diff options
Diffstat (limited to 'man/occuCOP.Rd')
| -rw-r--r-- | man/occuCOP.Rd | 16 |
1 files changed, 9 insertions, 7 deletions
diff --git a/man/occuCOP.Rd b/man/occuCOP.Rd index ca37e4e..aba49e3 100644 --- a/man/occuCOP.Rd +++ b/man/occuCOP.Rd @@ -7,10 +7,10 @@ \usage{ occuCOP(data, psiformula = ~1, lambdaformula = ~1, - psistarts, lambdastarts, + psistarts, lambdastarts, starts, method = "BFGS", se = TRUE, engine = c("C", "R"), na.rm = TRUE, - get.NLL.params = NULL, L1 = FALSE, ...)} + return.negloglik = NULL, L1 = FALSE, ...)} \arguments{ @@ -20,9 +20,11 @@ occuCOP(data, \item{lambdaformula}{Formula describing the detection covariates.} - \item{psistarts}{Vector of starting values for likelihood maximisation with \code{\link{optim}} for occupancy probability \eqn{\psi}{psi}. These values must be logit-transformed (with \code{\link{qlogis}}). See details. By default, optimisation will start at 0, corresponding to an occupancy probability of 0.5 (\code{plogis(0)} is 0.5).} + \item{psistarts}{Vector of starting values for likelihood maximisation with \code{\link{optim}} for occupancy probability \eqn{\psi}{psi}. These values must be logit-transformed (with \code{\link{qlogis}}) (see details). By default, optimisation will start at 0, corresponding to an occupancy probability of 0.5 (\code{plogis(0)} is 0.5).} - \item{lambdastarts}{Vector of starting values for likelihood maximisation with \code{\link{optim}} for detection rate \eqn{\lambda}{lambda}. These values must be log-transformed (with \code{\link{log}}). See details. By default, optimisation will start at 0, corresponding to detection rate of 1 (\code{exp(0)} is 1).} + \item{lambdastarts}{Vector of starting values for likelihood maximisation with \code{\link{optim}} for detection rate \eqn{\lambda}{lambda}. These values must be log-transformed (with \code{\link{log}}) (see details). By default, optimisation will start at 0, corresponding to detection rate of 1 (\code{exp(0)} is 1).} + + \item{starts}{Vector of starting values for likelihood maximisation with \code{\link{optim}}. If \code{psistarts} and \code{lambdastarts} are provided, \code{starts = c(psistarts, lambdastarts)}.} \item{method}{Optimisation method used by \code{\link{optim}}.} @@ -32,7 +34,7 @@ occuCOP(data, \item{na.rm}{Logical specifying whether to fit the model (\code{na.rm=TRUE}) or not (\code{na.rm=FALSE}) if there are NAs in the \code{\link{unmarkedFrameCOP}} object.} - \item{get.NLL.params}{A list of vectors of parameters (\code{c(psiparams, lambdaparams)}). If specified, the function will not maximise likelihood but return the likelihood for the those parameters. See an example below.} + \item{return.negloglik}{A list of vectors of parameters (\code{c(psiparams, lambdaparams)}). If specified, the function will not maximise likelihood but return the negative log-likelihood for the those parameters. See an example below.} \item{L1}{Logical specifying whether the length of observations (\code{L}) are purposefully set to 1 (\code{L1=TRUE}) or not (\code{L1=FALSE}).} @@ -222,11 +224,11 @@ occuCOP(data = umf, method = "Nelder-Mead") # We can run our model with a C++ or with a R likelihood function. ## They give the same result. -occuCOP(data = umf,engine = "C", psistarts = 0, lambdastarts = 0) +occuCOP(data = umf, engine = "C", psistarts = 0, lambdastarts = 0) occuCOP(data = umf, engine = "R", psistarts = 0, lambdastarts = 0) ## The C++ (the default) is faster. -system.time(occuCOP(data = umf,engine = "C", psistarts = 0, lambdastarts = 0)) +system.time(occuCOP(data = umf, engine = "C", psistarts = 0, lambdastarts = 0)) system.time(occuCOP(data = umf, engine = "R", psistarts = 0, lambdastarts = 0)) ## However, if you want to understand how the likelihood is calculated, |