Elmuti/g.lua

## g.lua
local PreBakedDeathFunction = {}
local random = math.random
local ceil = math.ceil
local floor = math.floor
local randomseed = math.randomseed
local prevActual = 0
local prevWeeks = 0

randomseed(1557007091)  --os.time()
random(); random(); random()


--16/4/19
--r-strategy simulation
--23/4/19
--r-strategy simulation expanded with population strata
--24/4/19

--first run for 1000 years (52000 weeks), results: 54.6 s with 1465 agents (i5 2500k)
--basedeathfactor was 0.0018 and basefertilityfactor was 0.008

--r-strategy simulation expanded to multiple repeated simulations with efficient logging
--28/4/19
--multiple simulation implemented (with inferior rolling average method) (will be replaced with superior full-averaging method)

--todo notes
--implement average agent pregnancies tracking (28/4/19)
--implement age strata size tracking (28/4/19)

--29/4/19
--multiple simulation (superior full average method) implemented


--mortality calculators
--(0.6(x+2)^2)(0.01(x-2)^2)(0.9(x-2)^2)+0.01

--big local list

local ResultsFileName = "C:/Users/Elmeri/Desktop/GregorSimData/GregorData"           --output file name (in general)
local pop_num = 1000                        --number of agents in the start
local desired_length = 1000                 --length in years to simulate
local desired_simulations = 5                --number of simulations
local verboseoutput = true                  --should the output include text (true) or just be numbers (false)
local runSingle = false                     --set to true if a single simulation is desired

local prerepro = 0.35                       --percent of population in the pre-reproductive stage
local repro = 0.6                           --percent of population in the reproductive stage of life
local postrepro = 0.05                      --percent of population in the post-reproductive stage

--small local list

--internal locals

local pop = {}                  --table to contain the agents
local week = 0                  --counts weeks, for ingest into Excel
local basedeathfactor = 0.0011
local basefertilityfactor = 0.007
local sim_length = (desired_length*52)  --simulation length in weeks
--local pop_actual = pop_num
local max_pop_size = 10000      --maximum population size to terminate the simulation
local simSettingsFile = (os.time().."RStratSimSettings.txt")        --simulation settings log file

local sim_interval = 10         --prints a progress message every n simulations to make sure the program is working as intended
local sim_number = 0            --keeps track of the current number of simulations
local sim_time_length = 0.83    --length in seconds of a single simulation per 1000 weeks in that simulation, to calculate estimated times

local simSingleOutput = "C:/Users/Elmeri/Desktop/GregorSimData/GregorData"
local preResults = {}

--sim length estimator

print("Expected run time (in seconds) "..( ((sim_length/1000) * sim_time_length) * desired_simulations))
os.execute("title GregorPopSim - Running "..desired_simulations.." simulations, each "..sim_length.." weeks")
--various verbose text

if desired_simulations ~= 0 then
print("Warning, multiple simulations ("..desired_simulations..") will be run!")
end

if simSingleOutput == nil then
print("Critical! Special simulation output folder not available!")
end

print("The program will now present various mission critical variables, and write them into a log file")
print("Strata: "..prerepro.." "..repro.." "..postrepro)
print("Factors: "..basedeathfactor.." "..basefertilityfactor)
print("Simulations: "..sim_length.." "..desired_simulations)
local F99 = io.open(simSettingsFile,"w")
F99:write("This is the settings log file for the simulation on "..os.date().."\n")
F99:write("Strata: "..prerepro.." "..repro.." "..postrepro.."\n")
F99:write("Factors: "..basedeathfactor.." "..basefertilityfactor.."\n")
F99:write("Simulations: "..sim_length.." "..desired_simulations.."\n")
F99:write("Agent characteristics")

print("script head complete "..os.clock().."\n")

local function PreBakeDeathCharts()
    local before = os.clock()
    for i = 1, 5200 do --assume 100 years is maximum age for pre-baked death function charts
        local age = i/1000
        PreBakedDeathFunction[i] = 0.1 * ( (0.6 * (age+0.1)^2) * (0.01 * (age-2.5)^2) * (0.9 * (age-2)^2) + basedeathfactor)
    end
    local timetaken = os.clock() - before
    print("Took "..timetaken.." seconds to pre-bake death function chart")
end

