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version 2.0.2, 2025-04-17
- calc_MO2():		when a single numeric value is entered as the bin width, the binning algorithm now starts the first bin with the first observation regardless of the numeric value of the duration input (e.g. if the data start at minute 23.17 in the O2 sensor output file and the bin widths are 10 minutes, then the first bin will be from minute mark 23.17 to 33.16).
- import_witrox():	fixed a bug when importing files with a non-English time locale.
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version 2.0.1, 2024-11-22
- import_firesting():		corrected a bug when a channel was turned off but still displayed in text file.
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version 2.0.0, 2024-07-18
- calc_pcrit() and plot_pcrit():	updated so that the classical "breakpoint" method of analysis is used by default. If other methods, or all methods are desired, they should be specified with the "method" parameter.
- calc_pcrit() and plot_pcrit():	for convenience, the output of calc_MO2() can now be inputted directly into these Pcrit functions with the mo2_data parameter, instead of adding po2 and mo2 parameters separately.
- closed():		clarified the usefulness of this function in documentation. Useful for estimating Pcrit trial length. Not ideal for analyzing collected data.
- calc_MO2():		corrected the "binning" behavior to not reuse data in multiple bins when a dataframe was provided for bin_width.
- make_bins():		(hopefully) clarified documentation and how to use make_bins(). Reversed order of rows from previous versions.
- conv_o2():	added support for nmol_per_ml
- For your convenience, added aliases so that calc_mo2() will work as calc_MO2() (for when you forget to capitalize the MO2 part. Same for Q10(), max_MO2(), and scale_MO2(). calc_q10() is now an alias for Q10().
- conv_o2():	No longer breaks when sal=NULL, but instead converts sal to 35psu (the default) and sends out a warning.
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version 1.5.0, 2024-02-09
- import_pyroscience_workbench():	new function: Import data from Pyroscience Workbench.
- import_firesting():	updated documentation to reflect the deprecated status of the software this supports.
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version 1.4.0, 2023-07-06
- adj_by_temp():		new function: Predict biological parameters at a new temperature.
- Q10():				fixed an error in one of the examples
- Q10():				improved documentation to be explicit that any temperature-dependent biological value could be used (e.g. Pcrit) and not just rates.
- calc_MO2():			improved readability of the documentation
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version 1.3.0, 2021-03-05
- calc_E():				new function: Calculate E temperature coefficient.
- calc_alpha():			includes an added parameter (avg_top_n) to calculate alpha based on the average of a defined number of observations rather than just the single highest value.
- calc_b():				added a "b0_start" parameter so the user can adjust the starting b0 value for the "nls" method when working with a tricky dataset to converge. Thanks to Alyssa Andres for the suggestion.
- calc_b():				can now handle 0 values in either the mass or MO2 parameters when using the "lm" mode.
- calc_MO2():			added a TEMP_MEAN column to the output data frame so that temperature within bins is also included. Thanks to Britney Firth for the suggestion.
- plot_pcrit():			improved the clarity of the plot by color coordinating the plot title.
- Q10():				the method of Q10 determination was changed from a nonlinear regression of R_vec values to a linear regression of log10(R_vec) values. This improves the accuracy and speed of determining the best Q10 value.
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version 1.2.1, 2020-11-04
- import_*():			improved compatibility with importing data files containing non-UTF-8 characters.
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version 1.2.0, 2020-08-14
- calc_alpha():			new function: Calculate the oxygen supply capacity (alpha).
- calc_pcrit():			added functionality to calculate Pcrit-alpha and Pcrit-LLO.
- calc_pcrit():			added a "return_models" parameter to optionally return a list of converged model parameters for subsequent personalized analyses. Thanks to Stefan Mucha for the suggestion.
- plot_pcrit():			added functionality to plot Pcrit-alpha and Pcrit-LLO.
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version 1.1.0, 2020-04-29
- calc_b():				added a "method" parameter, which allows the user to use a linear regression of log10 values rather than the default nonlinear regression, if desired.
- plot_pcrit():			allows plotting of just the MO2 v PO2 if Pcrit cannot be calculated.
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version 1.0.2, 2020-01-24
- import_presens():		fixes an error when Fibox 4 files were exported with PreSens Datamanager.
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version 1.0.1, 2019-09-26
- import_firesting():		now can tolerate files with less than four channels calibrated.
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version 1.0.0, 2019-05-24
- calc_pcrit():			new function: Calculate Pcrit (hypoxia tolerance)
- plot_pcrit():			new function: Plot Pcrit (hypoxia tolerance)
- calc_b():			output changed from a numeric value for b to a list of 1. the b value and 2. a vector of b0 values
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version 0.7.0, 2018-08-12
- make_bins():			new function: Make time bins for MO2 calculations.
