FLR and a4a for Quantitative Fisheries Science

https://github.com/iagomosqueira/FLRforQuantFishSci

SESSIONS

1. Introduction to R and FLR

1.1 Welcome and setup. 15'

[Presentation](./Sessions/01\ Intro\ to\ FLR/01.01\ Welcome/Welcome.md.pdf)

1.2 Introduction to FLR. 15'

[Presentation](./Sessions/01\ Intro\ to\ FLR/01.02\ Intro\ to\ FLR/Intro_FLR.md.pdf)

1.3 Introducing the FLQuant class. 45'

[Presentation](./Sessions/01\ Intro\ to\ FLR/01.03\ FLQuant/FLQuant.md.pdf)
[Tutorial](./Sessions/01\ Intro\ to\ FLR/01.03\ FLQuant/FLQuant.R)
[Exercise](./Sessions/01\ Intro\ to\ FLR/01.03\ FLQuant/Ex_FLQuant.R)

1.4 The FLCore package. 15'

[Presentation](./Sessions/01\ Intro\ to\ FLR/01.03\ FLCore/FLCore.md.pdf)

1.5 The FLStock class. 45'

2. Loading data, plotting and EDA

3. Stock-recruitment and reference points

3.1 Estimating SR models with FLSR

3.2 Residuals, profiles and quality of fit

3.3 Biological reference points using FLBRP

4. Modelling M and growth with a4a

4.1 a4a M methods

4.2 a4a Growth methods

4.3 Converting length to ages

5. Stock assessment using FLa4a

5.1 Sub-models

5.2 Diagnostics

5.3 Advanced features

5.4 Simulation

6. Short term forecasting for advice

7. Forecasting scenarios

8. From stock assessment to MSE

EXTRAS

A. Reproducible Research

B. Programming in FLR

C. High Performance Computing

D. Simulating datasets