DEPONS 3.0

DEPONS.rs/repast.simphony.action.data_set_14.xml

@@ -56,6 +56,14 @@
         <methodName>getReceivedSoundLevel</methodName>
       </repast.simphony.data2.engine.MethodDataSourceDefinition>
     </entry>
+    <entry>
+      <string>sourceSoundLevel</string>
+      <repast.simphony.data2.engine.MethodDataSourceDefinition>
+        <id>sourceSoundLevel</id>
+        <className>dk.au.bios.porpoise.Hydrophone</className>
+        <methodName>getSourceSoundLevel</methodName>
+      </repast.simphony.data2.engine.MethodDataSourceDefinition>
+    </entry>
   </methodDataSources>
   <countSources class="linked-hash-map"/>
   <customNADataSources class="linked-hash-map"/>

DEPONS.rs/repast.simphony.action.data_set_2.xml

@@ -80,6 +80,14 @@
         <methodName>getDeterStrength</methodName>
       </repast.simphony.data2.engine.MethodDataSourceDefinition>
     </entry>
+    <entry>
+      <string>LoudestShipSPL</string>
+      <repast.simphony.data2.engine.MethodDataSourceDefinition>
+        <id>LoudestShipSPL</id>
+        <className>dk.au.bios.porpoise.RandomPorpoiseReportProxy</className>
+        <methodName>getLoudestShipSPL</methodName>
+      </repast.simphony.data2.engine.MethodDataSourceDefinition>
+    </entry>
     <entry>
       <string>EnergyLevel</string>
       <repast.simphony.data2.engine.MethodDataSourceDefinition>

DEPONS.rs/repast.simphony.action.file_sink_15.xml

@@ -10,6 +10,7 @@
     <string>UtmY</string>
     <string>EnergyLevel</string>
     <string>DeterStrength</string>
+    <string>LoudestShipSPL</string>
     <string>DispersalMode</string>
     <string>PSMActive</string>
     <string>PSMTargetUtmX</string>

DEPONS.rs/repast.simphony.action.file_sink_18.xml

@@ -6,6 +6,7 @@
   <sourceIds class="linked-hash-set">
     <string>tick</string>
     <string>name</string>
+    <string>sourceSoundLevel</string>
     <string>receivedSoundLevel</string>
     <string>shipName</string>
     <string>shipUtmX</string>

README.md

@@ -1,8 +1,35 @@
-# DEPONS 2.3
-Simulating effects of disturbances on harbour porpoises in the North Sea.
+# DEPONS
+Simulating effects of disturbances on harbour porpoises in the North
+Sea.
 
-This is the second public version of the DEPONS model for simulation of population effects of noise for the harbour porpoise. Version 2.3 differs from version 2.2 in making it possible to simulate ship movements based on automatic identification system data (AIS) or based on user defined ship routes. Sound source levels now depend on ship speed, length and type in to make sound emission realistic. Sound transmission loss is based on power laws, and will be made more realistic in the next version of DEPONS. Harbour porpoise fine scale movements are calibrated based on animals tagged in the North Sea (see TRACE document for details).
+This is the third public version of the DEPONS model for simulating
+population effects of noise for the harbour porpoise. Version 3.0 differs
+from version 2.3 in making it possible to simulate the population impact
+of noise from ships, where sound emission from ships is related to the
+speed, length and type of the ships. Ship movements are defined by the
+user (potentially based on AIS data). Sound transmission loss is related
+to bathymetry and sediment type. Harbour porpoise fine scale
+movements are calibrated based on animals tagged in the North Sea,
+and their deterrence behaviour is related to both distance to ships and
+received sound levels, as observed for tagged animals (see TRACE
+document for details).
 
-The objective of the DEPONS model is to simulate how harbour porpoise population dynamics are affected by pile-driving noise associated with construction of offshore wind farms. The animals’ survival is directly related to their energy levels, and the population dynamics are affected by noise through its impact on the animals’ foraging behaviour. By ensuring that the animals’ movement patterns, space use and reactions to noise are realistic, the population dynamics in the model have the same causal drivers in the model as in nature.
+The objective of the DEPONS model is to simulate how harbour
+porpoise population dynamics are affected by disturbances, and was
+first developed to simulate effects of pile-driving noise associated with
+construction of offshore wind farms. Now it facilitates studies of
+cumulative impacts of pile-driving noise and ship noise. The animals’
+survival is directly related to their energy levels, and the population
+dynamics are affected by noise through its impact on the animals’
+foraging behaviour. By ensuring that the animals’ movement patterns,
+space use and reactions to noise are realistic, the population dynamics
+in the model have the same causal drivers in the model as in nature.
 
