From 69b9ba2fa3d22d54f724e14f3dacb00fdf1b8648 Mon Sep 17 00:00:00 2001
From: "patrick.lambert" <patrick.mh.lambert@inrae.fr>
Date: Wed, 17 Feb 2021 15:39:08 +0100
Subject: [PATCH] update of gitignore
---
.gitignore | 40 ++---
data/input/northeastamerica/RIO_obs_empty.xml | 147 ------------------
exploration/R_AS_GR3D/tryFromRougier.R | 54 ++++---
3 files changed, 53 insertions(+), 188 deletions(-)
diff --git a/.gitignore b/.gitignore
index 9df0b0a..08b864f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -100,29 +100,31 @@ target
.classpath
.project
org.*
+
+/src/main/java/environment/*.ucls
+/src/main/java/environment/TestShape.java
+/src/main/java/species/testAlea.java
+/src/main/java/species/Essai.java
/src/main/java/miscellaneous/Essai.java
->>>>>>> master
-/exploration/R/.Rhistory
-/exploration/R/.RData
+
/outcmaesaxlen.dat
/outcmaesdisp.dat
/outcmaesfit.dat
/outcmaesstddev.dat
/outcmaesxmean.dat
/outcmaesxrecentbest.dat
-/exploration/scriptR/BruchPrg.R.orig
-.Rproj.user
-/exploration/scriptR/.RData
-/exploration/scriptR/*.Rproj
-/exploration/scriptR/.Rhistory
-/exploration/scriptR/scriptR.Rproj
-/exploration/scriptR/.Rproj.user/
-/exploration/scriptR/.RData
-/src/main/java/environment/*.ucls
-/src/main/java/environment/TestShape.java
-/src/main/java/species/testAlea.java
-/data/input/northeastamerica/shape/*.qix
-/src/main/java/species/Essai.java
-/exploration/GR3D_Rdescription/.RData
-/exploration/GR3D_Rdescription/.Rhistory
-/exploration/GR3D_Rdescription/.~lock.*
+
+# R: files
+*.Rproj
+*.Rhistory
+*.RData
+*.Rproj.user
+*.~lock.*
+
+# qgis file
+*.qix
+
+
+
+
+
diff --git a/data/input/northeastamerica/RIO_obs_empty.xml b/data/input/northeastamerica/RIO_obs_empty.xml
index 8f9e49d..3ee9b0d 100644
--- a/data/input/northeastamerica/RIO_obs_empty.xml
+++ b/data/input/northeastamerica/RIO_obs_empty.xml
@@ -1,150 +1,3 @@
<hashtable>
- <entry>
- <!--
-
- <java-class>fr.cemagref.simaqualife.kernel.AquaticWorld</java-class>-->
- <java-class>environment.RIOBasinNetworkWithContinent</java-class>
- <fr.cemagref.observation.kernel.ObservablesHandler>
- <observers>
- <environment.RIOBasinNetworkObserverWithContinent>
- <title>North East America</title>
- <threshold>1000000</threshold>
- <colorScaleEnum>RedsScale</colorScaleEnum>
- </environment.RIOBasinNetworkObserverWithContinent>
-
- <environment.RIOBasinNetworkObserverPresence>
- <title>Shad presence in North East America</title>
- <presenceFileName>data/input/northeastamerica/nea_presence.csv</presenceFileName>
- <period>obs_1900_1950</period>
- </environment.RIOBasinNetworkObserverPresence>
- </observers>
- </fr.cemagref.observation.kernel.ObservablesHandler>
- </entry>
- <entry>
- <java-class>species.DiadromousFishGroup</java-class>
- <fr.cemagref.observation.kernel.ObservablesHandler>
- <observers>
- <fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <graphType>LINE</graphType>
- <title>Number of colonized
- basins
- </title>
- <xAxisLabel>Time (season)</xAxisLabel>
- <yAxisLabel>number of basins</yAxisLabel>
- <variableName>getNbColonizedBasins</variableName>
- </fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <graphType>LINE</graphType>
- <title>Total Abundance</title>
- <xAxisLabel>Time (season)</xAxisLabel>
- <yAxisLabel>number of fishes</yAxisLabel>
