rsimgmacs buck stockhausen afsc. rsimgmacs: an r-based simulation tool for testing/developing...

rsimGmacs

Buck StockhausenAFSC

rsimGmacs: An R-based simulation tool for testing/developing Gmacs

• Provides an independent testing platform– Embodies Gmacs equations– Coded in R– Provides redundancy checking

• Outputs:– R list object– Diagnostic plots– Data input file to Gmacs

• Available at https://github.com/seacode/rsimGmacs.git• Package dependencies: ggplot2, reshape2, tcltk

Package Documentation

Running rsimGmacs

• res<-runSim.BBRKC(pdf=‘rsimCIE.pdf’)

Configuration File (1)

Configuration File (2)

Configuration File (3)

Configuration File (4)

Configuration File (5)

Running rsimGmacs

• res<-runRsim.BBRKC()• res: list of lists

– mc: list object for model configuration• dims: list object with model dimensions info• params: list object with model parameters info

– mp: list object for model processes (rates)– mr: list object for model results

• R_yxz: recruitment by by y,x,z• iN_xmsz: initial abundance by x,m,s,z• N_yxmsz: 5-d array of population abundance by y,x,m,s,z• F_list: list of fisheries-related results• N_vyxmsz: 6-d array of abundance in surveys (v) by y,x,m,s,z

Diagnostic Plots

see rsimCIE.pdf

Gmacs input file

See gmacs.input.dat