Files in afsc-gap-products/gapctd
Process CTD data from bottom trawl surveys

.Rbuildignore

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.github/workflows/secretScan.yml

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

NEWS

R/align_oxygen.R R/alignment_functions.R R/calc_fixed_depth_bt.R R/calc_fixed_depth_var.R R/correct_density_inversion.R R/ctm_functions.R R/df_to_netcdf.R R/hex_to_cnv.R R/phfit.R R/profile_calcs.R R/qc_check.R R/review_profiles.R R/run_gapctd.R R/sbe_modules.R R/setup_gapctd_directory.R R/slowdown.R R/split_ctm.R R/utils.R R/window_filter.R README.md

analysis/.gitignore

analysis/00_select_stations.R analysis/01_get_data.R analysis/02_profiling_rate.R analysis/03_dynamic_correction_pars.R analysis/04_proportion_methods.R analysis/05_TSrate_methods.R analysis/06_align_segments.R analysis/07_map.R analysis/2024_ai_dissolved_oxygen.R analysis/97_tsa_spd_method.R analysis/98_tsa_spd_examples.R analysis/99_process_examples.R

analysis/algorithm_check/20240507/HAUL0002.BTD

analysis/algorithm_check/20240507/HAUL0002.BTH

analysis/algorithm_check/20240507/HAUL0162.BTD

analysis/algorithm_check/20240507/HAUL0162.BTH

analysis/algorithm_check/20240507/HAUL0176.BTD

analysis/algorithm_check/20240507/HAUL0176.BTH

analysis/algorithm_check/20240507/compare_racebase_to_algorithm.R

analysis/algorithm_check/20240507/st_comparison_20240507.csv

analysis/algorithm_check/20240517/HAUL0003.BTD

analysis/algorithm_check/20240517/HAUL0004.BTD

analysis/algorithm_check/20240517/HAUL0005.BTD

analysis/algorithm_check/20240517/HAUL0006.BTD

analysis/algorithm_check/20240517/HAUL0007.BTD

analysis/algorithm_check/20240517/HAUL0008.BTD

analysis/algorithm_check/20240517/HAUL0009.BTD

analysis/algorithm_check/20240517/HAUL0010.BTD

analysis/algorithm_check/20240517/HAUL0011.BTD

analysis/algorithm_check/20240517/HAUL0012.BTD

analysis/algorithm_check/20240517/HAUL0018.BTD

analysis/algorithm_check/20240517/HAUL0023.BTD

analysis/algorithm_check/20240517/Surface_Temp_Algorithm_Testing_R_to_Python_Javascript.xlsx

analysis/algorithm_check/20240517/st_comparison_20240517.csv

analysis/algorithm_check/20241216/Surface_Temp_Algorithm_Testing_R_to_Python_Javascript.xlsx

analysis/algorithm_check/20241216/compare_st_algorithm_20240517.R analysis/algorithm_check/20241216/compare_st_algorithm_20241216.R

analysis/algorithm_check/20241216/st_comparison_20240517.csv

analysis/algorithm_check/20241216/st_comparison_20241216.csv

analysis/ctd_trawl_height.R analysis/derive_and_bin.R analysis/efh_salinity.R analysis/ex_gapctd_workflow.R

analysis/ex_netcdf.zip

analysis/find_spd_profiles.R analysis/get_dynamic_correction_pars.R analysis/make_cast_pdfs.R analysis/make_pre_2019_summary.R analysis/temperature_salinity_sound_speed.R analysis/test_better_map.R analysis/test_oxygen_alignment.R analysis/test_r_workflow.R

