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

Source: R/detection_calculate.R
detection_calculate.Rd

This function calculates the number of survey effort units to necessary detect species presence using median estimated parameter values from joint_model(). 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

detection_calculate(
  model_fit,
  mu,
  cov_val = NULL,
  probability = 0.9,
  pcr_n = 3
)

Arguments

model_fit

An object of class stanfit.

mu

A numeric vector of species densities/capture rates. 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.

pcr_n

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

Value

A summary table of 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:

  • Input model fit is an object of class 'stanfit'.

  • Input mu is a numeric vector.

  • Input probability is a univariate numeric value.

  • If model fit contains alpha, cov_val must be provided.

  • Input cov_val is numeric.

  • Input cov_val is the same length as the number of estimated covariates.

  • Input model fit has converged (i.e. no divergent transitions after warm-up).

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

Examples

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

# Load data
data(goby_data)

# Fit a model including 'Filter_time' and 'Salinity' site-level covariates
fit_cov <- joint_model(data = goby_data, cov = c('Filter_time','Salinity'),
                       family = "poisson", p10_priors = c(1,20), q = FALSE,
                       multicore = FALSE)
#> 
#> SAMPLING FOR MODEL 'joint_count' NOW (CHAIN 1).
#> Chain 1: 
#> Chain 1: Gradient evaluation took 5.5e-05 seconds
#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.55 seconds.
#> Chain 1: Adjust your expectations accordingly!
#> Chain 1: 
#> Chain 1: 
#> Chain 1: Iteration:    1 / 3000 [  0%]  (Warmup)
#> Chain 1: Iteration:  500 / 3000 [ 16%]  (Warmup)
#> Chain 1: Iteration:  501 / 3000 [ 16%]  (Sampling)
#> Chain 1: Iteration: 1000 / 3000 [ 33%]  (Sampling)
#> Chain 1: Iteration: 1500 / 3000 [ 50%]  (Sampling)
#> Chain 1: Iteration: 2000 / 3000 [ 66%]  (Sampling)
#> Chain 1: Iteration: 2500 / 3000 [ 83%]  (Sampling)
#> Chain 1: Iteration: 3000 / 3000 [100%]  (Sampling)
#> Chain 1: 
#> Chain 1:  Elapsed Time: 0.487 seconds (Warm-up)
#> Chain 1:                0.848 seconds (Sampling)
#> Chain 1:                1.335 seconds (Total)
#> Chain 1: 
#> 
#> SAMPLING FOR MODEL 'joint_count' NOW (CHAIN 2).
#> Chain 2: 
#> Chain 2: Gradient evaluation took 3.3e-05 seconds
#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.33 seconds.
#> Chain 2: Adjust your expectations accordingly!
#> Chain 2: 
#> Chain 2: 
#> Chain 2: Iteration:    1 / 3000 [  0%]  (Warmup)
#> Chain 2: Iteration:  500 / 3000 [ 16%]  (Warmup)
#> Chain 2: Iteration:  501 / 3000 [ 16%]  (Sampling)
#> Chain 2: Iteration: 1000 / 3000 [ 33%]  (Sampling)
#> Chain 2: Iteration: 1500 / 3000 [ 50%]  (Sampling)
#> Chain 2: Iteration: 2000 / 3000 [ 66%]  (Sampling)
#> Chain 2: Iteration: 2500 / 3000 [ 83%]  (Sampling)
#> Chain 2: Iteration: 3000 / 3000 [100%]  (Sampling)
#> Chain 2: 
#> Chain 2:  Elapsed Time: 0.431 seconds (Warm-up)
#> Chain 2:                0.878 seconds (Sampling)
#> Chain 2:                1.309 seconds (Total)
#> Chain 2: 
#> 
#> SAMPLING FOR MODEL 'joint_count' NOW (CHAIN 3).
#> Chain 3: 
#> Chain 3: Gradient evaluation took 2.6e-05 seconds
#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
#> Chain 3: Adjust your expectations accordingly!
#> Chain 3: 
#> Chain 3: 
#> Chain 3: Iteration:    1 / 3000 [  0%]  (Warmup)
#> Chain 3: Iteration:  500 / 3000 [ 16%]  (Warmup)
#> Chain 3: Iteration:  501 / 3000 [ 16%]  (Sampling)
#> Chain 3: Iteration: 1000 / 3000 [ 33%]  (Sampling)
#> Chain 3: Iteration: 1500 / 3000 [ 50%]  (Sampling)
#> Chain 3: Iteration: 2000 / 3000 [ 66%]  (Sampling)
#> Chain 3: Iteration: 2500 / 3000 [ 83%]  (Sampling)
#> Chain 3: Iteration: 3000 / 3000 [100%]  (Sampling)
#> Chain 3: 
#> Chain 3:  Elapsed Time: 0.365 seconds (Warm-up)
#> Chain 3:                0.876 seconds (Sampling)
#> Chain 3:                1.241 seconds (Total)
#> Chain 3: 
#> 
#> SAMPLING FOR MODEL 'joint_count' NOW (CHAIN 4).
#> Chain 4: 
#> Chain 4: Gradient evaluation took 3.2e-05 seconds
#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds.
#> Chain 4: Adjust your expectations accordingly!
#> Chain 4: 
#> Chain 4: 
#> Chain 4: Iteration:    1 / 3000 [  0%]  (Warmup)
#> Chain 4: Iteration:  500 / 3000 [ 16%]  (Warmup)
#> Chain 4: Iteration:  501 / 3000 [ 16%]  (Sampling)
#> Chain 4: Iteration: 1000 / 3000 [ 33%]  (Sampling)
#> Chain 4: Iteration: 1500 / 3000 [ 50%]  (Sampling)
#> Chain 4: Iteration: 2000 / 3000 [ 66%]  (Sampling)
#> Chain 4: Iteration: 2500 / 3000 [ 83%]  (Sampling)
#> Chain 4: Iteration: 3000 / 3000 [100%]  (Sampling)
#> Chain 4: 
#> Chain 4:  Elapsed Time: 0.393 seconds (Warm-up)
#> Chain 4:                0.877 seconds (Sampling)
#> Chain 4:                1.27 seconds (Total)
#> Chain 4: 
#> Refer to the eDNAjoint guide for visualization tips:  https://ednajoint.netlify.app/tips#visualization-tips 

