Index.plots: Abundance Index plots from stock assessment models
In rcheshire/FishGraph: Visualizations for fishery stock-assessment.

Index.plots

R Documentation

Abundance Index plots from stock assessment models

Description

Plots observed and predicted and diagnostic plots for index development

Usage

Index.plots(
  x,
  DataName = deparse(substitute(x)),
  draft = TRUE,
  graphics.type = NULL,
  use.color = TRUE,
  connect.obsd = FALSE,
  from.zero = TRUE,
  two.panel = TRUE,
  log.resid = TRUE,
  err.bar = TRUE,
  resid.analysis = TRUE,
  resid.tests = NULL,
  runs.box = TRUE
)

Arguments

`x`	an R list with output from the assessment models.
`DataName`	string used in plot titles. Defaults to argument `x`.
`draft`	modifies plots for use in a report. When `FALSE` main titles are omitted.
`graphics.type`	a vector of graphics file types to which graphics are saved. When `NULL`, no plots are saved.
`use.color`	plots are made in grayscale when `FALSE`
`connect.obsd`	When `TRUE` a line connecting observed points is plotted
`from.zero`	When `TRUE`, the Y-axis of each plot (except recruitment deviations) starts at zero.
`two.panel`	when `TRUE`, the observed-predicted plot and residual time plot are drawn as two-panels. When `FALSE` they are drawn independently.
`log.resid`	When `TRUE` residuals are computed as `R = log(U \diagup\hat{U})`.
`err.bar`	When `TRUE`, error bars indicating plus/minus two standard errors of the observed index are plotted
`resid.analysis`	When `TRUE`, additional diagnostic plots of residuals are created
`resid.tests`	Runs statistical tests on residuals. Set to "runs" for runs test only or "multiple" for additional tests. Defaults to argument `NULL` for none.
`runs.box`	Boolean for if you want to print the runs test 3 times SD on the log residual plot for the 2 box