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Write a return bundle

Source: R/transport.R
write_transport.Rd

Serialises exactly the files a site is expected to return, and nothing else. Every filename is prefixed with the sample identifier, so bundles from different sites remain distinguishable when they are loose files in one directory rather than in separate folders.

Usage

write_transport(
  x,
  dir,
  sample_info = NULL,
  flow = NULL,
  caps_agreement = NULL,
  session_info = FALSE
)

Arguments

x

A ptsdiag_transport object.

dir

Directory to write into. Required, and must already exist: the function never creates directories and never guesses a location, so a mistyped path fails rather than scattering files.

sample_info, flow

Named lists of aggregate descriptives, or NULL.

caps_agreement

A data frame of counts against a clinician interview, or NULL.

session_info

Whether to write sessionInfo() alongside. FALSE by default, so nothing about the local machine leaves it unless you ask.

Value

The paths written, invisibly.

Details

sample_info and flow must be plain lists of aggregates. They are written as JSON deliberately: a gtsummary or ggplot2 object would carry a reference to the source data inside it.

See also

read_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"
)

# Write into a temporary directory, then clean up
out <- file.path(tempdir(), "transport_example")
dir.create(out, showWarnings = FALSE)
write_transport(bundle, out)
#> ✔ Wrote 2 files for "site_a" to /tmp/Rtmp2dnlav/transport_example.
#> ℹ Return all of them, and nothing else.
list.files(out)
#> [1] "site_a_named_sets.csv"        "site_a_transport_summary.csv"
unlink(out, recursive = TRUE)
# }