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added habitat example
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‎example-configs/habitat/habitat.xml‎

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<par version="1.0">
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<!--==================== -->
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<!--SIMULATION PARAMETERS-->
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<!--==================== -->
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<latitudeMin value="-25.0"/>
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<latitudeMax value="25.0"/>
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<longitudeMin value="155.0"/>
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<longitudeMax value="255.0"/>
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<nb_layer value="3"/>
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<deltaX value="120"/>
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<deltaY value="120"/>
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<deltaT value="30"/>
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<iterationNumber value="15"/>
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<save_first_date year="2000" month="1"/>
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<save_last_date year="2000" month="12"/>
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<nb_step_to_skip value="0"/>
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<!--===================-->
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<!--HABITAT SIMULATIONS-->
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<!--===================-->
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<!--0 - spawning_habitat, 1 - feeding habitat (give age in months)-->
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<habitat_run type="0" nb_ages="1"/>
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<!--If spawning_habitat run, ages are ignored-->
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<habitat_run_ages>2 3</habitat_run_ages>
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<!--==================== -->
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<!--LIKELIHOOD PARAMETERS-->
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<!--==================== -->
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<!--Written automatically in the newparfile.xml at the end of simulation-->
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<total_likelihood value="3366.679019188437"/>
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<!--DATA IN THE LIKELIHOOD:-->
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<!--LENGTH frequencies likelihood: 0 - do not take into account, 1 - account-->
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<frq_likelihood msp="0"/>
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<!--Likelihood functions: 1 - concentrated, 2 - log-normal, 3 - poisson, 4 - negative binomial, 5 - zero-inflated negbin, 6 - truncated poisson -->
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<!--can be different for each fishery (see below the fishery codes) -->
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<likelihood_types>
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<msp>3</msp>
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</likelihood_types>
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<!--==================== -->
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<!--FISHERIES DEFINITIONS-->
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<!--==================== -->
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<nb_fishery value="1"/>
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<list_fishery_name>F1</list_fishery_name>
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<!--1 - C in metric tones; 0 - C in numbers -->
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<fishery_catch_units>1</fishery_catch_units>
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<!--The resolution coarser than model grid, to be used for all fisheries-->
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<degrade_fishery_reso_deg value="5"/>
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<!--Mask for fishery data usage: 0 - do not take into account-->
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<mask_fishery_sp>
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<msp>1</msp>
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<!--<msp>0</msp>-->
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</mask_fishery_sp>
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<!--Fisheries without effort data (flagged 1) are to be accounted with catch removal method-->
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<mask_fishery_no_effort>
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<msp>0</msp>
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</mask_fishery_no_effort>
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<!--To exclude fishery from likelihood computation, flag it with 0, otherwise keep 1-->
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<mask_fishery_likelihood>
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<msp>1</msp>
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</mask_fishery_likelihood>
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<!--================= -->
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<!--MODEL INPUT-OUTPUT-->
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<!--================= -->
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<!-- Forcing Directory -->
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<strdir value="./input/"/>
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<!--Land mask and topo index files-->
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<str_file_mask value="mask.txt"/>
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<str_file_topo value="topo.txt"/>
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<!--Micronekton Files Sub-folder in Forcing Directory-->
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<strdir_forage value="forage/"/>
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<!--Forcing variables and file names-->
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<strfile_pp value="tpo_2x30d_pp.dym"/>
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<strfile_sst value="tpo_2x30d_sst.dym"/>
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<strfile_vld value="tpo_2x30d_zeu.dym"/>
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<strfile_u layer0="tpo_2x30d_U_L1.dym" layer1="tpo_2x30d_U_L2.dym" layer2="tpo_2x30d_U_L3.dym"/>
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<strfile_v layer0="tpo_2x30d_V_L1.dym" layer1="tpo_2x30d_V_L2.dym" layer2="tpo_2x30d_V_L3.dym"/>
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<strfile_t layer0="tpo_2x30d_T_L1.dym" layer1="tpo_2x30d_T_L2.dym" layer2="tpo_2x30d_T_L3.dym"/>
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<!--type of oxygen data: 0 for time series, 1 - for monthly, 2 for seasonal-->
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<type_oxy value="1"/>
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<strfile_oxy layer0="tpo_2x30d_O2_L1_CLM.dym" layer1="tpo_2x30d_O2_L2_CLM.dym" layer2="tpo_2x30d_O2_L3_CLM.dym"/>
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<!--Fisheries Data Directory-->
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<strdir_fisheries value="input/no-data"/>
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<!-- Output Directory and writing flags-->
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<strdir_output value="output/"/>
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<!--====================== -->
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<!--FORAGE MODEL PARAMETERS-->
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<!--====================== -->
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<Tr_max value="450"/>
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<Tr_exp value="-0.1"/>
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<inv_lambda_max value="1825"/>
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<inv_lambda_curv value="-0.1"/>
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<E value="0.00316"/>
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<c_pp value="0.0948"/>
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<nb_forage value="6"/>
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<frg_name>epi meso mmeso bathy mbathy hmbathy</frg_name>
