simNmix {AHMbook} | R Documentation |

This very general function generates single-season count data under variants of the binomial N-mixture model of Royle (2004) and of the multinomial N-mixture model of Royle et al (2007).

simNmix(nsites = 267, nvisits = 3, mean.theta = 1, mean.lam = 2, mean.p = 0.6, area = FALSE, beta1.theta = 0, beta2.theta = 0, beta3.theta = 0, beta2.lam = 0, beta3.lam = 0, beta4.lam = 0, beta3.p = 0, beta5.p = 0, beta6.p = 0, beta.p.survey = 0, beta.p.N = 0, sigma.lam = 0, dispersion = 10, sigma.p.site = 0, sigma.p.visit = 0, sigma.p.survey = 0, sigma.p.ind = 0, Neg.Bin = FALSE, open.N = FALSE, show.plots = TRUE, verbose = TRUE)

`nsites` |
number of sites |

`nvisits` |
number of visits per site |

`mean.theta` |
proportion of sites that can have non-zero abundance in principle: suitability model for zero-inflation |

`mean.lam` |
Expected abundance at the average value of all abundance covariates (and ignoring random site effects): abundance model |

`mean.p` |
Expected detection at the average value of all detection covariates (and ignoring all random effects): detection model |

`area` |
determines area of sites (A), defaults to A=1 (i.e., all identical), but you can supply a vector of site areas of length nsites instead. |

`beta1.theta` |
coefficient of site covariate 1 in suitability model |

`beta2.theta` |
coefficient of site covariate 2 in suitability model |

`beta3.theta` |
coefficient of site covariate 3 in suitability model |

`beta2.lam` |
coefficient of site covariate 2 in abundance model |

`beta3.lam` |
coefficient of site covariate 3 in abundance model |

`beta4.lam` |
coefficient of site covariate 4 in abundance model |

`beta3.p` |
coefficient of site covariate 3 in detection model |

`beta5.p` |
coefficient of site covariate 5 in detection model |

`beta6.p` |
coefficient of site covariate 6 in detection model |

`beta.p.survey` |
coefficient of survey ('observational') covariate on p |

`beta.p.N` |
coefficient of centered local population size (log(N+1)) in detection model (i.e., coef. for density-dependent detection prob.) |

`sigma.lam` |
"Overdispersion SD" in linear predictor of abundance |

`dispersion` |
'size' or extra-Poisson dispersion of Negative binomial |

`sigma.p.site` |
"Overdispersion SD" in linear predictor of detection coming from random site effects |

`sigma.p.visit` |
"Overdispersion SD" in linear predictor of detection coming from random visit effects |

`sigma.p.survey` |
"Overdispersion SD" in linear predictor of detection coming from random site-by-survey effects |

`sigma.p.ind` |
"Overdispersion SD" in linear predictor of detection coming from random site-by-individual effects |

`Neg.Bin` |
if FALSE, any overdispersion in abundance is modeled by a Poisson log-normal; if TRUE, abundance overdispersion is modeled by adoption of a Negative binomial distribution for latent N |

`open.N` |
if TRUE, data are simulated under one specific form of an open population, where N in the first occasion is drawn from the specified mixture distribution and for all further occasions j, we have N_ij ~ Poisson(N_i(j-1)). With open.N = TRUE, we must have sigma.p.ind = 0, show.plot = FALSE and nvisits >1. |

`show.plots` |
if TRUE, plots of the data will be displayed; set to FALSE if you are running simulations. |

`verbose` |
if TRUE, output will be written to the console. |

Data are simulated at the level of each individual and individual-specific detection heterogeneity can be included. As a side-effect, individual-specific detection histories are generated and hence, data are also be simulated under the corresponding multinomial N-mixture model.

Broadly, the function can generate data under this most general model:

'Suitability' (zero-inflation) ~ cov1 + cov2 + cov3

Abundance ~ offset + cov2 + cov3 + cov4 + overdispersion

Detection ~ cov3 + cov5 + cov6 + survey.covariate + log(N+1) + eps.site + eps.visit + eps.survey + eps.individual

Overdispersion in abundance is modeled either as a Poisson-log-normal with a normal random site effect in lambda or with a Negative binomial with mean lambda and a 'size', or dispersion, parameter. Variable site areas can be specified to affect abundance as in an offset.

