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Commit 5443206b authored by Laura Meier's avatar Laura Meier
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Merge branch 'main' of https://git.ufz.de/oesa/mastiff

parents f68b3129 9a547782
******************************************MASTIFF MODEL*********************************************
MASTIFF (Multiple Aquatic STressors In Flowing Food webs) is a spatially explivit simulation model
for multi-stressed riverine systems which supports systematic analyses of organismic drift and
dispersal processes and their functional importance for (i) the community structure of benthic
grazers, (ii) the performance of grazer-mediated control of eutrophication, and (iii) the ability to
counteract adverse effects of local stressors in the different river segments
# **MASTIFF MODEL**
MASTIFF (Multiple Aquatic STressors In Flowing Food webs) is a spatially explivit simulation model for multi-stressed riverine systems which supports systematic analyses of organismic drift and dispersal processes and their functional importance for (i) the community structure of benthic grazers, (ii) the performance of grazer-mediated control of eutrophication, and (iii) the ability to counteract adverse effects of local stressors in the different river segments.
INSTALLATION
## INSTALLATION
Requirements:
Java Version 1.8.0_271
> Java Version 1.8.0_271
Recommended software for development:
SceneBuilder (8.5.0)
Eclipse IDE for Java Developers (2019-09 R, 4.13.0)
> SceneBuilder (8.5.0)
>
> Eclipse IDE for Java Developers (2019-09 R, 4.13.0)
Open model GUI via:
(1) Run Main.java (in ...\MODEL_MASTIFF\Mastiff\Java model project\src\application) as Java
application (e.g. via Eclipse IDE)
(2) Double-click runMASTIFF.jar (if it does not open, check in 'Registrierungs-Editor' under
'Computer\HKEY_CLASSES_ROOT\jarfile\shell\open\command' the path points on the right java
version)
(3) via command line (cmd): 'java -jar runMASTIFF.jar' (check 'java -version' for version)
1. Run Main.java (in ...\MODEL_MASTIFF\Mastiff\Java model project\src\application) as Java application (e.g. via Eclipse IDE)
2. Double-click [runMASTIFF.jar](https://git.ufz.de/oesa/mastiff/-/blob/main/runMASTIFF.jar) (if it does not open, check in 'Registrierungs-Editor' under 'Computer\HKEY_CLASSES_ROOT\jarfile\shell\open\command' the path points on the right java version)
3. via command line (cmd): `java -jar runMASTIFF.jar` (check `java -version` for version)
...and choose scenarios options via GUI.
SET PARAMETERS
## SET PARAMETERS
Mastiff is modular in design. Therefore, you can switch on and off different processes in the GUI
interface, including options/functions/processes that are not included in ODD protocol yet.
Left side:
- Simulation parameters (amount segments, simulation time in months), initialisation for
biofilm biomass and abundances (x:y defines the range, e.g. increasing intial
abundance, if x = y every segmen has the same abundance)
- Button for intialize parameters (save parameters) and Button for run the model
- Number runs, Name Scenario, Path in which the output should be saved
- Simulation parameters (amount segments, simulation time in months), initialisation for biofilm biomass and abundances (x:y defines the range, e.g. increasing intial abundance, if x = y every segmen has the same abundance)
- Button for intialize parameters (save parameters) and Button for run the model
- Number runs, Name Scenario, Path in which the output should be saved
Middle:
- Environmental parameters: air temperature, land use profile by defining land use types
for each segment (options: individual by A-F, sequence (Holtemme), load file),
minimum nutrient factor (min eN)
- Biofilm parameters (growth rate, B0) and compartments (epsilon, my), Eutrophication
parameters (thresholds beta0 and beta 1, pfmax, betaf)
- Species characteristics: Mortality(mortality rates, scale, drift mortality), Reproduction
(offspring, dispersal probability and distances)
- Trohic interaction
- Environmental parameters: air temperature, land use profile by defining land use types for each segment (options: individual by A-F, sequence (Holtemme), load file), minimum nutrient factor (min eN)
