1.6.1 Release for Linux

• Fixed bug with Competition matrix not behaving exactly the same as Predation matrix
• Fixed bug with blanks sometimes written to fit to catch table
• Fixed bug with nmfDatabase::loadMatrix loading in column major order instead of row major when creating simulated biomass
• Fixed bug with paste sometimes omitting the last copied row (happened when pasting from a non-downloaded google spreadsheet)

1.6.0 Release for Windows

• Fixed bug with estimated parameter matrices being read col major instead of row major
• Fixed single estimation run with fixed seed resulting in different estimated parameters than when running a multi-run with same seed
• Fixed diagnostic bug due to precision error
• Fixed Run Summary not correct for multi-runs
• Fixed output estimated Cov Coeff numbers not being correct
• Fixed output SurveyQ values not being displayed with proper EE format
• Fixed output MSY tables not updated for multi-runs
• Fixed estimation checkboxes not working
• Fixed 3d plot not rescaling properly
• Fixed bug with Multi-Run when ”Using All” not working
• Fixed bug with stopping a Mohn’s Rhos causing the timer to get messed up
• Modified check logic to relax error if B0 > Kmin and make it only a warning
• Modified Load Est button to copy all the matrix parameters (i.e. predation, covariates) as well as the vector parameters
• Modified database. If updating table manually do the following, else import the latest sample database:
  -- alter table models add column LogScale int NULL after MinimizerType;
  -- alter table models add column Seed int NULL after Scaling;
• Added Log Scale to the multi-run data file
• Added functionality to save Log Scale with models file as well
• Added legend toggle for plots
• Added convergence information and tolerance value to the Run Summary
• Added functionality to copy estimated values to input data tables for local algorithm usage
• Added checkbox to only allow converged sub-runs in a multi-run
• Added log scale option in Scaling Algorithm combo box (and functionality)
• Added more troubleshooting questions/answers for what to do about poor estimation fits
• Added functionality to move columns in ModelReview
• Added right-click (context) menu to ModelReview with items: Hide Row(s), Show Row(s), and Delete Row(s)
• Added new function to MSSPMConversion r package to convert sim’d biomass data to MSSPM format

1.6.0 Release for Linux

• Fixed bug with estimated parameter matrices being read col major instead of row major
• Fixed single estimation run with fixed seed resulting in different estimated parameters than when running a multi-run with same seed
• Fixed diagnostic bug due to precision error
• Fixed Run Summary not correct for multi-runs
• Fixed output estimated Cov Coeff numbers not being correct
• Fixed output SurveyQ values not being displayed with proper EE format
• Fixed output MSY tables not updated for multi-runs
• Fixed estimation checkboxes not working
• Fixed 3d plot not rescaling properly
• Fixed bug with Multi-Run when ”Using All” not working
• Fixed bug with stopping a Mohn’s Rhos causing the timer to get messed up
• Modified check logic to relax error if B0 > Kmin and make it only a warning
• Modified Load Est button to copy all the matrix parameters (i.e. predation, covariates) as well as the vector parameters
• Modified database. If updating table manually do the following, else import the latest sample database:
  -- alter table models add column LogScale int NULL after MinimizerType;
  -- alter table models add column Seed int NULL after Scaling;
• Added Log Scale to the multi-run data file
• Added functionality to save Log Scale with models file as well
• Added legend toggle for plots
• Added convergence information and tolerance value to the Run Summary
• Added functionality to copy estimated values to input data tables for local algorithm usage
• Added checkbox to only allow converged sub-runs in a multi-run
• Added log scale option in Scaling Algorithm combo box (and functionality)
• Added more troubleshooting questions/answers for what to do about poor estimation fits
• Added functionality to move columns in ModelReview
• Added right-click (context) menu to ModelReview with items: Hide Row(s), Show Row(s), and Delete Row(s)
• Added new function to MSSPMConversion r package to convert sim’d biomass data to MSSPM format

