Example cat 3 stock assessment - ices-taf/doc GitHub Wiki

See also: Getting set up, Running a TAF analysis, Creating TAF datasets.

This page was based on using the icesTAF package version 4.2.0 dated 2023-03-21.

The resulting TAF analysis created from this example is on GitHub: github.com/ices-taf-dev/ices_cat_3_template, if you dont want to build up the code yourself by following the example, you can skip to the end and run on your computer by downloading the complete code and running it like this:

# get code
run_dir <- download.analysis("ices-taf-dev/ices_cat_3_template")
# view downloaded code
browseURL(run_dir)

# run analysis
run.analysis(run_dir)
# view result
browseURL(run_dir)

The final project should look like this:

                                      
 cat-3-example                        
  ¦--boot                             
  ¦   ¦--data                         
  ¦   ¦   ¦--advice_history.csv       
  ¦   ¦   ¦--FSP7e.csv                
  ¦   ¦   °--InterCatch_length.csv    
  ¦   ¦--DATA.bib                     
  ¦   °--initial                      
  ¦       °--data                     
  ¦           ¦--advice_history.csv   
  ¦           ¦--FSP7e.csv            
  ¦           °--InterCatch_length.csv
  ¦--data                             
  ¦   ¦--advice_history.csv           
  ¦   ¦--advice_history.rds           
  ¦   ¦--idx.csv                      
  ¦   ¦--idx.rds                      
  ¦   ¦--length_data.csv              
  ¦   °--length_data.rds              
  ¦--data.R                           
  ¦--model                            
  ¦   °--advice.rds                   
  ¦--model.R                          
  ¦--README.Rmd                       
  ¦--report                           
  ¦   ¦--figures                      
  ¦   ¦   ¦--rfb_b.png                
  ¦   ¦   ¦--rfb_f.png                
  ¦   ¦   ¦--rfb_Lc.png               
  ¦   ¦   ¦--rfb_Lmean.png            
  ¦   ¦   ¦--rfb_r.png                
  ¦   ¦   °--rfb_rb.png               
  ¦   °--tables                       
  ¦       °--advice_table.txt         
  ¦--report.R                         
  °--report_sg.R                      

And the figures that were produced are: