plot_sumz_density {TITAN2}

Plot community level change

Description

Plot community level change

Usage

plot_sumz_density(
  titan.out,
  filter = TRUE,
  sumz = TRUE,
  points = FALSE,
  ribbon = TRUE,
  density = TRUE,
  change_points = TRUE,
  sumz1 = TRUE,
  sumz2 = TRUE,
  xlim = c(min(titan.out$env), max(titan.out$envcls)),
  xlabel = "Environmental Gradient",
  y1label = NULL,
  y2label = "Density",
  alpha1 = 0.65,
  alpha2 = 0.5,
  col1 = "steelblue4",
  col2 = "red",
  trans = "identity",
  legend.position = c(0.9, 0.9),
  ...,
  axis.text.x,
  axis.text.y,
  axis.title.x,
  axis.title.y
)

Arguments

titan.out

A TITAN output object.

filter

A logical indicating whether only pure and reliable taxa should be used to create the plot.This is the recommended as a check of the unfiltered default to assess whether impure or unreliable taxa are substantially contributing to the distribution of sum(z) scores.

sumz

Plot sum z values? (Default = TRUE)

points

Plot points on sum z values? (Default = FALSE)

ribbon

Fill in axes under sum z values? (Default = TRUE)

density

Plot densities of change points? (Default = TRUE)

change_points

Plot ranges of change points? These are taken from the titan object. (Default = TRUE)

sumz1

A logical specifying whether decreasing changes should be plotted.

sumz2

A logical specifying whether increasing changes should be plotted.

xlim

x axis limits, e.g. xlim = c(0,10).

xlabel

A character string for the x axis label.

y1label

A character specifying the label of the second y axis

y2label

A character specifying the label of the second y axis

alpha1, alpha2

Transparency of Z- and Z+ values, respectively.

col1

A graphical argument specifying the color of group 1 symbols.

col2

A graphical argument specifying the color of group 2 symbols.

trans

a scale transformation to be applied to the x-axis through ggplot2. e.g. "log10" or "sqrt".

legend.position

ggplot2 legend position in relative coordinates of sum z plot. (Default = c(.9, .9))

...

An argument for passing generic plotting function parameters.

axis.text.x, axis.text.y, axis.title.x, axis.title.y

Font sizes of respective axis text. Passed as the size argument to the ggplot2 thematic elements of the same name. Defaults to current default ggplot2 theme.

Value

A plot

Note

Should not be used with output objects from TITAN v1.0.

Author(s)

M. Baker and R. King

References

Baker, ME and RS King. 2010. A new method for detecting and interpreting biodiversity and ecological community thresholds. Methods in Ecology and Evolution 1(1): 25:37.

King, RS and ME Baker 2010. Considerations for identifying and interpreting ecological community thresholds. Journal of the North American Benthological Association 29(3):998-1008.

See Also

plot_sumz(), plot_cps()

Examples

data(glades.titan)

plot_sumz_density(glades.titan)
plot_sumz_density(glades.titan, trans = "log10")