plot-sumz: Plots the pattern of community change along an environmental...

In dkahle/TITAN2: Threshold Indicator Taxa Analysis

Plots the pattern of community change along an environmental gradient

Description

Creates a plot of community-level sums of taxon-specific change along an environmental gradient and optionally conveys uncertainty associated with the maximum community change derived from decreasers or increasers.

Usage

plot_sumz(
  titan.out,
  filter = FALSE,
  cumfrq = TRUE,
  bootz1 = TRUE,
  bootz2 = TRUE,
  sumz1 = TRUE,
  sumz2 = TRUE,
  xmin = min(titan.out$env),
  xmax = max(titan.out$envcls) * 1.25,
  xlabel = "Environmental Gradient",
  y1label = NULL,
  y2label = "Cumulative Frequency",
  log = "",
  at = NULL,
  tck = 0.025,
  bty = "u",
  ntick = 6,
  prtty = TRUE,
  dig = 1,
  cex = 1.75,
  cex.axis = 1.75,
  cex.leg = 1.5,
  cex.lab = 1.75,
  leg.x = 0.8,
  leg.y = 0.8,
  legend = TRUE,
  pch1 = 16,
  pch2 = 1,
  col1 = "black",
  col2 = "black",
  ...
)

plotSumz(...)

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.
cumfrq	A logical specifying whether cumulative frequencies of sum(z) maxima across bootstrap replicates should be plotted.
bootz1	A logical specifying whether decreasing cumulative frequencies exist or should be plotted.
bootz2	A logical specifying whether increasing cumulative frequencies exist or should be plotted.
sumz1	A logical specifying whether decreasing changes should be plotted.
sumz2	A logical specifying whether increasing changes should be plotted.
xmin	A graphical argument specifying the value of the x axis minimum.
xmax	A graphical argument specifying the value of the x axis maximum.
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
log	A graphical argument specifying whether an axis should be log scaled.
at	A graphical argument for controling placement of the x axis label
tck	A graphical argument specifying the scale of axis tick marks.
bty	A graphical argument.
ntick	A graphical argument specifying the default number of axis tick marks.
prtty	A logical specifying whether pretty() should be used to plot axis labels.
dig	A numeric argument specifying the number of decimal digits in axes.
cex	A graphical argument specifying the scaling of the figure.
cex.axis	A graphical argument specifying the scaling of the axes.
cex.leg	A graphical argument specifying the scaling of the legend.
cex.lab	A graphical argument specifying the scaling of the lables.
leg.x	A graphical argument specifying the x coordinate of the legend.
leg.y	A graphical argument specifying the y coordinate of the legend.
legend	A logical specifying whether or not to plot the legend.
pch1	A graphical argument specifying the type of group 1 symbols.
pch2	A graphical argument specifying the type of group 2 symbols.
col1	A graphical argument specifying the color of group 1 symbols.
col2	A graphical argument specifying the color of group 2 symbols.
...	An argument for passing generic plotting function parameters.

Details

This function assumes that the TITAN object contains bootstrap summaries and filtering information and automatically determines whether this is the case. Without the bootstrap summaries, only unfiltered change magnitudes are plotted.

The original sum(z) plots (v1.0) did not filter taxa using purity and reliability. Because these taxa often have small z scores, they are unlikely to contribute significantly to the sum(z) profiles. However, subsequent investigation has demonstrated that when sufficient numbers of taxa are involved, it is possible for noisy data to generate artifactual peaks in low-magnitude sum(z) profiles or plateaus. Therefore, we recommend evaluating filtered versions of the sum(z) to assess this potential in v2.0.

Value

A plot of sum(z-) and sum(z+) profiles along the environmental gradient.

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_taxa(), plot_cps()

Examples

data(glades.titan)
plot_sumz(glades.titan, filter = FALSE)

dkahle/TITAN2 documentation built on Nov. 15, 2023, 2:49 p.m.