CMRFit: Model fitting

In CMRCT: Fit Capture-Mark-Recapture models in continuous time.

Description

'CMRFit' fit a Capture-Mark-Recapture model in continuous time.

Usage

CMRFit(surv, capt, cmrdata, start = 0, method = "BFGS", se.fit = TRUE,
latts = FALSE, ...)
## S3 method for class 'CMRCTFit'
print(x, ...)

Arguments

surv	an object of class 'formula': a symbolic description of the survival model to be fitted.
capt	an object of class 'formula': a symbolic description of the capture model to be fitted.
cmrdata	an object of class CMRData. See ?CMRData for details.
start	Initial values for the parameters to be optimized over. Either a single value applying for each parameters (0 fr each parameter by default) or a numeric vector containing a starting value for each parameter.
method	the method to be used in optim (see ?optim for details). Default is 'BFGS'.
se.fit	logical. If 'TRUE' (the default) the standad error of the parameter is derived from the Hessian matrix.
latts	logical. This argument is only present for experimental purpose and should not be used by the user.
x	an object of class 'CMRCTFit'.
...	additional arguments to be passed to or from other methods.

Details

Fit a Capture-Mark-Recapture model in continuous time.

Value

An object of class 'CMRCTFit' containing the following components:

Survival	a data.frame containing the survival parameter estimates and their associated standard errors (only if 'se.fit=TRUE')
Capture	a data.frame containing the capture parameter estimates and their associated standard errors (only if 'se.fit=TRUE')

Author(s)

Hugues Santin-Janin ([e-mail]) and David Fouchet ([e-mail])

References

Fouchet D., Santin-Janin H., Sauvage F., Yoccoz N.-G. & Pontier D. (submitted) An R package for analyzing survival using continuous-time open capture-recapture models: an example with feral cats on sub-Antarctic islands.

See Also

CMRData

Examples

## Not run: 
##Let define some arguments
start <- as.POSIXct(strptime("01/01/2000", "%d/%m/%Y"))
factind <- list(sex=c("M", "F"))
##numind <- list(weight=c(0.5, 4))
numtps <- list(rain=c(0, 100))

##Simulate the set of covariables
set.seed(123)
simvars <- CMRSimVars(n=15 , npop=4, start=start, step="6 months",
nstep=12, factind=factind, numtps=numtps, length="5 weeks",
clage=c(2), minage=0.1, maxage=20)

##Plot the simulated capture occasions
plot(simvars)

##True model
surv <- as.formula(~pop + age)
capt <- as.formula(~t)

##True model parameters values
#Survival parameters: Intercept, pop2, pop3, pop4, age1
surv.pars <- c(-2, 1.5, -0.1, -0.5, 0.3)
#Capture parameters: Intercept, t
capt.pars <- c(-1, 0.24)
theta <- c(surv.pars, capt.pars)

##Simulating a dataset
set.seed(456)
simdata <- CMRSimData(simvars=simvars, surv=surv, capt=capt, theta=theta)

##Plot the simulated capture occasions and capture histories
plot(simdata)

##Fit the model
fit <- CMRFit(surv=surv, capt=capt, cmrdata=simdata)
fit


## End(Not run)

CMRCT documentation built on May 2, 2019, 6:44 p.m.