Plot mean or variance shifts, with uncertainties and null hypothesis testing

plotShift(
  x,
  cl.color = "Reds",
  sf.fill = c("navy", "firebrick"),
  plot.sig.vlines = FALSE,
  label.sig = FALSE,
  qs = c(0.95, 0.9),
  x.axis.label = NA,
  x.lims = NA,
  y.axis.label = NA,
  y.lims.direction = 1,
  combine.plots = TRUE,
  shift.direction = "positive/negative",
  ...
)

Arguments

x

Output from actR::detectShift (tibble)

cl.color

Color palette, single color, or vector of colors to use for confidence intervals (default = "Reds"s)

sf.fill

Color palette, single color, or vector of colors to use for confidence intervals (default = c("grey"))

plot.sig.vlines

Plot vertical lines at significant change points? (default = TRUE)

label.sig

Label significant change points (default = TRUE)

qs

significance levels to plot. The first value will be used to calculate the alpha for significant shifts (default = c(0.95,0.9))

x.axis.label

Label the x-axis (default = NA, which will automatically generate from input)

x.lims

2-element vector to use as x-axis limits (default = NA)

y.axis.label

Label the y-axis (default = NA, which will automatically generate from input)

y.lims.direction

A value of -1 will flip the y-axis for both panels (default = 1) #TODO

combine.plots

Combine the probability and timeseries plots into a single plot (TRUE)? Or return a list with each plot as a separate object (FALSE)?

shift.direction

plot positive, negative or both ("positive/negative" - the default)

...

Arguments passed on to geoChronR::plotTimeseriesEnsRibbons

add.to.plot: A ggplot object to add this plot to. Default is ggplot() .
X: A LiPD variable list to plot, including values, units, names, and more
Y: A LiPD variable list to plot, including values, units, names, and more
alp: alpha (transparency) parameter for the ribbons
probs: a vector of probabilities to plot as ribbons. It will create bands as ribbons of quantiles moving inward. If there's an odd number, it plots the middle quantile as a line.
x.bin: vector of bin edges over which to bin.
y.bin: vector of bin edges over which to bin.
n.bins: number bins over which to calculate intervals. Used to calculate x.bin if not provided.
color.low: Color of the outermost band; the extreme quantiles of the distribution
color.high: Color of the innermost band; the central quantiles of the distribution
color.line: Line color (following ggplot rules)
color.vector: A vector (of length equal to the number of bands) that specifies the colors for the ribbons from the outermost band in (default = NA). Colors specified as string according to ggplot2 conventions. If present, this overrules color.high and color.low
line.width: Width of the line
export.quantiles: If TRUE, return the plotted quantiles rather than the plot

Value

a ggplot object