R/round-actions.R

In mesako/CancerSimulationR: What the Package Does (One Line, Title Case)

DeterminePatientAction <- function(current.map, patient.state, num.surgery,
                                   patient.pre.action.set, patient.post.action.set) {
  if (num.surgery < 2 & sum(current.map$data$value == "Cell") > round(nrow(current.map$data) * 0.66)) {
    if (patient.state == "post") {
      patient.action <- "surgery"
    } else {
      patient.action <- "doctor"
    }
  } else {
    patient.action <- GetPatientAction(patient.state, patient.pre.action.set,
                                       patient.post.action.set)
  }
  while (patient.action == "chemo1" | patient.action == "chemo2" | patient.action == "radtherapy" &
         sum(current.map$data$value == "Cell") < round(nrow(current.map$data) * 0.1)) {
    patient.action <- GetPatientAction(patient.state, patient.pre.action.set,
                                       patient.post.action.set)
  }
  while (patient.action == "surgery" & sum(current.map$data$value == "Cell") < round(nrow(current.map$data) * 0.25)) {
    patient.action <- GetPatientAction(patient.state, patient.pre.action.set,
                                       patient.post.action.set)
  }
  while (num.surgery >= 2 & patient.action == "surgery") {
    patient.action <- GetPatientAction(patient.state, patient.pre.action.set,
                                       patient.post.action.set)
  }
  return(patient.action)
}

