Skip to contents

Write a data file for the AgeingError package

Source: R/write_data_file.R
write_data_file.Rd

The resulting file has the format required by the load_data() function. In the future, this step could be bypassed by creating the list output from load_data() directly. Only one data set is supported (NDataSet = 1). This function is based on a subset of the RunFn() function in the older ADMB version of this package.

Usage

write_data_file(
  dat,
  dir = getwd(),
  file_name = "data.dat",
  minage = 0,
  maxage = NULL,
  refage = NULL,
  minusage = NULL,
  plusage = NULL
)

Arguments

dat

Dataframe or tibble with columns for each reader and rows for each age reading combination. This could either have a count column or not. If not, tally_repeats() will be called to add a count column. Order your reader/lab columns such that similar readers/labs are located next to one another because columns to the right can mirror columns to their immediate left in terms of parameter estimates.

dir

Directory where the data file will be saved.

file_name

Name of the data file.

minage

An integer, specifying the minimum possible "true" age.

maxage

An integer, specifying the maximum possible "true" age.

refage

An arbitrarily chosen age from which "true" age-composition fixed-effects are calculated as an offset. This has no effect on the answer but could potentially effect estimation speed. By default this will be set to the maxage / 4.

minusage

The minimum age for which an age-specific age-composition is estimated. Ages below minusage have "true" proportion-at-age (\(P_{a}\)) estimated as $$P_a = P_{minusage}*exp^{(\beta*(minusage - a))}$$, where beta is an estimated log-linear trend in the "true" proportion-at-age. If minusage = minage, beta is not estimated.

plusage

Identical to minusage except defining the age above with age-specific age composition is not estimated.

Value

Invisibly returns the path to the data file (file.path(dir, file_name)).

See also

write_files(), write_specs_file(), load_data(), tally_repeats()

Author

Ian G. Taylor, James T. Thorson, Ian J. Stewart, Andre E. Punt

Examples

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)
)
data_file <- write_data_file(data_test, dir = tempdir(), file_name = "test.dat")
#> ℹ Input 'dat' doesn't contain a column called 'count'; adding one via tally_repeats()
#> ℹ Total observations: 20
#> ℹ Aggregated unique combinations: 12
#> ℹ Range of observed ages in the data: 5 - 10
#> ℹ Number of readers: 3
#> ℹ Max age not specified; using 15 which is the multiple of 5 which is >120% of the observed maximum
#> ℹ Minus group set to the minimum observed age 5
#> ℹ Plus group set to the maximum observed age 10
#> ℹ Reference age not specified; using 7 = floor(median(c(minusage, plusage)))
#> ℹ Writing data file to /tmp/Rtmpk1RUGZ/test.dat