aggregateData: Aggregate and select data from Atlantis output

Description Usage Arguments Value Author(s) Examples

View source: R/aggregateData.R

Description

subsets data based on defined columns, and sums over layers, but enter NA for layers to keep the column names the same. Currently, the function works for a vector of defined species and polygons.

Usage

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aggregateData(dat, time, species, boxes, keepColumns = c("species",
  "agecl", "polygon", "time"))

Arguments

dat

A data.frame of numbers-at-age from reading in the Atlantis output

time

A single value or a vector of time steps for a survey. Time steps are specified as integers.

species

A vector of character values, where each entry is a species name that is sampled in the survey.

boxes

A vector of polygons where the survey samples within each specified polygon.

keepColumns

A vector of character values, specifying which columns to keep for the returned data.frame. The default is c("species", "agecl", "polygon", "time").

Value

The function returns a subsetted matrix with the same columns as the input data, i.e.,:

Author(s)

Allan Hicks

Examples

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dat <- data.frame(species = c(rep("spec1", 3*3),rep("spec2", 5*3)),
  agecl = c(rep(1:3, 3), rep(3:7, 3)),
  polygon = c(rep(1:3, each = 3), rep(1:3, each = 5)),
  layer = 1, time = 1)
dat$atoutput <- 10000/dat$agecl
tmp <- aggregateData(dat = dat, time = 1,
  species = c("spec1", "spec2"), boxes = 1:2)
rm(list = c("tmp", "dat"))

r4atlantis/atlantisom documentation built on Aug. 13, 2019, 12:58 p.m.