bsims_init {bSims}

bSims simulation functions

Description

Functions to initialize, populate, animate, detect, and transcribe simulated birds in a point count.

Usage

bsims_init(extent = 10, road = 0, edge = 0, offset = 0)

bsims_populate(x, density = 1, abund_fun = NULL, xy_fun = NULL,
  margin = 0, maxit = 100, fail = FALSE, ...)

bsims_animate(x, vocal_rate = 1, move_rate = 0, duration = 10,
  movement = 0, mixture = 1, avoid = c("none", "R", "ER"),
  initial_location=FALSE, allow_overlap=TRUE, ...)

bsims_detect(x, xy = c(0, 0), tau = 1, dist_fun = NULL,
  event_type = c("vocal", "move", "both"),
  sensitivity=1, direction=FALSE, ...)

bsims_transcribe(x, tint = NULL, rint = Inf,
  error = 0, bias = 1,
  condition=c("event1", "det1", "alldet"),
  event_type=NULL, perception=NULL, ...)

bsims_all(...)

## S3 method for class 'bsims_landscape'
print(x, ...)
## S3 method for class 'bsims_population'
print(x, ...)
## S3 method for class 'bsims_events'
print(x, ...)
## S3 method for class 'bsims_detections'
print(x, ...)
## S3 method for class 'bsims_transcript'
print(x, ...)
## S3 method for class 'bsims_all'
print(x, ...)

Arguments

extent

extent of simulation area, an extent x extent square with (0,0) at the center.

road

half width of the road stratum (perpendicular to the y axis).

edge

width of edge, same width on both sides of the road stratum.

offset

offset to apply to road and edge strata relative to the center in the x direction.

x

a simulation object.

density

population density, D, recycled 3x for the 3 strata (H: habitat, E: edge, R: road).

abund_fun

function to simulate abundance, N ~ Poisson(lambda), lambda=DA by default.

xy_fun

function used to simulate nest locations, see acceptreject. The function should return probability (value between 0 and 1), NULL means complete spatial randomness.

margin, maxit, fail

arguments passed to acceptreject when using xy_fun to simulate nest locations.

vocal_rate, move_rate

Vocal and movement rates (see events). Both of these rates can be: a single number; a vector of length length(mixture) (behavior based finite mixture groups); a vector of length 3 with mixture=1 (corresponding to HER strata); or a matrix of dimension 3 x length(mixture) (HER strata x number of behavior based groups).

duration

total time duration to consider (in minutes), passed to events.

movement

standard deviation for a bivariate Normal kernel to simulate locations centered at the nest location, passed to events. Can refer to the same stratum and behavior based groups as move_rate.

mixture

behavior based finite mixture group proportions.

avoid

range along the x axis to avoid with respect to movement locations, passed to events.

initial_location

logical, move_rate and vocal_rate are silently ignored if TRUE and nest locations are provided as part of the events table. This renders all individuals equally available for detection.

allow_overlap

logical, allowing overlap between neighboring nests when movement is involved. If FALSE, Voronoi tessellation is used to prevent overlap. If TRUE, the unconstrained bivariate Normal kernel is used.

xy

a vector of x and y coordinates describing the position of the observer.

tau

parameter of the distance function. Can be a single numeric value; a vector of length 2 to provide parameters for vocalization (1st value) and movement (2nd value) related events; (H: habitat, E: edge, R: road, in this order); a vector of length 3 to provide parameters for the 3 strata (H: habitat, E: edge, R: road); or a 3 x 2 matrix combining strata (rows) and vocalization/movement (columns) related parameters. Segmented sound attenuation is used when the values are different in the 3 strata (see dist_fun2).

dist_fun

distance function (1st argument is distance, second is tau).

event_type

type of events to access (vocal, movement, or both). Inherits value from input object when NULL.

tint

time interval break points in minutes.

rint

distance interval break points in units of 100 meter.

condition

conditioning type to define availability for each individual: "event1": the 1st event (detected or not); "det1": the 1st detection; "alldet": all detections (counting the same individual multiple times).

error

log scale standard deviation (SD) for distance estimation error, see rlnorm2. When direction=TRUE, error changes based on the angle between the observer and the individual's (random) singing direction. When the bird faces the observer (0 degrees) SD is 0, when the bird is facing away (180 degrees) SD is error. In the range between 0-180 degrees the SD is changing according to the cosine of the degree: SD*(0.5-cos(degree*pi/180)/2).

bias

nonnegative numeric, the distance estimation bias. The default value (1) means no bias, <1 indicates negative bias (perceived distance is less than true distance), >1 indicates positive bias (perceived distance is higher than true distance). This acts as a multiplier and can be combined with error. When direction=TRUE, bias changes based on the angle between the observer and the individual's (random) singing direction. When the bird faces the observer (0 degrees) perceived distance equals the true distance, when the bird is facing away (180 degrees) perceived distance is bias * true distance. In the range between 0-180 degrees the bias is changing according to the cosine of the degree: 1+(bias-1)*(0.5-cos(degree*pi/180)/2).

perception

perceived number of individuals relative to the actual number of individuals. A non-negative number (<1 values lead to under counting, >1 values lead to over counting), or NULL (observer correctly identifies all individuals).

sensitivity

non-negative numeric value indicating the sensitivity of the sensor receiving the signal. Can be of length 1 (applies to both vocal and movement events) or a named vector of length 2 (names should indicate which one is "vocal" or "move"). Sensitivity of 1 means that the process captured by tau is unaffected. Less than 1 values indicate lower sensitivity (effectively decreasing tau), larger than 1 values indicate higher sensitivity (effectively increasing tau).

direction

logical. When TRUE, tau for vocalizations (not for movement) changes based on the angle between the observer and the individual's (random) singing direction. When the bird faces the observer (0 degrees) tau is unaffected, when the bird is facing away (180 degrees) tau is sensitivity * tau. In the range between 0-180 degrees the effect is changing according to the cosine of the degree (0.5-cos(degree*pi/180)/2).

