reportAbundance: Calculate a summary of the bootstrap iterations (possibly...

Description Usage Arguments Value Examples

View source: R/rstox_reports.r

Description

reportAbundance is a wrapper function for the reportAbundance functions for the bootstrapMehtods "AcousticTrawl", "SweptAreaLength" and "SweptAreaTotal". reportAbundance_AcousticTrawl reports and writes to file the abundance with uncertanty for the different groups given by grp1 and (possibly) grp2. reportAbundance_SweptAreaLength is an alias for reportAbundance_AcousticTrawl. reportAbundance_SweptAreaTotal returns summary statistics generated from bootstrap replicates for projects with only total catch. reportAbundanceAtLevel is used in reportAbundance_AcousticTrawl and reportAbundance_SweptAreaLength for generating the report for each level "bootstra" or "bootstrapImpute".

Usage

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reportAbundance(projectName, bootstrapMethod = "AcousticTrawl",
  var = "Abundance", unit = NULL, baseunit = NULL, grp1 = "age",
  grp2 = NULL, numberscale = 1e+06, plotOutput = FALSE, write = FALSE,
  ...)

reportAbundance_SweptAreaLength(projectName, var = "Abundance", unit = NULL,
  baseunit = NULL, grp1 = "age", grp2 = NULL, numberscale = 1e+06,
  plotOutput = FALSE, write = FALSE, msg = TRUE, ...)

reportAbundance_AcousticTrawl(projectName, var = "Abundance", unit = NULL,
  baseunit = NULL, grp1 = "age", grp2 = NULL, numberscale = 1e+06,
  plotOutput = FALSE, write = FALSE, msg = TRUE, ...)

reportAbundance_SweptAreaTotal(projectName, unit = NULL, baseunit = NULL,
  write = FALSE, ...)

reportAbundanceAtLevel(projectName, var = "Abundance", unit = NULL,
  baseunit = NULL, level = "bootstrapImpute", grp1 = "age", grp2 = NULL,
  numberscale = 1e+06, plotOutput = FALSE, write = FALSE, digits = 6)

Arguments

projectName

The name or full path of the project, a baseline object (as returned from getBaseline or runBaseline, og a project object (as returned from openProject).

var

A key string indicating the variable to plot (see getPlottingUnit()$defaults$Rstox_var for available values).

unit

A unit key string indicating the unit, or alternatively a numeric value giving the scaling factor (run getPlottingUnit() to see available values).

baseunit

The unit used in the data.

grp1

Variable used to group results, e.g. "age", "LenGrp", "sex"

grp2

An optional second grouping variable

numberscale

Kept for compability with older versions. Use 'unit' instead. (Scale results with e.g. 1000 or 1000000).

plotOutput

Logical: if TRUE return a list of the recuired data in the function plotAbundance(). Otherwise, only the abundance data frame is returned.

write

Logical: if TRUE write the data to a tab-separated file.

level

A string naming the process level (see getRstoxEnv()$processLevels for available levels).

Value

A data frame of the abundance in sumary per grp2 and grp1 if plotOutput=FALSE, and a list holding this object (keeping "-" for missing values and not ordering) and other objects needed by plotAbundance().

Examples

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projectName <- "Test_Rstox"
reportAbundance(projectName, grp1=NULL, grp2=NULL)
reportAbundance(projectName, grp1="age", grp2=NULL)
reportAbundance(projectName, var="weight", grp1="age", grp2=NULL)
reportAbundance(projectName, grp1="age", grp2="Stratum")
reportAbundance(projectName, grp1="age", grp2="Stratum")

Sea2Data/Rstox documentation built on April 18, 2018, 11:11 p.m.