Combined Dredge, Habcam. Synch Mac, Win

.octaverc

@@ -1,3 +1,4 @@
+warning('off', 'Octave:shadowed-function');
 addpath mfiles/
 addpath mfiles/latlonutm/
 addpath PreProcess/

Configuration/Interpolation/UK.cfg

@@ -1,23 +1,23 @@
-# Set inputs for universal kriging
-Kriging variogram form = spherical
-#
-# Configuration files are expected to be in the Configuration directory
-#
-NLS Spatial Fcn File Name = SpatialFcns.cfg
-#
-# Save interim data by writing out supporting data files
-#
-Save Data = F
-#
-# Interpolation can sometimes create excessively large values.
-# To bypass, Use Saturate can be T or F, but set a larger threshold, i.e. 1E309 (Infinity).
-# The user can choose to saturate to the threshold, (T), or 
-# reset the value to 0.0 when exceeded, (F).
-#
-Use Saturate = F
-#
-# Threshold value to use
-# Use Saturate = T, if field > Threshold then field = Threshold
-# Use Saturate = F, if field > Threshold then field = 0.0
-#
-Overflow Threshold = 1E10
+# Set inputs for universal kriging
+Kriging variogram form = spherical
+#
+# Configuration files are expected to be in the Configuration directory
+#
+NLS Spatial Fcn File Name = SpatialFcns.cfg
+#
+# Save interim data by writing out supporting data files
+#
+Save Data = F
+#
+# Interpolation can sometimes create excessively large values.
+# To bypass, Use Saturate can be T or F, but set a larger threshold, i.e. 1E309 (Infinity).
+# The user can choose to saturate to the threshold, (T), or 
+# reset the value to 0.0 when exceeded, (F).
+#
+Use Saturate = F
+#
+# Threshold value to use
+# Use Saturate = T, if field > Threshold then field = Threshold
+# Use Saturate = F, if field > Threshold then field = 0.0
+#
+Overflow Threshold = 1E10

Configuration/Simulation/GridManager.cfg

@@ -1,6 +1,6 @@
-# configuration file for GridManager
-# The following is the file name with corner coordinates associated with Special Access Areas.
-# If not used then set to NONE or comment out line
-# NOTE: Setting to NONE will also cause Mortality to not read in
-# its special access fishing mortalities and default Fishing Mortalities are used.
-Special Access Config File = SpecialAreas.csv
+# configuration file for GridManager
+# The following is the file name with corner coordinates associated with Special Access Areas.
+# If not used then set to NONE or comment out line
+# NOTE: Setting to NONE will also cause Mortality to not read in
+# its special access fishing mortalities and default Fishing Mortalities are used.
+Special Access Config File = SpecialAreas.csv