- calc_b():			improved the ability to converge on the b value.
- calc_MO2():			fixed an issue where an error was returned if the bin_width dataframe had a 0 value.
- calc_b():			fixed an issue where the returned value was incorrect.
- import_firesting():		fixed an issue with the example.
- guess_TA():			fixed an issue where an error message would improperly say salinity was outside of bounds when temperature was outside of bounds.
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version 0.6.0, 2018-01-23
- import_presens():		added support for PreSens SDR SensorDish Reader txt files
- calc_MO2():			added support to enter a data frame as an argument for the "bin width" parameter
- calc_MO2():			fixed an issue where an error would be returned if an entire bin was full of O2 = NA
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version 0.5.0, 2017-11-01
- import_firesting():		now supports "Firesting Logger" software and 1st generation FireStingO2 meter
- Q10():			option added to return an nls object with the model fit if vectors are provided
- Q10():			fixed a bug where the returned value was 1 when the first two elements of T_vec were identical
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version 0.4.0, 2017-05-27
- calc_MO2():			parameter added: "pH" which allows pH data to be summarized along with oxygen and duration data for each bin
- calc_MO2():			parameter added: "time" to include time mean and range in output
- Q10():			added new functionality allowing a vector of rate and temperature values to be input to return the best fitting Q10 value
- calc_MO2():     		columns MEAN_DURATION, MEAN_O2, and MEAN_PH were renamed to DUR_MEAN, O2_MEAN, and PH_MEAN, respectively
- calc_MO2():     		the DUR_RANGE column in the returned data frame is no longer rounded
- calc_MO2():     		"bad" data identified by the parameter "good_data" now split their bin so that linear regressions are not fit through data that contain bad observations in the middle
- conv_o2():			added support for "volumes_percent"
- conv_nh4():			conv_NH4() was renamed and includes support for "mg_NH3" and "umol_NH3"
- predict_nh3():		predict_NH4() was renamed and now returns a list of NH3, NH4, and TAN
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version 0.3.1, 2016-12-31
- calc_MO2():			parameter added: "good_data" which allows identified O2 observations to be excluded from analyses
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version 0.3.0, 2016-11-29
- calc_b():			new function: Calculate the metabolic scaling coefficient, b
- calc_MO2():			new function: Calculate metabolic rate
- conv_resp_unit():		new function: Convert units related to respirometry
- import_firesting():		new function: Import data from a FireSting O2 transmitter
- conv_o2():			added support for ug_per_l and ug_per_kg
- flush_o2():			now returns just the missing value(s) rather than the missing value(s) within a list
- flush_water():		now returns just the missing value(s) rather than the missing value(s) within a list
- flush_water():		now gives a meaningful error message when parameters have a length >1 and plot = TRUE
- Q10():			now returns just the missing value(s) rather than the missing value(s) within a list
- scale_MO2():			now returns just the missing value(s) rather than the missing value(s) within a list
- import_presens():		improved efficiency
- import_witrox():		improved efficiency
- predict_pH():			improved efficiency
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version 0.2.0, 2016-10-07
- closed():			new function: Closed respirometry
- import_presens():		new function: Import data from a PreSens O2 transmitter
- import_witrox():		new function: Import data from a Loligo Systems Witrox transmitter
- scale_MO2():			new function: Scale metabolic rate by size
- conv_o2():			added support for mmol_per_l and mmol_per_kg
- flush_o2():			added support for calculating any parameter from the others, not just calculating final O2.
- mean_pH():			returns an NA rather than error when pH = NULL
- co2_*.R():			improved documentation
- flush_water():		improved documentation
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version 0.1.2, 2016-09-02
- guess_TA():			now allows calculations if salinity is <= 5 psu outside the bounds, but with a warning.
- guess_TA():			fixed a bug where an error occurred if any NAs were provided
- predict_pH():			fixed a bug where an error occurred if any NAs were provided
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version 0.1.1, 2016-08-23
- predict_pH():			fixed a bug where a single NA was returned if any NAs were provided
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version 0.1.0, 2016-08-22
- co2_add():			new function
- co2_flush():			new function
- co2_rate():			new function
- conv_NH4():			new function
- conv_o2():			new function
- correct_bubble():		new function
- flush_carb():			new function
- flush_o2():			new function
- flush_water():		new function
- goal_flush_pH():		new function
- guess_TA():			new function
- guess_when():			new function
- max_MO2():			new function
- mean_pH():			new function
- min_flow():			new function
- peri_pump():			new function
- predict_NH4():		new function
- predict_pH():			new function
- Q10():			new function
- RQ():				new function
