plotAgeTraces: Traceplot

In StoXProject/RstoxFDA: Fisheries Dependent Analysis with RstoX

Traceplot

Description

Plots a paneled plot with traces for age groups. That is the value for total catch at age in each iteration of eca.predict

Usage

plotAgeTraces(
  prediction,
  unit = "millions",
  plusGroup = NULL,
  nclust = 4,
  iter.max = 20,
  nstart = 10,
  agecolors = NULL,
  lowerquant = 0.05,
  upperquant = 0.95,
  catlimit = 8,
  title = ""
)

Arguments

prediction	as returned by eca.predict or runRECA.
unit	unit of traced estimates. See details.
plusGroup	Fish this age or older will be grouped in one trace.
nclust	the number of plots to distribute the ages and plus group on
iter.max	maximal number of iterations for k-means clustering deciding which ages are plotted in same plot.
nstart	the number of random sets chosen for the k-means clustering
agecolors	named vector matching ages to colors, if null a default color scheme is used
lowerquant	lower quantile in each age group to plot as points
upperquant	upper quantile in each age group to plot as points
catlimit	the upper limit for number of ages in a plot using categorical coloring. Plots with more than this number of ages will use a gradient coloring scheme
title	main title for plot

Details

The number of iterations of eca.predict is determined by the parameter 'nSamples' to eca.estimate or runRECA and the parameter 'caa.burnin' (different from parameter 'burnin') to eca.predict or runRECA

parameter 'unit' supports:

number

Catch at age as number of fish

thousands

Catch at age as number of fish in thousands

millions

Catch at age as number of fish in millions

kg

Catch at age as mass in kilogrammes

T

Catch at age as mass in tons

kT

Catch at age as mass in kilotonnes

In order to trade off readability of plots with the number of panels needed. the traces are clustered with a simple clustering algorithm and grouped in the same plots accordingly. Adjust clustering parameters, to get fewer or more plots.

Examples

 data(recaPrediction)
 plotAgeTraces(recaPrediction, plusGroup=13, nclust = 6)

StoXProject/RstoxFDA documentation built on Dec. 17, 2024, 10:58 a.m.