AndreasDuering

DPhil Candidate and Clarendon Scholar

Institute of Archaeology

University of Oxford

Email: andreas.duering@arch.ox.ac.uk

My profiles:

Adacemia.eu

ResearchGate

Clarendon Scholars

Links to the model

POPULATION & CEMETERY SIMULATOR beta 1.2                    

A more advanced version of the model: POPULATION & CEMETERY SIMULATOR beta 2.2

Please havea quick look at the introductory remarks and the brief user manual before usingthe model. If you have further questions, hints or technical difficulties, I wouldbe happy to help you out. You can contact me via the above mentioned details.

Introduction

ThePopulation & Cemetery Simulator (PCS) is an open-access toolkit based on theOxford IT department's modellig4all project (www.modelling4all.org). Itprovides (osteo-)archaeologists interested in the demography of single populationswith an agent-based model with which a dynamic living population and theaccumulating dead in a cemetery can be simulated. It can be used to checkdemographic data of archaeological cemetery sites and try out probable virtualscenarios in the case of missing data. It can also be tailored towardsanswering other research questions, such as the impact of heterogeneity,artefact & disease frequencies, catastrophes, stochasticity and population growth.It is designed to be easy to use and inclusive. At this point the model isstill a trial version and does not include all planned features. However, thesimple and self-explaining Behaviour Composer of the modelling4all projectmakes it possible that users tailor it to their specific interests right away.

The idea tocreate the Population & Cemetery Simulator evolved out of my interest inthe (bio-)archaeological problems of reconstructing the elusive sphere of lifefrom cemetery data presented by Wood et al. (1992) and the "RostockManifesto" for Palaeodemography by Hoppa & Vaupel (2002). With themodel I hope to illustrate the raised issues and translate them into a languageunderstandable by a wider range of archaeologists and osteologists. Kölbl 'sMonte Carlo simulations (2004) were also an important source of inspiration forthe project. I would like to thank Ken Kahn, Howard Noble, Anders Sandberg andThomas Woolley for the invaluable help I received over the time I developed themodel.

Share your results & find bugs

As thePopulation & Cemetery Simulator is the basic tool that I will use for myresearch at the interface of archaeology, osteoarchaeology and palaeodemographyat the Institute of Archaeology, University of Oxford, I would be very happy ifyou shared your experiences of the model with me, preferentially by directcontact via the above mentioned email addresses. Your feedback will help me toimprove the model in three ways:

Firstly, Iwould like it to be intuitive and therefore utilisable in a cross-disciplinarydiscourse. So please tell me what you do not understand and what should beincluded in the user manual.

Secondly, Iwould like to see which scenarios you are testing out and what you are doingwith the toolkit to find new ways of application and generate new ideas together.

Thirdly, ifyou have got an affinity towards mathematics and demography, please find bugsand help me to rule out logical problems which I might have overlooked.

Powers & limitations of the model

The model isstill work in progress and I cannot recommend it to be used for the generationof final results at this point. But the model is already very useful to broadenthe perspective of research questions and find new ways of challenging data andtheir interpretation. If you still believe in the data of a life-table youcalculated on the basis of a skeletal population, please prepare for asurprise.

User manual (for beta 1.2)

First steps

The Population& Cemetery Simulator simulates the life of a single virtual livingpopulation over the course of 300 years and the accumulating cemetery. Themodel represents an optimal scenario in which all individuals have beenpreserved and excavated. One step of time equals one year in the simulationroutine.

If youclick on the link to the model (see above) the Behaviour Composer of theOxford-based modelling4all project will open. The code of the model has beenpackaged in a form that visualises the logic of the agent-based modellingroutine and structures the coding procedure in a way that can be easily understoodby people who have no experience in computer modelling. The optional featuresdiscussed later in the guide can be activated here. This window is also theplace for more fundamental changes of the code.

But Irecommend that you proceed to the model interface by clicking on the RUN buttonon the upper left hand side if you are trying out the programme for the firsttime or if you do not want to change the initial settings. It is the modelinterface where you put in your data and where the simulation runs can beconducted. It might take some time to load because it will be opened as a JavaApplet. If your firewall blocks the Java Applet you must give it specificpermission to work, for instance by clicking on OK in a popup window.

If Java does not run, I recommend to download and install NetLogo on your computer. Then download the model via the Download function in the Behaviour Composer.

If you run the model or if you open it in NetLogo you will see the data entry interface in your browser or desktop.

Then put inyour data and start each new simulation run by a click on the SETUP button. Themodel will then apply your changes to the input data and by clicking on GO therun starts.

CAUTION! If you reload completely, for instanceif you load the link to the model again, the initial settings will reappear andyour individual changes in the interface will get lost.

Model datainput/ required data:

1. Arandomised initial population at time 0 with sliders to control the overallpopulation size, age distribution and sex ratio.

2.Age-specific mortality profile of a population in the form of the qx column ofa life-table that gives the probability of dying by input boxes for age groupsin 5 year steps.

3. The fertilityof the population with sliders for the reproductive phase of females, the childspacing and the probability of reproduction at each possible moment.

Dataoutput/ produced graphics:

The resultsappear in various continuous and accumulating graphics and monitors. Thegraphics are designed to illustrate the different dynamics of the dead and theliving populations, i.e. the living population and the cemetery.

There are monitorsand graphics for the total population size of the living population at eachpoint of time and the accumulating burials in the dead population. There arealso plots that show the age structure of the living and dead populations, theoverall input mortality profile, the mean age at death and the mean age in theliving group.

Options:

TheBehaviour Composer makes it possible to switch on and off specific parts of thecode. By right clicking on specific behaviours these pieces of code can beactivated and inactivated. This is why there are two optional ways of datainput for mortality data, a specific fertility routine that reducesreproduction success if there is no balance of sexes and an experimentalsimulation routine for disease and artefact rates.