assets/demos/2023_12_SCRUG/data/19-8102_Deploy2021.xmlcon

assets/demos/2023_12_SCRUG/data/202101_162_150_BT.csv

assets/demos/2023_12_SCRUG/data/2021_07_08_0001.hex

assets/demos/2023_12_SCRUG/data/2021_07_08_0001_raw.cnv

assets/demos/2023_12_SCRUG/data/2283_20170723_0733_downcast.nc

assets/demos/2023_12_SCRUG/data/2283_20170723_0733_upcast.nc

assets/demos/2023_12_SCRUG/data/GAPCTD_2021_EBS

assets/demos/2023_12_SCRUG/data/GAPCTD_2021_EBS.nc

assets/demos/2023_12_SCRUG/data/GAPCTD_2021_EBS.rds

assets/demos/2023_12_SCRUG/ex1_gapctd_data_product.R assets/demos/2023_12_SCRUG/ex2_sbe19plus_processing.R assets/demos/2023_12_SCRUG/ex3_sbe39tdr_cleaning.R assets/demos/2023_12_SCRUG/ex4_ctdnv_cleaning.R

assets/demos/compare_filters/SBE19plusV2_8106_ph_DO_leg2.xmlcon

assets/demos/compare_filters/SBE19plus_01908106_2023_06_14_0008_raw.cnv

assets/demos/compare_filters/SBE19plus_01908106_2023_06_14_0008_raw_boxcar.cnv

assets/demos/compare_filters/SBE19plus_01908106_2023_06_14_0008_raw_cosine.cnv

assets/demos/compare_filters/SBE19plus_01908106_2023_06_14_0008_raw_gaussian.cnv

assets/demos/compare_filters/SBE19plus_01908106_2023_06_14_0008_raw_median.cnv

assets/demos/compare_filters/SBE19plus_01908106_2023_06_14_0008_raw_triangle.cnv

assets/demos/compare_filters/boxcar_filter.psa

assets/demos/compare_filters/calibration_parameters.rds

assets/demos/compare_filters/compare_sbedp_gapctd_filters.R

assets/demos/compare_filters/cosine_filter.psa

assets/demos/compare_filters/gaussian_filter.psa

assets/demos/compare_filters/median_filter.psa

assets/demos/compare_filters/triangle_filter.psa

bottom_salinity.nc

doc/0_batch_processing.md doc/0_batch_processing.rmd

doc/2021_06_24_0001.cnv

doc/SBE19plus_01908106_2023_06_19_0001.cnv

doc/assets/batch_screenshots/align_ctd_method_salinity_104.png

doc/assets/batch_screenshots/align_plot.png

doc/assets/batch_screenshots/batch_0.png

doc/assets/batch_screenshots/batch_1.png

doc/assets/batch_screenshots/batch_10.png

doc/assets/batch_screenshots/batch_11.png

doc/assets/batch_screenshots/batch_12.png

doc/assets/batch_screenshots/batch_13.png

doc/assets/batch_screenshots/batch_14.png

doc/assets/batch_screenshots/batch_15.png

doc/assets/batch_screenshots/batch_16.png

doc/assets/batch_screenshots/batch_2.png

doc/assets/batch_screenshots/batch_3.png

doc/assets/batch_screenshots/batch_4.png

doc/assets/batch_screenshots/batch_5.png

doc/assets/batch_screenshots/batch_6.png

doc/assets/batch_screenshots/batch_7.png

doc/assets/batch_screenshots/batch_8.png

doc/assets/batch_screenshots/batch_9.png

doc/assets/batch_screenshots/mfi_1.png

doc/assets/batch_screenshots/mfi_2.png

doc/assets/batch_screenshots/mfi_3.png

doc/assets/batch_screenshots/mfi_4.png

doc/assets/batch_screenshots/mfi_5.png

doc/assets/batch_screenshots/mfi_6.png

doc/assets/cannot_finish_processing_1.png

doc/assets/cannot_finish_processing_2.png

doc/assets/cannot_finish_processing_3.png

doc/assets/cannot_finish_processing_4.png

doc/assets/ex2_profile_review.R

doc/assets/gapctd_workflow.png

doc/assets/r_process/13_finalize_data.png

doc/assets/r_process/1_setup_directory.png

doc/assets/r_process/1_setup_directory_1.png

