doc/assets/ex2_profile_review.R

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

# Examples of manually reviewing profiles
# Created by Sean Rohan <sean.rohan@noaa.gov>
# Updated: November 16, 2022

library(gapctd)

# Copy built-in example file and unzip to /output/ex_review_files/
ex_zip_path <- system.file(package = "gapctd", "extdata/example/ex_review_files.zip")
ex_dest_path <- gsub(pattern = system.file(package = "gapctd", "extdata/example/"),
                     replacement = here::here("output"),
                     x = ex_zip_path)
file.copy(from = ex_zip_path, to = ex_dest_path)

unzip(zipfile = ex_dest_path,
      exdir = here::here("output"))

# Select best method -----------------------------------------------------------------------------

# Review profile plots from data processing using four methods; choose the best method.
# Files chosen as the best will be renamed to end with "_best.rds"

gapctd::select_best_method(
  rds_dir_path = here::here("output", "ex_review_files"))


# Flag and interpolate --------------------------------------------------------------------------

# Visually inspect, flag, and interpolate
# Outputs written to /output/gapctd/ in rds files ending with "_qc.rds"

gapctd::wrapper_flag_interpolate(rds_dir_path = here::here("output", "ex_review_files"),
                                 review = c("density", "salinity"))


# Review ----------------------------------------------------------------------------------------

# Review profiles plots and select the casts that pass quality control checks.

gapctd::review_profiles(rds_dir_path = here::here("output", "ex_review_files"),
                        threshold = -1e-5, 
                        in_pattern = "_qc.rds")