A retrospective analysis tests the effect of peeling back the number of operating model years observable to the estimation model. This function alters the Stock Synthesis starter file to run a retrospective analysis.
change_retro(
str_file_in = "starter.ss",
str_file_out = "starter.ss",
retro_yr = 0
)A string providing the path to the input Stock Synthesis starter.ss file.
A string providing the path to the output Stock Synthesis starter.ss file.
Which retrospective year to enter into the starter file. Should be 0 (no retrospective analysis) or a negative value, which leads to the removal of data for the specified number of years. Positive values are not allowed.
A modified Stock Synthesis starter file.
Note that the starter file is set up to run a single retrospective run. Therefore, if you would like to run retrospective analyses for, say, 0, 1, 2, 3, 4, and 5 years, you will need to use this function to adjust the starter file 6 separate times.
Other change functions:
change_data(),
change_e(),
change_em_binning(),
change_f(),
change_o(),
change_tv()
# Create a temporary folder for the output:
temp_path <- file.path(tempdir(), "ss3sim-retro-example")
dir.create(temp_path, showWarnings = FALSE)
# Locate the package data:
starterfile <- system.file("extdata", "models", "cod-om",
"starter.ss",
package = "ss3sim"
)
# No retrospective analysis:
change_retro(starterfile, paste0(temp_path, "/retro-0-starter.ss"),
retro_yr = 0
)
# A retrospective analysis of 5 years:
change_retro(starterfile, paste0(temp_path, "/retro-5-starter.ss"),
retro_yr = -5
)