PreBakeDeathCharts()

print("Press ENTER to start simulation")
--io.read()

--agent types

--[[table positions agentID,
age,
death boolean for clean up,
age at reproductive maturity,
post-reproductive maturity,
pregnant boolean,
%chance of pregnancy,
week of pregnancy,
gestation period,
post-gestational regeneration (multiplier of gestation time),
post-gestational stage boolean,
numpregnancies,
is reproductive age (adult) boolean,
internal boolean to smooth out pregnancies at the start,
    ]]

local basicAgent = {

    ID = IDcount;
    Age = 0;
    Dead = false;
    Repro = 780;
    PRepro = 2080;
    Pregnant = false;
    FertilityRoll = basefertilityfactor;
    WeekP = 0;
    Gestation = 38;
    PGestation = 0.5;
    PGestational = false;
    PGestationalWeek = 0;
    Pregnancies = 0;
    Adult = false;
    Burnin = false;

    }

F99:write("Repro: "..basicAgent.Repro.."\n")
F99:write("PRepro: "..basicAgent.PRepro.."\n")
F99:write("Gestation "..basicAgent.Gestation.."\n")
F99:write("PGestation "..basicAgent.PGestation.."\n")
F99:close()

--samity checks

if prerepro+repro+postrepro ~= 1 then
print("The simulation cannot be started as the population strata do not sum to 1!")
print(prerepro)
print(repro)
print(postrepro)
print(prerepro+repro+postrepro)
error("Script has been halted!")
end

--script start

--local F = io.open(ResultsFile,"w")
--F:write("week \t deaths \t population \t births \t pregnancies \t burnins \t avg age")
local verboseLine = "week \t deaths \t population \t births \t pregnancies \t avg age"

--local F2 = io.open((os.time().."PopStart.txt"),"w")
--F2:write("agent \t age")

--establish the table


local function deepcopy(orig)
    local orig_type = type(orig)
    local copy
    if orig_type == 'table' then
        copy = {}
        for orig_key, orig_value in next, orig, nil do
            copy[deepcopy(orig_key)] = deepcopy(orig_value)
        end
        setmetatable(copy, deepcopy(getmetatable(orig)))
    else -- number, string, boolean, etc
        copy = orig
    end
    return copy
end

local function createAgents(numAgents,typeAgent,creationType)
    if creationType == "SimStart" then
        local IDcount = 0
        local prereprocount = ceil(pop_num * prerepro)
        local reprocount = ceil(pop_num * repro)
        local postreprocount = ceil(pop_num * postrepro)

        os.execute("cls")
        print("Currently running simulation #"..sim_number.." with agent configuration "..prereprocount.."/"..reprocount.."/"..postreprocount.." for a total of "..(prereprocount+reprocount+postreprocount).." agents")
        print("Previous simulation: "..prevActual.." agents and "..prevWeeks.." weeks")
        print("Total time running so far: ".. os.clock())
        reprocount = reprocount + prereprocount
        postreprocount = postreprocount + reprocount

        for i = 1, numAgents do
            if ((prereprocount > i) and (i >= 0)) then
                local copy = deepcopy(typeAgent)
                copy.Age = random(0,basicAgent.Repro)
                IDcount = IDcount + 1
                table.insert(pop,copy)
                --F2:write("\n"..IDcount.."\t"..copy.Age)
            elseif ((reprocount > i) and (i >= prereprocount)) then
                local copy = deepcopy(typeAgent)
                copy.Age = random(basicAgent.Repro,basicAgent.PRepro)
                local numReproAgents = ceil(pop_num * repro)
                local burninRoll = random()
                if burninRoll < 0.9 then
                    copy.Burnin = true
                end
                IDcount = IDcount + 1
                table.insert(pop,copy)
                --F2:write("\n"..IDcount.."\t"..copy.Age)
            elseif ((postreprocount > i) and (i >= reprocount)) then
                local copy = deepcopy(typeAgent)
                copy.Age = random(basicAgent.PRepro,3000)
                IDcount = IDcount + 1
                table.insert(pop,copy)
                --F2:write("\n"..IDcount.."\t"..copy.Age)
            end
        end
    elseif creationType == "Birth" then
        for i = 1, numAgents do
            table.insert(pop,deepcopy(typeAgent))
        end
    end
    --F2:close()
end