# Calculate at the mean covariate values
# (covariates are standardized, so mean = 0)
detection_calculate(fit_cov$model, mu = seq(from = 0.1, to = 1, by = 0.1),
                    cov_val = c(0,0), pcr_n = 3)
#>        mu n_traditional n_eDNA
#>  [1,] 0.1            24     14
#>  [2,] 0.2            12      7
#>  [3,] 0.3             8      5
#>  [4,] 0.4             6      4
#>  [5,] 0.5             5      4
#>  [6,] 0.6             4      3
#>  [7,] 0.7             4      3
#>  [8,] 0.8             3      3
#>  [9,] 0.9             3      2
#> [10,] 1.0             3      2

# Calculate mu_critical at salinity 0.5 z-scores greater than the mean
detection_calculate(fit_cov$model, mu = seq(from = 0.1, to = 1, by = 0.1),
                    cov_val = c(0,0.5), pcr_n = 3)
#>        mu n_traditional n_eDNA
#>  [1,] 0.1            24     12
#>  [2,] 0.2            12      6
#>  [3,] 0.3             8      5
#>  [4,] 0.4             6      4
#>  [5,] 0.5             5      3
#>  [6,] 0.6             4      3
#>  [7,] 0.7             4      2
#>  [8,] 0.8             3      2
#>  [9,] 0.9             3      2
#> [10,] 1.0             3      2