-The model was developed as part of the DEPONS project (Disturbance Effects of POrpoises in the North Sea) at Aarhus University, Denmark. The code was developed in Eclipse/Repast, and must be installed under this framework. See http://www.depons.dk or contact Jacob Nabe-Nielsen (jnn@ecos.au.dk) for more information.
+The model was developed as part of the DEPONS project (Disturbance
+Effects of POrpoises in the North Sea) at Aarhus University, Denmark.
+The extension that enabled simulations of responses to ships was part
+of the SATURN project (EU Horizon 2020; GA 101006443 ). The code
+was developed in Eclipse/Repast, and must be installed under this
+framework. See http://www.depons.dk or contact Jacob Nabe-Nielsen
+(jnn@ecos.au.dk) for more information.
+Simulating effects of disturbances on harbour porpoises in the North Sea.

Repast.settings

@@ -3,10 +3,12 @@
   <hashtable>
     <default>
       <loadFactor>0.75</loadFactor>
-      <threshold>8</threshold>
+      <threshold>3</threshold>
     </default>
-    <int>11</int>
-    <int>2</int>
+    <int>5</int>
+    <int>3</int>
+    <string>SettingsFileName</string>
+    <string>Repast.settings</string>
     <string>SettingsRegistryId</string>
     <string>Repast.registry</string>
     <string>LastLoadedScenario</string>

