Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

Figure 7.

Software Versions

Author information

Laurence Kell. laurie@seaplusplus.es

Acknowledgements

This vignette and many of the methods documented in it were developed under the MyDas project funded by the Irish exchequer and EMFF 2014-2020. The overall aim of MyDas is to develop and test a range of assessment models and methods to establish Maximum Sustainable Yield (MSY) reference points (or proxy MSY reference points) across the spectrum of data-limited stocks.

References

Session Info

R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] kernlab_0.9-27     mco_1.0-15.1       caret_6.0-84      
 [4] doParallel_1.0.14  foreach_1.4.4      mydas_1.0.3.0     
 [7] randtests_1.0      FLife_3.2.3.0      ggplotFL_2.6.6    
[10] FLasher_0.5.3.9001 FLFishery_0.1.6    FLBRP_2.5.3       
[13] FLCore_2.6.13      iterators_1.0.10   lattice_0.20-38   
[16] reshape_0.8.8      dplyr_0.8.0.1      plyr_1.8.4        
[19] ggplot2_3.1.1      knitr_1.22        

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1         lubridate_1.7.4    class_7.3-15      
 [4] assertthat_0.2.1   digest_0.6.19      ipred_0.9-9       
 [7] R6_2.4.0           stats4_3.5.2       evaluate_0.13     
[10] pillar_1.4.0       rlang_0.3.4        lazyeval_0.2.2    
[13] data.table_1.11.8  rstudioapi_0.10    rpart_4.1-13      
[16] Matrix_1.2-15      rmarkdown_1.12     labeling_0.3      
[19] splines_3.5.2      gower_0.2.1        stringr_1.4.0     
[22] munsell_0.5.0      compiler_3.5.2     xfun_0.6          
[25] pkgconfig_2.0.2    htmltools_0.3.6    nnet_7.3-12       
[28] tidyselect_0.2.5   tibble_2.1.1       gridExtra_2.3     
[31] prodlim_2018.04.18 codetools_0.2-16   crayon_1.3.4      
[34] withr_2.1.2        ModelMetrics_1.2.2 MASS_7.3-51.1     
[37] recipes_0.1.5      grid_3.5.2         nlme_3.1-137      
[40] gtable_0.3.0       magrittr_1.5       scales_1.0.0      
[43] stringi_1.4.3      reshape2_1.4.3     timeDate_3043.102 
[46] generics_0.0.2     lava_1.6.5         tools_3.5.2       
[49] glue_1.3.1         purrr_0.3.0        survival_2.43-3   
[52] yaml_2.2.0         colorspace_1.4-1