Plot chron ensemble

Source: R/plotting.geoChronR.R

Plot creates an age model plot with all the bells and whistles, including a spread of ensemble members, probability distributions, and a few example ensemble members.

plotChronEns(
  L,
  age.var = "ageEnsemble",
  depth.var = "depth",
  chron.number = NA,
  model.num = NA,
  probs = c(0.025, 0.25, 0.5, 0.75, 0.975),
  x.bin = NA,
  y.bin = NA,
  n.bins = 100,
  color.low = "white",
  color.high = "grey70",
  alp = 1,
  color.line = "Black",
  line.width = 1,
  add.to.plot = ggplot2::ggplot(),
  n.ens.plot = 5,
  color.ens.line = "red",
  alp.ens.line = 0.7,
  dist.alp = 0.3,
  dist.type = "violin",
  dist.color = "purple",
  dist.thick = 0.1,
  dist.scale = 0.02,
  truncate.dist = NA,
  add.paleo.age.depth = FALSE,
  paleo.number = NA,
  meas.num = NA,
  color.line.paleo = "cyan",
  plot.traces = TRUE
)

Arguments

L

A LiPD object - an R serialization of a single LiPD file. It's a list, and is typically created by `readLipd()`

age.var

ariableName to use for age ensemble ("ageEnsemble" by default)

depth.var

variableName to use for depth ("depth" by default)

chron.number

chron.numData object to use (NA by default, will ask if needed)

model.num

chron.numData model to use (NA by default, will ask if needed)

probs

quantiles to calculate and plot

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

Band color of the outer most band.

color.high

Band color of the inner most band.

alp

Transparency of the band plot

color.line

Line color (following ggplot rules)

line.width

Width of the line

add.to.plot

A ggplot object to add this plot to. Default is ggplot() .

n.ens.plot

Number of ensemble members to plot

color.ens.line

color of the ensemble lines

alp.ens.line

transparency of the lines

dist.alp

alpha of the distribution

dist.type

"violin" (default), "up" for one-sided distributions pointed up, "down" for one-sided distributions pointed down

dist.color

distribution color (following ggplot rules)

dist.thick

thickness of the line around the distribution

dist.scale

controls the vertical span of the probability distribution. Approximately the vertical fraction of the plot that the distribution will cover.

truncate.dist

truncate probability density values below this number. NA (default) means no truncation

add.paleo.age.depth

add a line that shows the paleoData age depth.

paleo.number

paleo.num number for the paleoData age-depth

meas.num

which measurement Table for the paleoData age-depth

color.line.paleo

line color of the paleoData age-depth (following ggplot rules)

plot.traces

Add timeseries lines to the plot (default = TRUE)

Value

A ggplot object

Author

Nick McKay