run EsayRun function in R:

still error

exploration/NEA_sensitivity_analysis/extractNumeroProcess.R

+library(tidyverse)
+#source("../GR3D_Rdescription/GR3D_NEA_XML_parameters.R")
+
+setwd("~/Documents/workspace/GR3D/exploration/NEA_sensitivity_analysis")
+fishXML <- xmlToList(xmlParse("../../data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml"))
+
+ fishXML[["species.DiadromousFishGroup"]][["processes"]]
+
+
+no_processesEachStep = tibble( process = names(fishXML[["species.DiadromousFishGroup"]][["processes"]][["processesEachStep"]][])) %>% 
+  mutate(no_R = row_number()) %>% 
+  filter(process != "comment") %>% 
+  mutate(no_java = row_number()-1) %>% 
+  select(no_R, no_java, process)
+
+no_processesAtEnd = tibble( process = names(fishXML[["species.DiadromousFishGroup"]][["processes"]][["processesAtEnd"]][])) %>% 
+  mutate(no_R = row_number()) %>% 
+  filter(process != "comment") %>% 
+  mutate(no_java = row_number()-1) %>% 
+  select(no_R, no_java, process)
+       
\ No newline at end of file

exploration/NEA_sensitivity_analysis/tryFromJava.R

@@ -23,6 +23,7 @@ rm(list = ls())
 
 # GR3D arguments -----------------------------------------
 ## to have the same working directory as GR3D
+#setwd("~/Documents/workspace/GR3D/exploration/NEA_sensitivity_analysis")
 setwd("../..")
 
 # path to outputs
@@ -51,13 +52,41 @@ arguments = c('-q','-simDuration', simDuration, '-simBegin',simBegin,
 .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)
+
+
+
+parametersNamesANG = c("processes.processesEachStep.11.Soffset") 
+thetasANG = c(0)
+
+parametersNamesENV = c("simulationName")
+thetasENV = c("noAllee")
+
+
+
+
+
+runEasyRun = function(arguments, parametersNamesANG,thetasANG, parametersNamesENV, thetasENV ){
+  # run the GR3D with updated parameter values in processes --------------------------------------------
+  .jclassPath()
+  .jcall("analysis.EasyRun", "V", "runSimulation", arguments, 
+         .jarray(parametersNamesANG), .jarray(thetasANG),
+         .jarray(parametersNamesENV), .jarray(thetasENV))
+  # call GR3D method to get model outputs ----------------------------------------------
+  #1. northern limit and distribution centroid ----
+  out = .jcall("analysis.EasyRun","[[Ljava/lang/String;","getValuesFromAquanismGroupProcess","processes.processesEachStep.10.exportToR")
+  range <- data.frame(matrix(convertToR(out[[2]]), nrow = 1,  dimnames = list(NULL, convertToR(out[[1]])))) %>% type_convert()
+  
+  return(list(range = range))
+}
+
+runEasyRun(arguments, parametersNamesANG,thetasANG, parametersNamesENV, thetasENV )
+
+
 # run the GR3D with updated parameter values in processes --------------------------------------------
 .jclassPath()
-.jcall("analysis.EasyRun", "V", "runSimulation", arguments, .jarray(parametersNames), .jarray(thetas))
+.jcall("analysis.EasyRun", "V", "runSimulation", arguments, 
+       .jarray(parametersNamesANG), .jarray(thetasANG),
+       .jarray(parametersNamesENV), .jarray(thetasENV))
 
 
 # call GR3D method to get model outputs ----------------------------------------------
@@ -65,14 +94,14 @@ thetas = c(10, 2, 0.7)
 #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)
+#       only basins with more than 50 recruits in average in the last 50 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
 
-out = .jcall("analysis.EasyRun","[[Ljava/lang/String;","getValuesFromAquanismGroupProcess","processes.processesEachStep.9.exportToR")
+out = .jcall("analysis.EasyRun","[[Ljava/lang/String;","getValuesFromAquanismGroupProcess","processes.processesEachStep.10.exportToR")
 range <- data.frame(matrix(convertToR(out[[2]]), nrow = 1,  dimnames = list(NULL, convertToR(out[[1]])))) %>% type_convert()
 
 
@@ -98,11 +127,16 @@ range <- data.frame(matrix(convertToR(out[[2]]), nrow = 1,  dimnames = list(NULL
 
 
 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()
 
+convertFromSALtoR = function(java_out){
+  require(jdx)
+  out2 = matrix(unlist(lapply(java_out, convertToR)), nrow = length(java_out) , byrow = TRUE)
+  out3 <- out2[-1,]
+  colnames(out3) <- unlist(out2[1,])
+  R_out <- as.data.frame(out3)  %>% type_convert()
+  return(R_out)
+}
+convertFromSALtoR(java_out = out)
 # ------------------------------------------------------------ #
 
 
@@ -118,23 +152,6 @@ as.data.frame(out3)  %>% type_convert()
 #TODO A FAIRE !!!
 
 # =================================================================================
-toto <- .jcall("analysis.EasyRun","Ljava/util/List;",
-                      "getAListFromAquanismGroupProcess","processes.processesAtEnd.1.getRecords")
 
-as.list(toto)
 
 
-
-# truc  = .jcall("analysis.EasyRun","Ljava/util/List;",
-#                "getAListFromAquanismGroupProcess","processes.processesAtEnd.1.getRecords")
-# 
-# trucMieux = .jcast(truc, "ljava/util/ArrayList", convert.array = FALSE)
-# 
-# i <- .jnew("java/lang/Integer", as.integer(10))
-# print(i)
-# print(.jsimplify(i))
-# .jcall(trucMieux, "java/lang/Object", "get", i)
-# 
-# with(trucMieux, {get(0)})
-# ArrayList = J("java.util.ArrayList")
-# .jclassPath()