              '-groups',"data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml",
-              '-env',"data/input/northeastamerica/RIOBNneaBasins_Rjava.xml",
-              '-observers',"data/input/northeastamerica/RIO_obs_empty.xml")
+#' jarfile = "target/GR3D-3.2-SNAPSHOT.jar"
+#' simDuration = 150
+#' simBegin = 1
+#' timeStepDuration = 1
+#' 
+#' seed = 1
+#' #'-q',
+#' arguments = c('-simDuration', simDuration, '-simBegin',simBegin,
+#'               '-timeStepDuration', timeStepDuration, 
+#'               '-RNGStatusIndex', format(seed,scientific = FALSE),
+#'               '-groups',"data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml",
+#'               '-env',"data/input/northeastamerica/RIOBNneaBasins_Rjava.xml",
+#'               '-observers',"data/input/northeastamerica/RIO_obs_empty.xml")
 
 
 # -----------------------------------------------------
 #  initializes the Java Virtual Machine -------------------------------------
+jarfile = "target/GR3D-3.2-SNAPSHOT.jar"
 .jinit(NULL, force.init = TRUE)
 .jinit(classpath = jarfile, force.init = TRUE)
 .jclassPath()
 
 #  modification of xlm parameters -----------------------
-parametersNamesANG = c("processes.processesEachStep.11.Soffset") 
-thetasANG = c(-1)
-
-parametersNamesENV = c("simulationName")
-thetasENV = c("Allee")
+# parametersNamesANG = c("processes.processesEachStep.11.Soffset") 
+# thetasANG = c(-1)
+# 
+# parametersNamesENV = c("simulationName")
+# thetasENV = c("Allee")
 
 # run the GR3D with updated parameter values in processes --------------------------------------------
-runEasyRun(arguments, parametersNamesANG,thetasANG, parametersNamesENV, thetasENV )
+# runEasyRun(arguments, parametersNamesANG,thetasANG, parametersNamesENV, thetasENV )
 
 # .jcall("analysis.EasyRun", "V", "runSimulation", arguments, 
 #        .jarray(parametersNamesANG), .jarray(thetasANG),
@@ -133,8 +137,6 @@ runEasyRun(arguments, parametersNamesANG,thetasANG, parametersNamesENV, thetasEN
 
 # call GR3D method to get model outputs ----------------------------------------------
 
-#
-
 
 runSimulation = function(simulationParameter) {
   arguments = c('-simDuration', 600, '-simBegin',2,
@@ -158,17 +160,6 @@ runSimulation = function(simulationParameter) {
 
 
 #============================
-listeSimulation <- list(list(replicat = 1, 
-                             parametersNamesANG = c("processes.processesEachStep.11.Soffset"), 
-                             thetasANG = c(-1),
-                             parametersNamesENV = c("simulationName"), 
-                             thetasENV = c("Allee")),
-                        list(replicat = 1, 
-                             parametersNamesANG = c("processes.processesEachStep.11.Soffset"), 
-                             thetasANG = c(0),
-                             parametersNamesENV = c("simulationName"), 
-                             thetasENV = c("no Allee")))
-
 listeSimulation <- list(list(replicat = 1, 
                              parametersNamesANG = c("processes.processesEachStep.11.Soffset",
                                                     "processes.processesEachStep.6.pHomingAfterEquil"), 
@@ -193,9 +184,12 @@ listeSimulation <- list(list(replicat = 1,
                         list(replicat = 1, 
                              parametersNamesANG = c("processes.processesEachStep.11.Soffset",
                                                     "processes.processesEachStep.6.pHomingAfterEquil"), 
-                             thetasANG = c(0, 0.97),
+                             thetasANG = c(0, 0.75),
                              parametersNamesENV = c("simulationName"), 
                              thetasENV = c("noAllee_lowHoming"))
                         )
+tic()
+resSimulation = lapply(listeSimulation, runSimulation)
+toc()
 
-lapply(listeSimulation, runSimulation)
\ No newline at end of file
+save(listeSimulation, resSimulation, file = 'simulation.Rdata')