powerAnalysis: Conduct a power analysis on an unmarked model

In rbchan/unmarked: Models for Data from Unmarked Animals

Conduct a power analysis on an unmarked model

Description

This function uses a simulation-based approach to estimate power for parameters in unmarked models. At a minimum, users must provide a fitted unmarked model object (preferably fit with simulated data) which ensures the model has been properly specified, a list of effect sizes for each parameter in the model (coefs), and the desired Type I error (alpha). It is also possible to get power for a range of other sample sizes besides the sample size in the fitted model object using the design argument to subsample within the provided dataset. See the unmarkedPower vignette for more details and examples.

Usage

  powerAnalysis(object, coefs=NULL, design=NULL, alpha=0.05, nulls=list(),
                datalist=NULL, 
                nsim=ifelse(is.null(datalist), 100, length(datalist)), 
                parallel=FALSE)

Arguments

object	A fitted model inheriting class unmarkedFit. This could potentially be fit using real data, but ideally you would simulate an appropriate dataset using simulate
coefs	A list containing the desired effect sizes for which you want to estimate power. This list must follow a specific format. There is one named entry in the list per submodel (e.g., occupancy, detection). To get the required submodel names call names(object) on your fitted model. Then, each list entry is a named vector with the names corresponding to the parameter names for that submodel, and the values corresponding to the desired effect sizes. It may be easier to leave coefs=NULL, which will generate an error message with a template that you can fill in.
design	An optional list of design/sample size parameters containing at a minimum two named elements: M, the number of sites, and J the number of observations per site. If this list is provided, unmarked will subsample the provided dataset to the specified number of sites and observations, allowing you to test power for different designs. If your model has multiple primary periods you must also include T, the number of periods, in the list.
alpha	Desired Type I error rate
nulls	If provided, a list matching the structure of coefs which defines the null hypothesis value for each parameter. By default the null is 0 for all parameters.
datalist	An optional list of previously-simulated datasets, in the form of unmarkedFrames matching the model type of object, which will be used for the power analysis simulations.
nsim	Number of simulations to conduct
parallel	If TRUE, run folds in parallel. This may speed up the power analysis in some situations

Value

unmarkedPower object containing the results of the power analysis

Author(s)

Ken Kellner [e-mail]

See Also

unmarkedPowerList

Examples

## Not run: 

# Simulate an occupancy dataset
# Covariates to include in simulation
forms <- list(state=~elev, det=~1)

# Covariate effects and intercept values
coefs <- list(state=c(intercept=0, elev=-0.4), det=c(intercept=0))

# Study design
design <- list(M=300, J=8) # 300 sites, 8 occasions per site

# Simulate an unmarkedFrameOccu
occu_umf <- simulate("occu", formulas=forms, coefs=coefs, design=design)

# Fit occupancy model to simulated data
# This will contain all the model structure info powerAnalysis needs
# The estimates from the model aren't used
template_model <- occu(~1~elev, occu_umf)

# If we run powerAnalysis without specifying coefs we'll get a template list
powerAnalysis(template_model)

# Set desired effect sizes to pass to coefs
effect_sizes <- list(state=c(intercept=0, elev=-0.4), det=c(intercept=0))

# Run power analysis and look at summary
(pa <- powerAnalysis(template_model, coefs=effect_sizes, alpha=0.05))

# Try a smaller sample size in the study design
(pa2 <- powerAnalysis(template_model, coefs=effect_sizes, alpha=0.05,
                      design=list(M=100, J=2)))


## End(Not run)

rbchan/unmarked documentation built on April 3, 2024, 10:11 p.m.