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#' Deprecated: Use \code{efast_netlogo_get_overall_medians}
#'
#' @inheritParams efast_get_overall_medians
#'
#' @export
efast_netlogo_get_overall_medians <-
function(FILEPATH, NUMCURVES, PARAMETERS, NUMSAMPLES, MEASURES,
TIMEPOINTS = NULL, TIMEPOINTSCALE = NULL) {
#message("Now Deprecated. Use efast_get_overall_medians instead")
.Deprecated("efast_get_overall_medians")
}
#' Deprecated: Use \code{efast_run_Analysis}
#'
#' @inheritParams efast_run_Analysis
#'
#' @export
efast_netlogo_run_Analysis <-
function(FILEPATH, MEASURES, PARAMETERS, NUMCURVES, NUMSAMPLES,
OUTPUTMEASURES_TO_TTEST, TTEST_CONF_INT, GRAPH_FLAG,
EFASTRESULTFILENAME, TIMEPOINTS, TIMEPOINTSCALE) {
.Deprecated("efast_run_Analysis")
}
#' Analyses Netlogo simulation data for parameter sets generated for eFAST
#'
#' Takes each parameter value set generated by eFAST in turn, and analyses the
#' Netlogo simulation results. For each parameter set, there will be n
#' simulation results. This method goes through these results, producing
#' a file containing the median of each output measure for each of the n runs.
#' Thus, if a Netlogo simulation was replicated 10 times, the median file will
#' contain 10 medians for each simulation output measure. The user should then
#' run \code{efast_get_overall_medians} and
#' \code{efast_run_Analysis} to analyse the results
#'
#' @param FILEPATH Directory where the simulation runs can be found
#' @param EFASTSAMPLE_RESULTFILENAME Name of the result file generated by
#' Netlogo, for an eFAST parameter sample.
#' @param PARAMETERS Array containing the names of the parameters of which
#' parameter samples will be generated
#' @param NUMCURVES The number of 'resamples' to perform
#' (see eFAST documentation) - recommend using at least 3.
#' @param NUMSAMPLES The number of parameter subsets that were generated
#' from each curve in the eFAST design
#' @param MEASURES Array containing the names of the Netlogo output measures
#' which are used to analyse the simulation.
#' @param RESULTFILENAME Name of the result file that will be produced which
#' summarises all results
#' @param TIMESTEP Timestep of the Netlogo simulation being analysed.
#'
#' @export
efast_process_netlogo_result <-
function(FILEPATH, EFASTSAMPLE_RESULTFILENAME, PARAMETERS, NUMCURVES,
NUMSAMPLES, MEASURES, RESULTFILENAME, TIMESTEP) {
# TO KEEP THIS IN LINE WITH TRADITIONAL SPARTAN, AND AS NETLOGO OFFERS
#THE CHANCE TO RUN REPEATED RUNS OF THE SAME EXPERIMENT
# WE ARE GOING TO CREATE A MEDIAN SET OF RESULTS FOR EACH SAMPLE.
# THEN THE OLD SPARTAN CODE CAN BE USED FROM THAT POINT
for (CURVENUM in 1:NUMCURVES) {
for (PARAMNUM in 1:length(PARAMETERS)) {
message(paste("Processing Curve: ", CURVENUM, " Parameter: ",
PARAMETERS[PARAMNUM], sep = ""))
# Open the parameter file
params <- read_from_csv(file.path(
FILEPATH, paste("Curve", CURVENUM, "_", PARAMETERS[PARAMNUM], ".csv",
sep = "")))
CURVE_PARAM_RESULT <- NULL
for (SAMPLE in 1:NUMSAMPLES) {
if (file.exists(paste(FILEPATH, "/", CURVENUM, "/", PARAMNUM,
"/", SAMPLE, "/", EFASTSAMPLE_RESULTFILENAME,
SAMPLE, ".csv", sep = ""))) {
message(paste("Processing EFAST Results for Curve: ", CURVENUM,
" Parameter: ", PARAMNUM, " Value Sample: ", SAMPLE,
sep = ""))
# READ IN THE RESULT FILE
# SKIP THE FIRST 6 LINES AS NONE OF THIS INFORMATION IS REQUIRED
NL_RESULT <- read.csv(paste(FILEPATH, "/", CURVENUM, "/", PARAMNUM,
"/", SAMPLE, "/",
EFASTSAMPLE_RESULTFILENAME, SAMPLE,
".csv", sep = ""), sep = ",",
skip = 6, check.names = FALSE)
# ORDER IT BY RUN FOR EFFICIENCY LATER
NL_RESULT_ORDERED <- NL_RESULT[order(NL_RESULT[, 1]), ]
TIMESTEP_RESULTS <- subset(NL_RESULT_ORDERED,
NL_RESULT_ORDERED["[step]"] == TIMESTEP)
# NOW TO CREATE THE RESULTS FOR THIS SAMPLE SET
# NETLOGO DOES GIVE THE OPTION OF RUNNING REPLICATES OF SAME EXPT
# THERE MAY BE A FEW ROWS HERE. SO SUMMARISE THESE
# FIRST LETS SET UP THE NUMBER OF PARAMETER ROWS
param_set <- params[SAMPLE, ]
# Make duplicates of the parameters to match number of replicate runs
PARAMS <- NULL
for (paramval in 1:ncol(param_set)) {
PARAMS <- cbind(PARAMS, param_set[[paramval]])
}
DUP_PARAMS <- NULL
for (r in 1:nrow(TIMESTEP_RESULTS) - 1) {
DUP_PARAMS <- rbind(DUP_PARAMS, PARAMS)
}
# NOW WE CAN ADD THE RESULTS FOR EACH NETLOGO RUN
for (RESPONSE in 1:length(MEASURES)) {
DUP_PARAMS <- cbind(DUP_PARAMS,
TIMESTEP_RESULTS[MEASURES[RESPONSE]][, 1])
}
CURVE_PARAM_RESULT <- rbind(CURVE_PARAM_RESULT, DUP_PARAMS)
}
}
colnames(CURVE_PARAM_RESULT) <- c(colnames(params), MEASURES)
# Write this file out to the FILEPATH
write_data_to_csv(CURVE_PARAM_RESULT, file.path(
FILEPATH, paste("Curve",CURVENUM,"_Parameter",PARAMNUM,"_Results.csv",sep="")))
}
message(paste("Analysis of Netlogo Results for Curve ", CURVENUM,
" Complete", sep = ""))
}
}
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