Run Seabird Data Processing using SBEBatch.exe

These functions generate suitable batch file specifications and run them using sbe_run_batch().

sbe_run_tool(
  tool,
  psa,
  input = NULL,
  con = NULL,
  output = sbe_temp_dir(),
  quiet = FALSE
)

sbe_psa_default(tool)

sbe_temp_dir()

is_sbe_temp_dir(path)

Arguments

tool	A vector of tool names. Currently supported names are alignctd, binavg, celltm, datcnv, derive, deriveteos_10, filter, loopedit, and wildedit.
psa	A vector of configuration files. See `sbe_psa_default()` for default configuration files for each tool.
input	A vector of input files. This can include the wildcard `*` to select multiple files.
con	A vector of .con or .xmlcon files, recycled along `input`.
output	An output directory, defaulting to `sbe_temp_dir()`.
quiet	Use `TRUE` to suppress non-error output.
path	A valid path in R.

Value

The output directory.

Examples

if (FALSE) {
# only works if SeaSoft has been installed
faroe_dir <- system.file("extdata/faroe", package = "sbe")
out_dir <- sbe_run_tool(
  "datcnv",
  psa = file.path(faroe_dir, "faroe.psa"),
  input = file.path(faroe_dir, "faroe.dat"),
  con = file.path(faroe_dir, "faroe.con")
)

out_sbe_cnv <- list.files(out_dir, full.names = TRUE)
read_sbe_cnv(out_sbe_cnv)
}