E.g. the twooptional ways of mortality input:

1. Acontinuous Siler Mortality Curve with known alpha and beta values.

2. A verysimple mortality structure with only three different age groups: children,reproducing adults & a post-reproductive phase.

CAUTION! If two redundant behaviours, such astwo mortality routines, have been activated at the same time, the model cannotwork properly and might produce error messages. Please switch on only one ofthe optional features per simulation run.

The optionsDOWNLOAD and SHARE can help you to download the programme and to save changesyou made in the Behaviour Composer. Both functions do not relate to yourindividual data you put in using the Java Applet interface.

For theDOWNLOAD option you will need to install the netLogo software which is freelyavailable online (http://ccl.northwestern.edu/netlogo/). Simulation runs aremuch faster in the downloaded version of the model.

If youclick on SHARE you will find four links with specific properties. These linkswill help you to save changes and share your results. I recommend using thefirst link (frozen model).

List of input and output data

The namingmight not adhere strictly to the common palaeodemographic nomenclature toimprove readability. Most of the parameters controlled by sliders or inputboxes must be named "the-NAME", such as "the-mortality_0to4".The use of "the-" as a suffix of the parameters is required by thelogic of the netLogo programming language.

time                                                 

1step of time equals one year

input

initialpopulation or starter generation

the-femalestartergeneration:    

number of female individuals at timestep 0

the-malestartergeneration:       

number of male individuals at timestep 0

the-lowerage:                                

minimumage of the individuals of the initial population

the-upperage:                                

maximum age ofthe individuals of the initial population

reproduction

the-minreprodage:                        

defines the minimum ageof reproduction for females

the-maxreprodage:                       

defines the maximum ageof reproduction for females

the-fbirthratio:                               

the ratio offemale versus male newborns

the-childspacing:                           

the temporal delaybetween briths

the-reprodprobability:                  

the probability of reproductionat a point of time a female could reproducedefined by age and childspacing

death

the-moratlity_0to4

...

the-mortality_60plus:                 

the age-dependant risk ofdying changes for each individual when theyage, each input box controls a 5-years increment

the-d:                                               

multipliesthe overall mortality of each individual by that value; this slidercan be used to change the mortality of the total population

the-y:                                               

subtractsthe value from the mortality of each individual; this slidercan be used to change the mortality of the total population

output

monitors

n females:                                       

totalnumber of living females at this point of time

n males:                                           

totalnumber of living males at this point of time

ndeadfemales:                              

accumulateddead females in the cemetery up to this point

ndeadmales:                                  

accumulateddead males in the cemetery up to this point

+age mean:                                     

mean ageat death of all individuals buried in the cemetery up to this point

age mean:                                       

mean ageof all living individuals, changes dynamically over time

mean nochildren per woman:    

the average numberof children which are being produced by the averagefemale in the living population with the current reproduction settings

graphics& plots

livingpopulation:                           

plotsthe size of the female population at each point of time in red andthat of the male population in blue

deadpopulation / cemetery:       

plots thetotal number of the accumulating dead females and males in thecemetery

livingpopulation structure:         

plots thenumber of individuals in each age category at each point of timeaccording to the sexes

agestructure in cemetery:           

plots theaccumulating number of individuals who die at a certain age accordingto age and sex; This equals the data you get from a cemeteryexcavation.    

inputmortality profile:                 

Thisis the overall risk of dying over age defined by the mortality data inputof the user.

mean ageplot:                                

plotsthe mean age at death, i.e. the average age at death of the cemeterypopulation, in black and the mean age of each living individualover time in green

% of traitplots:                              

theseplots show the frequency of an artefact/disease in the living anddead populations given to 20% of all male individuals aged 30 overtime in the subgroup of males aged 30 and over as well as in the completepopulation     

User manual (for beta 2.2)

(((in preparation)))

Copyright & citation

Please givethe source of the programme if you are using it when dealing with third partiesand contact me (details above) if you plan to use the tool in your ownresearch. I would be very happy to collaborate with you and share experienceswith the modelling tool.

Bibliography

Duering,A. (2012). Media vita in morte sumus. Differentdynamics of the living and dead populations at Bärenthal. In: Proceedings of theCultural Heritage and New Technologies Conference 17. Vienna, StadtarchäologieWien. Online resource, retrieved 15/01/2014, fromhttp://www.chnt.at/proceedings-chnt-17/.

Duering, A.(2014). Der Friedhof von Bärenthal aufder Scherra. Lebensverhältnisse und Bestattungsbrauch einer Dorfbevölkerung des7. bis 10. Jahrhunderts. Fundberichte aus Baden-Württemberg 2013, 34/2:391-490.

Duering,A. and J. Wahl (2014). A massacredvillage community? Agent-based modelling sheds new light on the demography ofthe Neolithic mass grave of Talheim. Journal of Biological and ClinicalAnthropology [in press].

Hoppa, R.D. & Vaupel, J. W. (Ed.) (2002). Paleodemography: Age distributions fromskeletal samples, Cambridge Studies in Biological and Evolutionary Anthropology31, Cambridge University Press, Cambridge.

Kahn, K. and H. Noble (2010). The BehaviourComposer 2.0: a web-based tool for composing NetLogo code fragments. Constructionism Paris 2010, 1-14.

Kölbl, S. (2004). Das Kinderdefizit im frühen Mittelalter –Realität oder Hypothese? – Zur Deutung demographischer Strukturen inGräberfeldern, Diss. Tübingen.

Wilensky, U. (1999). NetLogo, Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL. 2014, from http://ccl.northwestern.edu/netlogo/.