Example datasets 2 - ices-taf/doc GitHub Wiki

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

This example requires a package to be installed that is not on CRAN. Please ensure you have the package stockasessment by running

# Download and install stockassessment in R
install.packages("stockassessment", repos = "https://fishfollower.r-universe.dev")

The resulting TAF analysis created from this example is on GitHub: github.com/ices-taf-dev/wiki-example-2, 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/wiki-example-2")
# view downloaded code
browseURL(run_dir)

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

Creating an empty TAF project

First we create an empty TAF project, and in this case we will call it example-1, and then moving our working directory to this folder. We do this by running

taf.skeleton("example-2")
setwd("example-2")

resulting in the following:

                 
 example-2       
  ¦--boot        
  ¦   °--initial 
  ¦       °--data
  ¦--data.R      
  ¦--model.R     
  ¦--output.R    
  °--report.R

Adding SAM input data via a boot script

Tso get the input data for a stock asseement run on stockassessment.org/, we can use a short script. It is provided here as code that will create the script for you - normally you would create these scripts yourself.

cat('library(stockassessment)

# download model from stockassessment.org
fit <- fitfromweb("WBCod_2021_cand01")

# save to model folder
save(fit, file = "fit.rData")

',
  file = "boot/sam_fit.R"
)

bootsrap scripts such as this one, goes in the boot folder:

                  
 example-2        
  ¦--boot         
  ¦   ¦--initial  
  ¦   ¦   °--data 
  ¦   °--sam_fit.R
  ¦--data.R       
  ¦--model.R      
  ¦--output.R     
  °--report.R

a second script to get the fitted model object is given below:

cat('sam_assessment <- "WBCod_2021_cand01"

sam_dir <-
  paste0(
    "https://stockassessment.org/datadisk/stockassessment/userdirs/user3/",
    sam_assessment,
    "/data/"
  )

files <-
  paste0(
    c("cn", "cw", "dw", "lf", "lw", "mo", "nm", "pf", "pm", "survey", "sw"),
    ".dat"
  )

for (file in files) {
  download(paste0(sam_dir, file))
}

',
  file = "boot/sam_data.R"
)

We can then add records for these scripts in the DATA.bib file using:

draft.data(
  data.files = NULL,
  data.scripts = c("sam_data", "sam_fit"),
  originator = "WGBFAS",
  title = c("SAM input data for ...", "SAM fitted object for ..."),
  year = 2021,
  period = "1985-2020",
  file = TRUE,
  append = FALSE
)

resulting the project looking like this:

                   
 example-2         
  ¦--boot          
  ¦   ¦--DATA.bib  
  ¦   ¦--initial   
  ¦   ¦   °--data  
  ¦   ¦--sam_data.R
  ¦   °--sam_fit.R 
  ¦--data.R        
  ¦--model.R       
  ¦--output.R      
  °--report.R

and after running

taf.boot()

## [12:30:23] Boot procedure running...

## Processing DATA.bib

## [12:30:23] * sam_data

## [12:30:24] * sam_fit

## [12:30:25] Boot procedure done

your project should now look like this:

                           
 example-2                 
  ¦--boot                  
  ¦   ¦--data              
  ¦   ¦   ¦--sam_data      
  ¦   ¦   ¦   ¦--cn.dat    
  ¦   ¦   ¦   ¦--cw.dat    
  ¦   ¦   ¦   ¦--dw.dat    
  ¦   ¦   ¦   ¦--lf.dat    
  ¦   ¦   ¦   ¦--lw.dat    
  ¦   ¦   ¦   ¦--mo.dat    
  ¦   ¦   ¦   ¦--nm.dat    
  ¦   ¦   ¦   ¦--pf.dat    
  ¦   ¦   ¦   ¦--pm.dat    
  ¦   ¦   ¦   ¦--survey.dat
  ¦   ¦   ¦   °--sw.dat    
  ¦   ¦   °--sam_fit       
  ¦   ¦       °--fit.rData 
  ¦   ¦--DATA.bib          
  ¦   ¦--initial           
  ¦   ¦   °--data          
  ¦   ¦--sam_data.R        
  ¦   °--sam_fit.R         
  ¦--data.R                
  ¦--model.R               
  ¦--output.R              
  °--report.R

Now we have a folder with the same name as the script we created, and inside this is any files created by the script.