breeding: Caribou Conservation Breeding

In psolymos/CaribouBC: Caribou Population Forecasting

Description

Functions evaluate different options for conservation breeding.

Usage

caribou_matrix(settings, wild=TRUE,
    age.cens=3, age.1st.litter=3, age.calf.max=1)

caribou_breeding(settings,
    in.inds=10, out.prop=1, f.surv.trans=1,
    j.surv.trans=1, j.surv.red=1,
    tmax=20, pop.start=100)

## S3 method for class 'caribou_breeding'
print(x, ...)
## S3 method for class 'caribou_breeding'
summary(object, ...)
## S3 method for class 'caribou_breeding'
plot(x, plot = TRUE, ...)

Arguments

settings	a settings object returned by caribou_settings.
wild	logical, whether to use the penned or wild vital settings.
age.cens	censoring age. The projection matrix will contain one-year age classes up to age.cens, all age classes above this are combined into a single age class.
age.1st.litter	integer, female age at 1st litter; lower limit of the age class, default is 3 years, i.e. the [3, Inf] interval.
age.calf.max	integer, maximum age to be considered as calf; upper limit of the age class, default is 1 year, i.e. the [0, 1) interval.
in.inds	integer vector, number of adult females put into pen each year. 0s are appended to the value meaning that no females are added after the last value (up until year tmax).
out.prop	numeric vector between 0 and 1, the proportion of juvenile females transferred from the penned to the recipient herd. The last value is repeated when length is less than tmax. Can be useful if juvenile female transfer should be delayed to build up stock first.
f.surv.trans	numeric between 0 and 1, adult female survival during capture and transportation into the penned population.
j.surv.trans	numeric between 0 and 1, juvenile female survival during capture and transportation from penned to recipient herd.
j.surv.red	numeric between 0 and 1, transported juvenile female survival reduction factor for 1 year following capture and traportation.
tmax	positive integer, number of years to forecast after initial year 0.
pop.start	positive integer, initial population size in year 0 for the recipient and status quo populations (wild not receiving females).
x, object	an object to print, summarize, plot, etc.
plot	logical, whether a plot is to be produced.
...	additional arguments to functions.

Details

The conservation breeding functionality is based on vital rates provided via the settings argument. These rates are turned into a projection matrix using caribou_matrix. This projection matrix reflects survival and reproduction rates based on the settings, tracking females only based on a sex ratio of 0.5.

The caribou_breeding function tracks changes in the conservation population starting with adding females to produce offspring.

Juvenile females are captured and transferred to the recipient herd. The proportion of juvenile females transferred can be changed through out.prop (0: none, 1: all).

The output object tracks the number of adult females added to the penned population, and the number of juvenile females transferred from the penned to the recipient herd.

Besides these, a status quo (wild without receiving juveniles) population trajectory is used as a reference. This status quo population uses the same vital rates as the recipient herd, but does not get the extra juvenile females from the penned population.

Value

caribou_matrix returns a projection matrix.

caribou_breeding returns a conservation breeding object. It contains age specific population sizes for the penned, recipient, and status quo populations (females only).

The print method returns the input object x invisibly.

The summary method returns population summaries for the conservation breeding object.

The plot method return the plotted data invisibly and produces a plot as a side effect.

See Also

caribou_settings, caribou_forecast

Examples

## projection matrix
s <- caribou_settings()

caribou_matrix(s, wild=TRUE)  # wild
caribou_matrix(s, wild=FALSE) # captive

## out.prop = 0.5: move half of the juveniles
x0 <- caribou_breeding(s,
    tmax = 20,        # projection horizon
    in.inds = rep(10, 5),
    out.prop = 0.5)
x0
summary(x0)

## out.prop = 1: move all juveniles
x1 <- update(x0, out.prop = 1)
x1

op <- par(mfrow=c(1, 2))
plot(x0, main="out.prop = 0")
plot(x1, main="out.prop = 1")
par(op)

psolymos/CaribouBC documentation built on April 2, 2020, 3:54 a.m.