Fish Bioenergetics Model 4
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Main Inputs Add input files used in example Design files. Oct 31, 2018
Sub-Models
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FB4_Design_Bluegill_1.csv
FB4_Design_Check_Trout.csv
FB4_Design_Example_1.csv
FB4_Design_Example_5.csv Add example Design files. Oct 31, 2018
FB4_Design_Examples_1-4.csv
FB4_Design_Test_96_Models.csv
FB4_User_Guide.pdf
Output.csv
Parameters_official.csv
README.md
README_FB4.md
README_FB4.txt
_config.yml
server.R Update to v1.1.0, to allow Design files. Oct 31, 2018
ui.R

README.md

Welcome to Fish Bioenergetics 4.0

You can download the latest version of FB4 by clicking a button on this web page. The FB4 software, User Manual, and sample input files are all in the same zipped file. Instructions for getting started are in the User Manual (included in the zip file) and are also summarized below.

We are today (10/31/2018) releasing Version 1.1.0 of the FB4 software. Details for this update are explained at the bottom of this page.

FB4 v1.0.3 was released on 1/7/2018. FB4 v1.0.2 was released on 12/13/2017 FB4 v1.0.1 was released on 12/6/2017. FB4 v1.0.0 was released on 12/1/2017.

The Open Access article by Deslauriers et al. (2017) gives an introduction to this R-based modeling application.

There are two main goals of this website:

  • First, to make the current bioenergetics software available and easy to use;
  • Second, to facilitate the wider use and further development of the bioenergetics approach.

We hope to add information such as the following:

  • Online User's Manual, with full explanations
  • List of species for which bioenergetics parameters have been published
  • Table of parameter values (a .csv file comes with the code)
  • References to published models
  • Background material for an online introduction to fish bioenergetics
  • Suggestions for fitting bioenergetics models to data
  • Ideas for future modifications

Instructions

Steps to download, install and run Fish Bioenergetics 4.0

Fish Bioenergetics 4.0 (FB4) uses R as a computing language and Shiny through RStudio as the supporting interface. You will need both of these programs in order to be able to run FB4 on your computer.

  • Go to http://cran.r-project.org and download the latest version of R that is compatible with your computer (Windows or Mac).
  • Go to http://www.rstudio.com/products/rstudio/download/, click on the button to download the free RStudio Desktop version, then download the latest version of RStudio under "Installers for supported platforms" that is compatible with your computer (Windows or Mac) operating system.
  • Once both programs have been installed, save the FB4 folder downloaded from this website onto your desktop (or another suitable location).
  • In RStudio, select File -> Open File... and double click on the "server.R" file found in the FB4 folder on your desktop. This step only needs to be repeated if the server.R file has been modified or a different one is used, or if a different FB4 folder is used.
  • In RStudio, go to Session -> Set Working Directory -> Choose Directory... and select the FB4 folder you just saved. Once the folder has been selected, press the select (in Windows) or open (in Mac) tab. This step only needs to be performed once if the same FB4 folder is continually used. However, this step will have to be repeated if a different FB4 folder is created.
  • You will now need to download the "Shiny" package, which will allow you to run the application. To do so, go to Tools -> Install Packages... and type Shiny under Packages (separate multiple with space or comma). Then, click on Install. This might take 1-2 minutes.
  • You are now all set to run the application. To do so, press the down-arrow icon to the right of the Run App tab found in the upper right corner of the script window (upper left window) and select Run External. Once this is done, press the Run App tab and FB4 will start in a new window of your browser.

Note: In some versions of RStudio, the Run App tab does not appear. In that case, type runApp() in the Console window (lower left window) and insert the FB4 folder path inside the parentheses. The folder path should be inside quotation marks and should look something like: runApp("/Users/david/Desktop/Fish Bioen 4.0") Once done, press Enter and the application should run.

  • Warning: Any alteration to the R script will cause the application to either be modified or not function. If you inadvertently modify the code, just make sure you do not save the server.R or ui.R files before closing and re-opening them again (or save them under a different name).