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

# Load data
data(green_crab_data)

# Fit a model with no site-level covariates
fit_q <- joint_model(data = green_crab_data, cov = NULL, family = "negbin",
                     p10_priors = c(1,20), q = TRUE, multicore = FALSE)
#> 
#> SAMPLING FOR MODEL 'joint_count' NOW (CHAIN 1).
#> Chain 1: 
#> Chain 1: Gradient evaluation took 0.000457 seconds
#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 4.57 seconds.
#> Chain 1: Adjust your expectations accordingly!
#> Chain 1: 
#> Chain 1: 
#> Chain 1: Iteration:    1 / 3000 [  0%]  (Warmup)
#> Chain 1: Iteration:  500 / 3000 [ 16%]  (Warmup)
#> Chain 1: Iteration:  501 / 3000 [ 16%]  (Sampling)
#> Chain 1: Iteration: 1000 / 3000 [ 33%]  (Sampling)
#> Chain 1: Iteration: 1500 / 3000 [ 50%]  (Sampling)
#> Chain 1: Iteration: 2000 / 3000 [ 66%]  (Sampling)
#> Chain 1: Iteration: 2500 / 3000 [ 83%]  (Sampling)
#> Chain 1: Iteration: 3000 / 3000 [100%]  (Sampling)
#> Chain 1: 
#> Chain 1:  Elapsed Time: 4.768 seconds (Warm-up)
#> Chain 1:                12.844 seconds (Sampling)
#> Chain 1:                17.612 seconds (Total)
#> Chain 1: 
#> 
#> SAMPLING FOR MODEL 'joint_count' NOW (CHAIN 2).
#> Chain 2: 
#> Chain 2: Gradient evaluation took 0.000422 seconds
#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 4.22 seconds.
#> Chain 2: Adjust your expectations accordingly!
#> Chain 2: 
#> Chain 2: 
#> Chain 2: Iteration:    1 / 3000 [  0%]  (Warmup)
#> Chain 2: Iteration:  500 / 3000 [ 16%]  (Warmup)
#> Chain 2: Iteration:  501 / 3000 [ 16%]  (Sampling)
#> Chain 2: Iteration: 1000 / 3000 [ 33%]  (Sampling)
#> Chain 2: Iteration: 1500 / 3000 [ 50%]  (Sampling)
#> Chain 2: Iteration: 2000 / 3000 [ 66%]  (Sampling)
#> Chain 2: Iteration: 2500 / 3000 [ 83%]  (Sampling)
#> Chain 2: Iteration: 3000 / 3000 [100%]  (Sampling)
#> Chain 2: 
#> Chain 2:  Elapsed Time: 5.004 seconds (Warm-up)
#> Chain 2:                14.15 seconds (Sampling)
#> Chain 2:                19.154 seconds (Total)
#> Chain 2: 
#> 
#> SAMPLING FOR MODEL 'joint_count' NOW (CHAIN 3).
#> Chain 3: 
#> Chain 3: Gradient evaluation took 0.000401 seconds
#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 4.01 seconds.
#> Chain 3: Adjust your expectations accordingly!
#> Chain 3: 
#> Chain 3: 
#> Chain 3: Iteration:    1 / 3000 [  0%]  (Warmup)
#> Chain 3: Iteration:  500 / 3000 [ 16%]  (Warmup)
#> Chain 3: Iteration:  501 / 3000 [ 16%]  (Sampling)
#> Chain 3: Iteration: 1000 / 3000 [ 33%]  (Sampling)
#> Chain 3: Iteration: 1500 / 3000 [ 50%]  (Sampling)
#> Chain 3: Iteration: 2000 / 3000 [ 66%]  (Sampling)
#> Chain 3: Iteration: 2500 / 3000 [ 83%]  (Sampling)
#> Chain 3: Iteration: 3000 / 3000 [100%]  (Sampling)
#> Chain 3: 
#> Chain 3:  Elapsed Time: 4.799 seconds (Warm-up)
#> Chain 3:                14.303 seconds (Sampling)
#> Chain 3:                19.102 seconds (Total)
#> Chain 3: 
#> 
#> SAMPLING FOR MODEL 'joint_count' NOW (CHAIN 4).
#> Chain 4: 
#> Chain 4: Gradient evaluation took 0.000417 seconds
#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 4.17 seconds.
#> Chain 4: Adjust your expectations accordingly!
#> Chain 4: 
#> Chain 4: 
#> Chain 4: Iteration:    1 / 3000 [  0%]  (Warmup)
#> Chain 4: Iteration:  500 / 3000 [ 16%]  (Warmup)
#> Chain 4: Iteration:  501 / 3000 [ 16%]  (Sampling)
#> Chain 4: Iteration: 1000 / 3000 [ 33%]  (Sampling)
#> Chain 4: Iteration: 1500 / 3000 [ 50%]  (Sampling)
#> Chain 4: Iteration: 2000 / 3000 [ 66%]  (Sampling)
#> Chain 4: Iteration: 2500 / 3000 [ 83%]  (Sampling)
#> Chain 4: Iteration: 3000 / 3000 [100%]  (Sampling)
#> Chain 4: 
#> Chain 4:  Elapsed Time: 4.932 seconds (Warm-up)
#> Chain 4:                9.659 seconds (Sampling)
#> Chain 4:                14.591 seconds (Total)
#> Chain 4: 
#> Refer to the eDNAjoint guide for visualization tips:  https://ednajoint.netlify.app/tips#visualization-tips 

# Calculate
detection_calculate(fit_q$model, mu = seq(from = 0.1, to = 1, by = 0.1),
                    cov_val = NULL, pcr_n = 3)
#>        mu n_traditional_1 n_traditional_2 n_eDNA
#>  [1,] 0.1              25              32     28
#>  [2,] 0.2              13              17     15
#>  [3,] 0.3               9              12     10
#>  [4,] 0.4               7               9      8
#>  [5,] 0.5               6               8      6
#>  [6,] 0.6               6               7      5
#>  [7,] 0.7               5               6      5
#>  [8,] 0.8               5               5      4
#>  [9,] 0.9               4               5      4
#> [10,] 1.0               4               5      4

# Change probability of detecting presence to 0.95
detection_calculate(fit_q$model, mu = 0.1, cov_val = NULL,
                    probability = 0.95, pcr_n = 3)
#>       mu n_traditional_1 n_traditional_2 n_eDNA
#> [1,] 0.1              32              41     37
# }