respR 2.2.0

Version 2.2.0 – 2023-01-06

This update focuses on extending to the flowthrough respirometry workflow the functionality introduced in v2.1 for exploring and selecting final rates. The online vignette has been updated with some examples.

==================================== New =======================================

NEW: convert_rate.ft - Objects containing multiple rates can now be plotted in three different ways to help explore the results and decide how to summarise them. This pairs particularly well with select_rate.ft for exploring and selecting a final reportable rate. NEW: select_rate.ft - New function for selecting from amongst multiple rates in convert_rate.ft objects in flowthrough respirometry analyses. It is actually a simple wrapper for the select_rate function, so you can use either. NEW: select_rate - has the additional methods rep_omit, rank_omit, and manual_omit for omitting rates. NEW: select_rate - has the additional methods intercept and slope for selecting based on the respective summary table columns. This is mostly useful for selecting from flowthrough rate results where these parameters can indicate the stability of the delta oxygen region rates are derived from (in other analyses slope is essentially equivalent to the rate).

=================================== Changes ====================================

CHANGE: convert_rate.ft - Output objects have been restructured and new elements (e.g. $dataframe) brought forward from the input objects to enable plotting. CHANGE: convert_rate - The y-axis range in the lower panel of type = "rate" plots now adapts to the range of rate values plotted if pos has been used. You can use this to get a better idea of range of rates in a particular region. CHANGE: In summary tables the rate_b1 column (the slope in the linear regression model used to calculate the rate) has been renamed to slope_b1.

==================================== Fixes =====================================

FIX: convert_rate.ft - Now correctly converts rates to output units using nanomoles (nmol) and picomoles (pmol) (e.g. pmol/min, nmol/hr/ug, etc.).

Version 2.1.0 – 2022-12-06

This is a huge update that finally introduces what many users have been asking for - full support for analysing intermittent-flow respirometry data. This was always possible but required use of more advanced R methods. Now - no more for loops!

This version introduces two new functions for easily extracting rates from every replicate in intermittent-flow data, and

There is also a major focus on exploring and filtering results to help with outputting a final reportable rate for an experiment. There is a large update to convert_rate which adds new visualisation options, and the new function select_rate which is ideal for exploring and filtering the results of analyses using almost any criteria you can think of and outputting a final rate. It works with both intermittent-flow results and the outputs of other analyses. See the updated vignettes here and here for examples.

================================ Highlights ====================================

==================================== New =======================================

=================================== Changes ====================================

==================================== Fixes =====================================

Version 2.0.2 – 2022-03-23

Minor changes to help documentation.

Version 2.0.1 – 2022-03-14

Only a month after 2.0.0, this is a quick update that fixes a few bugs, adds a couple of enhancements, and has quite a large revision to the newest function select_rate.

==================================== New =======================================

=============================== select_rate() ==================================

=============================== General Changes ================================

==================================== Fixes =====================================


Version 2.0.0 – 2022-02-17

It’s been a long time - over two and a half years (!) since the last update. We are happy to see respR being used by the respirometry community in that time. Amazingly we have picked up over 30 citations, so we are very grateful and happy that so many scientists are finding the package of use.

We are glad to announce that respR has reached version 2.0 and is finally available on CRAN.

v2.0 has been a massive and thorough update where almost every corner of the package has been revised, rewritten, streamlined and tested. In addition, we have added a lot of new functionality which you can read about below.

We have also updated and added even more vignettes, function guides and more on our brand new website detailing all the old and new functionality.

Unfortunately, a major version update inevitably comes with some code breaking changes, and this one is no exception. We thought long and hard about introducing changes that might break code written for v1.1, but made the decision to fix as many as possible of the inconsistencies, bugs, and poor design decisions we made while we had the chance with this major version update. The upside of this is that the package will be much easier to update in the future without breaking existing code.

We have created a page on the new website to detail how v2.0 code has changed and how you may go about revising your earlier code to update it. The good news is most of these changes will be very easy to make. If you have submitted code or are in the process of submitting it as part of a publication, we want this code to remain reproducible long into the future. See here for how you can link to resources that will allow anyone to run v1.1 code and keep these analyses reproducible.

We are happy to say the package has never been more stable and even easier to use, and it is now on a great base upon which to build future functionality. Here are the major changes in this version:

================================== HIGHLIGHTS ==================================

=============================== General Changes ================================

======================== Function specific changes =============================

================================== inspect() ===================================

================================ calc_rate() ===================================

================================ auto_rate() ===================================

=============================== adjust_rate() ==================================

=============================== convert_rate() =================================

================================== oxy_crit() ==================================

================================ import_file() =================================

================================ format_time() =================================

================================ convert_val() =================================

=============================== =================================

================================ convert_DO() ==================================

================================ unit_args() ===================================

================================= subsample() ==================================

=============================== subset_data() ==================================

============================== flowthrough data ================================

==================================== data ======================================

NEW: New example datasets

================================= S3 Methods ===================================

Version 1.1.1

This is the final release of v1 of respR.

There is only one change, the addition of function called installation_help. This function simply opens its own help file. It contains resources which may be helpful in running v1 code in the future, such as a list of dependencies and the latest versions known to work with v1.1.1, and how to install them. This is intended for users who have recently submitted v1.1 code as part of a publication, and investigators who may wish to reproduce their analyses in the future.

The reason this may be necessary is because version 2.0 of respR will be released shortly and contains several code-breaking changes which means code written using v1.x will fail to run or return the same results. Using the information in this file an investigator should be able to install respR v1.1.1 and its dependencies and reproduce these analyses.

Version 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 Features



This is a quick fix for images not showing in the online vignettes.

Version 1.0.5

This version is aimed at improving the functionality and usability of our conversion functions. We have decided to remove the default values for temperature and salinity inputs in convert_DO() and convert_rate() (i.e. switched t and S numerics to NULL). This was no easy decision, but we noticed that some users were running the functions by default without considering (or even knowing the existence of) these two important input variables. With this change, existing workflows using calc_DO() and calc_rate()are likely to break. Do note that this is a very rare modification – we know that changing core functionality that breaks prior code is not something to be taken lightly. Please update these two functions respectively.

Version 1.0.4

This version updates the new functions from 1.0.0 and tries to improve piping workflows.

Version 1.0.0

The big update! Maybe it’s time to submit to CRAN?

Version 0.1.0

Version 0.0.7

Version 0.0.6

We are getting close to a 0.1 release, which will be ready for CRAN.

Version 0.0.5

Version 0.0.4

Version 0.0.3

Version 0.0.2

Version 0.0.1