Man pages for afsc-gap-products/gapctd
Process CTD data from bottom trawl surveys
| align_var | Align variables in time |
| append_haul_data | Find cast times and metadata for a haul (R workflow) |
| assign_metadata_fields | Assign metadata fields (R workflow) |
| bin_average | Bin average: Average variables by depth/pressure bin |
| calc_bottom_mean_oce | Calculate means for an oce object |
| calc_fixed_depth_var | Estimate value of a profile variable at a fixed depth |
| calc_fixed_depth_var_bt | Estimate value of a profile variable at a fixed depth |
| channel_correlation | Correlation between two channels (R workflow) |
| check_density_inversion | Check density inversion (R workflow) |
| conductivity_correction | Conductivity cell thermal inertia correction |
| convert_do_to_o2sat | Calculate oxygen saturation (percent) from dissolved oxygen... |
| ctm_correct_c_t | Conductivity thermal intertia correction factor (C[T]) |
| ctm_obj | Objective function for cell thermal mass calculations (R... |
| ctm_par_a | Conductivity thermal inertia correction parameter a |
| ctm_par_b | Conductivity thermal inertia correction parameter b |
| derive_eos | Derive EOS and GSW |
| derive_oxygen | Apply tau correction to oxygen voltage channel |
| df_to_ncdf | Data frame to netCDF (.nc) file |
| extract_calibration_xmlcon | Extract calibration parameters from xmlcon to a list |
| finalize_data | Move good and bad profiles to final directories (R workflow) |
| fixed_alignment | Calculate alignment correlation for fixed parameters |
| get_calibration_parameter | Extract variable from xmlcon file text |
| get_connected | Create a database connection using RODBC |
| get_haul_data | Get haul data from RACEBASE (R workflow) |
| hex_to_cnv | Convert SBE19plus V2 hex files to cnv |
| integer_to_conductivity | Convert SBE integer to conductivity |
| integer_to_ph | Convert SBE integer to pH |
| integer_to_pressure | Convert SBE integer to pressure |
| integer_to_temperature | Convert SBE integer to ITS-90 temperature |
| lowpass_filter | Low-pass filter |
| make_metadata_file | Calculate bottom variables and make metadata file from cast... |
| make_oce_ncdf | Make netCDF from profile and metadata rds files (R workflow) |
| make_oce_table | Write cast data to an oce or rds file |
| make_text_table | Write CTD data to a text file |
| median_filter | Median window filter |
| move_bad_rds | Remove rds files based on QA/QC flags (R workflow) |
| optim_align_par | Estimate channel alignment parameter (R workflow) |
| optim_ctm_pars | Optimize cell thermal mass correction parameters (R workflow) |
| oxygen_saturation | Calculate oxygen saturation (ml/l) |
| ph_calibration | Fit pH calibration parameters and generate new configuration... |
| phfit | This function fits pH calibration parameters This function... |
| profile_bld | Calculate bottom layer depth using a threshold method |
| profile_bld_from_t | Calculate bottom layer depth from temperature using a... |
| profile_cokelet_density_diff | Calculate density difference between reference depth and 30 m... |
| profile_mld_from_t | Calculate mixed layer depth from temperature using a... |
| profile_pycnocline | Calculate pycnocline depth as the maximum rate of increase in... |
| profile_tsrho_by_layer | Calculate temperature, salinity, and density for each layer |
| qc_check | Check profile for completeness (R workflow) |
| qc_flag_interpolate | Manually flag and interpolate bad data (R workflow) |
| remedial_ctm | UI and wrapper for split_ctm |
| review_oxygen_ph_profiles | Review oxygen and pH |
| review_profiles | Visually inspect temperature, salinity, and density profiles... |
| run_gapctd | Process an oce object using the gapctd workflow (R workflow) |
| section_oce | Section |
| select_best_method | Select best processing method (R workflow) |
| slowdown | Flag slowdowns and reversals |
| split_ctm | Remedial method to fix CTM errors using the best upcast or... |
| tau_par | Tau correction for dissolved oxygen voltage |
| ts_area | Calculate area between temperature-salinity curves (R... |
| vec_to_nc_class | Detect R vector class and return equivalent netCDF class |
| window_filter | Window filter |
| wrapper_flag_interpolate | Wrapper for qc_flag_interpolate (R workflow) |
| wrapper_run_gapctd | Wrapper function for run_ctd (R workflow) |
