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diff --git a/man/unmarkedPowerList.Rd b/man/unmarkedPowerList.Rd new file mode 100644 index 0000000..3dbbcf1 --- /dev/null +++ b/man/unmarkedPowerList.Rd @@ -0,0 +1,95 @@ +\name{unmarkedPowerList} +\alias{unmarkedPowerList} +\alias{unmarkedPowerList,list-method} +\alias{unmarkedPowerList,unmarkedFit-method} +\alias{unmarkedPowerList-class} +\alias{unmarkedPowerList-methods} +\alias{show,unmarkedPowerList-method} +\alias{summary,unmarkedPowerList-method} +\alias{plot,unmarkedPowerList,ANY-method} + +\title{Create or summarize a series of unmarked power analyses} + +\description{ + A list of power analyses created with \code{powerAnalysis} can be combined + using \code{unmarkedPowerList}, allowing comparison e.g. between different + study designs/sample sizes. Additionally an \code{unmarkedPowerList} can be + created directly from an \code{unmarkedFit} template model by specifying + a series of study designs (number of sites, number of observations) + as a \code{data.frame}. A series of methods for \code{unmarkedPowerList} + objects are available including a \code{plot} method. +} + +\usage{ +\S4method{unmarkedPowerList}{list}(object, ...) +\S4method{unmarkedPowerList}{unmarkedFit}(object, coefs, design, alpha=0.05, + nulls=list(), nsim=100, parallel=FALSE, ...) +\S4method{show}{unmarkedPowerList}(object) +\S4method{summary}{unmarkedPowerList}(object, ...) +\S4method{plot}{unmarkedPowerList,ANY}(x, power=NULL, param=NULL, ...) +} + +\arguments{ + \item{object,x}{A \code{list} of \code{unmarkedPower} objects, a fitted model + inheriting class \code{unmarkedFit}, or an \code{unmarkedPowerList} object, + depending on the method + } + \item{coefs}{A named list of effect sizes, see documentation for + \code{powerAnalysis}} + \item{design}{A \code{data.frame} with one row per study design to test, and + at least 2 named columns: \code{M} for number of sites and \code{J} for + number of observations. If you have >1 primary period a \code{T} column + must also be provided} + \item{alpha}{Type I error rate} + \item{nulls}{If provided, a list matching the structure of \code{coefs} which + defines the null hypothesis value for each parameter. By default the null + is 0 for all parameters. + } + \item{nsim}{The number of simulations to run for each scenario/study design} + \item{parallel}{If \code{TRUE}, run simulations in parallel} + \item{power}{When plotting, the target power. Draws a horizontal line + at a given value of power on the plot} + \item{param}{When plotting, the model parameter to plot power vs. sample size for. + By default this is the first parameter (which is usually an intercept, + so not very interesting)} + \item{...}{Not used} +} + +\value{A \code{unmarkedPowerList} object, a summary of the object in the console, + or a summary plot, depending on the method} + +\author{Ken Kellner \email{contact@kenkellner.com}} + +\seealso{ + \code{\link{powerAnalysis}} +} + +\examples{ + +\dontrun{ + +# Simulate an occupancy dataset and build template model +forms <- list(state=~elev, det=~1) +coefs <- list(state=c(intercept=0, elev=-0.4), det=c(intercept=0)) +design <- list(M=300, J=8) # 300 sites, 8 occasions per site +occu_umf <- simulate("occu", formulas=forms, coefs=coefs, design=design) +template_model <- occu(~1~elev, occu_umf) + +# Generate two power analysis +effect_sizes <- list(state=c(intercept=0, elev=-0.4), det=c(intercept=0)) +pa <- powerAnalysis(template_model, coefs=effect_sizes, alpha=0.05) +pa2 <- powerAnalysis(template_model, effect_sizes, design=list(M=100,J=2)) + +# Build unmarkedPowerList and look at summary +(pl <- unmarkedPowerList(list(pa,pa2))) + +# Run a bunch of power analyses for different scenarios all at once +scenarios <- expand.grid(M=c(50,200,400), + J=c(3,5,8)) +(pl2 <- unmarkedPowerList(template_model, effect_sizes, design=scenarios, nsim=20)) + +# Look at summary plot for elev effect +plot(pl2, power=0.8, param='elev') + +} +} |