Description Usage Arguments Details Value Note Author(s) References See Also
Original function designed for analyzing wolverine encounter histories in Ellis et al. 2013.
wolverine_analysis(n_yrs, ch = NULL, n_visit = NULL, sample_yr = 0, FPC = 1, ... )
Number of years in the encounter history. Run with all else NULL to produce an initial data.frame for setting up further results.
Character vector with encounters
Number of visits per year
Code for possible alternate model formulations
Finite population correction
This function provides an example of an analysis function, which will be called by
testReplicates on each individual encounter history. Should include appropriate model options for every subset of encounter histories. Returns a dataframe with results from current simulation, which will be compiled into a single output file by
testReplicates. Can include multiple model runs on the same encounter history by returning a data.frame with multiple lines.
The current function runs a robust design occupancy model through RMark with options for continuous or alternate year sampling. Trend is tested using variance.components procedure.
data.frame with model results
Default output from
wolverine_analysis include the estimated detection probability
p_est from the occupancy model, trend parameter estimate and standard error from GLM fit
trendSE, the number of singular parameters in the estimated occupancy model
singular, and the occupancy estimates by year
X10. Due to violation of closure assuption in RDoccup model
p_est includes effects of both imperfect detection (recorded via
detP) and underlying use/non-use for each cell in each year.
The analysis function you give
function_name will get called in two places in
testReplicates. First, it will get called by
RunAnalysis(n_yrs) to set up a header for the eventual results data.frame. Then it will get called in each step of the loop over all the subsetted encounter history files using
RunAnalysis(n_yrs, ch, n_visit, sample_yr,fpc , ... ). This is clunky, but for now, if you want to change
wolverine_analysis, you need to make sure the function you specify will work with those two function calls.
Jake Ivan, Martha Ellis
ELLIS, MARTHA M., JACOB S. IVAN, and MICHAEL K. SCHWARTZ. "Spatially Explicit Power Analyses for Occupancy-Based Monitoring of Wolverine in the US Rocky Mountains." Conservation Biology (2013).
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