msmod.Rmd

# Multispecies Models {#msmod}

As usual, course materials not in the github repository can be found in the course Google Drive [course-materials folder](https://drive.google.com/drive/folders/1Wt4fhAgCP92aBu_XSCQq50Xrkc-UVHnx?usp=sharing). Everything will of course be linked to here on the website.  

## 09/27 {.unlisted .unnumbered}

[Lecture slides](https://docs.google.com/presentation/d/1tDBnmVm4c0LZ9dH0goIi5yYA4L6yuP5Z/edit?usp=sharing&ouid=100082783551785338508&rtpof=true&sd=true)   

## 10/06 {.unlisted .unnumbered}

[recorded lecture by Dr. Sarah Gaichas, NOAA NEFSC, "what makes a good multispecies model?"](https://www.dropbox.com/s/sx1kgsxr9l5ovc4/Day2_S2_Sarah_Gaichas.mov?dl=0)  

[slide deck](https://www.dropbox.com/s/ua9ru1mt6n9kh1i/Gaichas_MMAW_Keynote.pdf?dl=0)

## Lab and Homework Assignment 3 {.unlisted .unnumbered}

[Estimating species interactions](https://github.com/gavinfay/mebm-models/blob/main/course-materials/assignments/hw-03/hw-03.pdf)

[HW3 materials](https://github.com/gavinfay/mebm-models/blob/main/course-materials/assignments/hw-03)

[MARSS user guide](https://cran.r-project.org/web/packages/MARSS/vignettes/UserGuide.pdf)

## 10/10-10/14 ICES WGSAM meeting

Parking is at the Northeast Fisheries Science Center in Woods Hole (166 Water Street). The meeting is at MBL, see Gavin's email with the agenda / room information.  

Accommodation is at the Inn on the Square in Falmouth, MA.  


## Reading {.unlisted .unnumbered}

Primary readings for 9/27, 10/4, 10/6

[Hall, S.J., Collie, J.S., Duplisea, D.E., Jennings, S., Bravington, M. and Link, J., 2006. A length-based multispecies model for evaluating community responses to fishing. Canadian Journal of Fisheries and Aquatic Sciences, 63(6), pp.1344-1359.](https://cdnsciencepub.com/doi/pdf/10.1139/f06-039)

[Ives, A.R., Dennis, B., Cottingham, K.L. and Carpenter, S.R., 2003. Estimating community stability and ecological interactions from time‐series data. Ecological monographs, 73(2), pp.301-330.](https://doi.org/10.1890/0012-9615(2003)073[0301:ECSAEI]2.0.CO;2)

[Plagányi, É.E., Punt, A.E., Hillary, R., Morello, E.B., Thébaud, O., Hutton, T., Pillans, R.D., Thorson, J.T., Fulton, E.A., Smith, A.D. and Smith, F., 2014. Multispecies fisheries management and conservation: tactical applications using models of intermediate complexity. Fish and Fisheries, 15(1), pp.1-22.]()


### Additional readings on these topics {.unlisted .unnumbered}

[Holsman, K.K., Ianelli, J., Aydin, K., Punt, A.E. and Moffitt, E.A., 2016. A comparison of fisheries biological reference points estimated from temperature-specific multi-species and single-species climate-enhanced stock assessment models. Deep Sea Research Part II: Topical Studies in Oceanography, 134, pp.360-378.](https://doi.org/10.1016/j.dsr2.2015.08.001)

[Thorpe, R.B., Le Quesne, W.J., Luxford, F., Collie, J.S. and Jennings, S., 2015. Evaluation and management implications of uncertainty in a multispecies size‐structured model of population and community responses to fishing. Methods in Ecology and Evolution, 6(1), pp.49-58.](https://doi.org/10.1111/2041-210X.12292)

[Trijoulet, V., Fay, G. and Miller, T.J., 2020. Performance of a state‐space multispecies model: What are the consequences of ignoring predation and process errors in stock assessments?. Journal of Applied Ecology, 57(1), pp.121-135.](https://doi.org/10.1111/1365-2664.13515)