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NEWS
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gapctd 2.1.7 (December 16, 2024)
----------------------------------------------------------------
NEW FEATURES
- Added calc_fixed_depth_var() function to implement RACE/GAP
bathythermic surface temperature algorithm.
gapctd 2.1.6 (September 19, 2024)
----------------------------------------------------------------
IMPROVEMENTS
- Added vessel metadata field to netCDF outputs generated using
make_oce_ncdf(vessel_attributes = [data.frame]), where the
input data.frame includes the following fields:
- vessel: AFSC/RACE vessel code
- vessel_name: Name of the vessel
- imo: International Maritime Organization (IMO) code
- call_sign: Vessel's maritime call sign
- flag: Flag country of the vessel
- year_built: Year the vessel was built
gapctd 2.1.5 (September 4, 2024)
----------------------------------------------------------------
BUG FIX
- Add numbers0() function from GAPsurvey package. Needed to run
convert_ctd_btd() using only gapctd functions.
IMPROVEMENTS
- Added option to set instrument timezone in wrapp_run_gapctd().
gapctd 2.1.4 (August 29, 2024)
----------------------------------------------------------------
BUG FIX
- Fix error where convert_ctd_to_btd() did not require latitude.
gapctd 2.1.3 (April 18, 2024)
----------------------------------------------------------------
IMPROVEMENTS
- Add informative messages to convert_ctd_btd().
gapctd 2.1.2 (January 17, 2024)
----------------------------------------------------------------
BUG FIX
- Fix error in lowpass_filter() automatic freq_n selection when
freq_n is NULL.
gapctd 2.1.1 (December 11, 2023)
----------------------------------------------------------------
NEW FEATURES
- Added two new functions for conducting pH calibration, phfit()
and ph_calibration().
phfit fits calibration slope and offset
parameters to pH calibration data, like the ph fit DOS program
included with SBE Data Processing.
ph_calibration() runs phfit() then writes calibration param-
eters to a new configuration(.xmlcon) file.
IMPROVEMENTS
- Added new code examples to documentation.
gapctd 2.1.0 (December 4, 2023)
----------------------------------------------------------------
NEW FEATURES
- Added a window_filter() function the implements SBEDP methods
for boxcar, cosine, triangle, and Gaussian window filters.
FUNCTIONALITY CHANGES
- Removed SBE Data Processing workflow functions from the package
due to lack of capacity to support parallel development. However,
processing methods will be implemented.
- hex_to_cnv() now expects default arguments for output_channels
and output_sig_digits.
BUG FIX
- Replaced instances where the default buoyancy frequency threshold
for density inversion checks was -1e-4 with the correct default
value of -1e-5, based on PMEL protocols.
IMPROVEMENTS
- Removed purrr, tibble, and stringr from dependencies and imports.
gapctd 2.0.2 (November 10, 2023)
----------------------------------------------------------------
IMPROVEMENTS
- Change section_oce() to allow sectioning when there are no
pressure data.
- Add error check to bin_average() for cases when there are no
data quality flags.
gapctd 2.0.1 (October 20, 2023)
----------------------------------------------------------------
BUG FIX
- Change filepath handling in align_oxygen() to use relative path
naming. This change allows the user to move the data processing
directory between setup and oxygen alignment steps.
IMPROVEMENTS
- Make qc_flag_interpolate() display oxygen units during flag/
interpolate step.
gapctd 2.0.0 (October 19, 2023)
----------------------------------------------------------------
This release includes substantial changes to data processing
functions in order to process data from SBE43 dissolved oxygen
and SBE18 pH sensors.
NEW FEATURES
- Modifications were made to numerous core functions to handle
data from dissolved oxygen and pH channels while retaining
functionality when the sensors are not used.
- derive_oxygen(): Converts SBE43 voltage into oxygen (ml/l)
using calibration parameters for the DO sensors. Currently
allows tau correction to voltage but not the hysteresis correct-
ion. References:
- Edwards, B., Murphy, D., Janzen, C., Larson, A.N., 2010.
Calibration, response, and hysteresis in deep-sea dissolved
oxygen measurements. J. Atmos. Ocean. Technol. 27, 920–931.
https://doi.org/10.1175/2009JTECHO693.1
- Garcia, H.E., Gordon, L.I., 1992. Oxygen solubility in seawater:
Better fitting equations. Limnol. Oceanogr. 37, 1307–1312.
https://doi.org/10.4319/lo.1992.37.6.1307
- extract_calibration_xmlcon(): Extracts calibration parameters
for temperature, pressure, conductivity, dissolved oxygen, and
pH sensors from a CTD configuration (.xmlcon) file.
- align_oxygen(): Aligns oxygen channel data using user-specified
offset value.
- wrapper_align_oxygen(): Aligns oxygen for multiple user-specified
alignment offset values using align_oxygen().
- select_best_oxygen_method(): Similar to select_best_method()
for temperature/salinity/density, an interface for users to
select the best oxygen alignment value based on visual inspection
of oxygen profiles.
- review_oxygen_ph_profiles(): Similar to review_profiles() for
temperature/salinity/density, an interface for users to select
oxygen and pH profiles to include in the final data product.
FUNCTIONALITY CHANGES
- qc_flag_interpolate(): Allows "oxygen" and "ph" as arguments
to 'review'
- .check_duplicates: Internal (AFSC) use. Checks hex files for
duplicate casts and multiple serial numbers to avoid processing
errors.
gapctd 1.5.1 (September 22, 2023)
----------------------------------------------------------------
FUNCTIONALITY CHANGES
- New error check for the Temperature-Salinity Error method in
run_gapctd() to handle cases where the temperature-salinity
area method doesn't converge because temperature-salinity curves
from upcasts and downcasts produce identical values.
- Added internal function to gapctd workflow to check for duplicate
casts and multiple CTDs in /data/ to avoid data processing errors.