TITAN2 (version 2.4)

plot-taxa: Plots taxon-specific change points

Description

Creates a plot of taxon-specific change points with optional quantiles conveying uncertainty resulting from bootstrapped samples and optional filtering by pure and reliable taxa.

Usage

plot_taxa(
  titan.out,
  z1 = TRUE,
  z2 = TRUE,
  interval = TRUE,
  prob95 = FALSE,
  z.med = FALSE,
  xlabel = "Environmental Gradient",
  log = "",
  at = NULL,
  xmin = min(titan.out$sppmax[, 8]),
  xmax = max(titan.out$sppmax[, 12]) * 1.05,
  tck = 0.025,
  bty = "u",
  ntick = 6,
  prtty = TRUE,
  dig = 1,
  leg.x = 0.8,
  leg.y = 10,
  cex.taxa = 0.75,
  cex = 1.25,
  cex.axis = 1.25,
  cex.leg = 1.25,
  cex.lab = 1.25,
  legend = TRUE,
  col1 = "black",
  fil1 = "black",
  col2 = "black",
  fil2 = "white",
  write = FALSE,
  all = FALSE,
  ...
)
plotTaxa(...)

Arguments

titan.out

A TITAN output object.

z1

A logical specifying whether decreasing taxa should be plotted.

z2

A logical specifying whether decreasing taxa should be plotted.

interval

A logical specifying whether quantiles of bootstrapped change points should be plotted.

prob95

A logical specifying whether change-point locations should be plotted on the basis of their 5th (for increasers) and 95th (for decreasers) quantile versus their observed values.

z.med

A logical specifying whether (1) change point magnitudes should be obtained from the median z score across bootstrap replicates and (2) whether the locations should be plotted on the basis of the 50th quantile of change-point locations (i.e., if prob95=FALSE).

xlabel

A character string for the x axis label.

log

A graphical argument specifying whether an axis should be log scaled.

at

A graphical argument controlling the locatino of the x axis label.

xmin

A graphical argument specifying the value of the x axis minimum.

xmax

A graphical argument specifying the value of the x axis maximum.

tck

A graphical argument specifying the scale of axis tick marks.

bty

A graphical argument specyfying the box type around the plot.

ntick

A graphical argument specifying the default number of axis tick marks.

prtty

A logical specifying whether pretty() should be used for axis plotting.

dig

A numeric argument controlling the number of decimal digits in axis labels.

leg.x

A graphical argument specifying the x coordinate of the legend.

leg.y

A graphical argument specifying the y coordinate of the legend.

cex.taxa

A graphical argument specifying the scaling of the taxa names.

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.

legend

A logical specifying whether or not to plot the legend.

col1

A graphical argument specifying the color of group 1 symbols.

fil1

A graphical argument specifying the color of group 1 fills.

col2

A graphical argument specifying the color of group 2 symbols.

fil2

A graphical argument specifying the color of group 2 fills.

write

A logical specifying whether summary tables are written to screen.

all

A logical specifying whether all taxa with p<0.05 should be plotted.

...

An argument for passing generic plotting function parameters.

Value

A plot of decreasing and/or increasing taxon-specific change points along the environmental gradient.

Details

The fuction assumes that TITAN objects contain bootstrap summaries and filtering information and automatically determines whether this is the case. Without bootstrap summaries, only observed change-point locations and z-score magnitudes will be plotted. The plotting function automatically interprets whether observed change-point values were obtained using IndVal or z-score maxima. The interval option is for turning off the intervals for TITAN objects that contain bootstrap information. The prob95 is recommended for communicating uncertainty involving management or policy action, whereas the z.med option is recommended for increasingly robust estimates (by incorporating uncertainty associated with the sample) of taxon-specific change-point locations beyond those provided by the default (i.e., observed values).

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

# NOT RUN {
data(glades.titan)
plot_taxa(glades.titan, xlabel = "Surface Water TP (ug/l)")


# }