simDemoDynocc {AHMbook} R Documentation

## Simulate data under a demographic dynamic occupancy model

### Description

Function to simulate detection/nondetection data under a variant of the demographic occupancy (or 'local survival') model of Roth & Amrhein (2010). Data are simulated in an 'unconditional' manner, i.e., for each site from first to last year. All parameters can be made year-dependent by specification of a range within which annual values will be drawn from uniform distributions.

### Usage

```simDemoDynocc(nsites = 100, nyears = 10, nvisits = 5, psi1 = 0.6,
range.phi = c(0.2, 0.9), range.r = c(0, 0.4), range.p = c(0.1, 0.9),
show.plot=TRUE)
```

### Arguments

 `nsites` Number of sites. `nyears` Number of years (or 'seasons', as they are somewhat confusingly often called in the occupancy literature). `nvisits` Number of replicate surveys (= occasions) within a year. `psi1` occupancy probability in first year. `range.phi` bounds of uniform distribution from which annual local probability of persistence is randomly drawn. `range.r` bounds of uniform distribution from which annual local probability of colonization is randomly drawn. `range.p` bounds of uniform distribution from which annual probability of detection is randomly drawn. `show.plot` If TRUE, plots of results are displayed; set to FALSE if running simulations.

### Value

A list with the values of the arguments input and the following additional elements:

 `phi ` persistence for each interval, a vector of length nyears - 1 `r ` colonization for each interval, a vector of length nyears - 1 `p ` detection probability for each year, a vector of length nyears `z ` true occurrence state, a nsites x nyears matrix of 0/1 `y ` the observed detection history, a nsites x nvisits x nyears array `f ` year of first detection, a vector of length nsites `nocc.true ` the true number of occupied sites, a vector of length nyears `nocc.true ` the observed number of occupied sites, a vector of length nyears

### Author(s)

Marc Kéry & Andy Royle

### References

Roth, T. & Amrhein, V. (2010), Estimating individual survival using territory occupancy data on unmarked animals. Journal of Applied Ecology, 47, 386-392.

Kéry, M. & Royle, J.A. (2021) Applied Hierarchical Modeling in Ecology AHM2 - 4.

### Examples

```# Generate data with the default arguments and look at the structure:
str(data <- simDemoDynocc() )                # Implicit defaults
str(data <- simDemoDynocc(psi1 = 1))         # All sites initially occupied
str(data <- simDemoDynocc(nsites = 1000))    # Plenty more sites
str(data <- simDemoDynocc(nyears = 100))     # Plenty more years
str(data <- simDemoDynocc(nvisits = 20))     # Plenty more visits
str(data <- simDemoDynocc(range.phi = c(0.8, 0.8))) # Constant survival
str(data <- simDemoDynocc(range.phi = c(0.2,0.3), range.r = c(0,0.2))) # Decline
str(data <- simDemoDynocc(range.phi = c(0.8,1), range.r = c(0.5,0.7))) # Increase
str(data <- simDemoDynocc(nvisits = 1))      # Single visit
str(data <- simDemoDynocc(range.p = c(1,1))) # Perfect detection
```

[Package AHMbook version 0.2.3 Index]