- Biofilm parameters (growth rate, B0) and compartments (epsilon, my), Eutrophication parameters (thresholds beta0 and beta 1, pfmax, betaf)
- Species characteristics: Mortality(mortality rates, scale, drift mortality), Reproduction (offspring, dispersal probability and distances)
- Trohic interaction
Right side:
- Stressors: constant input of herbicides and insecticides in segments with agriculture and
WWTP, input of pesticides by event
- Output Files (see OUTPUT/RESULT FILES)
- Stressors: constant input of herbicides and insecticides in segments with agriculture and WWTP, input of pesticides by event
- Output Files (see OUTPUT/RESULT FILES)
Table (lower right):
- segment specific parameters (number, land use type, maximal shading factor, epsilon, my,
drift mortality, nutrient factor, biofilm biomass, abundance for each species,
constant herbicide/insecticide input, beta1)
-> double-click: change a parameter in a segment individually
- segment specific parameters (number, land use type, maximal shading factor, epsilon, my, drift mortality, nutrient factor, biofilm biomass, abundance for each species, constant herbicide/insecticide input, beta1)
-> double-click: change a parameter in a segment individually
RUNNING
## RUNNING
Single scenario: choose tab single scenario, press 'Initialize Parameter' and afterwards 'Run Model'
Single scenario:
> Choose tab single scenario, press 'Initialize Parameter' and afterwards 'Run Model'
Multiple scenario (e.g. sensitive analysis): Define parameter variation in MainController.java
method onButtonClickvaryPar(). Choose tab multiple scenarios and define scenario name and path.
Decide if result files should be filtered by coexistence of species or/and rangeof abundance.
Press Run multiple.
Multiple scenario (e.g. sensitive analysis):
>Define parameter variation in MainController.java method onButtonClickvaryPar(). Choose tab multiple scenarios and define scenario name and path. Decide if result files should be filtered by coexistence of species or/and rangeof abundance. Press Run multiple.
OUTPUT/RESULT FILES
## OUTPUT/RESULT FILES
Output files could be choosen on the mid right. Possible are air temperature, water temperature,
biofilm biomass, biofilm condition, probability of filamentous algae (pf), abundance of each species,
demand of each species, Available feed, inflow and outflow of organisms, dispersal loss, abundance
in biomass, diffusive herbicide and insecticides, event herbicide and insecticides.
You can find result files starting with .jar in MODEL_MASTIFF\Data\Results
Output files could be choosen on the mid right. Possible are air temperature, water temperature, biofilm biomass, biofilm condition, probability of filamentous algae (pf), abundance of each species, demand of each species, Available feed, inflow and outflow of organisms, dispersal loss, abundance in biomass, diffusive herbicide and insecticides, event herbicide and insecticides.
You can find result files starting with [.jar](https://git.ufz.de/oesa/mastiff/-/blob/main/runMASTIFF.jar) in MODEL_MASTIFF\Data\Results
You can find result files starting manually in MODEL_MASTIFF\Mastiff\Java model project\data\Results
NOTE
## NOTE
A few options/function shown in GUI are implemented and tested but not relevant for publications and
not mentioned in ODD. For further studies interfaces are build (e.g. predator 'Stonefly' eating on
grazers, pesticide module) but not coupled or tested sufficiently.
A few options/function shown in GUI are implemented and tested but not relevant for publications and not mentioned in ODD. For further studies interfaces are build (e.g. predator 'Stonefly' eating on grazers, pesticide module) but not coupled or tested sufficiently.
## ODD protocol
A complete, detailed model description, following the ODD protocall is provided [here](https://git.ufz.de/oesa/mastiff/-/blob/main/Model%20description.pdf).
<img src="Mastiff/Java model project/src/application/Icon_Mastiff2.png" width = 100>
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