tseries_plot: Time series plot

In nikolaifish/bamExtras: Functions and Data in Support of Stock Assessments with the Beaufort Assessment Model (BAM)

Time series plot

Description

This is a simple plotting fucntion that is useful when plotting time series typically found in stock assessments (e.g. catch, indices)

Usage

tseries_plot(
  x,
  err,
  errType = "sd",
  errStyle = "bands",
  errUnits = "SE",
  nErrUnits = 2,
  errLim = c(0, Inf),
  plotLabel = NULL,
  matplot_args = list(col = rainbow(ncol(x)), type = "o", lty = 1, lwd = 2, pch = 16,
    ylim = NULL),
  polygon_args = list(border = NA, lwd = matplot_args$lwd),
  col_band_alpha = 0.3,
  pt_buffer = 0.1,
  ...
)

Arguments

x	data frame of mean observations by year, where columns are different groups (e.g. fleets)
err	error values for each value in x. Must be same dimensions as x
errType	type of error provided: "cv"= coefficient of variation or "sd"=standard deviation. If "cv" then x is multiplied by err to compute sd.
errStyle	Style of displaying error around the central tendency time series x. Can be"bars" or "bands"
errUnits	Units of err. Used only for displaying text on plot (e.g. "SE")
nErrUnits	Multiplied by err to determine how far above and below x to to plot the errors
errLim	Range for limiting the plotting of error bars or bands.
plotLabel	character string for labeling plot
matplot_args	list of additional arguments passed to matplot, which plots x.
polygon_args	list of additional arguments passed to polygon, which plots error bands when errStyle="bands".
col_band_alpha	alpha (transparency) value between 0 and 1 to adjust opacity of color bands
...	pass additional arguments to matplot
ylim	range of y on plot

Author(s)

Nikolai Klibansky

Examples

## Not run: 
rdat <- rdat_BlackSeaBass
tser <- rdat$t.series
U <- tser[,grepl("^U.*ob$",names(tser))]
Ucv <- tser[,grepl("^cv.U.",names(tser))]
tseries_plot(U,Ucv,xlab="year",ylab="index of abundance",plotLabel=rdat$info$species)

## End(Not run)

nikolaifish/bamExtras documentation built on July 21, 2023, 8:26 a.m.