Zonation is a spatial conservation prioritization framework for large-scale conservation planning. It identifies areas, or landscapes, important for retaining high habitat quality and connectivity for multiple biodiversity features (eg. species), providing a quantitative method for enhancing species' long term persistence.
Essentially, this software is a decision support tool for all non-commercial parties working on conservation issues. As Zonation operates on large grids, it provides a direct link between GIS, statistical distribution modeling and spatial conservation prioritization.
This repository contains the computational core of Zonation software. It does not contain the graphical user interface (GUI) components.
You can dowload the latest stable release installers (including the GUI) from the official website or from releases on Github.
Authors:
- Atte Moilanen <atte.moilanen@helsink.fi>
- Federico Montesino Pouzols
- Jarno Leppänen
Contributors:
- Joona Lehtomäki <joona.lehtomaki@helsink.fi>
These instruction describe the dynamic compilation of Zonation 4.0.0 on Ubuntu 14.04 (Trusty Tahr). Instructions have not been tested on other distributions/versions. For a set of bash scripts automating the steps below, please see this repository.
sudo apt-get update
sudo apt-get install cmake build-essential unzip libqt4-dev libfftw3-dev libqwt-dev libboost-all-dev libgdal-dev
Create a suitable download directory, fetch Zonation source code (version 4.0.0) from CBIG server, and extract the sources to the directory created:
mkdir zonation
wget https://github.com/cbig/zonation-core/archive/master.zip -P zonation
unzip zonation/master.zip -d zonation
or if you're using git, clone this repo
mkdir zonation
git clone https://github.com/cbig/zonation-core.git zonation/zonation-core-master
To build Zonation library (zig4lib) and Zonation CLI utility (zig4), do the following:
mkdir zonation/build
cd zonation/build
cmake ../zonation-core-master
make
If you have several cores available for compilation, you can pass switch -jX to make where X is the number of
designated cores (e.g. make -j4).
In order to call zig4 anywhere on the system (instead of just the build-location), create a symbolic link:
sudo ln -s FULL_PATH/zonation/build/zig4/zig4 /usr/local/bin/zig4
Replace FULL_PATH with the full path to the directory containing directory zonation created in step 2.
This stage is completely optional.
You can test that Zonation works by running some of the runs used in the
Hunter Valley tutorial. This is not a thorough test, but it will at least give you an overview on whether Zonationis working as intended. Tutorial data and setup files are fetched using
git and run using zrunner command line utility found in package ztools.
First, install git:
sudo apt-get -y install git
Then, install Python packages needed by zrunner:
sudo apt-get -y install python-yaml python-pip
ztools is installed directly from GitHub using pip.
sudo pip install https://github.com/cbig/ztools/archive/master.zip
With git installed, clone the tutorial repository with the following command:
git clone https://github.com/cbig/zonation-tutorial.git
You can run 5 basic tutorial variants defined in the configuration file basic/tests/ztests_basic.yaml by using zrunner:
zrunner -l tutorial_runs.yaml
zrunner will produce an output file results_XXX.yaml in the same folder. XXX will correspond to information about your system. If everything went fine, you should see no critical errors on the screen and the yaml-file should report execution times for successful runs.
Zonation computational core (zig4) is distributed under the GNU General Public License (GPL) version 3 (http://www.gnu.org/licenses/).
Zonation computational core © 2011-2014 Conservation Biology Informatics Group © 2004-2011 Atte Moilanen
Zonation computational core is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
Do not use this software if you disagree with the disclaimer or conditions of use. Even though the Zonation software has been done with the best of intentions, it is quite beyond one small research group to ensure its correct operation under all operating systems and environments. Anticipating all potential combinations of erroneous input has not been possible. Therefore, use the software with care and make an effort to understand how the inputs connect to outputs.
Zonation uses the following libraries:
- boost (http://www.boost.org)
- FFTW (http://www.fftw.org). We also used
- GDAL (http://www.gdal.org)
- Qt (http://qt-project.org)
- Qwt (http://qwt.sourceforge.net)
Various versions of GCC, the GNU compiler collection (http://gcc.gnu.org) were used as well.
These free open source software projects are greatly acknowledged!