new version to run Java from R

exploration/NEA_sensitivity_analysis/tryFromJava.R

-library(rJava)
+library(rJava) # see J4R
 #library(yaml)
-library(dplyr)
+library(tidyverse)
 
-rm(list=ls())
+rm(list = ls())
 
 # # parameters and prios=rs of parameters to be fitted
 # inputData = yaml.load_file("ABC_seq_2param_3stats_NewAfterSA.yaml")
@@ -20,36 +20,101 @@ rm(list=ls())
 # parametersNames = unlist(parametersNames)
 
 
-## to have the same working diretory as GR3D
+# GR3D arguments -----------------------------------------
+## to have the same working directory as GR3D
 setwd("../..")
+
 # path to outputs
-outputDir = "simus/"
+#outputDir = "simus/"
+outputFileName = paste0("SA/",seed)
+
 
 jarfile = "target/GR3D-3.2-SNAPSHOT.jar"
 simDuration = 48
 simBegin = 1
-timeStepDuration =1
+timeStepDuration = 1
 
 seed = 1
 
-parametersNames = c("processes.processesEachStep.8.tempMinRep",
-                    "processes.processesEachStep.8.ratioS95_S50",
+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 -------------------------------------
+.jinit(classpath = jarfile, force.init = TRUE)
+
+#  modification of xlm parameters -----------------------
+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 --------------------------------------------
 
-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")
+.jcall("analysis.EasyRun","V","runSimulation", arguments, outputFileName, .jarray(parametersNames), .jarray(thetas))
 
-outputFile = paste0("SA/",seed)
-.jinit(classpath = jarfile, force.init = TRUE)
-.jcall("miscellaneous.EasyRun","V","runSimulation",arguments, outputFile,.jarray(parametersNames),.jarray(thetas))
-.jcall("miscellaneous.EasyRun","[D","getValuesFromEnvironement","getMeanLastPercOfAut")
-.jcall("miscellaneous.EasyRun","[D","getValuesFromAquanismGroup","getRangeDistribution")
-# truc  = .jcall("miscellaneous.EasyRun","Ljava/util/List;",
+
+# call GR3D method to get model outputs ----------------------------------------------
+
+#TODO export [char] and then data.frame(toto) %>% type_convert()
+# ----------------------------------------------------------------------------------#
+# 1. northern limit and distribution centroid ----
+#       only basins with more than 50 recruits in average in the last 10 years (colonised basins)
+#       compute only in SPRING
+
+# access through getRangeDistribution in DiadromousFishGroup ==== NOT CORRECT
+#   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");
+# ------------------------------------------------------------ #
+# 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.
+#       Then a log-likelihood of a binomial distribution is computed
+
+# access through computeLikelihood in DiadromousFishGroup
+# see getProbOfNonNulRecruitmentDuringLastYears in BasinNetwork
+
+# ------------------------------------------------------------ #
+# 3. proportion of first-time spawners
+#     annual % of first-time spawners according to latitude (or basin_id)
+#     between 1920-1950
+#     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)
+
+# ------------------------------------------------------------ #
+# 5. number of metapopulation based on the exchange matrix ----
+#     annual exchange matrix between 1920 and 1950
+#     then in R: compute average matrix over the period,
+#     run metapopulationIdentification
+
+# moyenne sur les bassins versants des moyennes sur la peride  des moyennes des flux 
+# access through species.IdentifyPopulation in processesAtEnd
+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")
 # 
 # trucMieux = .jcast(truc, "ljava/util/ArrayList", convert.array = FALSE)