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Importing a Roman Transport Network with Netlogo, Tutorial Importing a Roman Transport Model in Netlogo version 01-09-2018 Importing a Roman Transport network with Netlogo, Tutorial By Tom Brughmans First version: Summer 2018 This version created 01/09/2018 Netlogo version used: 6.0.1 Extension used: nw (pre-packaged with Netlogo 6.0.1) https://ccl.northwestern.edu/netlogo/6.0-BETA1/docs/nw.html Cite this tutorial as: Brughmans, T. (2018). Importing a Roman Transport network with Netlogo, Tutorial, https://archaeologicalnetworks.wordpress.com/resources/#transport . 1 Importing a Roman Transport Model in Netlogo version 01-09-2018 1. Introduction This tutorial provides an introduction to downloading open Roman datasets via https://projectMERCURY.eu and importing them into a Netlogo model. We will use the ORBIS dataset (http://orbis.stanford.edu/) to create a set of Roman settlements and major routes between them. We will analyse the network using the techniques in the nw Netlogo extension. This tutorial will reveal the importance of checking downloaded open data for mistakes and how you can correct them. 2. Conventions, tips and assumed knowledge This tutorial assumes basic knowledge of Netlogo and of simulation. It is recommended to walk through the introductory tutorials on the Netlogo website or the tutorial on Netlogo for archaeologists on the Simulating Complexity blog: https://simulatingcomplexity.files.wordpress.com/2014/07/dispersal_tutorial.pdf https://ccl.northwestern.edu/netlogo/docs/ This tutorial will also refer to some network science jargon, concepts and techniques. You can get a basic definition of all of these from the glossary on my blog: https://archaeologicalnetworks.wordpress.com/resources/#glossary Good introductions to network science include the following: Brandes, U., Robins, G., McCranie, A., & Wasserman, S. 2013. What is network science? Network Science 1(01): p.1–15. Newman, M.E.J., 2010. Networks: an introduction, Oxford: Oxford University Press. Code written in this tutorial will be formatted as in the following example: breed [nodes node] Save your project! do this regularly and use multiple versions throughout the tutorial so that you can fall back on an earlier version at any time. I will remind you regularly throughout the tutorial to save your project. If you are familiar with Netlogo: skip to section 6! 2 Importing a Roman Transport Model in Netlogo version 01-09-2018 3. Download and install Netlogo Netlogo is open source software and can be downloaded free of charge for Windows, Mac OS X and Linux. Go to https://ccl.northwestern.edu/netlogo/download.shtml . download the Netlogo installer (this tutorial uses version 6.0.1). Run the installer and install Netlogo. 4. Netlogo resources, manual and interface Netlogo has great documentation about all its features and code in its user manual: https://ccl.northwestern.edu/netlogo/docs/ This manual includes tutorials, a reference to the software functions, a dictionary to its programming language, documentation of its extensions and much more. Additional external resources can be found on the resources page: https://ccl.northwestern.edu/netlogo/resources.shtml A detailed reference to Netlogo’s Interface can be found here: https://ccl.northwestern.edu/netlogo/docs/ This tutorial will only give a very brief introduction to the key elements of the Netlogo interface you will be using throughout the tutorial. 3 Importing a Roman Transport Model in Netlogo version 01-09-2018 When you open Netlogo it should look something like this: It has three tabs: Interface, Info, Code. The Interface tab is where you watch your model run. Throughout the tutorial you will add buttons and sliders to control the variables of your model, and you will add monitors and plots to inspect what your model is doing. You can speed up or slow down the simulation using the speed slider at the top of the interface. The command center at the bottom will display messages you ask the model to produce, and you can also use it to give to commands to the model from the interface tab. 4 Importing a Roman Transport Model in Netlogo version 01-09-2018 The Info tab is where you describe your model using a standardized set of questions. Adding this information when you share your model with other is crucial to enable them to work with your model. We will not work with the Info tab in this tutorial. The Code tab is where you write and store the code for the model. In this tutorial we will be mainly working in the Code tab. A useful feature is the Check function at the top of this tab: click this to let Netlogo check your code for errors. If it finds errors then you will be guided to the error and asked to resolve it before you can continue, if it does not find errors then you can proceed with coding or viewing your model in action. NOTE: this error checker only 5 Importing a Roman Transport Model in Netlogo version 01-09-2018 checks whether the primitives used and the order of the code comply with the Netlogo rules (i.e. the code’s vocabulary and grammar). It will not check whether the code does what you want it to do, so getting no errors is no guarantee that the code works the way it should or the way you think it does. The error checker will always need to be used alongside other error checking techniques, like reporting variable values and checking them against expectations, or testing submodels independently. 