------------------------------------------------- version 2.0.1, 2024-11-22 - import_firesting(): corrected a bug when a channel was turned off but still displayed in text file. ------------------------------------------------- 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. ------------------------------------------------- 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. ------------------------------------------------- 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 ------------------------------------------------- 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. ------------------------------------------------- version 1.2.1, 2020-11-04 - import_*(): improved compatibility with importing data files containing non-UTF-8 characters. ------------------------------------------------- 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. ------------------------------------------------- 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. ------------------------------------------------- version 1.0.2, 2020-01-24 - import_presens(): fixes an error when Fibox 4 files were exported with PreSens Datamanager. ------------------------------------------------- version 1.0.1, 2019-09-26 - import_firesting(): now can tolerate files with less than four channels calibrated. ------------------------------------------------- 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 ------------------------------------------------- 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. ------------------------------------------------- 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 ------------------------------------------------- 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 ------------------------------------------------- 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 ------------------------------------------------- version 0.3.1, 2016-12-31 - calc_MO2(): parameter added: "good_data" which allows identified O2 observations to be excluded from analyses ------------------------------------------------- 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 ------------------------------------------------- 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 ------------------------------------------------- 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 ------------------------------------------------- version 0.1.1, 2016-08-23 - predict_pH(): fixed a bug where a single NA was returned if any NAs were provided ------------------------------------------------- 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