Productivity
Western Mediterranean Hake
30 April, 2021
Introduction
The aim of this document is to evaluate the factors that affect productivity.
Installation
To run the code in this vignette a number of packages need to be installed, from CRAN and the FLR website, where tutorials are also available.
Libraries
FLR
The FLR packages can be installed from www.flr-project.org
library(FLCore)
library(FLBRP)
library(FLasher)
library(ggplotFL)CRAN
The examples make extensive use of the packages of Hadley Wickham. For example plotting is done using ggplot2 based on the Grammar of Graphics.1 Grammar is to specifies the individual building blocks and allows them to be combined to create the graphic desired2.
While ‘dplyr’ is a grammar of data manipulation, providing a consistent set of verbs that help solve the most common data manipulation challenges, while ‘plyr’ is a set of tools to split up a big data structure into homogeneous pieces, apply a function to each piece and then combine all the results back together.
library(ggplot2)
library(plyr)
library(dplyr)Install development version of FLife
library(devtools)
install_github("flr/FLife")Reference Points
Figure 1. Reference points and equilibrium curves for Beverton and Holt stock recruitment relationship.
Figure 2. Time series, with ICES PA and MSY reference points, along with MSY estimated with a Beverton and Holt stock recruitment relationship.
Productivity
Figure 3. Vectors of weigth, selectivity, maturity and M-at-age.
Figure 4. Time series of MSY benchmarks based on yield and spawner-per-recruit.
Figure 5. Production function with trajectory of catch v SSB.
Figure 6. Production function with trajectory of catch v SSB.
Figure 7. Time series of surplus production and process error.
Stock and recruitment
Figure 8. Stock recruitment fit for Beverton and Holt
Figure 9. Recruitment residuals, with regimes.
Steepness
Figure 10. Stock recruitment relationship by steepness.
Figure 11. Production functions by steepness.
Projections
Figure 12. Projection at MSY.
Software Versions
- R version 4.0.3 (2020-10-10)
- FLCore: 2.6.16
- FLPKG:
- Compiled: Fri Apr 30 08:58:20 2021
- Git Hash: 46f2d77
Acknowledgements
References
Wilkinson, L. 1999. The Grammar of Graphics, Springer. doi 10.1007/978-3-642-21551-3_13.↩