RunPatientSimulation <- function(num.rounds, starting.map, mutation.set,
                                 patient.pre.action.set, patient.post.action.set,
                                 mutation.encoding, cell.mut.rate, map.dim,
                                 cell.divisions, cell.states, max.divisions) {
  patient.summary.statement <- ""
  patient.log <- c()
  num.surgery <- 0
  patient.state <- "pre"
  current.map <- starting.map
  round.cell.num <- c()
  round.average.mut.num <- c()
  tumor.burden.count <- 0
  for (i in 1:num.rounds) {
    # print(paste("Round", i))
    patient.action <- DeterminePatientAction(current.map, patient.state, num.surgery,
                                             patient.pre.action.set, patient.post.action.set)
    # print(patient.action)
    patient.log <- c(patient.log, paste("Round", i, "-", patient.action))
    if (patient.action == "noaction") {
      cell.states <- AddMutations(cell.states, cell.mut.rate,
                                  map.dim, mutation.encoding, mutation.set)
      results <- RunBaselineCellActions(current.map, cell.states, cell.divisions, max.divisions, cell.mut.rate, mutation.encoding)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
    } else if (patient.action == "doctor") {
      cell.states <- AddMutations(cell.states, cell.mut.rate,
                                  map.dim, mutation.encoding, mutation.set)
      results <- RunBaselineCellActions(current.map, cell.states, cell.divisions, max.divisions, cell.mut.rate, mutation.encoding)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
      patient.state <- SwitchPrePost(cell.states, current.map, mutation.encoding)
      if (patient.state == "post") {
        patient.log <- c(patient.log, paste("Round", i, "-", "patient diagnosed with cancer"))
      }
    } else if (patient.action == "smoke" | patient.action == "asbestos" | patient.action == "radexpose") {
      temp.cell.mut.rate <- cell.mut.rate * 20
      cell.states <- AddMutations(cell.states, temp.cell.mut.rate,
                                  map.dim, mutation.encoding, mutation.set)
      results <- RunBaselineCellActions(current.map, cell.states, cell.divisions, max.divisions, cell.mut.rate, mutation.encoding)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
    } else if (patient.action == "deathinduct") {
      cell.states <- AddMutations(cell.states, cell.mut.rate,
                                  map.dim, mutation.encoding, mutation.set)
      results <- RunBaselineCellActions(current.map, cell.states, cell.divisions, max.divisions, cell.mut.rate, mutation.encoding)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
      results <- KillCellsSpace(cell.states, current.map, cell.divisions, cell.mut.rate, mutation.encoding)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
    } else if (patient.action == "immune" | patient.action == "growthinhibit" | patient.action == "targeted") {
      cell.states <- AddMutations(cell.states, cell.mut.rate,
                                  map.dim, mutation.encoding, mutation.set)
      results <- RunBaselineCellActions(current.map, cell.states, cell.divisions, max.divisions, cell.mut.rate, mutation.encoding)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
      results <- KillCellsGrowth(cell.states, current.map, cell.divisions, cell.mut.rate, mutation.encoding)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
    } else if (patient.action == "chemo1") {
      cell.states <- AddMutations(cell.states, cell.mut.rate,
                                  map.dim, mutation.encoding, mutation.set)
      results <- MarkDeadCells(cell.states, current.map, cell.divisions, cell.mut.rate)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
      results <- CheckEnergyNeed(current.map, cell.states, cell.divisions, cell.mut.rate, mutation.encoding)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
      results <- KillCellsCycling(cell.states, current.map, cell.divisions, cell.mut.rate, mutation.encoding)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
    } else if (patient.action == "chemo2" | patient.action == "radtherapy") {
      temp.cell.mut.rate <- cell.mut.rate * 10
      cell.states <- AddMutations(cell.states, temp.cell.mut.rate,
                                  map.dim, mutation.encoding, mutation.set)
      results <- MarkDeadCells(cell.states, current.map, cell.divisions, cell.mut.rate)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
      results <- CheckEnergyNeed(current.map, cell.states, cell.divisions, cell.mut.rate, mutation.encoding)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
      results <- KillCellsDNA(cell.states, current.map, cell.divisions, cell.mut.rate, mutation.encoding)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
    } else if (patient.action == "angblock") {
      cell.states <- AddMutations(cell.states, cell.mut.rate,
                                  map.dim, mutation.encoding, mutation.set)
      results <- RunBaselineCellActions(current.map, cell.states, cell.divisions, max.divisions, cell.mut.rate, mutation.encoding)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
      results <- KillCellsEnergy(cell.states, current.map, cell.divisions, cell.mut.rate, mutation.encoding)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
    } else if (patient.action == "surgery") {
      cell.states <- AddMutations(cell.states, cell.mut.rate,
                                  map.dim, mutation.encoding, mutation.set)
      results <- RunBaselineCellActions(current.map, cell.states, cell.divisions, max.divisions, cell.mut.rate, mutation.encoding)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
      results <- KillCellsSurgery(cell.states, current.map, cell.divisions, cell.mut.rate)
      current.map <- results[[1]]
      cell.states <- results[[2]]
      cell.divisions <- results[[3]]
      cell.mut.rate <- results[[4]]
      num.surgery <- num.surgery + 1
    }
    cell.meet.cond <- CheckPatientDeath(cell.states, mutation.encoding)
    if (length(cell.meet.cond) > round(length(cell.states) * 0.1) && !is.null(cell.meet.cond)) {
      patient.summary.statement <- paste("Patient has died from aggressive, metastastatic tumor at round ", i, ".", sep = "")
      # has mutations: E, T, D, G, C, S
      # EMT, telomerase, death inhibition,
      # growth activation, cell cycle, metastasis
      patient.log <- c(patient.log, paste("Round", i, "-", "patient died"))
      break
    }
    if (sum(current.map$data$value == "Cell") > round(nrow(current.map$data) * 0.80)) {
      tumor.burden.count <- tumor.burden.count + 1
      if (tumor.burden.count >= 3) {
        patient.summary.statement <- paste("Patient has died from high ongoing tumor burden at round ", i, ".", sep = "")
        patient.log <- c(patient.log, paste("Round", i, "-", "patient died"))
        break
      }
    }
    if (nchar(patient.summary.statement) < 1) {
      patient.summary.statement <- "Patient is still alive."
    }
    round.cell.num <- c(round.cell.num, GetCellNumbers(current.map))
    round.average.mut.num <- c(round.average.mut.num,
                               GetAverageMutationNum(cell.states, GetCellNumbers(current.map)))
  }
  return(list(current.map, cell.states, cell.divisions, cell.mut.rate,
              round.cell.num, round.average.mut.num, patient.summary.statement,
              patient.log))
}