--simulation


local function simulate(dsrlngth,startPop)
    local pop_actual = startPop
    --print(dsrlngth)
    for i = 1, dsrlngth do
        if pop_actual > max_pop_size or pop_actual <= 10 then
            --createLastLog()
            local time_length = os.clock()
            --print("The simulation has ended after "..time_length.." seconds with "..pop_actual.." agents and "..week.." weeks")
            prevActual = pop_actual
            prevWeeks = week
            break
        end
        --print(pop_actual)
        local deaths = 0
        local births = 0
        local pregnants = 0
        local burnins = 0
        local checkavg = 0
        --age all the agents
        for numAgent, agent in pairs(pop) do
            agent.Age = agent.Age + 1
            --DEATH FUNCTION
            if random() <= PreBakedDeathFunction[agent.Age] then
                agent.Dead = true
                deaths = deaths + 1
            end
        end
        --remove dead ones to prevent dead ones from being pregnant
        for numAgent, agent in pairs(pop) do
            if agent.Dead == true then
                table.remove(pop,numAgent)
            end
        end


        --count burnin agents during burnin period
        if week < 781 then
            for numAgent, agent in pairs(pop) do
                if agent.Burnin == true then
                    burnins = burnins + 1
                end
            end
        else end
        --make agents pregnant, advance their fetal ages, check for whether it is time for birth, check whether the agent can be returned to a fertile status (post-gestational period)
        for numAgent, agent in pairs(pop) do
            --check for Burnin and adjust the agent accordingly
            if agent.Burnin == true or (week > dsrlngth+1) then
                if week > dsrlngth then
                    agent.Burnin = false
                else
                    local chance_unburn = random()
                    if chance_unburn < (1/burnins) then
                        agent.Burnin = false
                    end
                end
            end
            --check for pregnant or post-gestational
            if agent.Pregnant == true then
                pregnants = pregnants + 1
                --check for whether its delivery time
                if agent.WeekP >= agent.Gestation then
                    agent.Pregnant = false
                    agent.Pregnancies = agent.Pregnancies + 1
                    agent.PGestational = true
                    agent.WeekP = 0
                    createAgents(1,basicAgent,"Birth")
                    births = births + 1
                end
                agent.WeekP = agent.WeekP + 1
            elseif agent.PGestational then
                --check for whether the post-birth recovery period is over
                if agent.PGestationalWeek >= (agent.Gestation * agent.PGestation ) then
                    agent.PGestational = false
                    agent.PGestationalWeek = 0
                end
                agent.PGestationalWeek = agent.PGestationalWeek + 1
            elseif not agent.Pregnant and not agent.PGestational and not agent.Burnin then
                --calculate chance of pregnancy and manipulate the agent accordingly
                if agent.Age > agent.Repro and agent.Age < agent.PRepro then
                    if random() < agent.FertilityRoll then
                        agent.Pregnant = true
                    else
                        agent.Pregnant = false
                    end
                end
            end
            checkavg = checkavg + agent.Age
        end
        pop_actual = (pop_actual - deaths) + births
        local checkavg2 = floor(checkavg/pop_actual)
        --print(checkavg2)
        --createLogLine(week,deaths,pop_actual,births,pregnants,burnins,checkavg2) [single simulation]
        --[[if sim_number == 0 then
        local startlogline = (week.."\t"..deaths.."\t"..pop_actual.."\t"..births.."\t"..pregnants.."\t"..burnins.."\t"..checkavg2)
        preResults[week] = startlogline
        elseif sim_number > 0 then
        createLogLine2(week,deaths,pop_actual,births,pregnants,burnins,checkavg2)
        end --deprecated multiple simulations]]
        if runSingle == false then
            local currentLogLine = tostring((week.."\t"..deaths.."\t"..pop_actual.."\t"..births.."\t"..pregnants.."\t"..checkavg2))
            --preResults[week] = currentLogLine
            table.insert(preResults,currentLogLine)
        end
        week = week + 1
        checkavg = 0
    end
end

