Plot community level change
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
)
A TITAN output object.
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.
Plot sum z values? (Default = TRUE
)
Plot points on sum z values? (Default = FALSE
)
Fill in axes under sum z values? (Default = TRUE
)
Plot densities of change points? (Default = TRUE
)
Plot ranges of change points? These are taken from the
titan object. (Default = TRUE
)
A logical specifying whether decreasing changes should be plotted.
A logical specifying whether increasing changes should be plotted.
x axis limits, e.g. xlim = c(0,10)
.
A character string for the x axis label.
A character specifying the label of the second y axis
A character specifying the label of the second y axis
Transparency of Z- and Z+ values, respectively.
A graphical argument specifying the color of group 1 symbols.
A graphical argument specifying the color of group 2 symbols.
a scale transformation to be applied to the x-axis through
ggplot2. e.g. "log10"
or "sqrt"
.
ggplot2 legend position in relative coordinates of sum
z plot. (Default = c(.9, .9)
)
An argument for passing generic plotting function parameters.
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.
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.
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.
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.
A plot
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.
# NOT RUN {
data(glades.titan)
plot_sumz_density(glades.titan)
plot_sumz_density(glades.titan, trans = "log10")
# }
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