Description Usage Arguments Details Value See Also Examples
Functions evaluate different options for conservation breeding.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | 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, ...)
|
settings |
a settings object returned by |
wild |
logical, whether to use the penned or wild vital |
age.cens |
censoring age. The projection matrix will contain one-year
age classes up to |
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 |
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 |
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. |
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.
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.
caribou_settings
, caribou_forecast
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ## 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)
|
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