baRcodeR: An open‐source R package for sample labelling

Abstract

Reproducibility is a foundation of the scientific method that is difficult to achieve in practice, contributing to a perceived 'crisis' in peer-reviewed research (Baker, 2016). A push towards more transparent, reproducible methods has inspired rapid development of new tools for data science, including R Markdown and R Notebooks with R Studio (RStudio Team, 2016) to generate reproducible analysis and reports in R (R Core Team, 2018). In contrast, tools to reduce errors and improve transparency at earlier stages have received relatively little attention. In biological studies, these earlier stages may include sample collecting, labelling, measuring, subsampling and tracking. Documenting these earlier stages is crucial for data sharing and scientific inquiry because errors in sample labelling and data collection propagate through all downstream analyses. As such, a reproducible analysis on faulty data can be scientifically less robust than an irreproducible analysis on carefully curated data.In many of the biological sciences, samples are collected under arduous field conditions that pose challenges for labelling, organizing, measuring and analysing samples. A common approach is to collect and preserve samples for later analysis, which may involve multiple users, movement to different locations, transferring to different storage media or vessels, subsampling and archiving. Misinterpreted labels, ambiguous handwriting, cut-and-paste errors, typographical

Identification of Arctic Food Fish Species for Anthropogenic Contaminant Testing Using Geography and Genetics

“…We selected Hg, As, and PCBs for assay at the behest of the people of Gjoa Haven, an Inuit community on the shores of the lower Northwest Passage, who, as indicated, rely on anadromous salmonids as an important part of their traditional diet. Success in sampling depended upon a respect and integration of ITK and interactive mapping and atlases as well as sample tracking using a newly developed R-based barcoding system [ 36 , 38 ]. A large number of samples were obtained and, overall, 6% (31/540) of the fish tested for Hg exceeded Canadian guidelines for commercial sale (0.5 mg·kg −1 wet weight) [ 55 ], with preliminary analysis of a few fish showing that much of the Hg was in the neurotoxic methylated form.…”

“…After capture, fish were assigned a unique numeric barcode identifier [ 38 ], photographed, measured for fork length, weighed, and otoliths were dissected and subsequently dried for age analysis [ 35 , 39 ]. Muscle and other tissue samples including fin clips for contaminant and genomic DNA isolation were placed in barcode-tagged sterile whirl-paks ® , empty tubes, or tubes containing 70% ethanol, respectively, and frozen at –20 °C and shipped with freezer packs to Queen’s University for analysis, as previously detailed [ 32 , 37 ].…”

Direct and indirect fitness effects of plant metabolites and genetic constraints limit evolution of allelopathy in an invading plant

“…To limit human error in labelling and data collection, we used the baRcodeR package in R to generate a unique, scannable 2-dimensional barcode for each plant (Wu et al 2020). As detailed in Appendix A of the Supporting Information, we stratified seeds of Alliaria petiolata in petri dishes and transferred germinated seedlings into 2cm x 2cm plug trays at a constant 10°C (12h half daylight) in a growth chamber to limit growth of early-germinating seeds.…”

Characterization of skin- and intestine microbial communities in migrating high Arctic lake whitefish and cisco

“…Fish were catalogued and weighed, fork length (mm) was measured, and dissected otoliths were aged as previously described (Campana et al 2008;Casselman et al, 2019). All samples were given a unique barcode linked to each fish (Wu et al, 2020). Fish skin and intestine samples were aseptically collected from fish caught in commercial and subsistence fishing nets or occasionally on fish spears, frozen at -20 °C then shipped frozen to the laboratory, as previously described (Hamilton et al, 2019).…”