NEWS

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respirometry 2.0.1 (2024-11-22)

• import_firesting(): corrected a bug when a channel was turned off but still displayed in text file.

respirometry 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.

respirometry 1.5.0 (2024-02-10)

• import_pyroscience_workbench(): new function: Import data from Pyroscience Workbench.
• import_firesting(): updated documentation to reflect the deprecated status of the software this supports.

respirometry 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

respirometry 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.

respirometry 1.2.1 (2020-11-04)

• import_*(): improved compatibility with importing data files containing non-UTF-8 characters.

respirometry 1.2.0 (2020-08-26)

• 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.

respirometry 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.

respirometry 1.0.2 (2020-01-26)

• import_presens(): fixes an error when Fibox 4 files were exported with PreSens Datamanager.

respirometry 1.0.1 (2019-09-27)

• import_firesting(): now can tolerate files with less than four channels calibrated.

respirometry 1.0.0 (2019-05-27)

• 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

respirometry 0.7.0 (2018-08-13)

• 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.

respirometry 0.6.0 (2018-01-24)

• 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

respirometry 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

respirometry 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

respirometry 0.3.1 (2016-12-31)

• calc_MO2(): parameter added: "good_data" which allows identified O2 observations to be excluded from analyses

respirometry 0.3.0 (2016-11-30)

• 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

respirometry 0.2.0 (2016-10-08)

• 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

respirometry 0.1.2

• 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

respirometry 0.1.1

• predict_pH(): fixed a bug where a single NA was returned if any NAs were provided

respirometry 0.1.0 (2016-08-23)

• 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