A similar set of instructions for getting started is in the FB Wiki: FB Wiki

Simulation Setup

Setting up the files needed to run bioenergetics simulations

Once you successfully install and open FB4 you are ready to run bioenergetics simulations. To run a basic simulation, you will need to supplement the program with Initial Settings and Input Files.

Initial Settings

  • Species

You must first decide on the species you want to use for the simulation. Under the Initial Settings tab, select the species of interest by scrolling through the dropdown menu under Species. You can see the species’ common and scientific name, along with the reference and parameters value on the right-hand side of the screen.

  • Duration

You must then select the duration of your simulation. The duration of the simulation must not exceed the length of time found in the Input Files. In addition, the simulation days are arbitrary and do not fall under any calendar constraints (i.e., day of year). Type your first day in the Initial Day box and your last day in the Final Day box. The days you input here will be used to determine the range of data from the input files to run the simulations.

  • Initial weight

All simulations require you to input an initial weight (in grams of wet weight) for the fish used in the simulation. Make sure you use a relevant weight that corresponds to the life stage of the species model you are using.

  • Oxycalorific coefficient

This parameter is used to convert oxygen consumption into an energy unit (Joules/grams of O2) that is compatible with the modeling process. The default value was taken from Stewart et al. (1983) but be aware that all species do not require the same coefficient (see Elliot & Davison 1975 for more information).

  • Fit to

This is where you decide what kind of simulation you want to run. By selecting Final Weight, you are telling the program that you want your fish’s final weight (in grams of wet weight) to equal the value you input in the box. The program will then iteratively adjust daily consumption so that the final weight calculated from the simulation matches the final weight you used as an input.

If you select Consumption, the program will use the value you input in the box (in grams of total prey wet weight) and assign the fish a daily consumption value so that the total consumption value from the simulation matches the consumption value you used as an input.

By selecting Ration, you are telling the program to feed the fish a % of the fish’s wet body weight every day.

Lastly, if you select P-value, the program will calculate a consumption value based on maximum consumption (Cmax) on any given day. Remember that Cmax will vary depending on water temperature and fish body mass.

Input Files

Input data files contain information that might have been collected in the field, retrieved from historical archives, or pulled from scientific literature. These files are created outside FB4 and are loaded automatically by the program once it is launched. Not all simulations require the same input files but all simulations require the files in the Main Inputs folder to be filled out.

  • Main Inputs

The Main Input files include: Temperature, Prey Energy Density (Prey_E), Prey Proportions (Diet_prop), Predator Energy Density (Pred_E), and Indigestible Prey (only if using Equation 3 for waste losses; see Stewart et al. 1983). All files are saved in .csv format. Default files have been provided with the Fish Bioen 4.0 folder but these can be modified to reflect your own data. To do so, simply replace the days and input data with your own data and save the .csv file before launching FB4. Data are linearly interpolated for the days where the data are missing. You must always have the same number of prey items for each of the input files (except Predator Energy Density) that you plan on using for the simulations.

The mortalify file is the one case where daily values are not interpolated. The value specified for one day remains in effect until a different value is specified (see User Manual for details).

Note: All input files must start on day 1. Failure to do so will result in FB4 using the wrong set of days for the simulation.

  • Input Files

Once you give FB4 the input data you want to use for your simulation, you can visualize them by selecting the Input Files tab. However, you must make sure that you filled out the Initial Day and Final Day sections under the Initial Settings tab. This will allow you to visualize the input data for the time range you want to run your simulation for. You will also notice that the plots generated under the Input Files tab are reactive. This means that the plots will automatically adjust to reflect the Initial Day and Final Day of your simulation.

  • Output (to run the program)

Once you have inspected your input data and arranged your initial settings, you can run your simulation. To do so, go to the Output tab and the program will run. Under this tab, you can see the results of the simulation on a daily basis under the Table tab. To view different outputs, select within the Variables box and many output options will become available. Select the ones of interest and they will appear in the table. Once you have all the data you need, you can download them into a .csv file onto the Fish Bioen 4.0 folder. To do so, select the Download button and save the file to the folder.

