aggregateBySpeciesCategory: Generate species matrix with biotic stations as rows and...

Description Usage Arguments Value

View source: R/rstox_reports.r

Description

Generate species matrix with biotic stations as rows and station information and the species present in the ref file as columns. One matrix generated per variable var.

Usage

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aggregateBySpeciesCategory(projectName, ref, specVar = "noname",
  specVar.bio = specVar, specVar.ref = specVar, catVar = "SpecCat",
  bioticProc = "FilterBiotic", stationVar = c("cruise", "serialno"),
  var = c("weight", "count"), na.as = 0, drop.out = TRUE, close = TRUE,
  msg = FALSE, ...)

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).

ref

The path to a file linking species to species categories, specifically named by specVar or specVar.ref and catVar. The file must be a CSV (comma separated) file with UTF-8 encoding.

specVar, specVar.bio, specVar.ref

Names of the species columns in the data and in the ref file. When only specifying specVar, a common column name is assumed.

catVar

The name of the species category column in the ref file.

bioticProc

The process from which the biotic data should be extracted from the project.

stationVar

The names of the columns of the biotic data identifying the biotic stations. These columns will be concatenated.

var

The names of the columns for which the species matrices should be generated.

na.as

The value to use for missing data (e.g., species categories that are not present in a station).

drop.out

Logical: If TRUE (default) unlist if only one variable is given in var.

close

Logical: If TRUE (default) close the project after reading the data.

...

Parameters passed on to getBaseline(), e.g. for changing the baseline parameters (adding filters).

Value

A list of matrices (dropped to a matrix if only one variable is specified in var) with stations as rows and station information and the species present in the ref file as columns.


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