Nothing
## ----eval=FALSE----------------------------------------------------------
# library(spartan)
# # Directory where the sample file should be stored
# FILEPATH<-"/home/user/robustness/"
# # Name to give the setup file. No need for file extension
# NETLOGO_SETUPFILE_NAME<-"nl_robustness_setup"
# # Parameters in simulation. List all the parameters that Netlogo is
# # required to know,
# PARAMETERS<-c("people","infectiousness","chance-recover","duration")
# # Now values for each of the parameters above
# # For parameters not being analysed, simply list the value
# # For parameters being analysed, put the min, max and increment values
# # of the parameter in square brackets, in double quotes, e.g.
# # "[0.1,0.5,0.1]"
# PARAMVALS<-c(150,"[10,90,10]","[10,90,10]","[5,40,5]")
# # Name of the setup simulation function in Netlogo simulation
# # Usually setup
# NETLOGO_SETUP_FUNCTION<-"setup"
# # Name of the function that starts the simulation. Usually go
# NETLOGO_RUN_FUNCTION<-"go"
# # Simulation output measures
# MEASURES<-c("death-thru-sickness","death-but-immune",
# "death-old-age","death-old-and-sick")
# # Number of times Netlogo should repeat the experiment for each
# # parameter set
# EXPERIMENT_REPETITIONS<-1
# # Whether Netlogo should collect metrics at each timestep
# RUNMETRICS_EVERYSTEP<-"true"
## ----eval=FALSE----------------------------------------------------------
# oat_generate_netlogo_behaviour_space_XML(FILEPATH, NETLOGO_SETUPFILE_NAME, PARAMETERS,
# PARAMVALS, NETLOGO_SETUP_FUNCTION, NETLOGO_RUN_FUNCTION,
# MEASURES, EXPERIMENT_REPETITIONS, RUNMETRICS_EVERYSTEP)
## ----eval=FALSE----------------------------------------------------------
# # Import the package
# library(spartan)
# library(XML)
# # Folder containing the Netlogo Behaviour Space table, AND where the
# # processed results will be written to
# FILEPATH<-"/home/user/robustness/"
# # Name of the Netlogo Behaviour Space Table file
# NETLOGO_BEHAVIOURSPACEFILE<-"virus_oat.csv"
# # Array of the parameters to be analysed, but ONLY those perturbed
# PARAMETERS<-c("infectiousness","chance-recover","duration")
# # Value assigned to each parameter at calibration (the baseline value)
# BASELINE<-c(60,50,20)
# # The maximum value for each parameter
# PMAX<-c(90,90,40)
# # The minimum value explored for each parameter
# PMIN<-c(10,10,5)
# # Amount the parameter value was incremened during sampling
# PINC<-c(10,10,5)
# # Timestep of interest. The behaviour space table is likely to contain
# # all timesteps - this narrows the analysis
# TIMESTEP<-5200
# # The simulation output measures being examined. Should be specified
# # as they are in the Netlogo file
# MEASURES<-c("death-thru-sickness","death-but-immune","death-old-age",
# "death-old-and-sick")
# # For each parameter value being analysed, a file is created
# # containing the median of each output measure, of each simulation run
# # for that value. This sets the name of this file.
# RESULTFILENAME<-"ParamValResponses.csv"
# # The results of the A-Test comparisons of each parameter value
# # against that of the parameters baseline value are output as a file.
# # This sets the name of this file.
# ATESTRESULTSFILENAME<-"VirusOAT_ATests.csv"
# # A-Test result value either side of 0.5 at which the difference
# # between two sets of results is significant
# ATESTSIGLEVEL<-0.21
# # What each measure represents. Used in graphing results
# MEASURE_SCALE<-c("Number of People","Number of People",
# "Number of People","Number of People")
# # Not used in this case, but when a simulation is analysed at multiple
# # timepoints (see tutorials 1-4)
# TIMEPOINTS<-NULL; TIMEPOINTSCALE<-NULL
#
# oat_process_netlogo_result(FILEPATH,NETLOGO_BEHAVIOURSPACEFILE, PARAMETERS,
# BASELINE, PMIN, PMAX, PINC, MEASURES, RESULTFILENAME,
# ATESTRESULTSFILENAME, TIMESTEP)
#
# # Note that PARAMVALS is set to NULL - we don't use that for Netlogo
# oat_graphATestsForSampleSize(FILEPATH, PARAMETERS, MEASURES, ATESTSIGLEVEL,
# ATESTRESULTSFILENAME, BASELINE, PMIN, PMAX, PINC, NULL,
# TIMEPOINTS, TIMEPOINTSCALE)
## ----eval=FALSE----------------------------------------------------------
# library(spartan)
# # Directory where the samples should be stored
# FILEPATH<-"/home/user/LHC/"
# # Parameters