  • Plot

It is also possible to visualize the outputs in a plot format. To do so, select the Plot tab. This will bring you to a plot with 2 y-axes. You can modify the variables found on either y-axes or the x-axis by scrolling down the dropdown menus below Plot Output.

  • Summary

Finally, by selecting the Summary tab, you will be able to see the final weight, consumption and p-value calculated or used for the simulation. Keep in mind that the p-value is irrelevant if you choose to run a simulation using the Fit to: Ration option.

FB4 versions:

  • Latest version: FB4 v1.1.0. was released 10/31/2018. Click the "Download .zip" button at the top of the web page to obtain the latest version. This version can be used in the same way as earlier versions. There are two minor changes and one major change. One minor change is that the number of decimal places for output of the p-value is increased from 4 to 6 decimal places. A second minor change is the addition of some warning messages if fish weight becomes negative or if the program cannot calculate the new weight at the end of a day, to help in debugging simulations. The major change with this version is the ability to use a Design File to run a series of simulations, each with different input values and input files (e.g., Temperature.csv, Temperature_plus2C.csv, Pred_E.csv, Pred_E_4500.csv). For example, users could compare food consumption by different sizes of fish, or food consumption under different temperature regimes or prey energy densities. The summary output from the series of simulations is written to a separate log file, which the user specifies in the Design File. See the example Design Files that are included. To try using a Design file, pick one of the examples in lines 15-20 of the R code, and remove the starting "#" so that the chosen line of code becomes active. For example, line 17 (Design_File = "FB4_Design_Examples_1-4.csv") specifies a Design file which has input values for all the runs for Examples 1, 2, 3, and 4 in the User Guide. (Example 5 is a separate Design file.) Then go to line 53 of the R code and change FALSE to TRUE: UseDesignFile <- TRUE Then, from the top menu in RStudio, click File > Save to save these changes in the code. Then run the model. In this version, you need to pick a Species, set initial and final days, select the fit option and value, in order to start the model going. But if UseDesignFile is TRUE, these user inputs are ignored: only the input values in the Design File are used in the runs. Note that the user can create multiple input files, e.g., for different temperature regimes, different diet files, different energy density files, etc., and can specify the desired files to use for each separate run in the Design File. (A future update will probably allow users to choose a Design file from a menu.) To stop using a Design File, go to line 53 of the R code, make UseDesignFile <- FALSE and save that change in the R code by clicking File > Save in the top menu in RStudio.

  • FB4 v1.0.3, was released 1/7/2018. This minor update adds the creation of a log file (FB4_Log_File.csv), which is written to the current directory after each run. After the file is first created, information from subsequent runs is appended to the previous file. This log file records the date-time, program version, input values, file names used for the simulation run, and summary output values. These input and output values are also printed to the RStudio Console. If you open FB4_Log_File.csv in Excel to see the values, be sure to close the file before doing another run, or else you will get an error: R will not be able to write (append) new information to the log file while it is open in Excel.

  • FB4 v1.0.2 was released 12/13/2017. This minor update includes checks to avoid reading some additional input files that are not needed for a particular run. The Mortality input file is not read unless that sub-model is selected. Reproduction file is not read unless that sub-model is selected. If the last day of values in these two files are less than the Final Day of the simulation entered in Initial Values, then a caution message is displayed on the Sub-Model graph to remind the user there may be a problem unless more days are added to the file. The purpose of these changes is to help prevent file errors for new users, who may delete files or forget to update files they don't think they need.

  • FB4 v1.0.1 was released 12/6/2017. This minor update includes checks to avoid reading input files that are not needed for the selected species parameters. The Indigestible_prey file is not read unless EGEQ == 3; the program needs this file only if Egestion Model 3 is being used. Similarly, the Pred_E file is not read unless PREDEDEQ == 1; this file is not needed if predator energy density is based on weight (PREDEDEQ 2 or 3). The purpose of these changes is to help prevent file errors for new users, who may delete files or forget to update prey types in files they don't think they need.

  • FB4 v1.0.0 was released on 12/1/2017.