batch/batch_params.xml

@@ -1 +1 @@
-<?xml version="1.0" ?><sweep runs="1"><parameter name="Euse" type="constant" constant_type="double" value="4.5"></parameter><parameter name="tdisp" type="constant" constant_type="int" value="3"></parameter><parameter name="b0" type="constant" constant_type="double" value="-0.024"></parameter><parameter name="b1" type="constant" constant_type="double" value="-0.008"></parameter><parameter name="b2" type="constant" constant_type="double" value="0.93"></parameter><parameter name="b3" type="constant" constant_type="double" value="-14.0"></parameter><parameter name="simYears" type="constant" constant_type="int" value="50"></parameter><parameter name="Elact" type="constant" constant_type="double" value="1.4"></parameter><parameter name="tmating" type="constant" constant_type="java.lang.String" value="N(225;20)"></parameter><parameter name="bycatchProb" type="constant" constant_type="double" value="0.0"></parameter><parameter name="alpha_hat" type="constant" constant_type="java.lang.String" value="0.0"></parameter><parameter name="tmature" type="constant" constant_type="double" value="3.44"></parameter><parameter name="dmax_mov" type="constant" constant_type="double" value="1.73"></parameter><parameter name="R1" type="constant" constant_type="java.lang.String" value="N(1.25;0.15)"></parameter><parameter name="rR" type="constant" constant_type="double" value="0.04"></parameter><parameter name="tgest" type="constant" constant_type="int" value="300"></parameter><parameter name="R2" type="constant" constant_type="java.lang.String" value="N(0;4)"></parameter><parameter name="rS" type="constant" constant_type="double" value="0.04"></parameter><parameter name="T_ships" type="constant" constant_type="double" value="152.9"></parameter><parameter name="wdisp" type="constant" constant_type="double" value="4.0"></parameter><parameter name="rU" type="constant" constant_type="double" value="0.1"></parameter><parameter name="trackedPorpoiseCount" type="constant" constant_type="int" value="1"></parameter><parameter name="Einit" type="constant" constant_type="java.lang.String" value="N(10.0;1)"></parameter><parameter name="tnurs" type="constant" constant_type="int" value="240"></parameter><parameter name="tdeter" type="constant" constant_type="int" value="0"></parameter><parameter name="ships" type="constant" constant_type="boolean" value="false"></parameter><parameter name="beta_hat" type="constant" constant_type="java.lang.String" value="20.0"></parameter><parameter name="PSM_angle" type="constant" constant_type="double" value="20.0"></parameter><parameter name="ddisp" type="constant" constant_type="double" value="1.05"></parameter><parameter name="PSM_tol" type="constant" constant_type="double" value="5.0"></parameter><parameter name="RT" type="constant" constant_type="double" value="152.9"></parameter><parameter name="dispersal" type="constant" constant_type="java.lang.String" value="PSM-Type2"></parameter><parameter name="PSM_dist" type="constant" constant_type="java.lang.String" value="N(300;100)"></parameter><parameter name="Ewarm" type="constant" constant_type="double" value="1.3"></parameter><parameter name="wmin" type="constant" constant_type="double" value="1.0"></parameter><parameter name="PSM_log" type="constant" constant_type="java.lang.String" value="0.6"></parameter><parameter name="beta" type="constant" constant_type="double" value="0.4"></parameter><parameter name="dmax_deter" type="constant" constant_type="double" value="1000.0"></parameter><parameter name="q1" type="constant" constant_type="double" value="0.02"></parameter><parameter name="porpoiseCount" type="constant" constant_type="int" value="10000"></parameter><parameter name="Psi_deter" type="constant" constant_type="double" value="50.0"></parameter><parameter name="debug" type="constant" constant_type="int" value="0"></parameter><parameter name="c" type="constant" constant_type="double" value="0.07"></parameter><parameter name="turbines" type="constant" constant_type="java.lang.String" value="off"></parameter><parameter name="h" type="constant" constant_type="double" value="0.68"></parameter><parameter name="k" type="constant" constant_type="double" value="0.001"></parameter><parameter name="tmaxage" type="constant" constant_type="double" value="30.0"></parameter><parameter name="a0" type="constant" constant_type="double" value="0.35"></parameter><parameter name="a1" type="constant" constant_type="double" value="5.0E-4"></parameter><parameter name="a2" type="constant" constant_type="double" value="-0.02"></parameter><parameter name="c_ships" type="constant" constant_type="double" value="0.07"></parameter><parameter name="Umin" type="constant" constant_type="double" value="0.001"></parameter><parameter name="wrapBorderHomo" type="constant" constant_type="boolean" value="true"></parameter><parameter name="landscape" type="constant" constant_type="java.lang.String" value="NorthSea"></parameter></sweep>
+<?xml version="1.0" ?><sweep runs="1"><parameter name="Euse" type="constant" constant_type="java.lang.String" value="4.5"></parameter><parameter name="cship_noise_day" type="constant" constant_type="java.lang.String" value="0.0472709"></parameter><parameter name="tdisp" type="constant" constant_type="int" value="3"></parameter><parameter name="pship_dist_x_noise_day" type="constant" constant_type="java.lang.String" value="0.0293443"></parameter><parameter name="cship_noise_night" type="constant" constant_type="java.lang.String" value="0.0"></parameter><parameter name="b0" type="constant" constant_type="java.lang.String" value="-0.024"></parameter><parameter name="b1" type="constant" constant_type="java.lang.String" value="-0.008"></parameter><parameter name="dmin_deter_ships" type="constant" constant_type="java.lang.String" value="0.1"></parameter><parameter name="b2" type="constant" constant_type="java.lang.String" value="0.93"></parameter><parameter