...

other arguments passed to underlying functions. For the bsims_all wrapper, it means all the arguments (except for x) that the underlying bsims_* functions have. bsims_all can also take a single list as its argument.

Details

The functions capturing the simulation layers are supposed to be called in sequence, allowing to simulate multiple realities by keeping preceding layers intact. Construction allows easy piping. The bsims_all function is a wrapper for the bsims_* layer functions.

The simulations follow time-removal and distance sampling models based on Matsuoka et al. (2012) <doi:10.1525/auk.2012.11190>, Solymos et al. (2013) <doi:10.1111/2041-210X.12106>, and Solymos et al. (2018) <doi:10.1650/CONDOR-18-32.1>, and sound attenuation experiments by Yip et al. (2017) <doi:10.1650/CONDOR-16-93.1>.

Value

bsims_init returns a landscape object.

bsims_populate returns a population object.

bsims_animate returns an events object.

bsims_detect returns a detections object.

bsims_transcribe returns a transcript object.

get_table returns the removal table.

bsims_all returns a closure with $settings(), $new(recover = FALSE), and $replicate(B, recover = FALSE, cl = NULL) functions. The settings function returns the input arguments as a list; the new function returns a single transcript object; the replicate function takes an argument for the number of replicates (B) and returns a list of transcript objects with B elements. The cl argument is used to parallelize the work, can be a numeric value on Unix/Linux/OSX, or a cluster object on any OS, see examples. The 'recover = TRUE' argument allows to run simulations with error catching based on try.

Note that simulated objects returned by bsims_all will contain different realizations and all the conditionally independent layers. Use a layered approach if former layers are meant to be kept identical across runs.

Author(s)

Peter Solymos

References

Matsuoka, S. M., Bayne, E. M., Solymos, P., Fontaine, P., Cumming, S. G., Schmiegelow, F. K. A., & Song, S. A., 2012. Using binomial distance-sampling models to estimate the effective detection radius of point-counts surveys across boreal Canada. Auk, 129: 268–282. <doi:10.1525/auk.2012.11190>

Solymos, P., Matsuoka, S. M., Bayne, E. M., Lele, S. R., Fontaine, P., Cumming, S. G., Stralberg, D., Schmiegelow, F. K. A. & Song, S. J., 2013. Calibrating indices of avian density from non-standardized survey data: making the most of a messy situation. Methods in Ecology and Evolution, 4: 1047–1058. <doi:10.1111/2041-210X.12106>

Solymos, P., Matsuoka, S. M., Cumming, S. G., Stralberg, D., Fontaine, P., Schmiegelow, F. K. A., Song, S. J., and Bayne, E. M., 2018. Evaluating time-removal models for estimating availability of boreal birds during point-count surveys: sample size requirements and model complexity. Condor, 120: 765–786. <doi:10.1650/CONDOR-18-32.1>

Yip, D. A., Bayne, E. M., Solymos, P., Campbell, J., and Proppe, J. D., 2017. Sound attenuation in forested and roadside environments: implications for avian point count surveys. Condor, 119: 73–84. <doi:10.1650/CONDOR-16-93.1>

See Also

Plotting functions: plot.bsims_landscape

Getter functions: get_nests, get_events, get_detections, get_abundance, get_density get_table

Shiny apps: run_app

acceptreject, events, estimate

Examples

phi <- 0.5
tau <- 1:3
dur <- 10
rbr <- c(0.5, 1, 1.5, Inf)
tbr <- c(3, 5, 10)
(l <- bsims_init(10, 0.5, 1))
(p <- bsims_populate(l, 1))
(a <- bsims_animate(p, vocal_rate=phi, duration=dur))
(o <- bsims_detect(a, tau=tau))
(x <- bsims_transcribe(o, tint=tbr, rint=rbr))

plot(x)
get_table(x, "removal")
get_table(x, "visits")

head(get_events(a))
plot(get_events(a))

head(get_detections(o))
plot(get_detections(o), "time")
plot(get_detections(o), "distance")

## wrapper function for all the bsims_* layers
b <- bsims_all(road=1, density=0.5, tint=tbr, rint=rbr)
## alternatively: supply a list
#settings <- list(road=1, density=0.5, tint=tbr, rint=rbr)
#b <- bsims_all(settings)
b$settings()
b$new()
bb <- b$replicate(3)
lapply(bb, get_table)


## parallel simulations
library(parallel)
b <- bsims_all(density=0.5)
B <- 4  # number of runs
nc <- 2 # number of cores
## sequential
system.time(bb <- b$replicate(B, cl=NULL))
## parallel clusters
cl <- makeCluster(nc)
## note: loading the package is optional
system.time(clusterEvalQ(cl, library(bSims)))
system.time(bb <- b$replicate(B, cl=cl))
stopCluster(cl)
## parallel forking
if (.Platform$OS.type != "windows") {
  system.time(bb <- b$replicate(B, cl=nc))
}