Read a return bundle

The inverse of write_transport. Optional parts that a site did not produce come back as NULL rather than erroring.

Usage

read_transport(dir, sample_id = NULL)

Arguments

dir

Directory holding the bundle.

sample_id

Sample identifier, which is also the filename prefix. If NULL, it is inferred from the single *_transport_summary.csv present, and an error is raised if there is more than one.

Value

A list of six elements:

• sample_id: the identifier the bundle was written under, whether it was supplied or inferred from the filenames.

• summary, named: the two tables described in transport_plateau.

• caps_agreement, sample_info, flow: the optional parts, or NULL where the site did not produce them.

See also

write_transport, transport_plateau.

Examples

# \donttest{
ptsd_data <- rename_ptsd_columns(
  simulated_ptsd_genpop[1:400, c("patient_id", paste0("S", 1:20))],
  id_col = "patient_id")
fit <- score_all_combinations(ptsd_data, n_symptoms = 3, n_required = 2,
                              show_progress = FALSE)
plateau <- compute_plateau(fit, delta = 1)
bundle <- transport_plateau(
  ptsd_data,
  plateau_specs = list(list(derivation = "example", rule_form = "flat_2_3",
                            delta = 1, n_required = 2, clusters = NULL,
                            sets = plateau$sets$combination_id)),
  named_specs = list(list(derivation = "example", rule_form = "flat_2_3",
                          n_required = 2, clusters = NULL,
                          sets = fit$combination_id[1:3], ranks = 1:3)),
  sample_id = "site_a"
)

out <- file.path(tempdir(), "transport_roundtrip")
dir.create(out, showWarnings = FALSE)
write_transport(bundle, out)
#> ✔ Wrote 2 files for "site_a" to /tmp/Rtmp2dnlav/transport_roundtrip.
#> ℹ Return all of them, and nothing else.

returned <- read_transport(out)
returned$sample_id
#> [1] "site_a"
returned$summary
#>   sample_id payload_id derivation rule_form delta      metric n_sets       min
#> 1    site_a         NA    example  flat_2_3     1          ba      1 0.9204812
#> 2    site_a         NA    example  flat_2_3     1 sensitivity      1 0.9213483
#> 3    site_a         NA    example  flat_2_3     1 specificity      1 0.9196141
#>          q1    median        q3       max
#> 1 0.9204812 0.9204812 0.9204812 0.9204812
#> 2 0.9213483 0.9213483 0.9213483 0.9213483
#> 3 0.9196141 0.9196141 0.9196141 0.9196141
unlink(out, recursive = TRUE)
# }