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<source_frg epi="0.08" meso="0.17" mmeso="0.08" bathy="0.56" mbathy="0.07" hmbathy="0.04"/>
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<day_layer epi="0" meso="1" mmeso="1" bathy="2" mbathy="2" hmbathy="2"/>
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<night_layer epi="0" meso="1" mmeso="0" bathy="2" mbathy="1" hmbathy="0"/>
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<tstep_forage value="30"/>
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<sigma_fcte value="10"/>
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<max_NPP value="200"/>
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<b_F_habitat value="20000"/>
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<!-- daily food ration -->
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<forage_ration msp="0.06"/>
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<!--===========================================-->
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<!--PREDATOR MODEL AGE and LIFE STAGE STRUCTURE-->
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<!--===========================================-->
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<nb_species value="1"/>
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<sp_name>msp</sp_name>
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<nb_life_stages msp="3"/>
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<life_stage>
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<msp>larvae juvenile adult</msp>
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</life_stage>
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<nb_cohort_life_stage>
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<msp>1 2 7</msp>
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</nb_cohort_life_stage>
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<age_recruit msp="3"/>
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<age_mature msp="5"/>
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<sp_unit_cohort>
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<msp> 30 30 30 30 30 30 30 30 30 810</msp>
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</sp_unit_cohort>
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<length>
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<msp>0.5 1.5 2.5 3.5 4.5 5.5 6.5 7.5 8.5 22.5</msp>
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</length>
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<weight>
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<msp>0.001 0.008 0.027 0.064 0.125 0.216 0.343 0.512 0.729 11.4 </msp>
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</weight>
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<!--======================== -->
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<!--PREDATOR MODEL PARAMETERS-->
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<!--======================== -->
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<!--=== 1. Available OPTIONS =====-->
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<!--=== 2. Spawning habitat parameters =======-->
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<a_sst_larvae msp="1.5">
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<variable min="0.5" max="2.5" use="false"/>
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</a_sst_larvae>
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<b_sst_larvae msp="28.5">
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<variable min="28.0" max="30.0" use="false"/>
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</b_sst_larvae>
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<a_sst_spawning msp="2.0">
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<variable min="0.0" max="3.0" use="true"/>
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</a_sst_spawning>
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<b_sst_spawning msp="25.0">
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<variable min="20.0" max="31.0" use="true"/>
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</b_sst_spawning>
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<alpha_hsp_prey msp="0.005">
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<variable min="0.0" max="1.0" use="true"/>
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</alpha_hsp_prey>
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<alpha_hsp_predator msp="0.1">
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<variable min="0.0" max="2.5" use="true"/>
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</alpha_hsp_predator>
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<beta_hsp_predator msp="1.5">
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<variable min="0.0" max="3.0" use="true"/>
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</beta_hsp_predator>
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<!--=== end of Spawning habitat parameters =====-->
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<!--=== 3. Recruitment function =============-->
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<nb_recruitment msp="0.1">
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<variable min="0.005" max="0.1" use="false"/>
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</nb_recruitment>
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<a_adults_spawning msp="0.5">
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<variable min="0.005" max="0.5" use="false"/>
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</a_adults_spawning>
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<!--=== end of Recruitment function ===========-->
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<!--=== 4. Juvenile habitat parameters =========-->
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<hp_cannibalism msp="0.0">
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<variable min="0.002" max="0.3" use="false"/>
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</hp_cannibalism>
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<!--=== end of Juvenile habitat parameters =====-->
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<!--=== 5. Adult seasonal migrations ===========-->
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<spawning_season_peak msp="120">
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<variable min="0" max="360" use="false"/>
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</spawning_season_peak>
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<spawning_season_start msp="1.15">
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<variable min="1.0" max="1.5" use="false"/>
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</spawning_season_start>
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<!--=== end of Adult seasonal migrations =======-->
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<a_sst_habitat msp="3.0">
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<variable min="1.0" max="5.0" use="false"/>
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</a_sst_habitat>
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<!--=== 6. Adult feeding habitat ===============-->
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<b_sst_habitat msp="20.0">
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<variable min="18.0" max="26.0" use="false"/>
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</b_sst_habitat>
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<T_age_size_slope msp="2.5">
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<variable min="0.5" max="3.0" use="false"/>
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</T_age_size_slope>
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<thermal_func>
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<delta1 skj="0.04">
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<variable min="0.0" max="0.05" use="false"/>
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</delta1>
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<delta2 skj="0.015">
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<variable min="0.0" max="0.25" use="false"/>
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</delta2>
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<delta3 skj="0.25">
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<variable min="0.0" max="10.0" use="false"/>
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</delta3>
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</thermal_func>
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<a_oxy_habitat msp="0.0001">
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<variable min="0.0" max="0.1" use="false"/>
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</a_oxy_habitat>