--increment logging

local function doAverage(num1,num2)

    local doneAverage = ((num1+num2)/2)
    return doneAverage
end

local function createLogLine2(whatWeek, numDead, numPopulation, numBorn, numPregnant, numBurnin, numAvg)
    local loglineOld = preResults[whatWeek]
    local llOstrings = splitString(loglineOld,"\t")
    print(llOstrings)
    local logline = tostring((whatWeek.."\t"..(doAverage(llOstrings[2],numDead)).."\t"..(doAverage(llOstrings[3],numPopulation)).."\t"..(doAverage(llOstrings[4],numBorn)).."\t"..(doAverage(llOstrings[5],numPregnant)).."\t"..(doAverage(llOstrings[6],numBurnin)).."\t"..(doAverage(llOstrings[7],numAvg))))
    preResults[whatWeek] = logline
end

local function splitString(inputstr, sep)
        if sep == nil then
                sep = "%s"
        end
        local t={}
        for str in string.gmatch(inputstr, "([^"..sep.."]+)") do
                table.insert(t, str)
        end
        return t
end

local function createSimTable(weekLength)
    --tracking for 7 datapoints
    local newLine = "0 \t 1 \t 2 \t 3 \t 4 \t 5"
    for i = 1, weekLength do
    table.insert(preResults,newLine)
    --print(newLine)
    end
    print("Data gathering table with "..weekLength.." weeks has been prepared! "..os.clock())
end

local function writeWholeLog(simNumber)
    --F:write("week \t deaths \t population \t births \t pregnancies \t burnins \t avg age")
    local currentResult = (ResultsFileName..simNumber..".txt")
    local F9 = io.open(currentResult,"w")
    for i = 1, sim_length do
        F9:write("\n"..tostring(preResults[i]))
    end
    F9:close()
end

local function createLogLine(numDead, numPopulation, numBorn, numPregnant, numBurnin, numAvg)
    local logline
    logline = ("\n"..week.."\t"..numDead.."\t"..numPopulation.."\t"..numBorn.."\t"..numPregnant.."\t"..numBurnin.."\t"..numAvg)
    F:write(logline)
end

local function createLastLog()
    if verboseoutput == false then return end
    local lastlogline
    lastlogline = ("\n*At week "..week.." the simulation ended with "..pop_actual.." agents")
    --F = io.open(ResultsFile,"w")
    F:write(lastlogline)
    --F:close()
end

--simulation

--setup simulation
--createAgents(pop_num,basicAgent,"SimStart")

--[[do simulation (single)

simulate(sim_length)

writeWholeLog()

print("In "..os.clock().." seconds "..desired_simulations.." simulations with a length of "..desired_length.." years were run and the averages reported in "..tostring(ResultsFile))

if os.clock() > 60 then
local minutes = os.clock()/60
print(minutes.." minutes")
end

if os.clock() > 3600 then
local hours = os.clock()/3600
print(hours.." hours")
end

F:close()]]

--do simulation (multiple)

local function runSimulations(howMany,howLong)
    --createSimTable(howLong)
    local lastTime = os.clock()
    for X = 1, howMany do
        preResults = {}
        pop = {}
        createAgents(pop_num,basicAgent,"SimStart")
        --createSimTable(howLong)
        week = 0
        simulate(howLong,pop_num)
        writeWholeLog(sim_number)
        sim_number = sim_number + 1
        local completion = (X/desired_simulations)*100
        if desired_simulations < 51 then
            print(completion.."% complete")
        else
            local checkInteger = completion/sim_interval
            if completion == checkInteger then
                local currentTime = (os.clock() - lastTime)
                print(completion.."% complete (simulation "..sim_number..") in time "..currentTime.." seconds")
            end
        end
    end
end

runSimulations(desired_simulations,sim_length)

--writeWholeLog()

print("In "..os.clock().." seconds "..desired_simulations.." simulations with a length of "..desired_length.." years were run and the averages reported in "..tostring(ResultsFile))

if os.clock() > 60 then
local minutes = os.clock()/60
print(minutes.." minutes")
end

if os.clock() > 3600 then
local hours = os.clock()/3600
print(hours.." hours")
end
	local PreBakedDeathFunction = {}
	local random = math.random
	local ceil = math.ceil
	local floor = math.floor
	local randomseed = math.randomseed
	local prevActual = 0
	local prevWeeks = 0

	randomseed(1557007091) --os.time()
	random(); random(); random()



