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NEWS.md

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Wish list:

  • Figure out what to do if both DO and Cond have single point calibration - in which case either the start or the end of the calibration window will be missing.
  • Calculate conductivity calibration ratio - pulling from raw data.
  • Add tide height plots?

BuzzardsBay 0.1.0.9011

  • Fix bug with date times in prior deployment. Problem was that excel is changing the date format for the prior deployment which when read to add to report plots resulted in an error.

    • Add example data BD1/2024-09-23 (target) and BD1/2024-09-17 (prior deployment)
    • Add test to reproduce bug
    • Add new function format_csv_date_time() used to cleanup date time data that is either in the expected format or in the format excel changes it to. This is similar to format_csv_date() but works for date-time columns.

BuzzardsBay 0.1.0.9010

  • Fix namespace bug. tide_station_info is a dataset included in the package but was erroneously listed as an exported object. This caused the package to fail to install cleanly.

BuzzardsBay 0.1.0.9009

  • New convert_to_utc() allows converting the local date times to UTC utilizing the GMT offset that HOBOware uses in place of a timezone.

  • New function is_daylight() returns TRUE for date-times that correspond to daylight.

  • Update day and night plotting in reports to reflect actual sunrise and sunset time and increase contrast between day and night shading.

  • Add functions for estimating and plotting tide height: get_tideheight() and plot_tide_sun() NOTE, however, that due to limitation in the rtide package it doesn't work for most of the tide stations in Buzzards Bay and tide height has not been added to the reports.

  • Reports now include any portion of the prior deployment that is within six hours of the current deployment. In the static plots the last observation of the preceding deployment and the first of the current are both highlighted with a red circle.

BuzzardsBay 0.1.0.9008

  • Add a bunch more test data see setup_example_dir() for a description of the test data files and why they were added.
  • Update setup_example_dir() so that a subset of the data can be specified, in which case only that data is copied into the example directory.
  • qc_deployment() now works when conductivity is calibrated with a single calibration point. DO is not set up this way yet, and there is a conceptual problem that if both DO and Cond. use single point calibration than qc_deployment() cannot determine the start and end of the calibration window.
  • Add "calibration_points" to metadata for conductivity.
  • Delete duplicated "High Range" in conductivity column heading if present. The BD1 sensor is generating a "High Range High Range (μS/cm)" column.
  • Fix bug that caused sensor swaps to result in rejected placements due to overly strict data comparison with placements table.
  • Replace "temperature Temp" in calibrated CSV headings with "Temp" similar to the "High Range" issue this appears in some of the calibrated files for example in Ob1/2024-05-31 and subsequent deployments in the conductivity file.
  • Allow serial numbers to be missing from calibrated file headings. Again as in OB1/2024-05-31 calibrated conductivity. If they are missing then the SN is pulled from the details file to populate the metadata and the two are not checked against each other.

BuzzardsBay 0.1.0.9007

  • Allow dates in placements.csv to be either month/day/year or year-month-day
  • New internal function format_csv_date() takes text dates in either month/day/year or year-month-day and converts to year-month-day text. This is intended for using with dates from CSV files that might have been edited with excel which messes with dates.

BuzzardsBay 0.1.0.9006

  • Add 2024 example data - so now there are two example datasets.
  • setup_example_dir() return list has new item deployments which is a vector of deployment directories. The deployment item still exists and is the first item. It also sets up both deployment directories and metadata files for each year.
  • Fixed bug in the QAQC report code that caused temperature flags from the DO logger to be considered both temperature and DO flags when plotting.
  • Updated qc_deployment() and helper functions to handle changes in CSV file column names between 2023 and 2024 example data.
    It will now work with both formats.

BuzzardsBay 0.1.0.9005

  • Minor edits to README
  • Updated parse_do_details() and parse_cond_details()
    • Work with new 2024 example files
    • Have greater flexibility in identifying series names in each file.
      • in the conductivity file the site id and a number were added to the series name.
      • in the DO file "Conc" was dropped from the series name that is now: "Series: DO Adj, mg/L""
    • For both types of files the old and new versions should both be processed correctly with the updated code.

BuzzardsBay 0.1.0.9004

  • Add bb_options() for setting and retrieving global parameters which are stored in a private environment, bbp.
  • Move auto qc parameters from `[qc_deployment()] and helper functions into global parameters.
  • Add tide_station_info dataset containing locations of NOAA tide stations in Buzzard's bay.
  • Add inst/rmd/QAQC_report.rmd with plots and summary information to facilitate quality control and quality assurance.
  • Add make_deployment_report() to make QAQC report from data in a deployment directory.
  • qc_deployment() now makes the report automatically unless the new report argument is set to FALSE.

BuzzardsBay 0.1.0.9003

2024-05-10

  • Update example dataset. In prior example data the Conductivity didn't match in the DO and Cond. data and it should.
  • Update Details.txt processing to work with newer data that has different line endings. It now works with any combination of CR and LF line endings.
  • Add test for consistent conductivity and dropped duplicate conductivity column.
  • Add test for consistent calibration start and end time in the two details files and consolidated the start and end times in the metadata file.
  • Drop _flag columns. "Flags" covers all flags.
  • Adopt standard "year-month-day" date, and "year-month-day h:m:s" date time formats everywhere.
  • Add more checks for consistency against sites table and placements table.
    • Logger SN's must be in placement table at the site indicated by the deployment path.
    • Deployment date from path must match date of last observation in data.
  • Add range checks against sites table for DO, both Temperature Columns, DO Pct. Saturation, and
  • Add DO ratios to metadata - this is the "meter/titration value (mg/L)" divided by the "DO conc" from the DO details.txt file created by HOBOware for both the start and end calibrations
  • Add sites.csv and placements.csv to example data and to files created by setup_example_data()
  • Cut off the pre and post calibration observations from the head and tail of the file.
  • Add "pct_calibrated", "n_records", "pct_immediate_rejection", and "pct_flagged_for_review" to metadata.
  • Add warning if "pct_calibrated" is less than 95.

BuzzardsBay 0.1.0.9002

  • Add README.Rmd and NEWS.md files.
  • Update temperature flags so they indicate which dataset they are associated with.

BuzzardsBay 0.1.0.9001

Initial package