Bycatch estimation using design-based estimators

Produces estimates of bycatch using design-based ratio estimator and delta estimator, with the option of pooling across stratification variables.

Usage

bycatchDesign(
  setupObj = setupObj,
  designScenario,
  designMethods = "Ratio",
  designVars = "Year",
  groupVar = "Year",
  designPooling = FALSE,
  poolTypes = NULL,
  pooledVar = NULL,
  adjacentNum = NULL,
  minStrataUnit = 1,
  baseDir = getwd(),
  reportType = "html"
)

Arguments

setupObj

An object produced by bycatchSetup.

designScenario

Short name, e.g. noPool, or Pool1, to distinguish outputs made with the same setupObj.

designMethods

Character vector of methods to use for design based estimation. Current options are Ratio and Delta (for a delta-lognormal estimator).

designVars

Specify strata that must be included in design based estimates, in order across which data should be pooled. Order of these variables determines order for which pooling will occur.

groupVar

Specify variable to keep separate in summaries. Defaults to Year. Put "NA" to summarize over whole dataset

designPooling

TRUE if design-based estimates should be pooled for strata with missing data

poolTypes

Type of pooling for each variable in designVars, as a character vector in the same order. Options are "none", where data will not be pooled over this variable, "all" where data will be pooled over all levels of the variable, "pooledVar" where the variable named in pooledVar will be used to pool, and (currently for year only) "adjacent" to pool over adjacent years.

pooledVar

Variables to pool over for any variable with pooledVar in the previous line, as a character vector in the same order as designVars. Use NA for variables with other pooling methods. This can be used to pool (for example) months into seasons when pooling is needed.

adjacentNum

Number of adjacent years to include for adjacent pooling, as a numerical vector in the same order as designVars. NA for anything other than year, in the same order as designVars.

minStrataUnit

The smallest sample size in the strata defined by designVars that is acceptable, in sample units (e.g. trips); below that pooling will occur.

baseDir

Character. A directory to save output. Defaults to current working directory.

reportType

Character. Choose type of report to be produced. Options are pdf, html (default) or both.

Examples

if (FALSE) { # \dontrun{
library(BycatchEstimator)
#-------------------------------------------------
#Step 1. Run the datasetup function and review data inputs
setupObj<-bycatchSetup(
obsdat = obsdatExample,
logdat = logdatExample,
yearVar = "Year",
obsEffort = "sampled.sets",
logEffort = "sets",
obsCatch = "Catch",
catchUnit = "number",
catchType = "dead discard",
logNum = NA,
sampleUnit = "trips",
factorVariables = c("Year","season"),
numericVariables = NA,
EstimateBycatch = TRUE,
baseDir = getwd(),
runName = "SimulatedExample",
runDescription = "Example with simulated data",
common = "Simulated species",
sp = "Genus species",
reportType = "html"
)

#-------------
#Step 2. Design-based estimators (with pooling)
bycatchDesign(
setupObj = setupObj,
designScenario = "noPool",
designMethods = c("Ratio", "Delta"),
designVars = c("Year","season"),
groupVar = "Year",
designPooling = TRUE,
poolTypes=c("adjacent","all"),
pooledVar=c(NA,NA),
adjacentNum=c(1,NA),
minStrataUnit = 1
)} # }