Traceplot

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)