in simulation. List all the parameters that Netlogo is
# # required to know,
# PARAMETERS<-c("people","infectiousness","chance-recover","duration")
# # Now values for each of the parameters above
# # For parameters not being analysed, simply list the value
# # For parameters being analysed, put the min and max values of the
# # parameter in square brackets, in double quotes, e.g. "[0.1,0.5]"
# # Encapsulate strings, i.e.: "\"/home/user/Experiment/\""
# PARAMVALS<-c(150,"[10,90]","[10,90]","[5,40]")
# # Number of parameter samples to take from hypercube
# NUMSAMPLES<-500
# # Name of function that sets up Netlogo simulation. Usually setup
# NETLOGO_SETUP_FUNCTION<-"setup"
# # Name of function that starts Netlogo simulation. Usually go
# NETLOGO_RUN_FUNCTION<-"go"
# # Simulation output measures
# MEASURES<-c("death-thru-sickness","death-but-immune","death-old-age",
# "death-old-and-sick")
# # Number of times the Netlogo experiment is repeated for each parameter
# # set
# EXPERIMENT_REPETITIONS<-1
# # Whether Netlogo metrics should be collected at each timestep
# RUNMETRICS_EVERYSTEP<-"true"
# # Algorithm to use to generate the hypercube (normal or optimal)
# ALGORITHM<-"normal"
#
# lhc_generate_lhc_sample_netlogo(FILEPATH,PARAMETERS,PARAMVALS,NUMSAMPLES,ALGORITHM,
# EXPERIMENT_REPETITIONS,RUNMETRICS_EVERYSTEP,NETLOGO_SETUP_FUNCTION,
# NETLOGO_RUN_FUNCTION,MEASURES)
## ----eval=FALSE----------------------------------------------------------
# # Import the package
# library(spartan)
# # Folder containing the Netlogo Behaviour Space table,
# # and where the processed results will be written to
# FILEPATH<-"/home/user/LHC/"
# # Name of the result file (csv) generated by Netlogo, with no file
# # extension
# LHCSAMPLE_RESULTFILENAME<-"lhcResult"
# # Location of a file containing the parameter value sets
# # generated by the hypercube sampling (i.e. the file generated
# # in the previous method of this tutorial. U
# SPARTAN_PARAMETER_FILE<-"LHC_Parameters_for_Runs.csv"
# # Number of parameter samples generated from the hypercube
# NUMSAMPLES<-500
# # The simulation output measures being examined. Should be specified
# # as they are in the Netlogo file
# MEASURES<-c("death-thru-sickness","death-but-immune","death-old-age",
# "death-old-and-sick")
# # File name to give to the summary file that is produced showing
# # the parameter value sets alongside the median results for each
# # simulation output measure.
# LHC_ALL_SIM_RESULTS_FILE<-"Virus_LHCSummary.csv"
# # Timestep of interest. The behaviour space table is likely to contain
# # all timesteps - this narrows the analysis
# TIMESTEP<-5200
# # Parameters of interest in this analysis
# PARAMETERS<-c("infectiousness","chance-recover","duration")
# # What each measure represents. Used in graphing results
# MEASURE_SCALE<-c("Number of People","Number of People",
# "Number of People","Number of People")
# # File name to give to the file showing the Partial Rank Correlation
# # Coefficients for each parameter. Again note no file extension
# CORCOEFFSOUTPUTFILE<-"EgSet_corCoeffs"
# # Not used in this case, but when a simulation is analysed at
# # multiple timepoints (see Tutorials 1-4)
# TIMEPOINTS<-NULL; TIMEPOINTSCALE<-NULL
#
# lhc_process_netlogo_result(FILEPATH, LHCSAMPLE_RESULTFILENAME, SPARTAN_PARAMETER_FILE, NUMSAMPLES, MEASURES, LHC_ALL_SIM_RESULTS_FILE, TIMESTEP)
#
# lhc_generatePRCoEffs(FILEPATH, PARAMETERS, MEASURES, LHC_ALL_SIM_RESULTS_FILE, CORCOEFFSOUTPUTFILE)
#
# lhc_graphMeasuresForParameterChange(FILEPATH, PARAMETERS, MEASURES, MEASURE_SCALE, CORCOEFFSOUTPUTFILE, LHC_ALL_SIM_RESULTS_FILE)
#
## ----eval=FALSE----------------------------------------------------------
# library(spartan)
# # The directory where the samples should be stored
# FILEPATH<-"/home/user/eFAST/"
# # Parameters for this simulation. List ALL the parameters that Netlogo needs to know, even those not being perturbed. Make # sure you include the dummy
# PARAMETERS<-c("people","infectiousness","chance-recover","duration", "dummy")
# # Now values for each of the parameters above. For parameters not being analysed, simply list the value
# # For parameters being analysed, put the min and max values of the parameter in square brackets, in double quotes, e.g.
