Monthly Archives: January 2018

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‘FishResp’, version 0.2.0: stability and flexibility

Both the R package and its GUI implementation were upgraded to the version 0.2.0. New options for import, correction and calculation of respirometry data suppose to make ‘FishResp’ a more flexible tool than before. In addition, several bugs and technical problems were revealed and fixed, which should improve the stability of the software. Please, see the list of updates below to get detailed information on the changes applied to the new version of ‘FishResp’.

Major updates

•  seven new methods of slope extraction are integrated into the function extract.slope (including ones described in Chabot et al, 2016*)

•  ‘progressive’ method for correction of background respiration was split into ‘linear’ and ‘exponential’ in the function correct.meas

•  ability to work with different date formats (DMY, MDY and YMD) and time formats (24h, AM/PM)

•  several DO units are acceptable for analyzing respirometry data: mg O2/L, mmol O2/L, ml O2/L

•  two new functions convert.respirometry and convert.rMR were created to convert other DO units to acceptable ones. These functions represents modifications of the functions conv_o2 and DO.unit.convert from the packages ‘respirometry’ and ‘rMR’ packages, respectively.

GUI updates

•  new extensions module for integration with other R packages, scripts and functions

•  graphical interfaces for extensions ‘respirometry’ and ‘rMR’ (only converter functions have been used from those packages)

•  opportunity to create a log file to record commands and error messages on the hard drive

•  design structure is slightly changed due to major updates

•  ‘FishResp’ logo inserted into an empty graphical module

Minor updates

•  renamed the ‘Standard’ oxygen logger format to ‘FishResp’

•  new package dependencies: ‘mclust’, ‘respirometry’,’rMR

•  new trial datasets are used in the R package (see examples there)

•  DO unit is changed automatically in all plots after using the function input.info

•  change point and font sizes in all functions for a better readability of plots

•  legends to plots of the function QC.slopes were added

•  automatic plot was removed from the function extract.slopes

•  initial DO point is changed form 30s to 5s in the function import.test 

•  fixed a bug with plotting >24 slopes in the function QC.slopes

•  fixed a bug in functions import.meas and import.test, when the first Measure Phase is not ‘M1’

        •  fixed a bug in the ‘parallel’ method (now ‘linear’)

References

* Chabot, D., Steffensen, J. F., & Farrell, A. P. (2016). The determination of standard metabolic rate
in fishes. Journal of Fish Biology, 88(1), 81-121.