eDNA_data: eDNA_data
In artemis: Analysis and Simulation of Environmental DNA Experiments
Description
Usage
Format
Details
Description
Data from Delta Smelt (Hypomesus transpacificus) eDNA experiments, collected at the Central Valley Project facility in California.
Usage
1
Format
A data frame of 180 observations and 9 variables associated with individual qPCR replicates within filters.
- Date
Date of sample, yyyy-mm-dd
- FilterID
Represents a single Sterivex filter. Each unique FilterID is associated with 3 qPCR reactions (technical replicates)
- TechRep
Index of technical replicate from a given SampleID.
- Cq
Quantification cycle of qPCR. For this assay, the limit of detection was set at 40.0
- Distance_m
Distance (in meters) from the 'source' of eDNA, which was a small underwater enclosure containing 100 live individual (cultured) Delta Smelt.
- Volume_mL
Volume (in milliliters) of water pulled through the Sterivex filter in the sample.
- Biomass_N
The number of individual Delta Smelt carcasses present in the submerged cage.
- StdCrvAlpha_lnForm
The intercept of the standard curve equation associated with these filters, in ln form
- StdCrvBeta_lnForm
The slope of the standard curve equation associated with these filters, in ln form
Details
This sample dataset is designed to be representative of the type of data collected in a semi-controlled eDNA survey study. The data consists of 180 technical replicates processed from samples filtered at different distances from the 'source' of eDNA, which was a small underwater enclosure containing 100 live individual (cultured) Delta Smelt. All samples were filtered from water flowing unidirectionally at the surface (depth < 1.0m). Filtered volume was fixed at either 50mL or 200mL. From distances of 10-50m, three filters were taken in series every 10m at 50mL and 200mL, sampled from near to far relative to live car. Note that the live car itself (Distance_m = ~0) was not actually sampled. Full details on this data are presented in Espe et al. 2021 (in prep).
The standard curve equation associated with this data is: Cq_star = -1.529*ln[eDNA concentration] + 21.168, where Cq_star is the Cq value estimated by the standard curve for the assay.
artemis documentation built on Sept. 9, 2021, 1:07 a.m.
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Description Usage Format Details
Description
Data from Delta Smelt (Hypomesus transpacificus) eDNA experiments, collected at the Central Valley Project facility in California.
Usage
1 |
Format
A data frame of 180 observations and 9 variables associated with individual qPCR replicates within filters.
- Date
Date of sample, yyyy-mm-dd
- FilterID
Represents a single Sterivex filter. Each unique FilterID is associated with 3 qPCR reactions (technical replicates)
- TechRep
Index of technical replicate from a given SampleID.
- Cq
Quantification cycle of qPCR. For this assay, the limit of detection was set at 40.0
- Distance_m
Distance (in meters) from the 'source' of eDNA, which was a small underwater enclosure containing 100 live individual (cultured) Delta Smelt.
- Volume_mL
Volume (in milliliters) of water pulled through the Sterivex filter in the sample.
- Biomass_N
The number of individual Delta Smelt carcasses present in the submerged cage.
- StdCrvAlpha_lnForm
The intercept of the standard curve equation associated with these filters, in ln form
- StdCrvBeta_lnForm
The slope of the standard curve equation associated with these filters, in ln form
Details
This sample dataset is designed to be representative of the type of data collected in a semi-controlled eDNA survey study. The data consists of 180 technical replicates processed from samples filtered at different distances from the 'source' of eDNA, which was a small underwater enclosure containing 100 live individual (cultured) Delta Smelt. All samples were filtered from water flowing unidirectionally at the surface (depth < 1.0m). Filtered volume was fixed at either 50mL or 200mL. From distances of 10-50m, three filters were taken in series every 10m at 50mL and 200mL, sampled from near to far relative to live car. Note that the live car itself (Distance_m = ~0) was not actually sampled. Full details on this data are presented in Espe et al. 2021 (in prep).
The standard curve equation associated with this data is: Cq_star = -1.529*ln[eDNA concentration] + 21.168, where Cq_star is the Cq value estimated by the standard curve for the assay.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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