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Sea lamprey quantitative environmental DNA surveillance - Code

Citation

Nicholas Schloesser, 2018, Sea lamprey quantitative environmental DNA surveillance - Code: U.S. Geological Survey code release. https://doi.org/10.5066/F7DR2TD0

Summary

## Descriptions for each of the code files are listed below. ## 1) Adult SL density The file “Adult_density_Rscript_code_release.R” contains R code for running linear mixed models of log-transformed copy numbers using tank as the random effect and density as the fixed effect (log10(copies) ~ log10(density) + (1|Tank)). Required data includes: tank ID, density of sea lamprey in the tank, and copy numbers detected in the qPCR assays. Outputs include: The mean copy numbers, log transformed mean copy numbers, slope of the equation for the linear mixed models, p-values. ## 2) Larval SL density The file “larval_density_Rscript_IPDS.R” contains R code for running a linear model to looks for trends between copy numbers and SL densities. [...]

Contacts

Point of Contact :
Nicholas A Schloesser

Attached Files

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Adult_density_Rscript_code_release_Merkes.R 6.46 KB
larval_density_Rscript_IPDS.R 9.54 KB
LOD IPDS.R 8.78 KB
readme.md 3.99 KB
LICENSE 2.6 KB

Purpose

Three R code files were used to analyze data for this study and they included: 1) code to determine if adult SL density in tanks correlates with copies of eDNA detected in samples taken from the tanks, and 2) code to determine if larval SL density in tanks correlates with copies and detection rate of eDNA detected in samples taken from tanks, and 3) code to determine the limit of detection of 4 separate qPCR assays to detect SL

Communities

  • Upper Midwest Environmental Sciences Center (UMESC)

Provenance

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