	--16/4/19
	--r-strategy simulation
	--23/4/19
	--r-strategy simulation expanded with population strata
	--24/4/19

	--first run for 1000 years (52000 weeks), results: 54.6 s with 1465 agents (i5 2500k)
	--basedeathfactor was 0.0018 and basefertilityfactor was 0.008

	--r-strategy simulation expanded to multiple repeated simulations with efficient logging
	--28/4/19
	--multiple simulation implemented (with inferior rolling average method) (will be replaced with superior full-averaging method)

	--todo notes
	--implement average agent pregnancies tracking (28/4/19)
	--implement age strata size tracking (28/4/19)

	--29/4/19
	--multiple simulation (superior full average method) implemented



	--mortality calculators
	--(0.6(x+2)^2)(0.01(x-2)^2)(0.9(x-2)^2)+0.01

	--big local list

	local ResultsFileName = "C:/Users/Elmeri/Desktop/GregorSimData/GregorData" --output file name (in general)
	local pop_num = 1000 --number of agents in the start
	local desired_length = 1000 --length in years to simulate
	local desired_simulations = 5 --number of simulations
	local verboseoutput = true --should the output include text (true) or just be numbers (false)
	local runSingle = false --set to true if a single simulation is desired

	local prerepro = 0.35 --percent of population in the pre-reproductive stage
	local repro = 0.6 --percent of population in the reproductive stage of life
	local postrepro = 0.05 --percent of population in the post-reproductive stage

	--small local list

	--internal locals

	local pop = {} --table to contain the agents
	local week = 0 --counts weeks, for ingest into Excel
	local basedeathfactor = 0.0011
	local basefertilityfactor = 0.007
	local sim_length = (desired_length*52) --simulation length in weeks
	--local pop_actual = pop_num
	local max_pop_size = 10000 --maximum population size to terminate the simulation
	local simSettingsFile = (os.time().."RStratSimSettings.txt") --simulation settings log file

	local sim_interval = 10 --prints a progress message every n simulations to make sure the program is working as intended
	local sim_number = 0 --keeps track of the current number of simulations
	local sim_time_length = 0.83 --length in seconds of a single simulation per 1000 weeks in that simulation, to calculate estimated times

	local simSingleOutput = "C:/Users/Elmeri/Desktop/GregorSimData/GregorData"
	local preResults = {}

	--sim length estimator

	print("Expected run time (in seconds) "..( ((sim_length/1000) * sim_time_length) * desired_simulations))
	os.execute("title GregorPopSim - Running "..desired_simulations.." simulations, each "..sim_length.." weeks")
	--various verbose text

	if desired_simulations ~= 0 then
	print("Warning, multiple simulations ("..desired_simulations..") will be run!")
	end

	if simSingleOutput == nil then
	print("Critical! Special simulation output folder not available!")
	end

	print("The program will now present various mission critical variables, and write them into a log file")
	print("Strata: "..prerepro.." "..repro.." "..postrepro)
	print("Factors: "..basedeathfactor.." "..basefertilityfactor)
	print("Simulations: "..sim_length.." "..desired_simulations)
	local F99 = io.open(simSettingsFile,"w")
	F99:write("This is the settings log file for the simulation on "..os.date().."\n")
	F99:write("Strata: "..prerepro.." "..repro.." "..postrepro.."\n")
	F99:write("Factors: "..basedeathfactor.." "..basefertilityfactor.."\n")
	F99:write("Simulations: "..sim_length.." "..desired_simulations.."\n")
	F99:write("Agent characteristics")

	print("script head complete "..os.clock().."\n")

	local function PreBakeDeathCharts()
	local before = os.clock()
	for i = 1, 5200 do --assume 100 years is maximum age for pre-baked death function charts
	local age = i/1000
	PreBakedDeathFunction[i] = 0.1 * ( (0.6 * (age+0.1)^2) * (0.01 * (age-2.5)^2) * (0.9 * (age-2)^2) + basedeathfactor)
	end
	local timetaken = os.clock() - before
	print("Took "..timetaken.." seconds to pre-bake death function chart")
	end

