Plots a line graph showing how the AICc changed over the forward and backward phases of a SURFACE analysis. surfaceAICPlot
can optionally show the change in the deviance or 'partial AICc' for each trait separately as well as for the analysis as a whole. surfaceAICMultiPlot
plots lines from multiple runs on the same plot, allowing comparison among analyses done on alternate tree topologies or with stochasticity added using sample_shifts
surfaceAICPlot(fwd = NULL, bwd = NULL, out = NULL, summ = NULL,
traitplot = "none", cols = NULL, daic = FALSE, ...)
surfaceAICMultiPlot(fwd = NULL, bwd = NULL, out = NULL, summ = NULL,
cols = NULL, daic = FALSE, ...)
Plots AIC values from a SURFACE analysis on the current graphics device
List resulting from a surfaceForward
run, or a list of such lists if calling surfaceAICMultiPlot
List resulting from a surfaceBackward
run, or a list of such lists if calling surfaceAICMultiPlot
List resulting from a runSurface
run, consisting of elements fwd
and bwd
, or a list of such lists if calling surfaceAICMultiPlot
Object returned by surfaceSummary
(run on the forward and backward phases of an analysis together), or a list of such objects if calling surfaceAICMultiPlot
String indicating what values to use to draw lines corresponding to individual traits: "none"
, "dev"
or "aic"
(see details); defaults to "none"
An optional character vector of colors for the AICc lines, used to color the different runs in surfaceAICMultiPlot
. Only used in surfaceAICPlot
if traitplot = "aic"
or traitplot = "dev"
, in which case the colors are used for the trait lines (the overall AICc line is drawn in black)
A logical indicating whether to rescale all delta-AICc (and delta-deviance) values to the value from the starting model; defaults to FALSE
, but is automatically set to TRUE
if traitplot = "aic"
or traitplot = "dev"
Additional arguments to be passed to the plot
or points
functions
Travis Ingram
If values are plotted on a trait-by-trait basis, either traitplot="dev"
or traitplot="aic"
can be specified. If traitplot="dev"
, the deviance (-2*log likelihood) at each step is shown for each trait. If traitplot="aic"
, a "partial AICc" at each step is shown for each of the m
traits, consisting of the deviance and 1/m of the "penalty" part of the overall AICc, where m is the number of traits. Note that this is not a proper statistical construct, but its property of adding to give the overall AICc can be useful in visualizing the patterns among traits
Ingram, T. & Mahler, D.L. (2013) SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise AIC. Methods in Ecology and Evolution 4: 416-425.
Mahler, D.L., Ingram, T., Revell, L.J. & Losos, J.B. (2013) Exceptional convergence on the macroevolutionary landscape in island lizard radiations. Science 341: 292-295.
surfaceForward
, surfaceBackward
, surfaceSimulate
, surfaceSummary
, surfaceTreePlot
, surfaceTraitPlot
if (FALSE) {
data(surfaceDemo)
tree<-surfaceDemo$tree
dat<-surfaceDemo$sim$dat
result<-runSurface(tree,dat)
surfaceAICPlot(result$fwd,result$bwd)
}
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