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

In Sea2Data/Rstox: Running Stox functionality independently in 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

generateSpeciesMatrix(projectName, ref, years, check = TRUE,
  downloadProjects = FALSE, timeout = 600,
  model = list("ReadBioticXML", FilterBiotic = list(BioticData =
  "ReadBioticXML")), specVar = "noname", catVar = "Speccat",
  stationVar = c("cruise", "serialno"), bioticProc = "FilterBiotic",
  var = c("weight", "count"), max.sampletype = 49, list.out = TRUE,
  ...)

mergeSpeciesMatrix(...)

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 = TRUE, ...)

Arguments

projectName	A vector of cruise series names providing the data.
ref	Either a data frame with the reference information about the species, containing the variables specied in "specVar", "catVar", or the path to a csv file holding this data frame.
years	A vector of the years to process.
downloadProjects	Logical: If TRUE download the projects, which must be done the first time, or if one needs to re-download.
timeout	Used on Windows if problems with incompletely downloded data occurs (server problems).
model	The model to use in the projects. Per default only two processes are needed: ReadBioticXML reads the biotic data, and FilterBiotic filters away stations, gear, species and so on. Set FilterBiotic to filter data from ReadBioticXML.
specVar	The name of the variable identifying the species the data. This variable must be present also in 'ref'.
catVar	The name of the variable identifying the species categories to which the data should be grouped.
stationVar	The variables in the data defining biotic stations (the combination of these variables is used).
bioticProc	The StoX process from which the data are extracted (one of "ReadBioticXML" and "FilterBiotic" (the default, useful for filtering out e.g. gears)).
var	The variables to return data of.
...	Parameters passed on to getBaseline(), e.g. for changing the baseline parameters (adding filters).
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.
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.
model	Parameters such as FilterBiotic <- list(BioticData="ReadBioticXML", FishStationExpr = "gear =~['3270','3271', '3293', ”] and gearcondition < 3 and trawlquality =~['1','3'] and fishstationtype != ['2','C']", SampleExpr = "genetics != '7'").
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).

Value

A list of data frames with stations as rows and station information and the species present in the ref file as columns.

Sea2Data/Rstox documentation built on May 14, 2019, 8:58 a.m.