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author | Ken Kellner <ken@kenkellner.com> | 2023-08-04 16:03:41 -0400 |
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committer | Ken Kellner <ken@kenkellner.com> | 2023-08-04 16:03:41 -0400 |
commit | f51ecca33c6a38596d6f3100bb8a1c76a7a1c843 (patch) | |
tree | 90a707c4d16486b71f03d62f1105a0d6368293b9 | |
parent | 74e73f176d019b9ad64fa7199f00b04785ae7668 (diff) |
Add docs
-rw-r--r-- | man/fitted-methods.Rd | 1 | ||||
-rw-r--r-- | man/getP-methods.Rd | 1 | ||||
-rw-r--r-- | man/goccu.Rd | 105 | ||||
-rw-r--r-- | man/ranef-methods.Rd | 1 | ||||
-rw-r--r-- | man/simulate-methods.Rd | 1 | ||||
-rw-r--r-- | man/unmarkedFit-class.Rd | 1 | ||||
-rw-r--r-- | man/unmarkedMultFrame.Rd | 1 |
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} |