name="b3" type="constant" constant_type="java.lang.String" value="-14"></parameter><parameter name="simYears" type="constant" constant_type="int" value="50"></parameter><parameter name="Elact" type="constant" constant_type="java.lang.String" value="1.4"></parameter><parameter name="tmating" type="constant" constant_type="java.lang.String" value="N(225;20)"></parameter><parameter name="bycatchProb" type="constant" constant_type="java.lang.String" value="0.0"></parameter><parameter name="pship_noise_night" type="constant" constant_type="java.lang.String" value="0.0"></parameter><parameter name="alpha_hat" type="constant" constant_type="java.lang.String" value="0.0"></parameter><parameter name="tmature" type="constant" constant_type="java.lang.String" value="3.44"></parameter><parameter name="dmax_mov" type="constant" constant_type="java.lang.String" value="1.73"></parameter><parameter name="cship_int_day" type="constant" constant_type="java.lang.String" value="2.9647996"></parameter><parameter name="R1" type="constant" constant_type="java.lang.String" value="N(1.25;0.15)"></parameter><parameter name="rR" type="constant" constant_type="java.lang.String" value="0.04"></parameter><parameter name="cship_dist_night" type="constant" constant_type="java.lang.String" value="0.0284629"></parameter><parameter name="tgest" type="constant" constant_type="int" value="300"></parameter><parameter name="R2" type="constant" constant_type="java.lang.String" value="N(0;4)"></parameter><parameter name="rS" type="constant" constant_type="java.lang.String" value="0.04"></parameter><parameter name="wdisp" type="constant" constant_type="java.lang.String" value="4.0"></parameter><parameter name="rU" type="constant" constant_type="java.lang.String" value="0.1"></parameter><parameter name="pship_dist_day" type="constant" constant_type="java.lang.String" value="-0.1303880"></parameter><parameter name="trackedPorpoiseCount" type="constant" constant_type="int" value="1"></parameter><parameter name="Einit" type="constant" constant_type="java.lang.String" value="N(10.0;1)"></parameter><parameter name="tnurs" type="constant" constant_type="int" value="240"></parameter><parameter name="tdeter" type="constant" constant_type="int" value="0"></parameter><parameter name="ships" type="constant" constant_type="boolean" value="false"></parameter><parameter name="beta_hat" type="constant" constant_type="java.lang.String" value="20.0"></parameter><parameter name="PSM_angle" type="constant" constant_type="java.lang.String" value="20.0"></parameter><parameter name="ddisp" type="constant" constant_type="java.lang.String" value="1.05"></parameter><parameter name="cship_dist_x_noise_day" type="constant" constant_type="java.lang.String" value="0.0"></parameter><parameter name="PSM_tol" type="constant" constant_type="java.lang.String" value="5.0"></parameter><parameter name="RT" type="constant" constant_type="java.lang.String" value="152.9"></parameter><parameter name="dispersal" type="constant" constant_type="java.lang.String" value="PSM-Type2"></parameter><parameter name="PSM_dist" type="constant" constant_type="java.lang.String" value="N(300;100)"></parameter><parameter name="Ewarm" type="constant" constant_type="java.lang.String" value="1.3"></parameter><parameter name="cship_int_night" type="constant" constant_type="java.lang.String" value="2.7543376"></parameter><parameter name="wmin" type="constant" constant_type="java.lang.String" value="1.0"></parameter><parameter name="pship_dist_x_noise_night" type="constant" constant_type="java.lang.String" value="0.0"></parameter><parameter name="PSM_log" type="constant" constant_type="java.lang.String" value="0.6"></parameter><parameter name="pship_dist_night" type="constant" constant_type="java.lang.String" value="0.085242"></parameter><parameter name="pship_noise_day" type="constant" constant_type="java.lang.String" value="0.2172813"></parameter><parameter name="beta" type="constant" constant_type="java.lang.String" value="0.4"></parameter><parameter name="dmax_deter" type="constant" constant_type="java.lang.String" value="1000.0"></parameter><parameter name="porpoiseCount" type="constant" constant_type="int" value="10000"></parameter><parameter name="Psi_deter" type="constant" constant_type="java.lang.String" value="50.0"></parameter><parameter name="pship_int_day" type="constant" constant_type="java.lang.String" value="-3.0569351"></parameter><parameter name="debug" type="constant" constant_type="int" value="0"></parameter><parameter name="c" type="constant" constant_type="java.lang.String" value="0.07"></parameter><parameter name="turbines" type="constant" constant_type="java.lang.String" value="off"></parameter><parameter name="h" type="constant" constant_type="java.lang.String" value="0.68"></parameter><parameter name="k" type="constant" constant_type="java.lang.String" value="0.001"></parameter><parameter name="tmaxage" type="constant" constant_type="java.lang.String" value="30.0"></parameter><parameter name="a0" type="constant" constant_type="java.lang.String" value="0.35"></parameter><parameter name="a1" type="constant" constant_type="java.lang.String" value="0.0005"></parameter><parameter name="a2" type="constant" constant_type="java.lang.String" value="-0.02"></parameter><parameter name="cship_dist_x_noise_night" type="constant" constant_type="java.lang.String" value="0.0"></parameter><parameter name="cship_dist_day" type="constant" constant_type="java.lang.String" value="-0.0355541"></parameter><parameter name="Umin" type="constant" constant_type="java.lang.String" value="0.001"></parameter><parameter name="pship_int_night" type="constant" constant_type="java.lang.String" value="-3.233771"></parameter><parameter name="wrapBorderHomo" type="constant" constant_type="boolean" value="true"></parameter><parameter name="landscape" type="constant" constant_type="java.lang.String" value="NorthSea"></parameter></sweep>