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#' Generates spartan-compatible timepoint files if simulation results over
#' time are in one file
#'
#' @param FILEPATH Filepath to all LHC results being analysed
#' @param SPARTAN_PARAMETER_FILE CSV file generated by spartan, containing
#' all parameter sets under which the simulation was run
#' @param RUN_SUMMARY_FILE_NAME Simulation output file, containing multiple
#' timepoints
#' @param NUMSAMPLES Number of parameter samples generated using the hypercube
#' @param NUMRUNSPERSAMPLE Number of replicate runs performed for each sample
#' @param TIMEPOINTS Simulation timepoints to extract from the result file
#'
#' @export
lhc_generateTimepointFiles <- function(FILEPATH, SPARTAN_PARAMETER_FILE,
RUN_SUMMARY_FILE_NAME, NUMSAMPLES,
NUMRUNSPERSAMPLE, TIMEPOINTS) {
# USED WHEN A SIMULATION IS BEING PROCESSED WHERE THE RESULTS OF EACH
# TIMEPOINT ARE IN THE SAME FILE (AS IN LEISHSIM)
## RATHER THAN REMAKE SPARTAN TO PROCESS THESE, WE INSTEAD MAKE INDIVIDUAL
# TIMEPOINT FILES FOR THIS DATA SO THE FILES ARE COMPATIBLE WITH SPARTAN
if (file.exists(FILEPATH)) {
message("Generating Simulation Timestep files compatible for
Spartan Analysis")
# READ IN THE SPARTAN PARAMETER FILE
LHCTABLE <- read.csv(paste(FILEPATH, "/", SPARTAN_PARAMETER_FILE,
sep = ""), header = TRUE)
# NOW FOR LEISHSIM WE NEED TO DO 168 ROWS, SO:
for (t in 1:length(TIMEPOINTS)) {
current_timepoint <- TIMEPOINTS[t]
message(paste("Processing Timepoint: ", current_timepoint, sep = ""))
ALL_SIM_RESULTS_FOR_TIMEPOINT <- NULL
for (k in 1:NUMSAMPLES) {
# GET THE MEDIAN RESULTS FILE, CONTAINING THE MEDIAN OF EACH TIMEPOINT
MEDIAN_RESULTS <- read.csv(paste(FILEPATH, "/", k, "/",
RUN_SUMMARY_FILE_NAME, sep = ""),
header = TRUE)
RESULT <- cbind(LHCTABLE[k, ], MEDIAN_RESULTS[current_timepoint, ])
# NOW ADD THIS TO THE LIST OF ALL MEDIANS BEING PROCESSED IN THIS
# ANALYSIS
ALL_SIM_RESULTS_FOR_TIMEPOINT <- rbind(ALL_SIM_RESULTS_FOR_TIMEPOINT,
RESULT)
}
# WRITE THE RESULTS FILE FOR THIS TIMEPOINT
if (!is.null(ALL_SIM_RESULTS_FOR_TIMEPOINT)) {
RESULTSFILE <- paste(FILEPATH, "/Results_Time_", current_timepoint,
".csv", sep = "")
write.csv(ALL_SIM_RESULTS_FOR_TIMEPOINT,
RESULTSFILE, quote = FALSE, row.names = FALSE)
}
}
}
}
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