Commit 69b9ba2f authored by patrick.lambert's avatar patrick.lambert
Browse files

update of gitignore

parent 6a44a26e
......@@ -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
<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
......@@ -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) {
......
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