run_gapctd: Process an oce object using the gapctd workflow (R workflow)

In afsc-gap-products/gapctd: Process CTD data from bottom trawl surveys

Process an oce object using the gapctd workflow (R workflow)

Description

Run gapctd modules in the order described in Rohan et al. (2023) to process data from an oce object.

Usage

run_gapctd(
  x,
  haul_df,
  return_stage = "full",
  ctd_tzone = "America/Anchorage",
  ctm_pars = list(),
  align_pars = c(),
  cal_rds_path = NULL,
  cor_var = "conductivity"
)

Arguments

x	oce object
haul_df	data.frame containing haul data from RACEBASE that includes metadata for the cnv file.
return_stage	Character vector denoting which stages of processing should be included in the output (options "typical", "split", "align", "tmcorrect", "full"). Can return multiple stages simultaneously. Default = "full"
ctd_tzone	timezone for CTD as a character vector or numeric that is valid for POSIXct.
ctm_pars	Used for remedial cell thermal mass corrections. Optional list of parameters to use for cell thermal mass correction. Must contain alpha_C and beta_C.
align_pars	A list object with alignment parameters for a variable, e.g., list(temperature = -0.5)
cal_rds_path	Filepath to RDS containing calibration parameters. Required for oxygen data processing.
cor_var	Channel to use for optimizing temperature alignment. For exploratory purposes only.

Value

A list of oce objects at stages of processing specified in return_stage.

Author(s)

Sean Rohan

References

Rohan, S. K., Charriere, N. E., Riggle, B., O’Leary, C. A., and Raring, N. W. 2023. A flexible approach for processing data collected using trawl-mounted CTDs during Alaska bottom-trawl surveys. U.S. Dep. Commer., NOAA Tech. Memo. NMFS-AFSC-475, 43 p.

afsc-gap-products/gapctd documentation built on March 5, 2025, 3:42 a.m.