FishResp: R Package and GUI Application for Analysis of Aquatic Respirometry Data

Abstract

32Intermittent-flow respirometry is widely used to measure oxygen uptake rates and subsequently 33 estimate aerobic metabolic rates of aquatic animals. However, the lack of a standard quality-control 34 software to detect technical problems represents a potential impediment to comparisons across studies. 35Here, we introduce 'FishResp', a versatile R package and its graphical implementation for quality-36 control and filtering of raw respirometry data. Our goal is to provide a straightforward, cross-platform 37and free software to help improve the quality and comparability of metabolic rate estimates for 38 reducing methodological fragmentation in the field of aquatic respirometry. FishResp accepts data from 39 various respirometry systems, allows users to detect potential mechanical problems which can occur 40 during oxygen uptake measurements (e.g. chamber leaking, poor water circulation), and offers six 41 options to correct raw data for microbial oxygen consumption. The software performs filtering of raw 42 data based on user criteria, and produces accurate and unbiased estimates of absolute and mass-specific 43 metabolic rates. Using data from three-spined sticklebacks (Gasterosteus aculeatus) and Trinidadian 44 guppies (Poecilia reticulata), we demonstrate the virtues of FishResp, highlighting the importance of 45 detecting mechanical problems and correcting measurements for background respiration. 46

Does parental angling selection affect the behavior or metabolism of brown trout parr?

“…No measurable respiration was detected without fish. The slope of the decrease in oxygen level during each 3.5‐min measurement period was calculated using linear regression with FishResp (Morozov et al., 2019) in R. An initial acclimation period was excluded by including only measurements taken after 16:00 in the analysis. We accepted all slopes where the R 2 was > 0.9 in the calculation: This resulted in 12–70 slopes being accepted for each individual, after data from one individual with only 7 accepted slopes were excluded.…”

Coevolution between life-history and metabolic rate depends on ontogenetic stage

“…with no fish) before and after SMR measurements, and subtracting the extrapolated value from the total oxygen consumption. The respirometry analysis, including correction for background respiration, was conducted using the R package FishResp (42). We performed a Cook’s D outlier analysis on a model with log 10 oxygen consumption as response, and log 10 mass as a covariate, including species as a random effect (fit using restricted maximum likelihood in the R-library lme4), and the most deviating observations (i.e.…”

Genetic coupling of life-history and aerobic performance in Atlantic salmon

“…Based on blank tests conducted before and after the SMR measurement, background respiration was accounted for using the R package FishResp (Morozov et al 2019), assuming linear growth of microorganisms inside a respirometry chamber over time (only weak background respiration was observed). Oxygen consumption rate (MO2, mg O2 h -1 ) for each linear measurement phase, represented as a slope, was derived from best-fit linear regression of dissolved oxygen concentration over time (details in online supplementary material).…”

“…MMR was calculated from the O2 concentrations (mg O2 L -1 ) after background correction was performed in FishResp (Morozov et al 2019). We used two methods to identify the slope of the steepest decrease in O2 saturation.…”