Add docs

7 files changed, 111 insertions, 0 deletions

diff --git a/man/fitted-methods.Rd b/man/fitted-methods.Rd
index a06b930..8868565 100644
--- a/man/fitted-methods.Rd
+++ b/man/fitted-methods.Rd
@@ -15,6 +15,7 @@
 \alias{fitted,unmarkedFitGMM-method}
 \alias{fitted,unmarkedFitGDR-method}
 \alias{fitted,unmarkedFitDailMadsen-method}
+\alias{fitted,unmarkedFitGOccu-method}
 \title{Methods for Function fitted in Package `unmarked'}
 \description{Extracted fitted values from a fitted model.
 }
diff --git a/man/getP-methods.Rd b/man/getP-methods.Rd
index f44ec68..c554ebe 100644
--- a/man/getP-methods.Rd
+++ b/man/getP-methods.Rd
@@ -17,6 +17,7 @@
 \alias{getP,unmarkedFitDSO-method}
 \alias{getP,unmarkedFitMMO-method}
 \alias{getP,unmarkedFitGDR-method}
+\alias{getP,unmarkedFitGOccu-method}
 \title{Methods for Function getP in Package `unmarked'}
 \description{
 Methods for function \code{getP} in Package `unmarked'. These methods
diff --git a/man/goccu.Rd b/man/goccu.Rd
new file mode 100644
index 0000000..ef9f08c
--- /dev/null
+++ b/man/goccu.Rd
@@ -0,0 +1,105 @@
+\name{goccu}
+\alias{goccu}
+\title{
+Fit multi-scale occupancy models
+}
+\description{
+Fit multi-scale occupancy models as described in Nichols et al. (2008) to
+repeated presence-absence data collected using the robust design. This model
+allows for inference about occupancy, availability, and detection probability.
+}
+\usage{
+goccu(psiformula, phiformula, pformula, data, linkPsi = c("logit", "cloglog"),
+      starts, method = "BFGS", se = TRUE, ...)
+}
+\arguments{
+  \item{psiformula}{
+    Right-hand sided formula describing occupancy covariates
+}
+  \item{phiformula}{
+    Right-hand sided formula describing availability covariates
+}
+  \item{pformula}{
+    Right-hand sided formula for detection probability covariates
+}
+  \item{data}{
+    An object of class unmarkedFrameGOccu or unmarkedMultFrame
+}
+\item{linkPsi}{Link function for the occupancy model. Options are  
+      \code{"logit"} for the standard occupancy model or \code{"cloglog"} 
+      for the complimentary log-log link, which relates occupancy
+      to site-level abundance.
+}
+\item{starts}{
+    Starting values
+}
+  \item{method}{
+    Optimization method used by \code{\link{optim}}
+}
+  \item{se}{
+    Logical. Should standard errors be calculated?
+}
+\item{\dots}{
+    Additional arguments to \code{\link{optim}}, such as lower and upper
+    bounds
+}
+}
+\details{
+  Primary periods could represent spatial or temporal sampling replicates.
+  For example, you could have several spatial sub-units within each site, where each
+  sub-unit was then sampled repeatedly. This is a frequent design for eDNA studies.
+  Or, you could have multiple primary periods of sampling at each site
+  (conducted at different times within a season), each of which contains 
+  several secondary sampling periods. In both cases the robust design structure
+  can be used to estimate an availability probability in addition to