- <variableName>getFishEffective</variableName>
- </fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <graphType>LINE</graphType>
- <title>Abundance of spawners</title>
- <xAxisLabel>Time (season)</xAxisLabel>
- <yAxisLabel>number
- of fishes
- </yAxisLabel>
- <variableName>getSpawnerEffective</variableName>
- </fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <graphType>LINE</graphType>
- <title>Abundance of male spawners</title>
- <xAxisLabel>Time (season)</xAxisLabel>
- <yAxisLabel>number of fishes</yAxisLabel>
- <variableName>getMaleSpawnerEffective</variableName>
- </fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <graphType>LINE</graphType>
- <title>Abundance of female spawners</title>
- <xAxisLabel>Time (season)</xAxisLabel>
- <yAxisLabel>number
- of fishes
- </yAxisLabel>
- <variableName>getFemaleSpawnerEffective</variableName>
- </fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <observer.TemporalRangeSerieChart>
- <title>Range distribution</title>
- <xAxisLabel>Time (season)</xAxisLabel>
- <yAxisLabel>latitude</yAxisLabel>
- <variableName>getRangeDistributionWithLat</variableName>
- </observer.TemporalRangeSerieChart>
- <fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <graphType>LINE</graphType>
- <title>Mean age at first reproduction for female</title>
- <xAxisLabel>Time (season)</xAxisLabel>
- <yAxisLabel>age (year)</yAxisLabel>
- <variableName>getMeanAgeOfFirstReprodutionForFemale</variableName>
- </fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <graphType>LINE</graphType>
- <title>Mean age at first reproduction
- for male
- </title>
- <xAxisLabel>Time (season)</xAxisLabel>
- <yAxisLabel>age (year)</yAxisLabel>
- <variableName>getMeanAgeOfFirstReprodutionForMale</variableName>
- </fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <graphType>LINE</graphType>
- <title>Statistic for male spawners age</title>
- <xAxisLabel>Time (season)</xAxisLabel>
- <yAxisLabel></yAxisLabel>
- <variableName>computeMaleSpawnerForFirstTimeSummaryStatistic</variableName>
- </fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <graphType>LINE</graphType>
- <title>Statistic for female
- spawners age
- </title>
- <xAxisLabel>Time (season)</xAxisLabel>
- <yAxisLabel></yAxisLabel>
- <variableName>computeFemaleSpawnerForFirstTimeSummaryStatistic</variableName>
- </fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <graphType>LINE</graphType>
- <title>Mean length at first reproduction for female</title>
- <xAxisLabel>Time (season)</xAxisLabel>
- <yAxisLabel>length (cm)</yAxisLabel>
- <variableName>getMeanLengthOfFirstReprodutionForFemale</variableName>
- </fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- <graphType>LINE</graphType>
- <title>Mean length at first
- reproduction for male
- </title>
- <xAxisLabel>Time (season)</xAxisLabel>
- <yAxisLabel>length (cm)</yAxisLabel>
- <variableName>getMeanLengthOfFirstReprodutionForMale</variableName>
- </fr.cemagref.observation.observers.jfreechart.TemporalSerieChart>
- </observers>
- </fr.cemagref.observation.kernel.ObservablesHandler>
- </entry>
- <entry>
- <java-class>environment.RiverBasin</java-class>
- <fr.cemagref.observation.kernel.ObservablesHandler>
- <observers>
- <observer.TemporalSerieChartForBasin>
- <graphType>LINE</graphType>