Abundance can be zero-inflated (this is the 'suitability' model). Note that the zero-inflation parameter is called theta here (in unmarked it is called psi). mean.phi is the probability that a site is suitable (i.e., 1 minus the expected proportion of sites with structural zero abundance.

Site covariate 2 can affect both suitability and abundance, while covariate 3 may affect all three levels. Hence, the function permits to simulate the case where a single site covariate affects different levels in the process (e.g., abundance and detection) in opposing directions (as for instance in Kéry, 2008)

Density-dependent detection can be modeled as a logistic-linear effect of local abundance (centered and log(x+1) transformed). Overdispersion in detection is modeled via normal random effects (the eps terms above) specific to sites, visits, surveys or individuals.

Effects of covariates and random-effects factors are modeled as additive on the link scale (log for abundance and logit for suitability and detection).

Data may be generated under one specific open-population model when argument 'open.N' is set to TRUE.

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

`nobs ` |
The total number of visits |

`site.cov ` |
An nsites x 6 matrix of values for 6 site covariates |

`survey.cov ` |
An nsites x nvisits matrix of values for a survey covariate |

`log.lam ` |
Linear predictor of PLN abundance model including random effects, a vector of length nsites |

`s ` |
Site suitability indicator, a vector of length nsites |

`N ` |
Number of individuals at each site, a vector of length nsites |

`p ` |
Probability of detection, an array with dimensions sites occupied x visits x max(N) |

`DH ` |
Detection history (1/0), an array with dimensions sites occupied x visits x max(N) |

`N.open ` |
Number of individuals at each site for open model, a sites x visits matrix |

`C ` |
Summary of DH: number of individuals detected for each site and visit |

`eta.lam ` |
Random site effects in lambda, a vector of length nsites, zero if Neg.Bin == TRUE |

`eta.p.site ` |
Random site effects in p, a vector of length nsites |

`eta.p.visit ` |
Random visit effects in p, a vector of length nvisits |

`eta.p.survey ` |
Random survey (= site-by-survey) effects in p, a nsites x nvisits matrix |

`eta.p.ind ` |
Random individual (= site-by-ind) effects in p (NOT site-ind-visit !), a nsites x max(N) matrix |

`odcN ` |
Naive overdispersion measure (var/mean) for true abundance (N) |

`odcC ` |
Naive overdispersion measure (var/mean) for observed counts (C) |

`Ntotal ` |
Total abundance summed over all sites |

`summax ` |
The sum of maximum counts over all sites |

Marc Kéry & Andy Royle

Royle, J.A. (2004) N-mixture models for estimating population size from spatially replicated counts. *Biometrics*, 60, 108-115.

Royle, J.A., et al (2007) Hierarchical spatial models of abundance and occurrence from imperfect survey data. *Ecological Monographs*, 77, 465-481.

Kéry, M. (2008) Estimating abundance from bird counts: binomial mixture models uncover complex covariate relationships, *Auk*, 125, 336-345

Kéry, M. & Royle, J.A. (2016) *Applied Hierarchical Modeling in Ecology* AHM1 - 6.5.

# Generate data with the default arguments and look at the structure: tmp <- simNmix() str(tmp) str(data <- simNmix()) # Null data-generating model str(data <- simNmix(mean.theta = 0.60)) # ZIP with 40% structural zeroes str(data <- simNmix(sigma.lam = 1)) # Poisson-lognormal (PLN) mixture str(data <- simNmix(Neg.Bin = TRUE)) # Negative-binomial mixture str(data <- simNmix(mean.theta = 0.6, sigma.lam = 1)) # Zero-inflated PLN str(data <- simNmix(mean.theta = 0.6, Neg.Bin = TRUE)) # Zero-infl. NegBin str(data <- simNmix(mean.p = 1)) # Perfect detection (p = 1) str(data <- simNmix(mean.theta = 0.6, mean.p = 1)) # ZIP with p = 1 str(data <- simNmix(sigma.lam = 1, mean.p = 1)) # PLN with p = 1

[Package *AHMbook* version 0.2.3 Index]