doc/assets/r_process/1_setup_directory_2.png

doc/assets/r_process/5_run_gapctd.png

doc/assets/r_process/5_run_gapctd_1.png

doc/assets/r_process/5_run_gapctd_2.png

doc/assets/r_process/6_select_best_1.png

doc/assets/r_process/6_select_best_2.png

doc/assets/r_process/8_flag_interpolate.png

doc/assets/r_process/8_flag_interpolate_1.png

doc/assets/r_process/8_flag_interpolate_2.png

doc/assets/r_process/8_flag_interpolate_3.png

doc/assets/r_process/8_flag_interpolate_4.png

doc/assets/r_process/9_review_profiles.png

doc/assets/r_process/9_review_profiles_1.png

doc/assets/r_process/9_review_profiles_2.png

doc/batch_processing_steps.md doc/batch_processing_steps.rmd doc/convert_hex.R doc/convert_hex_files.Rmd doc/convert_hex_files.md

doc/convert_hex_files_files/figure-markdown_strict/do_ph-1.png

doc/convert_hex_files_files/figure-markdown_strict/hex_to_cnv-1.png

doc/data_processing_modules.Rmd doc/data_processing_modules.md

doc/data_processing_modules_files/figure-gfm/unnamed-chunk-1-1.png

doc/data_processing_modules_files/figure-gfm/unnamed-chunk-10-1.png

doc/data_processing_modules_files/figure-gfm/unnamed-chunk-14-1.png

doc/data_processing_modules_files/figure-gfm/unnamed-chunk-16-1.png

doc/data_processing_modules_files/figure-gfm/unnamed-chunk-16-2.png

doc/data_processing_modules_files/figure-gfm/unnamed-chunk-17-1.png

doc/data_processing_modules_files/figure-gfm/unnamed-chunk-2-1.png

doc/data_processing_modules_files/figure-gfm/unnamed-chunk-4-1.png

doc/data_processing_modules_files/figure-gfm/unnamed-chunk-6-1.png

doc/data_processing_modules_files/figure-gfm/unnamed-chunk-8-1.png

doc/ex1_processing.R doc/ex2_profile_review.R

doc/example_gapctd.nc

inst/CITATION

inst/extdata/atsea/DatCnv.psa

inst/extdata/atsea/atsea_getdata.bat

inst/extdata/example/19-8102_Deploy2021.xmlcon

inst/extdata/example/2021_06_24_0001.hex

inst/extdata/example/2021_06_24_0001_final.rds

inst/extdata/example/2021_06_24_0001_raw.cnv

inst/extdata/example/SBE19plusV2_8106_ph_DO_leg2.xmlcon

inst/extdata/example/SBE19plus_01908106_2023_06_19_0001.hex

inst/extdata/gapctd/DatCnv.psa

inst/extdata/gapctd/gapctd_getdata.bat

inst/extdata/nc/Bottom_Trawl_Survey_CTD_data_2008.nc

inst/extdata/nc/Bottom_Trawl_Survey_CTD_data_2009.nc

inst/extdata/nc/Bottom_Trawl_Survey_CTD_data_2010.nc

inst/extdata/nc/Bottom_Trawl_Survey_CTD_data_2011.nc

inst/extdata/nc/Bottom_Trawl_Survey_CTD_data_2012.nc

inst/extdata/nc/Bottom_Trawl_Survey_CTD_data_2013.nc

inst/extdata/nc/Bottom_Trawl_Survey_CTD_data_2014.nc

inst/extdata/nc/Bottom_Trawl_Survey_CTD_data_2015.nc

inst/extdata/nc/Bottom_Trawl_Survey_CTD_data_2016.nc

inst/extdata/nc/Bottom_Trawl_Survey_CTD_data_2017.nc

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

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

Files in afsc-gap-products/gapctd
Process CTD data from bottom trawl surveys

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

Files in afsc-gap-products/gapctd Process CTD data from bottom trawl surveys

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

Files in afsc-gap-products/gapctd
Process CTD data from bottom trawl surveys