run in JAva and R

exploration/NEA_sensitivity_analysis/tryFromJava.R

 library(rJava) # see J4R
 #library(yaml)
 library(tidyverse)
+library(jdx)
 
 rm(list = ls())
 
@@ -26,18 +27,18 @@ setwd("../..")
 
 # path to outputs
 #outputDir = "simus/"
-outputFileName = paste0("SA/",seed)
+#outputFileName = paste0("SA/",seed)
 
 
 jarfile = "target/GR3D-3.2-SNAPSHOT.jar"
-simDuration = 48
+simDuration = 150
 simBegin = 1
 timeStepDuration = 1
 
 seed = 1
 
-arguments = c('-simDuration',simDuration, '-simBegin',simBegin,
-              '-timeStepDuration',timeStepDuration, 
+arguments = c('-q','-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",
@@ -46,6 +47,7 @@ arguments = c('-simDuration',simDuration, '-simBegin',simBegin,
 
 
 #  initializes the Java Virtual Machine -------------------------------------
+.jinit(classpath ="", force.init = TRUE)
 .jinit(classpath = jarfile, force.init = TRUE)
 
 #  modification of xlm parameters -----------------------
@@ -53,9 +55,9 @@ parametersNames = c("processes.processesEachStep.10.tempMinRep",
                     "processes.processesEachStep.10.ratioS95_S50",
                     "processes.processesEachStep.6.pHomingAfterEquil")
 thetas = c(10, 2, 0.7)
-# run the GR3D with update xlm parameters --------------------------------------------
-
-.jcall("analysis.EasyRun","V","runSimulation", arguments, outputFileName, .jarray(parametersNames), .jarray(thetas))
+# run the GR3D with updated parameter values in processes --------------------------------------------
+.jclassPath()
+.jcall("analysis.EasyRun", "V", "runSimulation", arguments, .jarray(parametersNames), .jarray(thetas))
 
 
 # call GR3D method to get model outputs ----------------------------------------------
@@ -70,17 +72,17 @@ thetas = c(10, 2, 0.7)
 #   range[1] = latitude of the median distribution ( 50 % of effectives are northern)
 #   range[2] = southern limit latitude of the fish distribution
 
-#range = .jcall("miscellaneous.EasyRun","[D","getValuesFromAquaNismsGroup","getRangeDistribution")
-.jcall("analysis.EasyRun", "D", "getSingleValueFromAquanismGroupProcess", "processes.processesAtEnd.0.getLogLikelihood");
+out = .jcall("analysis.EasyRun","[[Ljava/lang/String;","getValuesFromAquanismGroupProcess","processes.processesEachStep.9.exportToR")
+range <- data.frame(matrix(convertToR(out[[2]]), nrow = 1,  dimnames = list(NULL, convertToR(out[[1]])))) %>% type_convert()
+
+
 # ------------------------------------------------------------ #
 # 2. log-likelihood ----
 #       the proportion of reproductions leading to a recruitment > 50 over the 1920-1950 period was used 
-#       as a proxy of predicted probability of presecen in a  basin.
+#       as a proxy of predicted probability of presence in a  basin.
 #       Then a log-likelihood of a binomial distribution is computed
 
-# access through computeLikelihood in DiadromousFishGroup
-# see getProbOfNonNulRecruitmentDuringLastYears in BasinNetwork
-
+.jcall("analysis.EasyRun", "D", "getSingleValueFromAquanismGroupProcess", "processes.processesAtEnd.0.getLogLikelihood");
 # ------------------------------------------------------------ #
 # 3. proportion of first-time spawners
 #     annual % of first-time spawners according to latitude (or basin_id)
@@ -88,16 +90,21 @@ thetas = c(10, 2, 0.7)
 #     then in R: annual slope of the linear regression
 #     and average over the period
 
-# mean (+sd) and slpe after
-
-# access through AnalyseSpawnerRun in [processesAtEnd]
-
-
-# ------------------------------------------------------------ #
 # 4. Mean age of the spawner for male and female ----
 #     annual mean age in each basin, 
 #     then in R: average per year,
 #     and average over the period (1920 and 1950)
+# mean (+sd) and slope after
+
+
+out = .jcall("analysis.EasyRun","[[Ljava/lang/String;","getValuesFromAquanismGroupProcess","processes.processesEachStep.8.exportToR")
+out2 = matrix(unlist(lapply(out, convertToR)), nrow = length(out) , byrow = TRUE)
+out3 <- out2[-1,]
+colnames(out3) <- unlist(out2[1,])
+as.data.frame(out3)  %>% type_convert()
+
+# ------------------------------------------------------------ #
+
 
 # ------------------------------------------------------------ #
 # 5. number of metapopulation based on the exchange matrix ----
@@ -107,12 +114,16 @@ thetas = c(10, 2, 0.7)
 
 # moyenne sur les bassins versants des moyennes sur la peride  des moyennes des flux 
 # access through species.IdentifyPopulation in processesAtEnd
+
+#TODO A FAIRE !!!
+
+# =================================================================================
 toto <- .jcall("analysis.EasyRun","Ljava/util/List;",
                       "getAListFromAquanismGroupProcess","processes.processesAtEnd.1.getRecords")
 
 as.list(toto)
 
-.jcall("miscellaneous.EasyRun","[D","getValuesFromEnvironment","getMeanLastPercOfAut")
+
 
 # truc  = .jcall("analysis.EasyRun","Ljava/util/List;",
 #                "getAListFromAquanismGroupProcess","processes.processesAtEnd.1.getRecords")

src/main/java/analysis/EasyRun.java

@@ -26,8 +26,7 @@ public class EasyRun {
 
 	static Pilot pilot;
 
-	public static void runSimulation(String[] batchArgs, String outputfilename, String[] paramNames, double[] paramValues)
-			throws Exception {
+	public static void runSimulation(String[] batchArgs, String[] paramNames, double[] paramValues) throws Exception {
 
 		try {
 			pilot = new Pilot();
@@ -96,7 +95,7 @@ public class EasyRun {
 
 		double[] parameterValues = new double[] { 10, 2, 0.7 };
 
-		runSimulation(batchArguments, "tsointsoin", parameterNames, parameterValues);
+		runSimulation(batchArguments, parameterNames, parameterValues);
 
 		System.out.println("\n== AnalyseSpawnerFeatures ==");
 		String[][] spawnerRunResults = getValuesFromAquanismGroupProcess("processes.processesEachStep.8.exportToR");