Configuration/Simulation/Growth.cfg

@@ -1,35 +1,35 @@
-# Was configuration file for mortality
-# Actually contains parameters that define both Growth and Mortality
-#
-Fishing Mortality = 0.4
-# Fishing Mortality proportional to LPUE^alpha
-Alpha Mortality = 1.0
-MA Cull size = 90.0
-MA Discard = 0.2
-GB Cull size = 100.0
-GB Discard = 0.2
-# increasing logistic function
-MA FSelectA = 20.5079
-MA FSelectB = 0.19845
-GB Closed FSelectA = 17.72
-GB Closed FSelectB = 0.15795
-GB Open FSelectA = 21.7345
-GB Open FSelectB = 0.2193
-# Natural adult mortality
-MA Adult Mortality = 0.25
-GB Adult Mortality = 0.2
-MA Incidental = 0.05
-GB Incidental = 0.1
-MA Length_0 = 65.0
-GB Length_0 = 70.0
-# special area fishing mortalities
-# if not used set to NONE
-Fishing Mortality File = FishingMortality.csv
-# Used to compute LPUE
-LPUE Slope = 0.6556
-LPUE Slope2 = 2.3
-LPUE Intercept = 1094 # slope and intercept of regression
-Max Per Day = 56000  # max scallops shucked per day
-Max Time = 19  # Max hours dredging per day  
-Dredge Width = 9.144    # average total dredge width meters
-Towing Speed = 4.8  # knots, mean towing speed
+# Was configuration file for mortality
+# Actually contains parameters that define both Growth and Mortality
+#
+Fishing Mortality = 0.4
+# Fishing Mortality proportional to LPUE^alpha
+Alpha Mortality = 1.0
+MA Cull size = 90.0
+MA Discard = 0.2
+GB Cull size = 100.0
+GB Discard = 0.2
+# increasing logistic function
+MA FSelectA = 20.5079
+MA FSelectB = 0.19845
+GB Closed FSelectA = 17.72
+GB Closed FSelectB = 0.15795
+GB Open FSelectA = 21.7345
+GB Open FSelectB = 0.2193
+# Natural adult mortality
+MA Adult Mortality = 0.25
+GB Adult Mortality = 0.2
+MA Incidental = 0.05
+GB Incidental = 0.1
+MA Length_0 = 65.0
+GB Length_0 = 70.0
+# special area fishing mortalities
+# if not used set to NONE
+Fishing Mortality File = FishingMortality.csv
+# Used to compute LPUE
+LPUE Slope = 0.6556
+LPUE Slope2 = 2.3
+LPUE Intercept = 1094 # slope and intercept of regression
+Max Per Day = 56000  # max scallops shucked per day
+Max Time = 19  # Max hours dredging per day  
+Dredge Width = 9.144    # average total dredge width meters
+Towing Speed = 4.8  # knots, mean towing speed

Configuration/Simulation/Recruitment.cfg

@@ -1,3 +1,3 @@
-# configuration file for Recruitment
-Start Period = 0  # Jan 1 is 0
-Stop Period = 100 # converted to fraction of year, i.e. /365
+# configuration file for Recruitment
+Start Period = 0  # Jan 1 is 0
+Stop Period = 100 # converted to fraction of year, i.e. /365

Configuration/Simulation/Scallop.cfg

@@ -1,20 +1,18 @@
-# input file for Scallops 
-Time steps per Year = 13
-Save By Stratum = T
-Use HabCam Data = T
-# Configuration files are expected to be in the Configuration directory
-Mortality Config File = Growth.cfg
-Recruit Config File = Recruitment.cfg
-Grid Manager Config File = GridManager.cfg
-# The following items determine the parameters for output and plotting
-# One need only select the desired parameters, the default is to not show them
-# Anything after = is ignored.
-Select Abundance          =# ABUN abundance scallops per square meter
-Select BMS                =# BMMT biomass in metric tons
-Select Expl BMS           =# EBMS exploitable biomass in metric tons
-Select Fishing Effort     =# FEFF Fishing Effort
-Select Fishing Mortality  =# FMOR Fishing Mortality
-Select Landings by Number =# LAND Landings by number of scallops
-Select Landings by Weight =# LNDW Landings by weight in grams
-Select LPUE               =# LPUE Landing Per Unit Effort, (per day)
-Select RECR               =# Recruitment
+# input file for Scallops 
+Time steps per Year = 13
+# Configuration files are expected to be in the Configuration directory
+Mortality Config File = Growth.cfg
+Recruit Config File = Recruitment.cfg
+Grid Manager Config File = GridManager.cfg
+# The following items determine the parameters for output and plotting
+# One need only select the desired parameters, the default is to not show them
+# Anything after = is ignored.
+Select Abundance          =# ABUN abundance scallops per square meter
+Select BMS                =# BMMT biomass in metric tons
+Select Expl BMS           =# EBMS exploitable biomass in metric tons
+Select Fishing Effort     =# FEFF Fishing Effort
+Select Fishing Mortality  =# FMOR Fishing Mortality
+Select Landings by Number =# LAND Landings by number of scallops
+Select Landings by Weight =# LNDW Landings by weight in grams
+Select LPUE               =# LPUE Landing Per Unit Effort, (per day)
+Select RECR               =# Recruitment