pbs-software / pbs-ddiff

R-code for GUI control of an iSCAM delay-difference model

PBSddiff: GUI control for delay-difference output from iSCAM

© Fisheries and Oceans Canada (2017-2023)

PBSddiff contains R code for GUI control of delay-difference model output for multiple scenarios using iSCAM. The code was originally created by Chris Grandin (PBS) for a Pacific Cod (Gadus macrocephalus ) assessment, hence the prefix pcod in many R functions, and subsequently adapted by Rowan Haigh (PBS) and Paul Starr (CGRCS) for use in stock assessments of Shortspine Thornyhead [1] (Sebastolubus alascanus) and Walleye Pollock [2] (Theragra chalcogramma).

Warning

The repository is set up to mimic an R package source repository; however, it currently does not meet requirements for building an R package (e.g., no Rd documentation files, direct sourcing of R code).

Note

The tpl code to convert to C++ via ADMB and then compile to a Windows binary (and perhaps an appliance on the African operating system Ubuntu) comes from Steve Martell originally and has subsequently been modified by us and others (e.g., https://github.com/cgrandin/iSCAM).

Acronyms

ADMB -- Automatic Differentiation Model Builder
CGRCS -- Canadian Groundfish Research and Conservation Society
GUI -- Graphical User Interface
iSCAM -- Integrated Statistical Catch Age Model
PBS -- Pacific Biological Station (Nanaimo BC)

References

[1] Starr, P.J., and Haigh, R. (2017). Stock assessment of the coastwide population of Shortspine Thornyhead (Sebastolobus alascanus) in 2015 off the British Columbia coast. DFO Can. Sci. Advis. Sec. Res. Doc. 2017/015: ix + 174 p.

[2] Starr, P.J., and Haigh, R. (2021) Walleye Pollock (Theragra chalcogramma) stock assessment for British Columbia in 2017. DFO Can. Sci. Advis. Sec. Res. Doc. 2021/004: viii + 294 p.