januarharianto/respR: respR 1.1.0

Lots of updates! First, we have a new function, calc_pcrit(), which we will use to include new methods in the future. We've also made some improvements to import_file() with increased support to more files from Vernier, PRESENS and Loligo systems.

Vignettes have been migrated into a new repository on GitHub, and are now updated separately. This gives us several advantages -- the documentation can be updated without needing to compile a new package, and the size of the package is significantly reduced. Users can also contribute to the documentation more easily now that it is not tied to the package.

• NEW: You can now grab the reference for respR by running citation("respR").
• NEW: Loading respR will print a startup message containing links to our published manuscript and vignettes.
• NEW: inspect() can now plot data with multiple columns when more than 2 columns are detected. For some people, this may provide a great overview of the data.
• NEW: calc_pcrit() is a new function that will be developed in parallel to the current pcrit() function. In the future we intend to use calc_pcrit() to incorporate new methods.
• NEW: import_file() supports even more files! Added more parsers for Vernier, PRESENS and Loligo systems.
• NEW: format_time() can now calculate time elapsed even if date information is not provided (e.g. "HMS"-only data).
• NEW: The by argument in auto_rate(), calc_rate(), calc_rate.bg() and subset_data() is now more forgiving with string input values (e.g. "o2", "O2", "oxygen" and "Oxygen" are recognised). To achieve this we created a string matching function, verify_by() which uses brute force matching to recognise different ways of writing the same text.

• convert_DO():
  • FIX: Argument for "P" (pressure) was ignored even when a value was already specified, resulting in the default used. The function will now respect the "P" value provided.
  • FIX: The error message for an unrecognised unit was... cryptic. It has been changed and will now instruct the user on the proper syntax required to recognise units properly.
• inspect():
  • FIX: Positive rates were not reflected accurately in plots.
  • FIX: Plot of rolling regression was not sensitive for smaller changes in datasets. The rolling window has been reduced to 10% of the length of the dataset to address this.
• convert_rate():
  • FIX: Now stops if a "mass" argument is provided but "output.unit" is not a mass-specific unit.
  • FIX: Properly accepts objects of class calc_rate.bg.
  • FIX: Optimised the syntax for the recognition of output.unit in the code.
• calc_rate.ft():
  • FIX: Critical error in returned rates sometimes outputting values with the wrong sign.
  • FIX: Optimised code - the "time" argument has been removed as it was not used.
  • FIX: Properly accepts objects of class inspect.
• pcrit():
  • FIX: Properly accepts objects of class inspect and inspect_data. Please note that the inspect_data() function is deprecated and will be removed in the near future.