eDNA-experiments-in-turbid-water

Holmes et al. (2023)

Data processing workflow and supplementary files for:

Holmes et al. (2023). Evaluating eDNA detection a rare fish in turbid water using field and experimental approaches

Contents

Generic LOD/LOQ calculator from Merkes et al. 2019; modifications commented in script

R script for Figure 2: Maps showing delta smelt trawl detections (A) and eDNA detections (B) December 2016 to March 2017 and collection sites for estuary water used in the experiment (C)

R script for Figure 5: Boxplots showing filtration experiment results

R script for imputation of nondetects using the R package 'nondetects' (McCall et al. 2014) Data file (csv) for readCt in 'nondetects.' This is the input raw Ct values for Supplementary File S7.

R script for statistical comparisons and models

References

McCall, M. N., McMurray, H. R., Land, H., & Almudevar, A. (2014). On non-detects in qPCR data. Bioinformatics, 30(16), 2310–2316. https://doi.org/10.1093/bioinformatics/btu239

Merkes C. M., Klymus K. E., Allison M. J., Goldberg C., Helbing C. C., Hunter M. E., Jackson C. A., Lance R. F., Mangan A. M., Monroe E. M., Piaggio A. J., Stokdyk J. P., Wilson C. C., & Richter C. (2019). Generic qPCR Limit of Detection (LOD) / Limit of Quantification (LOQ) calculator. R Script. Available at: https://github.com/cmerkes/qPCR_LOD_Calc. https://doi.org/10.5066/P9GT00GB (Accessed: 2022-07-26)