+  detection probability. See Kery and Royle (2015) 10.10 for more details.
+}
+\value{
+  An object of class unmarkedFitGOccu
+}
+\references{
+  Kery, M., & Royle, J. A. (2015). Applied hierarchical modeling in ecology: 
+  Volume 1: Prelude and static models. Elsevier Science.
+  
+  Nichols, J. D., Bailey, L. L., O'Connell Jr, A. F., Talancy, N. W., 
+  Campbell Grant, E. H., Gilbert, A. T., Annand E. M., Husband, T. P., & Hines, J. E.
+  (2008). Multi-scale occupancy estimation and modelling using multiple detection methods. 
+  Journal of Applied Ecology, 45(5), 1321-1329.
+}
+\author{
+  Ken Kellner \email{contact@kenkellner.com}
+}
+
+\seealso{
+\code{\link{occu}}, \code{\link{colext}},
+  \code{\link{unmarkedMultFrame}}, \code{\link{unmarkedFrameGOccu}}
+}
+
+\examples{
+
+set.seed(123)
+M <- 100
+T <- 5
+J <- 4
+
+psi <- 0.5
+phi <- 0.3
+p <- 0.4
+
+z <- rbinom(M, 1, psi)
+zmat <- matrix(z, nrow=M, ncol=T)
+
+zz <- rbinom(M*T, 1, zmat*phi)
+zz <- matrix(zz, nrow=M, ncol=T)
+
+zzmat <- zz[,rep(1:T, each=J)]
+y <- rbinom(M*T*J, 1, zzmat*p)
+y <- matrix(y, M, J*T)
+umf <- unmarkedMultFrame(y=y, numPrimary=T)
+
+\dontrun{
+  mod <- goccu(psiformula = ~1, phiformula = ~1, pformula = ~1, umf)
+  plogis(coef(mod))
+}
+
+}
diff --git a/man/ranef-methods.Rd b/man/ranef-methods.Rd
index abf0c68..c38e82e 100644
--- a/man/ranef-methods.Rd
+++ b/man/ranef-methods.Rd
@@ -20,6 +20,7 @@
 \alias{ranef,unmarkedFitNmixTTD-method}
 \alias{ranef,unmarkedFitGDR-method}
 \alias{ranef,unmarkedFitDailMadsen-method}
+\alias{ranef,unmarkedFitGOccu-method}
 \title{ Methods for Function \code{ranef} in Package \pkg{unmarked} }
 \description{
 Estimate posterior distributions of the random variables (latent
diff --git a/man/simulate-methods.Rd b/man/simulate-methods.Rd
index 67d942d..fc8a008 100644
--- a/man/simulate-methods.Rd
+++ b/man/simulate-methods.Rd
@@ -18,6 +18,7 @@
 \alias{simulate,unmarkedFitGPC-method}
 \alias{simulate,unmarkedFitGDR-method}
 \alias{simulate,unmarkedFitDailMadsen-method}
+\alias{simulate,unmarkedFitGOccu-method}
 \alias{simulate,character-method}
 \title{Methods for Function simulate in Package `unmarked'}
 \description{
diff --git a/man/unmarkedFit-class.Rd b/man/unmarkedFit-class.Rd
index 91e1723..4d7aa8f 100644
--- a/man/unmarkedFit-class.Rd
+++ b/man/unmarkedFit-class.Rd
@@ -35,6 +35,7 @@
 \alias{update,unmarkedFitNmixTTD-method}
 \alias{update,unmarkedFitGDR-method}
 \alias{update,unmarkedFitDailMadsen-method}
+\alias{update,unmarkedFitGOccu-method}
 \alias{sampleSize}
 \alias{sampleSize,unmarkedFit-method}
 \alias{unmarkedFitOccu-class}
diff --git a/man/unmarkedMultFrame.Rd b/man/unmarkedMultFrame.Rd
index 622b3ff..383b905 100644
--- a/man/unmarkedMultFrame.Rd
+++ b/man/unmarkedMultFrame.Rd
@@ -8,6 +8,7 @@
 \alias{unmarkedFrameGMM}
 \alias{unmarkedFrameGDS}
 \alias{unmarkedFrameGPC}
+\alias{unmarkedFrameGOccu}
 
 \title{Create an unmarkedMultFrame, unmarkedFrameGMM, unmarkedFrameGDS,
   or unmarkedFrameGPC object}