	PreBakeDeathCharts()

	print("Press ENTER to start simulation")
	--io.read()

	--agent types

	--[[table positions agentID,
	age,
	death boolean for clean up,
	age at reproductive maturity,
	post-reproductive maturity,
	pregnant boolean,
	%chance of pregnancy,
	week of pregnancy,
	gestation period,
	post-gestational regeneration (multiplier of gestation time),
	post-gestational stage boolean,
	numpregnancies,
	is reproductive age (adult) boolean,
	internal boolean to smooth out pregnancies at the start,
	]]

	local basicAgent = {

	ID = IDcount;
	Age = 0;
	Dead = false;
	Repro = 780;
	PRepro = 2080;
	Pregnant = false;
	FertilityRoll = basefertilityfactor;
	WeekP = 0;
	Gestation = 38;
	PGestation = 0.5;
	PGestational = false;
	PGestationalWeek = 0;
	Pregnancies = 0;
	Adult = false;
	Burnin = false;

	}

	F99:write("Repro: "..basicAgent.Repro.."\n")
	F99:write("PRepro: "..basicAgent.PRepro.."\n")
	F99:write("Gestation "..basicAgent.Gestation.."\n")
	F99:write("PGestation "..basicAgent.PGestation.."\n")
	F99:close()

	--samity checks

	if prerepro+repro+postrepro ~= 1 then
	print("The simulation cannot be started as the population strata do not sum to 1!")
	print(prerepro)
	print(repro)
	print(postrepro)
	print(prerepro+repro+postrepro)
	error("Script has been halted!")
	end

	--script start

	--local F = io.open(ResultsFile,"w")
	--F:write("week \t deaths \t population \t births \t pregnancies \t burnins \t avg age")
	local verboseLine = "week \t deaths \t population \t births \t pregnancies \t avg age"

	--local F2 = io.open((os.time().."PopStart.txt"),"w")
	--F2:write("agent \t age")

	--establish the table


	local function deepcopy(orig)
	local orig_type = type(orig)
	local copy
	if orig_type == 'table' then
	copy = {}
	for orig_key, orig_value in next, orig, nil do
	copy[deepcopy(orig_key)] = deepcopy(orig_value)
	end
	setmetatable(copy, deepcopy(getmetatable(orig)))
	else -- number, string, boolean, etc
	copy = orig
	end
	return copy
	end

	local function createAgents(numAgents,typeAgent,creationType)
	if creationType == "SimStart" then
	local IDcount = 0
	local prereprocount = ceil(pop_num * prerepro)
	local reprocount = ceil(pop_num * repro)
	local postreprocount = ceil(pop_num * postrepro)

	os.execute("cls")
	print("Currently running simulation #"..sim_number.." with agent configuration "..prereprocount.."/"..reprocount.."/"..postreprocount.." for a total of "..(prereprocount+reprocount+postreprocount).." agents")
	print("Previous simulation: "..prevActual.." agents and "..prevWeeks.." weeks")
	print("Total time running so far: ".. os.clock())
	reprocount = reprocount + prereprocount
	postreprocount = postreprocount + reprocount

	for i = 1, numAgents do
	if ((prereprocount > i) and (i >= 0)) then
	local copy = deepcopy(typeAgent)
	copy.Age = random(0,basicAgent.Repro)
	IDcount = IDcount + 1
	table.insert(pop,copy)
	--F2:write("\n"..IDcount.."\t"..copy.Age)
	elseif ((reprocount > i) and (i >= prereprocount)) then
	local copy = deepcopy(typeAgent)
	copy.Age = random(basicAgent.Repro,basicAgent.PRepro)
	local numReproAgents = ceil(pop_num * repro)
	local burninRoll = random()
	if burninRoll < 0.9 then
	copy.Burnin = true
	end
	IDcount = IDcount + 1
	table.insert(pop,copy)
	--F2:write("\n"..IDcount.."\t"..copy.Age)
	elseif ((postreprocount > i) and (i >= reprocount)) then
	local copy = deepcopy(typeAgent)
	copy.Age = random(basicAgent.PRepro,3000)
	IDcount = IDcount + 1
	table.insert(pop,copy)
	--F2:write("\n"..IDcount.."\t"..copy.Age)
	end
	end
	elseif creationType == "Birth" then
	for i = 1, numAgents do
	table.insert(pop,deepcopy(typeAgent))
	end
	end
	--F2:close()
	end

