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Life and Fishery","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"\n\nFind your way with DISPLACE\n======\n\nFor DISPLACE users and possibly interested persons to contribute, see [DISPLACE documentation](https://frabas.github.io/DISPLACE_GUI/)\n\n\u003e **📚 New Documentation System Available for DISPLACE developers!**  \n\u003e We've created a comprehensive Quarto-based documentation system that makes it easy to expand and contribute documentation.  \n\u003e **See [DOCUMENTATION.md](DOCUMENTATION.md) for the new documentation guide** or explore the `docs/` directory directly.\n\nFurther below is some initial documentation.\n\n## Summary\n- [What is for?](#what-is-for)\n- [How to contribute](#how-to-contribute)\n- [How to install](#how-to-install)\n- [Quick start for running a DISPLACE simulation](#quick-start-for-running-a-displace-simulation)\n- [Simulation output formats](#simulation-output-formats)\n- [How to build from scratch](#how-to-build-from-scratch)\n- [DISPLACE doxygen documentation](#displace-doxygen-documentation)\n- [GDAL notes](#gdal-notes)\n- [Unit testing](#unit-testing)\n- [Build a new case study](#build-a-new-case-study)\n- [How to cite](#how-to-cite)\n\n\n\n## What is for?\n\n\nDISPLACE is a dynamic, individual-based model for spatial fishing planning and effort displacement \nintegrating underlying fish population models. The DISPLACE project develops and provides a \nplatform primarily for research purposes to transform the fishermen detailed knowledge into models,\nevaluation tools, and methods that can provide the fisheries with research and advice. \nBy conducting a ecological and socio-economic impact assessment the model intends to serve as an aid to decision-making for (fishery) managers.\nAn impact assessment will help answering on what are the impacts of the different policy options and who will be affected.\nBy quantifying the effects the assessment will measure how the different options compare, for example \nhow different the options perform in achieving the objective(s) of the policy.\n\n## How to contribute\n\n[Please read our CONTRIBUTING statement here](CONTRIBUTING.md)\n\n\n## How to install DISPLACE\n\n\nLook at the [Release section](https://github.com/frabas/DISPLACE_GUI/releases) on this GitHub repository \nto download an installer for Windows. Alternatively, look at the \n[google drive for DISPLACE](https://drive.google.com/drive/folders/0ByuO_4j-1PxtfnZBblpQNmh2a2Z4SmpkRC16T1kwR0t1RWUyOVUxdHlEZzZwZWVpaVJac00)\nfor Unix or MacOSX packages, also hosting additional files i.e. possible dependencies and the DISPLACE software development kit.\n\n\n### Install on Windows\n\nLaunch the installer application, and follow the guide. There are no prerequisites on Windows, and the application\nshould work out of the box.\n\n### Install on MacOS\n\nOpen the DMG file, then drop the program in the Application folder.\nThere are no prerequisites on MacOS, and the application should work out of the box.\n\n### Install on Ubuntu Linux\n\nUbuntu 18.04LTS has a few prerequisites that must be installed before installing the displace package itself.\n\nRun the following command to install the prerequisites:\n\n```bash\n\n$ sudo apt install libgdal20 libgdal-dev libcgal13 libcgal-dev libboost1.65-all-dev libgeographic17 libqt5gui5 libqt5widgets5 libqt5xml5\n\n```\n\nThen install the `msqlitecpp` packages provided in the download section:\n\n```bash\n$ sudo dpkg -i msqlitecpp0_0.9.4_amd64.deb msqlitecpp-dev_0.9.4_amd64.deb \n```\n\n\nFinally, install the displace package:\n\n```bash\n$ sudo dpkg -i displace_0.9.22_amd64.deb\n```\n\nIf you have any difficulty, try fixing the package dependencies by running: \n\n```bash\n$ sudo apt --fix-broken install\n```\n\nAny missing package should be automatically installed.\n\n## How to compile from the code source\n\n\n[compiling with CMake (preferred)](docs/Building-cmake.md)\n\n[compiling on HPC (simulator only)](docs/Building-on-hpc.md)\n\n[making the displace sdk (optional)](docs/building.md)\n\n[compiling on Windows (deprecated)](docs/Building.win)\n\n[compiling on Unix deprecated)](docs/Building.unix)\n\n[compiling on MacOSX deprecated)](docs/Building.MacOSX)\n\n\n## DISPLACE doxygen documentation [DEPRECATED]\n\nCan be found [here](https://frabas.github.io/DISPLACE_GUI/doxygen/doc/html/index.html)\n\nProcedure for updating the doxygen documentation without keeping track of git history [here](https://github.com/robotology/how-to-document-modules/blob/master/README.md)\n\n## Quick start for running a basic DISPLACE simulation\n\n[DISPLACE Example datasets](https://displace-project.org/blog/download/) are available for download. \nYou need to unzip the downloaded file to a folder that name the dataset with the pattern DISPLACE_input_xx,\nfor example DISPLACE_input_minitest which is the minimal dataset typically used for demonstration purpose.\n\n\nRun DISPLACE with e.g. displacegui\n\n\nBy default the Model Objects is set to 4. If you want to run a scenario, first make sure your Model Objects is set to [0].