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U.S. Geological Survey - Great Lakes Science Center

artiFISHal

A pelagic fish community simulator

Program artiFISHal is a pelagic fish community simulator developed using the R programming language (R Core Team 2013). It is freely available for download from this web page. Program artiFISHal can be used to create artificial lakes and populate them with known numbers of fish (identified in species-size groups) to mimic pelagic fish communities. Program artiFISHal can then be used to sample these fish with virtual acoustic and midwater trawl surveys. Program artiFISHal was used by Yule et al. (in press) to evaluate several different approaches for estimating the biomass of pelagic fish species in the Great Lakes. Send questions and comments on this program to Jean Adams, USGS Great Lakes Science Center Statistician, jvadams@usgs.gov.

Instructions In order to run program artiFISHal, follow the steps outlined below:

  1. Download the zip file from this website. It contains three files:
    1. Inputs.xls
    2. SimulateFish.r
    3. SampleFish.r
  2. Edit the three worksheets in the Excel workbook, Inputs.xls.
    1. SimLake -- edit the inputs for the shape of the artificial lake you wish to create
    2. SimFish -- edit the inputs for the fish population you wish to create
    3. Sample -- edit the inputs for the acoustic and midwater trawl survey
  3. Edit the inputs in the R script SimulateFish.r
    1. dir -- directory for reading input data (location of Inputs.xls)
    2. subdir -- directory for saving output data
    3. sel.lk -- the lake you wish to create (LC in Inputs.xls tab SimFish)
    4. cap.no.fish -- set the maximum number of fish
    5. save.plots -- specify whether to save plots to a pdf or show them on the screen
  4. Run the R script SimulateFish.r, which will create four output files, one comma delimited data file, one pdf document, and two Rdata files
    1. Truth-lake#.csv -- number and biomass of true population of fish in lake
    2. Diagnostic-lake#.pdf -- diagnostic plots of fish population
    3. inputs-lake#.Rdata -- collection of R objects
    4. fish-lake#.Rdata -- true population of fish in lake, one row per fish
  5. Edit the inputs in the R script SampleFish.r
    1. dir -- directory for reading input data (location of Inputs.xls)
    2. subdir -- directory for saving output data
    3. sel.run -- the survey run you wish to execute (run.id in Inputs.xls tab Sample)
    4. save.plots -- specify whether to save plots to a pdf or show them on the screen
    5. min.no.fish.per.haul -- set the minimum number of fish required for a valid trawl sample
  6. Run the R script SampleFish.r, which will create five output files, four comma delimited data files and one pdf document
    1. ACTargets-lake#-run#.csv -- individual acoustic targets
    2. ACSummaryI-lake#-run#.csv -- summary of acoustic targets by interval (I)
    3. ACSummaryIL-lake#-run#.csv -- summary of acoustic targets by interval (I) and layer (L)
    4. MTRCatch-lake#-run#.csv -- individual fish captured in midwater trawl
    5. Survey-lake#-run#.pdf -- diagnostic plots of acoustics and midwater trawl sampling

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

This flowchart shows the relationship among program artiFISHal inputs (blue), R scripts (green), and outputs (orange, yellow, and red). Follow the black arrows (top) to create a fish population in a lake. Follow the gray arrows to survey the lake with down-looking acoustics and midwater trawls.

References

R Core Team. 2013. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. www.R-project.org.

Yule, D.L., J.V. Adams, D.M. Warner, T.R. Hrabik, P.M. Kocovsky, B.C. Weidel, L.G. Rudstam, and P.J. Sullivan. 2013. Evaluating approaches for estimating biomass of pelagic fish species using simulated fish communities. Canadian Journal of Fisheries and Aquatic Sciences 70:1845-1857.

artiFISHal
U.S. Geological Survey (USGS) Computer Program "artiFISHal" version 2014-04
Written by Jean V. Adams, USGS - Great Lakes Science Center, Ann Arbor, Michigan, USA
Use of this program was first described by Jean V. Adams in a publication by
Yule et al. (2013) in the Canadian Journal of Fisheries and Aquatic Sciences.
Written in programming language R (R Core Team, 2013, www.R-project.org),
Version 3.0.1 (2013-05-16)
Run on a PC with Intel(R) Core(TM)2 Duo CPU P8600 @ 2.40 GHz processor, 8.00 GB RAM,
and Microsoft Windows 7 Enterprise operating system 2009 Service Pack 1
Source code is available from Jean V. Adams, jvadams@usgs.gov

 

Disclaimer
Although this program has been used by the USGS, no warranty, expressed or implied, is made by the USGS or the United States Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.

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