green_crab_data

data

Models integrate environmental DNA (eDNA) detection data and traditional survey data to jointly estimate species catch rate (see package vignette: <https://ednajoint.netlify.app/>). Models can be used with count data via traditional survey methods (i.e., trapping, electrofishing, visual) and replicated eDNA detection/nondetection data via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey locations. Estimated parameters include probability of a false positive eDNA detection, a site-level covariates that scale the sensitivity of eDNA surveys relative to traditional surveys, and gear scaling coefficients for traditional gear types. Models are implemented with a Bayesian framework (Markov chain Monte Carlo) using the 'Stan' probabilistic programming language.

Abigail G. Keller

eDNAjoint

Joint Modeling of Traditional and Environmental DNA Survey Data
in a Bayesian Framework

Ryan P. Kelly

Chitra M. Saraswati

Saras M. Windecker

green_crab_data function

A list with four matrices representing eDNA sampling data (pcr_n and
pcr_k) and trap sampling data (count and count_type).<dl>
<dt>pcr_n</dt>
<dd>Total number of eDNA qPCR replicates at each site (row) and
eDNA sample replicate (column). Data includes 20 total sites and 5 eDNA
sample replicates.</dd><dt>pcr_k</dt>
<dd>Total number of positive eDNA qPCR detections at each site
(row) and eDNA sample replicate (column). Data includes 20 total sites
and 5 eDNA sample replicates.</dd><dt>count</dt>
<dd>Count of green crab individuals in trap samples at each site
(row) and trap sample replicate (column). Data includes 20 total sites
and a maximum of 420 trap replicates. NA indicates that fewer trap
samples were collected than the maximum at a site.</dd><dt>count_type</dt>
<dd>Integer indicating the traditional gear type used at each
site (row) and trap sample replicate (column). '1' refers to Fukui traps,
and '2' refers to Minnow traps. Data includes 20 total sites and a
maximum of 420 trap replicates. NA indicates that fewer trap samples
were collected than the maximum at a site.</dd>
</dl>

Format

green_crab_data — green_crab_data

A list with four matrices representing eDNA sampling data (pcr_n and
pcr_k) and trap sampling data (count and count_type).<dl>
<dt>pcr_n</dt>
<dd>Total number of eDNA qPCR replicates at each site (row) and
eDNA sample replicate (column). Data includes 20 total sites and 5 eDNA
sample replicates.</dd>

<dt>pcr_k</dt>
<dd>Total number of positive eDNA qPCR detections at each site
(row) and eDNA sample replicate (column). Data includes 20 total sites
and 5 eDNA sample replicates.</dd>

<dt>count</dt>
<dd>Count of green crab individuals in trap samples at each site
(row) and trap sample replicate (column). Data includes 20 total sites
and a maximum of 420 trap replicates. NA indicates that fewer trap
samples were collected than the maximum at a site.</dd>

<dt>count_type</dt>
<dd>Integer indicating the traditional gear type used at each
site (row) and trap sample replicate (column). '1' refers to Fukui traps,
and '2' refers to Minnow traps. Data includes 20 total sites and a
maximum of 420 trap replicates. NA indicates that fewer trap samples
were collected than the maximum at a site.</dd>


</dl>

green_crab_data: green_crab_data

Description

Usage

Arguments

Format

References