SightabilityPopR {SightabilityModel}

R function that interfaces with the SightabilityModel package and gives similar functionality as the AerialSurvey program

Description

A stratified random sample of blocks in a survey area is conducted. In each block, groups of moose are observed (usually through an aerial survey). For each group of moose, the number of moose is recorded along with attributes such as sex or age.

The SightabilityPopR() function adjusts for sightability < 100%.

Usage

SightabilityPopR(
  survey.data,
  survey.block.area,
  stratum.data,
  density = NULL,
  abundance = NULL,
  numerator = NULL,
  denominator = NULL,
  sight.formula = observed ~ 1,
  sight.beta = 10,
  sight.beta.cov = matrix(0, nrow = 1, ncol = 1),
  sight.logCI = TRUE,
  sight.var.method = c("Wong", "SS")[1],
  block.id.var = "Block.ID",
  block.area.var = "Block.Area",
  stratum.var = "Stratum",
  stratum.blocks.var = "Stratum.Blocks",
  stratum.area.var = "Stratum.Area",
  conf.level = 0.9
)

Arguments

survey.data

A data frame containing counts of moose in each group along with a variable identifying the stratum (see stratum.var) and block (see block.id.var)

survey.block.area

A data frame containing for each block, the block id (see block.id.var), the area of the block (see block.area.var). The data frame can contain information for other blocks that were not surveyed (e.g. for the entire population of blocks) and information from these additional blocks will be ignored.

stratum.data

A data frame containing for each stratum, the stratum id (see stratum.var), the total number of blocks in the stratum (see stratum.blocks.var) and the total area of the stratum (see stratum.area.var)

density, abundance, numerator, denominator

Right-handed formula identifying the variable(s) in the survey.data data frame for which the density, abundance, or ratio (numerator/denominator) are to be estimated.

sight.formula

A formula that identifies the model used to estimate sightability. For example observed ~ VegCoverClass would indicate that sightability is a function of the VegCoverClass variable in the survey data. The left hand variable is arbitrary. The right hand variables must be present in the survey.data data frame.

sight.beta

The vector of estimated coefficients for the logistic regression sightability model.

sight.beta.cov

The covariance matrix of sight.beta

sight.logCI

Should confidence intervals for the sightability adjusted estimates be computed using a normal-based confidence interval on log(abundance)

sight.var.method

What method should be used to estimate the variances after adjusting for sightability.

block.id.var

Name of the variable in the data frames that identifies the block.id (the sampling unit)

block.area.var

Name of the variable in data frames that contains the area of the blocks (area of sampling unit)

stratum.var

Name of the variable in the data frames that identifies the classical stratum

stratum.blocks.var

Name of the variable in the stratum.data data frame that contains the total number of blocks in the stratum.

stratum.area.var

Name of the variable in the stratum.data data.frame that contains the total stratum area.

conf.level

Confidence level used to create confidence intervals.

Value

A data frame containing for each stratum and for all strata (identified as stratum id .OVERALL), the density, or abundance or ratio estimate along with its estimated standard error and large-sample normal-based confidence interval. Additional information on the components of variance is also reported.

Author(s)

Schwarz, C. J. [e-mail].

References

To Be Added.

Examples

 
##---- See the vignettes for examples on how to run this analysis.