	--simulation


	local function simulate(dsrlngth,startPop)
	local pop_actual = startPop
	--print(dsrlngth)
	for i = 1, dsrlngth do
	if pop_actual > max_pop_size or pop_actual <= 10 then
	--createLastLog()
	local time_length = os.clock()
	--print("The simulation has ended after "..time_length.." seconds with "..pop_actual.." agents and "..week.." weeks")
	prevActual = pop_actual
	prevWeeks = week
	break
	end
	--print(pop_actual)
	local deaths = 0
	local births = 0
	local pregnants = 0
	local burnins = 0
	local checkavg = 0
	--age all the agents
	for numAgent, agent in pairs(pop) do
	agent.Age = agent.Age + 1
	--DEATH FUNCTION
	if random() <= PreBakedDeathFunction[agent.Age] then
	agent.Dead = true
	deaths = deaths + 1
	end
	end
	--remove dead ones to prevent dead ones from being pregnant
	for numAgent, agent in pairs(pop) do
	if agent.Dead == true then
	table.remove(pop,numAgent)
	end
	end


	--count burnin agents during burnin period
	if week < 781 then
	for numAgent, agent in pairs(pop) do
	if agent.Burnin == true then
	burnins = burnins + 1
	end
	end
	else end
	--make agents pregnant, advance their fetal ages, check for whether it is time for birth, check whether the agent can be returned to a fertile status (post-gestational period)
	for numAgent, agent in pairs(pop) do
	--check for Burnin and adjust the agent accordingly
	if agent.Burnin == true or (week > dsrlngth+1) then
	if week > dsrlngth then
	agent.Burnin = false
	else
	local chance_unburn = random()
	if chance_unburn < (1/burnins) then
	agent.Burnin = false
	end
	end
	end
	--check for pregnant or post-gestational
	if agent.Pregnant == true then
	pregnants = pregnants + 1
	--check for whether its delivery time
	if agent.WeekP >= agent.Gestation then
	agent.Pregnant = false
	agent.Pregnancies = agent.Pregnancies + 1
	agent.PGestational = true
	agent.WeekP = 0
	createAgents(1,basicAgent,"Birth")
	births = births + 1
	end
	agent.WeekP = agent.WeekP + 1
	elseif agent.PGestational then
	--check for whether the post-birth recovery period is over
	if agent.PGestationalWeek >= (agent.Gestation * agent.PGestation ) then
	agent.PGestational = false
	agent.PGestationalWeek = 0
	end
	agent.PGestationalWeek = agent.PGestationalWeek + 1
	elseif not agent.Pregnant and not agent.PGestational and not agent.Burnin then
	--calculate chance of pregnancy and manipulate the agent accordingly
	if agent.Age > agent.Repro and agent.Age < agent.PRepro then
	if random() < agent.FertilityRoll then
	agent.Pregnant = true
	else
	agent.Pregnant = false
	end
	end
	end
	checkavg = checkavg + agent.Age
	end
	pop_actual = (pop_actual - deaths) + births
	local checkavg2 = floor(checkavg/pop_actual)
	--print(checkavg2)
	--createLogLine(week,deaths,pop_actual,births,pregnants,burnins,checkavg2) [single simulation]
	--[[if sim_number == 0 then
	local startlogline = (week.."\t"..deaths.."\t"..pop_actual.."\t"..births.."\t"..pregnants.."\t"..burnins.."\t"..checkavg2)
	preResults[week] = startlogline
	elseif sim_number > 0 then
	createLogLine2(week,deaths,pop_actual,births,pregnants,burnins,checkavg2)
	end --deprecated multiple simulations]]
	if runSingle == false then
	local currentLogLine = tostring((week.."\t"..deaths.."\t"..pop_actual.."\t"..births.."\t"..pregnants.."\t"..checkavg2))
	--preResults[week] = currentLogLine
	table.insert(preResults,currentLogLine)
	end
	week = week + 1
	checkavg = 0
	end
	end

