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FishResp: an R‐package for Filtering and Analyzing Raw Data in Aquatic Respirometry
Author(s) -
Morozov Sergey,
McCairns Scott R.J.,
Merilä Juha
Publication year - 2017
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.31.1_supplement.719.13
Subject(s) - respirometry , raw data , comparability , environmental science , biochemical engineering , biology , statistics , engineering , mathematics , biochemistry , combinatorics
One of the most common approaches for measuring metabolic rate of aquatic animals is whole‐body respirometry. Respirometry systems that are currently available on the market allow researchers to get raw respirometry data of high accuracy. However, further data processing, including quality‐control tests, is left to researchers' discretion. There is currently no universal tool for filtering raw data and extraction of key parameters from the massive datasets consisting point observations. This methodological disunity affects further comparability of research findings, and published studies contain contradictory estimations of metabolic rates in different fish species. For example, background respiration of microorganisms present inside chambers and tubing is one of the most significant factors that influence the quality and reliability of raw respirometry data. Different methodologies are known to correct for microbial oxygen consumption, but a lack of such correction appears to be common in many published studies. The problem is especially relevant when respirometry measurements are performed in conditions favorable for microbial growth, e.g. at high water temperatures. Consequently, without proper quality controls and data filtering, oxygen consumption in aquatic animals may be significantly overestimated. To overcome problems associated with raw respirometry data processing, we have developed an R‐package ‘FishResp’. This package is freely available, versatile and easy‐to‐use. Being compatible with raw data from various commercial respirometry systems, it allows users to perform quality control checks for chamber leaking and microbial oxygen consumption. We demonstrate the virtues of FishResp and its applicability in correcting for background respiration, using raw data obtained from metabolic rate measurements of the Trinidadian guppy ( Poecilia reticulata ). This example is peculiar as the species' reported mean standard metabolic rate measured at 25–26°C temperature varies substantially in different studies (100–500 mgO 2 /kg/h). Using FishResp software, we show that background respiration in chambers may make up to 75% of the total oxygen consumption during a long‐term experiment with a regular cleaning protocol. We wish to promote FishResp as a common tool for raw data processing in metabolic rate estimation in aquatic animals. A user‐friendly GUI version and a simple user manual are under development and will be available at the official website fishresp.org in 2017. Support or Funding Information SM: LUOVA doctoral programme, Alfred Kordelin Foundation, Oskar Öflund Foundation; RJSM, JM: Academy of Finland