1.5.1 Release for Windows

• Fixed stop button not stopping an estimation properly
• Fixed enable-ness issue with estimation checkboxes causing predation to not estimate in multi-runs
• Added seed spin box and allow user to set a specific seed value per run
• Added seed functionality to multi-runs (user designates one fixed seed or an incremented seed)

1.5.1 Release for Linux

• Fixed stop button not stopping an estimation properly
• Fixed enable-ness issue with estimation checkboxes causing predation to not estimate in multi-runs
• Added seed spin box and allow user to set a specific seed value per run
• Added seed functionality to multi-runs (user designates one fixed seed or an incremented seed)

1.5.0 Release for Windows

Prior to running, please:

1. Resave current model by clicking save in Setup -> Model Setup tab
2. Confirm that the appropriate parameters are checked on Estimation Data Input -> Run Estimation tab

Release Notes

• Added log scaling checkbox for parameters ranges (i.e., log prior to estimation and exponentiated post estimation)
• Added logic to handle case of range having a 0 (use 1e-20 under the covers); it won’t work with log scaling
• Added user notification when model converges
• Added tolerance label so user can see which algorithms abide by tolerance stop value
• Added default button to set the default tolerance to 1E-06
• Fixed "Load Model" button behavior on Estimation Tab 8 (doesn’t auto switch to run page after loading)
• Fixed predation matrix on input having different orientation than that of output (should be predators across and prey down)
• Fixed state and enable-ness of Estimation Tab7 checkboxes
• Fixed check if any Predation/Competition initial values are outside ranges
• Fixed multi-runs not recognizing the new stop tolerance

1.5.0 Release for Linux

Prior to running, please:

1. Resave current model by clicking save in Setup -> Model Setup tab
2. Confirm that the appropriate parameters are checked on Estimation Data Input -> Run Estimation tab

Release Notes

• Added log scaling checkbox for parameters ranges (i.e., log prior to estimation and exponentiated post estimation)
• Added logic to handle case of range having a 0 (use 1e-20 under the covers); it won’t work with log scaling
• Added user notification when model converges
• Added tolerance label so user can see which algorithms abide by tolerance stop value
• Added default button to set the default tolerance to 1E-06
• Fixed "Load Model" button behavior on Estimation Tab 8 (doesn’t auto switch to run page after loading)
• Fixed predation matrix on input having different orientation than that of output (should be predators across and prey down)
• Fixed state and enable-ness of Estimation Tab7 checkboxes
• Fixed check if any Predation/Competition initial values are outside ranges
• Fixed multi-runs not recognizing the new stop tolerance

1.4.1a Release for Windows

This is a temporary release with half of the most recent post-WGSAM changes implemented.

Release Instructions

Changes to the database have been made and the user should either:

1. To create a new database:
    1.1. Click: Utilities -> Create Tables
    1.2. Create their own database
    1.3. Import their own data

  or

2. To import an existing database:
    2.1. Click: Utilities -> Create Tables
    2.2. Create a project: preWGSAM
    2.3. Import the database included with this release in the sample_data directory: Keyrun_preWGSAM

  or

3. To patch a current database:
    3.1. Run the following commands at the MySQL command line prior to running this version of MSSPM:
    -- alter table species add column Weight float NULL after ExploitationRate
    -- alter table species add column GrowthRateShape float NULL after GrowthRate
    -- alter table species add column GrowthRateShapeMin float NULL after GrowthRateMax
    -- alter table species add column GrowthRateShapeMax float NULL after GrowthRateShapeMin
    -- alter table species drop column SpeciesKCovarCoeff, drop column GrowthRateCovarCoeff
    -- alter table summarydiagnostic add column GrowthRateShape varchar(50) NULL after GrowthRate
    -- alter table forecastmontecarloparameters add column GrowthRateShape double NULL after GrowthRate
    -- alter table forecastuncertainty add column GrowthRateShape float NOT NULL after GrowthRate
    -- alter table modelreview add column isEstGrowthRateShapeEnabled varchar(10) NOT NULL after isEstGrowthRateChecked
    -- alter table modelreview add column isEstGrowthRateShapeChecked varchar(10) NOT NULL after isEstGrowthRateShapeEnabled
    -- alter table models add column EstimateGrowthRateShape int(11) NULL after EstimateGrowthRate
    3.2. Run MSSPM and reset GUI and Settings prior to application start up
    3.3. Make sure project database and project name are: Keyrun_preWGSAM and preWGSAM (if planning on importing the sample db)
    3.4. Click: Utilities -> Create Tables