	--increment logging

	local function doAverage(num1,num2)

	local doneAverage = ((num1+num2)/2)
	return doneAverage
	end

	local function createLogLine2(whatWeek, numDead, numPopulation, numBorn, numPregnant, numBurnin, numAvg)
	local loglineOld = preResults[whatWeek]
	local llOstrings = splitString(loglineOld,"\t")
	print(llOstrings)
	local logline = tostring((whatWeek.."\t"..(doAverage(llOstrings[2],numDead)).."\t"..(doAverage(llOstrings[3],numPopulation)).."\t"..(doAverage(llOstrings[4],numBorn)).."\t"..(doAverage(llOstrings[5],numPregnant)).."\t"..(doAverage(llOstrings[6],numBurnin)).."\t"..(doAverage(llOstrings[7],numAvg))))
	preResults[whatWeek] = logline
	end

	local function splitString(inputstr, sep)
	if sep == nil then
	sep = "%s"
	end
	local t={}
	for str in string.gmatch(inputstr, "([^"..sep.."]+)") do
	table.insert(t, str)
	end
	return t
	end

	local function createSimTable(weekLength)
	--tracking for 7 datapoints
	local newLine = "0 \t 1 \t 2 \t 3 \t 4 \t 5"
	for i = 1, weekLength do
	table.insert(preResults,newLine)
	--print(newLine)
	end
	print("Data gathering table with "..weekLength.." weeks has been prepared! "..os.clock())
	end

	local function writeWholeLog(simNumber)
	--F:write("week \t deaths \t population \t births \t pregnancies \t burnins \t avg age")
	local currentResult = (ResultsFileName..simNumber..".txt")
	local F9 = io.open(currentResult,"w")
	for i = 1, sim_length do
	F9:write("\n"..tostring(preResults[i]))
	end
	F9:close()
	end

	local function createLogLine(numDead, numPopulation, numBorn, numPregnant, numBurnin, numAvg)
	local logline
	logline = ("\n"..week.."\t"..numDead.."\t"..numPopulation.."\t"..numBorn.."\t"..numPregnant.."\t"..numBurnin.."\t"..numAvg)
	F:write(logline)
	end

	local function createLastLog()
	if verboseoutput == false then return end
	local lastlogline
	lastlogline = ("\n*At week "..week.." the simulation ended with "..pop_actual.." agents")
	--F = io.open(ResultsFile,"w")
	F:write(lastlogline)
	--F:close()
	end

	--simulation

	--setup simulation
	--createAgents(pop_num,basicAgent,"SimStart")

	--[[do simulation (single)

	simulate(sim_length)

	writeWholeLog()

	print("In "..os.clock().." seconds "..desired_simulations.." simulations with a length of "..desired_length.." years were run and the averages reported in "..tostring(ResultsFile))

	if os.clock() > 60 then
	local minutes = os.clock()/60
	print(minutes.." minutes")
	end

	if os.clock() > 3600 then
	local hours = os.clock()/3600
	print(hours.." hours")
	end

	F:close()]]

	--do simulation (multiple)

	local function runSimulations(howMany,howLong)
	--createSimTable(howLong)
	local lastTime = os.clock()
	for X = 1, howMany do
	preResults = {}
	pop = {}
	createAgents(pop_num,basicAgent,"SimStart")
	--createSimTable(howLong)
	week = 0
	simulate(howLong,pop_num)
	writeWholeLog(sim_number)
	sim_number = sim_number + 1
	local completion = (X/desired_simulations)*100
	if desired_simulations < 51 then
	print(completion.."% complete")
	else
	local checkInteger = completion/sim_interval
	if completion == checkInteger then
	local currentTime = (os.clock() - lastTime)
	print(completion.."% complete (simulation "..sim_number..") in time "..currentTime.." seconds")
	end
	end
	end
	end

	runSimulations(desired_simulations,sim_length)

	--writeWholeLog()

	print("In "..os.clock().." seconds "..desired_simulations.." simulations with a length of "..desired_length.." years were run and the averages reported in "..tostring(ResultsFile))

	if os.clock() > 60 then
	local minutes = os.clock()/60
	print(minutes.." minutes")
	end

	if os.clock() > 3600 then
	local hours = os.clock()/3600
	print(hours.." hours")
	end