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Combine saved checkpoint files from a checkpointed cleangrowth() run

Source: R/cleangrowth_checkpoint.R
cleangrowth_checkpoint_combine.Rd

Reads all checkpoint .rds files from a directory and combines them into a single data.table. Use this when a checkpointed cleangrowth run (checkpoint_dir set) completed all checkpoints but the combine step failed - you can re-combine without re-running the algorithm.

Usage

cleangrowth_checkpoint_combine(
  checkpoint_dir,
  id_order = NULL,
  log_file = NULL,
  quietly = FALSE,
  verbose = FALSE
)

Arguments

checkpoint_dir

Directory containing checkpoint .rds files named checkpoint_0001.rds, checkpoint_0002.rds, etc.

id_order

Optional vector of id values specifying the desired output row order (typically your_data$id). If NULL, rows are returned in checkpoint order (subjects grouped together but not in the original row order).

log_file

Optional path to append log messages.

quietly

Logical (default FALSE). When FALSE, prints a short start and completion line (and writes them to log_file if set). When TRUE, the console is silent; log_file still receives the log.

verbose

Logical (default FALSE). When TRUE, additionally prints the per-file read progress. Implies quietly = FALSE.

Value

A long-format data.table with growthcleanr's standard column names (id, subjid, param, agedays, sex, measurement, plus result columns). Unlike cleangrowth(), it does not restore the user's column names, carried-through columns, or wide/semi-wide layout; if growthcleanr generated id values (because id was missing or not unique), id holds those generated values.

Details

All .rds files matching checkpoint_NNNN.rds in checkpoint_dir are read and combined in numeric order. Every matching file is included, so the directory should hold checkpoints from a single run only. (A checkpointed cleangrowth() run with checkpoint_resume = FALSE, the default, removes earlier checkpoint files from the directory at the start, so after a run only that run's files remain.)

See also

cleangrowth_checkpoint

Examples

if (FALSE) { # \dontrun{
# If the combine step failed at the end of a run, re-combine like this:
result <- cleangrowth_checkpoint_combine(
  checkpoint_dir = "results/gc_checkpoints",
  id_order       = dt$id   # original row order; needs a unique id column named id
)
saveRDS(result, "results/gc_output.rds")
} # }