Commit 54962b4b authored by patrick.lambert's avatar patrick.lambert
Browse files

last version

parent ecd192a5
......@@ -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')
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