- <title>Number of juveniles</title>
- <xAxisLabel>Time
- (season)
- </xAxisLabel>
- <yAxisLabel>number of juveniles</yAxisLabel>
- <variableName>getJuvenileNumber</variableName>
- </observer.TemporalSerieChartForBasin>
- <observer.TemporalSerieChartForBasin>
- <graphType>LINE</graphType>
- <title>% Autochtone</title>
- <xAxisLabel>Time (season)</xAxisLabel>
- <yAxisLabel>% Autochtone</yAxisLabel>
- <variableName>getLastPercentageOfAutochtone</variableName>
- </observer.TemporalSerieChartForBasin>
- </observers>
- </fr.cemagref.observation.kernel.ObservablesHandler>
- </entry>
-
</hashtable>
\ No newline at end of file
diff --git a/exploration/R_AS_GR3D/tryFromRougier.R b/exploration/R_AS_GR3D/tryFromRougier.R
index 349ad01..e793ccb 100644
--- a/exploration/R_AS_GR3D/tryFromRougier.R
+++ b/exploration/R_AS_GR3D/tryFromRougier.R
@@ -6,22 +6,25 @@ rm(list=ls())
set.seed(1)
-# parameters and prios=rs of parameters to be fitted
-inputData = yaml.load_file("ABC_seq_2param_3stats_NewAfterSA.yaml")
-# load prior
-prior = list()
-for (i in 1:length(inputData$parameters)) {
- p = inputData$parameters[[i]]
- prior[[i]] = unlist(p$prior)
-}
-
-parametersNames = list()
-for (i in 1:length(inputData$parameters)) {
- parametersNames = c(parametersNames, inputData$parameters[[i]]$javapath)
-}
-
-
-thetas = c(0.45, 10.5)
+# # parameters and prios=rs of parameters to be fitted
+# inputData = yaml.load_file("ABC_seq_2param_3stats_NewAfterSA.yaml")
+# # load prior
+# prior = list()
+# for (i in 1:length(inputData$parameters)) {
+# p = inputData$parameters[[i]]
+# prior[[i]] = unlist(p$prior)
+# }
+#
+# parametersNames = list()
+# for (i in 1:length(inputData$parameters)) {
+# parametersNames = c(parametersNames, inputData$parameters[[i]]$javapath)
+# }
+# parametersNames = unlist(parametersNames)
+
+parametersNames = c("processes.processesEachStep.8.tempMinRep",
+ "processes.processesEachStep.8.ratioS95_S50",
+ "processes.processesEachStep.6.pHomingAfterEquil")
+thetas = c(10, 2, 0.7)
# path to outputs
outputDir = "simus/"
@@ -33,19 +36,26 @@ timeStepDuration =1
seed = 1
+## to have the same working diretory as GR3D
+setwd("../..")
-
-arguments = c('-d','-simDuration',simDuration, '-simBegin',simBegin,
+arguments = c('','-simDuration',simDuration, '-simBegin',simBegin,
'-timeStepDuration',timeStepDuration,
'-RNGStatusIndex', format(seed,scientific = FALSE),
- '-groups',"../../data/input/northeastamerica/fishRIOBasin_Sapidissima_PL.xml",
- '-env',"../../data/input/northeastamerica/RIOBNneaBasins.xml",
- '-observers',"../../data/input/northeastamerica/RIO_obs_empty.xml")
+ '-groups',"data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml",
+ '-env',"data/input/northeastamerica/RIOBNneaBasins_Rjava.xml",
+ '-observers',"data/input/northeastamerica/RIO_obs_empty.xml")
outputFile = paste0(outputDir,"output",seed)
.jinit(classpath = jarfile, force.init = TRUE)
-.jcall("miscellaneous.EasyRun","V","runSimulation",arguments, outputFile,.jarray(unlist(parametersNames)),.jarray(thetas))
+.jcall("miscellaneous.EasyRun","V","runSimulation",arguments, outputFile,.jarray(parametersNames),.jarray(thetas))
+
+
+
+
+
+
# return a function to run the model with parameters as arguments
salrun <- function(jarfile, simDuration, simBegin, timeStepDuration = 1) {
--
GitLab