# # "[0.1,0.5]" Encapsulate strings, i.e.: "\"/home/user/Experiment/\""
# PARAMVALS<-c(150,"[10,90]","[10,90]","[5,40]","[1,10]")
# # Number of resampling curves to use
# NUMCURVES<-3
# # Number of value samples to take from each parameter curve
# NUMSAMPLES<-65
# # The name of the function in Netlogo that sets up the simulation (Usually setup)
# NETLOGO_SETUP_FUNCTION<-"setup"
# # Name of the function in Netlogo that starts the simulation (Usually go)
# NETLOGO_RUN_FUNCTION<-"go"
# MEASURES<-c("death-thru-sickness","death-but-immune","death-old-age","death-old-and-sick")
# # Number of times the Netlogo run should be repeated for each parameter set
# EXPERIMENT_REPETITIONS<-1
# # Whether Netlogo should collect metrics at all timesteps
# RUNMETRICS_EVERYSTEP<-"true"
#
# efast_generate_sample_netlogo(FILEPATH,NUMCURVES,NUMSAMPLES,MEASURES,PARAMETERS,PARAMVALS,EXPERIMENT_REPETITIONS,
# RUNMETRICS_EVERYSTEP,NETLOGO_SETUP_FUNCTION,NETLOGO_RUN_FUNCTION)
## ----eval=FALSE----------------------------------------------------------
# library(spartan)
# # The directory where the netlogo experiment file should be stored
# FILEPATH<-"/home/kieran/Documents/Tutorial/eFAST/"
# # Name of the result file generated by Netlogo. The sample number and
# # .csv are added to this
# EFASTSAMPLE_RESULTFILENAME<-"efast_result_set"
# # The parameters being examined in this analysis. Include the dummy
# PARAMETERS<-c("infectiousness","chance-recover","duration","dummy")
# # Number of resampling curves to use
# NUMCURVES<-3
# # Number of value samples to take from each curve
# NUMSAMPLES<-65
# # The output measures by which you are analysing the results.
# MEASURES<-c("death-thru-sickness","death-but-immune","death-old-age","death-old-and-sick")
# # File created containing the median of each output measure, of each
# # simulation for this parameter set. Note no file extension
# RESULTFILENAME<-"ParamValResponses"
# # Timestep of interest. The behaviour space table is likely to contain
# # all timesteps. This narrows the analysis
# TIMESTEP<-5200
# # Output measures to t-test to gain statistical significance
# OUTPUTMEASURES_TO_TTEST<-1:4
# # T-Test confidence interval
# TTEST_CONF_INT<-0.95
# # Boolean noting whether graphs should be produced
# GRAPH_FLAG<-TRUE
# # Name of the final result file summarising the analysis, showing the
# # partitioning of the variance between parameters. Note no file
# # extension
# EFASTRESULTFILENAME<-"Virus_eFAST_Analysis"
# # Not used in this case, but when a simulation is analysed at
# # multiple timepoints (see Tutorials 1-4)
# TIMEPOINTS<-NULL; TIMEPOINTSCALE<-NULL
#
# efast_process_netlogo_result(FILEPATH, EFASTSAMPLE_RESULTFILENAME, PARAMETERS, NUMCURVES,
# NUMSAMPLES, MEASURES, RESULTFILENAME, TIMESTEP)
#
# # Get all the results for each curve into one summary file for each curve
# efast_get_overall_medians(FILEPATH, NUMCURVES, PARAMETERS, NUMSAMPLES, MEASURES)
#
# # Run the eFAST analysis
# efast_run_Analysis(FILEPATH, MEASURES, PARAMETERS, NUMCURVES, NUMSAMPLES, OUTPUTMEASURES_TO_TTEST, TTEST_CONF_INT,
# GRAPH_FLAG, EFASTRESULTFILENAME, TIMEPOINTS, TIMEPOINTSCALE)
#
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