simCountData: Simulates Breeding Bird Survey-style count data
In SMBC-NZP/MigConnectivity: Estimate Migratory Connectivity for Migratory Animals

simCountData

R Documentation

Simulates Breeding Bird Survey-style count data

Description

Recently updated (version 0.4.3) to more properly match current BBS models. modelCountDataJAGS has not been updated yet

Usage

simCountData(
  nStrata,
  routesPerStrata,
  nYears,
  alphaStrat,
  beta = 0,
  eta = 0,
  sdRoute = 0,
  sdYear = 0,
  sdObs = 0,
  sdCount = 0,
  model = c("S", "Sh", "D", "Dh"),
  obsSurvival = 1,
  fixedyear = round(nYears/2),
  nuCount = 1
)

Arguments

`nStrata`	Number of populations/regions/strata
`routesPerStrata`	Vector of length 1 or nStrata containing the number of routes (i.e. counts) per stratum. If length(routesPerStrata) == 1, number of routes is identical for each population
`nYears`	Number of years surveys were conducted
`alphaStrat`	Vector of length 1 or nStrata containing the log expected number of individuals counted at each route for each population. If length(alphaStrat) == 1, expected counts are identical for each population
`beta`	Coefficient of linear year effect (default 0)
`eta`	Coefficient of first time run effect (default 0)
`sdRoute`	Standard deviation of random route-level variation. Default is 0, and if you're setting sdObs, it's probably best to keep it that way
`sdYear`	Standard deviation of random year-level variation (default 0)
`sdObs`	Standard deviation of random observer variation (default 0)
`sdCount`	Standard deviation of random count-level variation (default 0)
`model`	One of "S" (default), "Sh", "D", and "Dh". See Link et al. (2020) for descriptions of these models
`obsSurvival`	Annual probability that the observer that ran a route one year will run it the next. Default 1 (each route has only one observer)
`fixedyear`	The year within nYears that alphaStrat applies directly to (default halfway through)
`nuCount`	For the "h" models, parameter for extra variation in counts (default 1)

Value

simCountData returns a list containing:

nStrata: Number of populations/regions.
nRoutes: Total number of routes.
nYears: Number of years.
routesPerStrata: Number of routes per population.
year: Vector of length nYears with standardized year values.
strat: Vector of length nRoutes indicating the population/region in which each route is located.
alphaStrat: log expected count for each populations.
epsRoute: realized deviation from alphaStrat for each route.
epsYear: realized deviation from alphaStrat for each year.
beta: linear year effect.
sdRoute: standard deviation of random route-level variation.
sdYear: standard deviation of random year-level variation.
expectedCount: nRoutes by nYears matrix containing deterministic expected counts.
C: nRoutes by nYears matrix containing observed counts.

References

Cohen, E. B., J. A. Hostetler, M. T. Hallworth, C. S. Rushing, T. S. Sillett, and P. P. Marra. 2018. Quantifying the strength of migratory connectivity. Methods in Ecology and Evolution 9: 513-524. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/2041-210X.12916")}

Link, W. A., J. R. Sauer, and D. K. Niven. 2020. Model selection for the North American Breeding Bird Survey. Ecological Applications 30: e02137. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/eap.2137")}

Examples

set.seed(150)

### Set parameters for simulation ----

# Number of populations
nStrata. <- 4
# Number of routes w/i each population (assumed to be balanced)
routePerStrat. <- 30 # reduced from 90 for example speed
# Number of years
nYears. <- 5 # reduced from 10 for example speed
# log(Expected number of birds counted at each route)
alphaStrat. <- 1.95
# standard deviation of normal distribution assumed for route/observer random
# effects
sdRoute. <- 0.6
# standard deviation of normal distribution assumed for year random effects
sdYear. <- 0.18


# Number of simulated datasets to create and model
nsims <- 50 # reduced from 100 for example speed
# Number of MCMC iterations
ni. <- 1000 # reduced from 15000 for example speed
# Number of iterations to thin from posterior (reduced from 5)
nt. <- 1
# Number of iterations to discard as burn-in
nb. <- 500 # reduced from 5000 for example speed
# Number of MCMC chains
nc. <- 1 # reduced from 3 for example speed

### Create empty matrix to store model output ---
sim_in <- vector("list", nsims)
sim_out <- vector("list", nsims)


# Simulation ---

system.time(for(s in 1:nsims){
  cat("Simulation",s,"of",nsims,"\n")

  # Simulate data
  sim_data <- simCountData(nStrata = nStrata., routesPerStrata = routePerStrat.,
                           nYears = nYears., alphaStrat = alphaStrat.,
                           sdRoute = sdRoute., sdYear = sdYear.)
  sim_in[[s]] <- sim_data


  # Estimate population-level abundance
  out_mcmc <- modelCountDataJAGS(count_data = sim_data, ni = ni., nt = nt.,
                                 nb = nb., nc = nc.)

  # Store model output
  sim_out[[s]] <- out_mcmc
  remove(out_mcmc)

})


### Check that relative abundance is, on average, equal for each population
prop.table(sapply(sim_in, function(x) return(rowsum(colSums(x$C), x$strat))), 2)

rel_names <- paste0('relN[', 1:nStrata., ']')
rel_abund1 <- data.frame(sim=1:nsims,
                         ra1.mean=NA, ra2.mean=NA, ra3.mean=NA, ra4.mean=NA,
                         ra1.low=NA, ra2.low=NA, ra3.low=NA, ra4.low=NA,
                         ra1.high=NA, ra2.high=NA, ra3.high=NA, ra4.high=NA,
                         ra1.cover=0, ra2.cover=0, ra3.cover=0, ra4.cover=0)
for (s in 1:nsims) {
  rel_abund1[s, 2:5] <- summary(sim_out[[s]])$statistics[rel_names, "Mean"]
  rel_abund1[s, 6:9] <- summary(sim_out[[s]])$quantiles[rel_names, 1]
  rel_abund1[s, 10:13] <- summary(sim_out[[s]])$quantiles[rel_names, 5]
}
rel_abund1 <- transform(rel_abund1,
                        ra1.cover = (ra1.low<=0.25 & ra1.high>=0.25),
                        ra2.cover = (ra2.low<=0.25 & ra2.high>=0.25),
                        ra3.cover = (ra3.low<=0.25 & ra3.high>=0.25),
                        ra4.cover = (ra4.low<=0.25 & ra4.high>=0.25))

summary(rel_abund1)

SMBC-NZP/MigConnectivity documentation built on March 26, 2024, 4:22 p.m.