Release Notes

• Added plot of Catch and Observed together vs time
• Added tooltip on Observed Biomass to show the actual coordinates and not just "Obs Biomass"
• Added functionality where user can set the scale factor in Remora larger than 4
• Added Weight functionality for species (N.B. required changes to database tables)
• Added Growth Rate Shape parameter functionality (N.B. required changes to database tables)
• Added a None scaling type to give user full control as to whether and when to use which Scaling algorithm
• Added whatsThis help to Model Review table
• Added error checking for case of no db loaded
• Fixed issue with Remora sometimes resizing larger than the laptop height
• Fixed issue with Setup Tab3 Export not asking user if they want a non-default name for the .csv file
• Fixed issue with Setup Tab3 Export not working correctly when on Guild page

1.4.1a Temp Release for Linux

• Added error checking for case of no db loaded

1.4.0a Temp Release for Linux

This is a temporary release with half of the most recent post-WGSAM changes implemented.

Release Instructions

Changes to the database have been made and the user should either:

1. To create a new database:
    1.1. Click: Utilities -> Create Tables
    1.2. Create their own database
    1.3. Import their own data

  or

2. To import an existing database:
    2.1. Click: Utilities -> Create Tables
    2.2. Create a project: preWGSAM
    2.3. Import the database included with this release in the sample_data directory: Keyrun_preWGSAM

  or

3. To patch a current database:
    3.1. Run the following commands at the MySQL command line prior to running this version of MSSPM:
    -- alter table species add column Weight float NULL after ExploitationRate
    -- alter table species add column GrowthRateShape float NULL after GrowthRate
    -- alter table species add column GrowthRateShapeMin float NULL after GrowthRateMax
    -- alter table species add column GrowthRateShapeMax float NULL after GrowthRateShapeMin
    -- alter table species drop column SpeciesKCovarCoeff, drop column GrowthRateCovarCoeff
    -- alter table summarydiagnostic add column GrowthRateShape varchar(50) NULL after GrowthRate
    -- alter table forecastmontecarloparameters add column GrowthRateShape double NULL after GrowthRate
    -- alter table forecastuncertainty add column GrowthRateShape float NOT NULL after GrowthRate
    -- alter table modelreview add column isEstGrowthRateShapeEnabled varchar(10) NOT NULL after isEstGrowthRateChecked
    -- alter table modelreview add column isEstGrowthRateShapeChecked varchar(10) NOT NULL after isEstGrowthRateShapeEnabled
    -- alter table models add column EstimateGrowthRateShape int(11) NULL after EstimateGrowthRate
    3.2. Run MSSPM and reset GUI and Settings prior to application start up
    3.3. Make sure project database and project name are: Keyrun_preWGSAM and preWGSAM (if planning on importing the sample db)
    3.4. Click: Utilities -> Create Tables

Release Notes

• Added plot of Catch and Observed together vs time
• Added tooltip on Observed Biomass to show the actual coordinates and not just "Obs Biomass"
• Added functionality where user can set the scale factor in Remora larger than 4
• Added Weight functionality for species (N.B. required changes to database tables)
• Added Growth Rate Shape parameter functionality (N.B. required changes to database tables)
• Added a None scaling type to give user full control as to whether and when to use which Scaling algorithm
• Added whatsThis help to Model Review table
• Fixed issue with Remora sometimes resizing larger than the laptop height
• Fixed issue with Setup Tab3 Export not asking user if they want a non-default name for the .csv file
• Fixed issue with Setup Tab3 Export not working correctly when on Guild page