\n\n\n![alt text](./docs/images/quickstart_select_model_0.png)\n\n\nIf yes then in the main menu do a \"File\"\u003e\"Load a Scenario Model, \n\n\n ![alt text](./docs/images/quickstart_load_scenario_file.png)\n\n\nand choose a scenario file (a .dat file) you´ll find in the\\simusspe subfolder of your DISPLACE dataset.\nSelect the file, click Ok and wait to see the DISPLACE graph plotted on the map.\n\n\n ![alt text](./docs/images/quickstart_scenario_file_is.png)\n\n\nYou can now click Start in the DISPLACE command panel for a DISPLACE simulation to start:\n\n\n ![alt text](./docs/images/quickstart_click_start.png)\n\nAfter some object creation and initialization the time step window will shortly update and the simulation run to the end time step. \nBy default, 8762 hourly time steps will be simulated which is approx. the number of hours in one year.\nin Setup menu the total number of time step can be changed to up to 52586 for a maximal 6-years horizon. \nBecause of the computation time, running more than one year simulation and many replicates are better done on a HPC cluster.\nAutomated shell scripts to run many DISPLACE simulations in parallel on a HPC cluster can be provided on request. \n\n ## Simulation output formats\n\n\nLook at the [description](./docs/output_fileformats.md) of the list of files produced by a DISPLACE simulation. \nA [displaceplot](https://github.com/frabas/displaceplot/releases) R package has been developed to handle these output text files and produced some plots out of them. \nSimulation outcomes are also exported as a SQLite database which can be re-loaded within DISPLACE in a Replay mode. The internal structure and simulated data\ncan be further retrieved from the database when using an external SQLite DB browser. \n\nTo load a result database into DISPLACE: \n\n\n\n ![alt text](./docs/images/quickstart_load_db_menu.png)\n\nSelect a DISPLACE db file:\n\n ![alt text](./docs/images/quickstart_load_db_file.png)\n\nOnce loaded, the simulation can be replayed with the Replay command:\n\n ![alt text](./docs/images/quickstart_replay_command.png)\n\n\n\n\n## GDAL Notes\n\n\nCurrent version of QMapControl supports shapefiles loading ONLY for WGS84 Coordinates system. This is because QMapControl itself uses WGS84 coordinates.\nSo you need to convert your shapefiles if not using this CRS.\nYou can use ogr2ogr or the provided script in the scripts/ directory.\n\n$ ogr2ogr -t_srs WGS84 DEST.shp SRC.shp\n\nNote that DEST file is specified before the source!\n\n\n## Unit testing\n\n\nUnit testing is performed using the Boost::Test framework. It can be compiled and linked in two ways:\n\n- Dynamic linked, using the system installed boost::test library. This option is enabled by default on Unix\n- Compiled in, using the boost/test/included/unit_test.hpp (included in main.cpp). This is suitable for Windows, where boost::test is not available with our version of mingw64. A standard installation of boost::test is required.\n\nThe two methods can be selected by defining boost_test_included in the CONFIG line of the Qt Project. It is enabled by default on Windows (see localconfig.pri).\n\nIf boost::test is not available in any form, it can be disabled by removing the units-test option from the CONFIG variable in the pro file.\n\n## Build a new case study\n\nA set of [R routines](https://github.com/frabas/DISPLACE_R_inputs) are available to create a new DISPLACE case study from scratch. These routines are quite data-hungry \nand would require to be adapted to each case. Ideally a R package should be build soon to wrap them in a consistent tool. \nAnother way is to scrutinize the DISPLACE_input_mintest github repository to see all the required input files required \nto run a minimal case study. Because it can be currently tricky to understand the logic behind all the input text files \nwe will think one day to build a unique input database to DISPLACE instead of using so many individual text files.\n\n## How to cite\n\n* Bastardie F, Nielsen JR, Miethe T. 2014. DISPLACE: a dynamic, individual-based model for \nspatial fishing planning and effort displacement - integrating underlying \nfish population models. Canadian Journal of Fisheries and Aquatic Sciences. 71(3):366-386. [link here](https://www.nrcresearchpress.com/doi/full/10.1139/cjfas-2013-0126#.XJs-ubh7nmE) \n\n* Bastardie, F., Nielsen, J. R., Eigaard, O. R., Fock, H. O., Jonsson, P., and Bartolino, V. \nCompetition for marine space: modelling the Baltic Sea fisheries and effort displacement \nunder spatial restrictions. ICES Journal of Marine Science, doi: 10.1093/icesjms/fsu215. [link to a free copy](https://academic.oup.com/icesjms/article/72/3/824/701817) \n\n* Bastardie, F., Nielsen, J. R., Eero, M., Fuga, F. Rindorf., A. 2017. Effects of changes\nin stock productivity and mixing on sustainable fishing and economic viability,\nICES Journal of Marine Science, Volume 74, Issue 2, Pages 535–551\n[link to a free copy](https://academic.oup.com/icesjms/article/74/2/535/2669542)\n\n* Bastardie, F., Angelini, S., Bolognini, L., Fuga, F., Manfredi, C., Martinelli, M.,\nNielsen, J. R., Santojanni, A., Scarcella, G., and Grati, F.. 2017. \nSpatial planning for fisheries in the Northern Adriatic: working toward viable and sustainable fishing.\nEcosphere 8( 2):e01696. 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