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

In Sea2Data/Rstox: Running Stox functionality independently in 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

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

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 May 14, 2019, 8:58 a.m.