detectionPlot {eDNAjoint}R Documentation

Plot the survey effort necessary to detect species presence, given the species expected catch rate.

Description

This function plots the number of survey effort units to necessary detect species presence, calculated using median estimated parameter values from jointModel(). Detecting species presence is defined as producing at least one true positive eDNA detection or catching at least one individual. See more examples in the Package Vignette.

Usage

detectionPlot(
  modelfit,
  mu.min,
  mu.max,
  cov.val = NULL,
  probability = 0.9,
  qPCR.N = 3
)

Arguments

modelfit

An object of class stanfit.

mu.min

A value indicating the minimum expected species catch rate for plotting. If multiple traditional gear types are represented in the model, mu is the catch rate of gear type 1.

mu.max

A value indicating the maximum expected species catch rate for plotting. If multiple traditional gear types are represented in the model, mu is the catch rate of gear type 1.

cov.val

A numeric vector indicating the values of site-level covariates to use for prediction. Default is NULL.

probability

A numeric value indicating the probability of detecting presence. The default is 0.9.

qPCR.N

An integer indicating the number of qPCR replicates per eDNA sample. The default is 3.

Value

A plot displaying survey efforts necessary to detect species presence, given mu, for each survey type.

Note

Before fitting the model, this function checks to ensure that the function is possible given the inputs. These checks include:

If any of these checks fail, the function returns an error message.

Examples


# Ex. 1: Calculating necessary effort for detection with site-level
# covariates

# Load data
data(gobyData)

# Fit a model including 'Filter_time' and 'Salinity' site-level covariates
fit.cov <- jointModel(data = gobyData, cov = c('Filter_time','Salinity'),
                      family = "poisson", p10priors = c(1,20), q = FALSE,
                      multicore = FALSE)

# Plot at the mean covariate values (covariates are standardized, so mean=0)
detectionPlot(fit.cov$model, mu.min = 0.1, mu.max = 1,
              cov.val = c(0,0), qPCR.N = 3)

# Calculate mu_critical at salinity 0.5 z-scores greater than the mean
detectionPlot(fit.cov$model, mu.min = 0.1, mu.max = 1, cov.val = c(0,0.5),
              qPCR.N = 3)

# Ex. 2: Calculating necessary effort for detection with multiple
# traditional gear types

# Load data
data(greencrabData)

# Fit a model with no site-level covariates
fit.q <- jointModel(data = greencrabData, cov = NULL, family = "negbin",
                    p10priors = c(1,20), q = TRUE,
                    multicore = FALSE)

# Calculate
detectionPlot(fit.q$model, mu.min = 0.1, mu.max = 1,
              cov.val = NULL, qPCR.N = 3)

# Change probability of detecting presence to 0.95
detectionPlot(fit.q$model, mu.min = 0.1, mu.max = 1, cov.val = NULL,
              probability = 0.95, qPCR.N = 3)



[Package eDNAjoint version 0.2 Index]