R Interface for Program PRESENCE

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Documentation for package ‘RPresence’ version 2.13.47

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RPresence-package R Interface for Program PRESENCE
Blue_Ridge.csv Blue-Ridge salamander data (single-season example with covariate)
cal_owl_multistate_data.csv Occupancy detection data for California Spotted Owls (single-season, multi-state analysis)
coef.occMod Extract regression coefficients from occupancy model, i.e., real parameter estimates
createAicTable Create AIC table
createPao Create a pao data object.
delete_unused_covs get rid of unused covariates in pao object 'simplify_dm'
exampleBobcats Second RPresence example using real data, bobcats
exampleGenpres Example intro script for RPresence using expected-value data generated by 'genpres'
exampleSalamanders Example intro script for RPresence using Salamander data from book.
exampleSkinks Example intro script for RPresence using Skinks data from book.
exampleWeta Second RPresence example using real data, Giant Weta
fitted.occMod Extract fitted values from occupancy model, i.e., real parameter estimates
genpresEV generate expected value detection histories
genpresEV2sp generate expected value detection histories for multi-state models
genpresEVcd generate expected value detection histories for corr. det. model
genpresEVhet generate expected value detection histories for model with heterogeneous detections
genpresEVmm generate expected value detection histories for multi-method model
genpresEVms generate expected value detection histories for multi-state models
genpresRPC generate simulated data detection histories Royle point-count model
genpresSD generate simulated data (single or multi-season) detection histories
genpresSD2sp generate simulated data detection histories for 2-species models
genpresSDcd generate stochastic data detection histories for corr. det. model
genpresSDmm generate simulated single-season, multi-method data detection histories
genpresSDms generate SIMULATED detection histories for multi-state model w/ psi/R parameterization.
getbetas Get beta estimates from output file
get_dmats Get design matrices from output file
get_not01_dm get site/survey covarite names which are not all 0 or 1 in the design matrix so the 0/1 covariate names (eg., Intercept) can be omitted from the temp.pao file.
importProject Import a PRESENCE project into R.
is.pao check if object is pao object
LRTpower compute expected power using non-central chi-square function
makeHtmlFromAicTable write html file with links based on AIC table
modAvg Calculate model averaged estimates
modCombos Create a list of formulae for all possible first-order combinations for a set of variables.
occMod Fit an occupancy model using Program PRESENCE
occMod_2SP Fit two species, static occupancy (single season), or dynamic occupancy (multi-season) model
occMod_2SPfp Fit two species, static occupancy (single season) model with false positive detections
occMod_DO Fit dynamic (multi-season) occupancy model using the first parameterisation in PRESENCE.
occMod_DO2 Fit dynamic (multi-season) occupancy model using the first parameterisation in PRESENCE.
occMod_DO4 Fit dynamic (multi-season) occupancy model using the fourth parameterisation (random changes in occupancy, epsilon=1-gamma) in PRESENCE.
occMod_DO_fp Fit static occupancy/single season model
occMod_DO_het Fit static occupancy/single season model
occMod_DO_ms1 Fit multi-state dynamic (multi-season) occupancy model using the 1st parameterisation (psi/phi).
occMod_DO_ms2 Fit multi-state dynamic occupancy (multi-season) occupancy model using the second (conditional binomial) parameterisation in PRESENCE.
occMod_mm Fit multi-method (or multi-scale) static occupancy/single season model
occMod_RPC Fit static occupancy/single season model
occMod_SO Fit static occupancy/single season model
occMod_SO_2SP_cd Fit two species, static occupancy (single season) model with correlated detectoins
occMod_SO_cd Fit static occupancy, correlated detections model
occMod_SO_fp Fit static occupancy/single season model
occMod_SO_het Fit static occupancy/single season model
patch.data Middle Earth patch covariate data
predict.occMod Predict real parameter values.
print_one_site_estimates Print real param estimates for i-th site only
psi_cond get conditional occupancy estimates from single-season ("so") model
readPao Read a pao data object.
RPresence R Interface for Program PRESENCE
runPresence call PRESENCE to produce model estimates (replaces "write_dm_and_run")
simplify_dm simplify design matrix by replacing all individual covariates which are all one or zero with '1' or '0' in the design matrix. This makes the design matrix much easier to read and faster for the model. 'simplify_dm' Replaces ind. covariates which are all 0 or 1, with 0 or 1.
summary.aicTable Summary of 'aic.table' object
summary.occMod Summary of occupancy model
summary.pao Summary of occupancy data object
summedWgt Calculate summed model weights for a set of variables for a specific parameter.
trolls Middle Earth troll data (single-season example with covariates)
trolls_ms This dataset contains fictional data from a multi-season occupancy study.
trolls_ss Middle Earth troll data (single-season example with covariates)
writePao Write a pao data object to disk file.