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<b_oxy_habitat msp="3.0">
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<variable min="1.0" max="4.0" use="false"/>
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</b_oxy_habitat>
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<eF_habitat>
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<epi msp="1.0">
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<variable min="0.0" max="4.0" use="false"/>
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</epi>
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<meso msp="1.0">
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<variable min="0.0" max="4.0" use="false"/>
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</meso>
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<mmeso msp="1.0">
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<variable min="0.0" max="2.0" use="false"/>
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</mmeso>
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<bathy msp="0.0">
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<variable min="0.0" max="1.0" use="false"/>
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</bathy>
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<mbathy msp="0.0">
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<variable min="0.0" max="1.0" use="false"/>
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</mbathy>
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<hmbathy msp="1.0">
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<variable min="0.0" max="4.0" use="false"/>
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</hmbathy>
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</eF_habitat>
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<!--=== end of Adult feeding habitat ===========-->
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<!--=== 7. Movement parameters ==============-->
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<sigma_species msp="4.0">
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<variable min="0.0001" max="5" use="false"/>
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</sigma_species>
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<c_diff_fish msp="0.9">
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<variable min="0.1" max="1.0" use="false"/>
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</c_diff_fish>
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<MSS_species msp="0.5">
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<variable min="0.0" max="5.0" use="false"/>
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</MSS_species>
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<MSS_size_slope msp="0.43">
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<variable min="0.4" max="1.15" use="false"/>
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</MSS_size_slope>
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<!--=== end of Movement parameters ==========-->
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<!--=== 8. Mortality parameters ==============-->
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<Mp_mean_max msp="0.25">
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<variable min="0.0" max="0.5" use="false"/>
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</Mp_mean_max>
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<Mp_mean_exp msp="0.05">
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<variable min="0.0" max="0.5" use="false"/>
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</Mp_mean_exp>
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<Ms_mean_max msp="0.004">
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<variable min="0.0" max="0.01" use="false"/>
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</Ms_mean_max>
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<Ms_mean_slope msp="1.1">
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<variable min="0.5" max="2.0" use="false"/>
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</Ms_mean_slope>
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<M_mean_range msp="0.0">
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<variable min="0.0" max="2.0" use="false"/>
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</M_mean_range>
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<!--=== end of Mortality parameters ===========-->
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<!--========================== -->
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<!-- FISHERY PARAMETERS -->
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<!--========================== -->
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<q_sp_fishery>
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<variables use="false"/>
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<F1 msp="0.001">
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<variable min="0.0" max="0.1" use="true" dyn="0.0"/>
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</F1>
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</q_sp_fishery>
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<!--selectivities as functions of length-->
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<!--1 - logistic, 1 parameter: main parameter is used as a slope coefficient-->
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<!--2 - sigmoid, 2 parameters: main parameter as slope coefficient + length_threshold-->
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<!--3 - asymmetric Gaussian, 3 parameters: length_threshold as optimal value, main as sigma, right_asymptote as the function min on the right -->
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<s_sp_fishery>
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<variables use="false"/>
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<F1 msp="5.0">
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<variable min="0.05" max="20.0" use="true"/>
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<function_type value="3"/>
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<length_threshold msp="15.0" use="true"/>
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<right_asymptote msp="0.5" min="0.0" max="1" use="true"/>
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</F1>
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</s_sp_fishery>
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<!--================ -->
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<!--AGGREGATION ZONES-->
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<!--================ -->
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<nb_region value="1"/>
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<use_mask_catch value="0"/>
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<area0 area_id="1" lgmin="170" lgmax="210" ltmin="-20" ltmax="20"/>
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<nb_region_sp_B msp="1"/>
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<area_sp_B>
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<msp>1</msp>
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</area_sp_B>
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<nb_EEZ value="0"/>
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<!-- Negative binomial likelihood parameters. Used only and only for those fisheries, for which the Negbin-like is set up in likelihood types -->
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<likelihood_parameters>
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<variables use="false"/>
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<F1 msp="0.0"/>
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</likelihood_parameters>
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<prob_zero>
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<F1 msp="0.0"/>
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</prob_zero>
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</par>

‎example-configs/habitat/input/forage/Fbiom_bathy.dym‎

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‎example-configs/habitat/input/forage/Fbiom_epi.dym‎

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‎example-configs/habitat/input/forage/Fbiom_hmbathy.dym‎

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‎example-configs/habitat/input/forage/Fbiom_mbathy.dym‎

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‎example-configs/habitat/input/forage/Fbiom_meso.dym‎

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‎example-configs/habitat/input/forage/Fbiom_mmeso.dym‎

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