5. Netlogo dictionary A crucial resource when coding in Netlogo is its dictionary: https://ccl.northwestern.edu/netlogo/docs/ For this tutorial, you will find the section on ‘Links’ in the Netlogo dictionary particularly useful, as well as the documentation of the ‘nw’ extension. You can get direct access (even offline) to the entry about a particular primitive by right- clicking it and selecting Quick Help. 6 Importing a Roman Transport Model in Netlogo version 01-09-2018 6. Create a working folder Make a folder on your computer called ‘Roman-transport’. All data we will use and the model we will create will be saved in this folder. When importing data into Netlogo models, as we will do in this tutorial, it is crucial that all data used is in the model is saved in the same location as the model itself. 7. Download ORBIS data ORBIS is the Stanford Geospatial Network Model of the Roman World (http://orbis.stanford.edu). It is a coarse-grained representation of the major terrestrial and maritime routes connecting the major settlements across the Roman world. Check out the ORBIS website if you want to learn more about it, or read the following publications: • http://orbis.stanford.edu/assets/Scheidel_64.pdf • http://orbis.stanford.edu/assets/Scheidel_59.pdf What is most crucial for this tutorial is that the ORBIS model can be reused with accreditation for research purposes. It offers a great starting point for studies of the Roman world that concern flows of goods, ideas and people. Before we download this open dataset we need to think about how we want to use it in Netlogo. What we want to achieve in this tutorial is to have an agent-based model with a network representation of the Roman transport system where nodes represent settlements and edges represent routes. It will therefore be best to download the network data version of ORBIS. Go to the MERCURY.eu page listing open Roman datasets: https://projectmercury.eu/datasets/ Scroll down the list and navigate to ‘Transport System (ORBIS)’. You will notice from the description of this resource that we will need to download two datasets: a list of settlements/sites and a list of routes. Click the link to download ORBIS Network data which will take you to a Stanford webpage: https://purl.stanford.edu/mn425tz9757 7 Importing a Roman Transport Model in Netlogo version 01-09-2018 download the two .csv files for the nodes and edges in this network (the nodes represent settlements and the edges represent routes). Right-click each file and select ‘download Linked File As …’ and save them in the ‘Roman-transport’ folder: A .csv file is a comma separated value file in which each line represents a data entry and each value in this entry is separated by a comma. It can be opened with a text editor or with a spreadsheet programme like Excel to view it as rows and columns. The edges file with the route data has six data columns: the source node of the edge, the target node of the edge, the length of the route in km, the number of days to traverse the route, the expense of doing so, and the route type (road, coastal, overseas, …). The nodes file with the settlement has four data columns: a unique node id, the settlement name as a label, the X and Y spatial coordinates. 8. Errors in the data it’s crucial to always thoroughly check downloaded open data to identify mistakes and omissions and to get an idea of how the data should be critically used in your study. Look through the nodes file and try to find some of the settlements that have “x” as their label. Notice any mistakes? They don’t have any coordinate information! In fact, there are a few issues with this nodes file. First, the X and Y coordinates are correct for some but switched around for most settlements. Second, the crossroads in the ORBIS model that are not towns do not have spatial coordinates associated with them. For these reasons it is advised to use 8 Importing a Roman Transport Model in Netlogo version 01-09-2018 another settlement dataset provided by the ORBIS team, which solves most issues with this file (but introduces others, wait and see…).
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