run: Run ageing error routine

In nwfsc-assess/nwfscAgeingError: Estimating ageing error with 'TMB' from double reads

Run ageing error routine

Description

A wrapper for running a TMB model to estimate ageing error for a given data set and specification file.

Usage

run(directory, file_data = "data.dat", file_specs = "data.spc")

Arguments

directory	A string specifying a file path to a directory where you would like to save the results.
file_data	A string specifying the data file within 'directory'.
file_specs	A string specifying the specifications file within 'directory'.

Value

Invisibly return model output.

Author(s)

Kelli F. Johnson

See Also

write_files()

Examples

## Not run: 
data_test <- data.frame(
  reader1 = c(7, 10, 7, 6, 6, 10, 7, 9, 8, 10, 10, 5, 6, 7, 9, 7, 7, 5, 8, 5),
  reader2 = c(8, 10, 7, 6, 6, 10, 7, 9, 8, 10, 10, 5, 6, 7, 9, 7, 7, NA, NA, NA),
  reader3 = c(7, 10, 7, 6, 6, 8, 7, 9, 8, 10, 10, 5, 6, 7, NA, NA, NA, 5, 8, 5)
)
write_files(dat = data_test, dir = tempdir())
out <- run(dir = tempdir())
# see estimated parameters
out$model$par
# see model selection results
out$output$ModelSelection
# see ageing error matrices
out$output$ErrorAndBiasArray
# add to an SS3 model (assumes the model already has a single
# ageing error matrix and a maxage <= maxage in the ageing error model)
ss3_inputs <- r4ss::SS_read()
maxage <- ss3_inputs$dat$Nages
ss3_inputs$dat$ageerror <-
  out$output$ErrorAndBiasArray[c("Expected_age", "SD"), 1 + 0:maxage, "Reader 1"] |>
  as.data.frame()
r4ss::SS_write(inputlist = ss3_inputs)

## End(Not run)

nwfsc-assess/nwfscAgeingError documentation built on July 4, 2025, 9:49 a.m.