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Extracts the most important results from the output of the forward, backward, or both phases of a SURFACE analysis
● Data Source:
CranContrib
● Keywords: manip
● Alias: surfaceSummary
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surface provides a wrapper to the ouch package, fitting a series of Hansen multiple-peak stabilizing selection models using stepwise AIC, and identifying cases of convergence where independent lineages discovered the same adaptive peak
● Data Source:
CranContrib
● Keywords: package
● Alias: surface, surface-package
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Plotting functions to visualize the results of a SURFACE analysis, with colors depicting regime structure: surfaceTreePlot produces a customized plot.phylo figure, and surfaceTraitPlot produces a scatterplot of trait values and optima
● Data Source:
CranContrib
● Keywords: hplot
● Alias: surfaceTraitPlot, surfaceTreePlot
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A wrapper to the paint function in ouch to ensure that regime paintings are automatically formatted for SURFACE analysis (painting the stem branch of a clade and ensuring that the root is assigned a regime)
● Data Source:
CranContrib
● Keywords: manip
● Alias: repaint
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Provides several ways to simulate data sets on phylogenetic trees in conjunction with SURFACE analyses. Can simulate under simple models without regime shifts, under a Hansen model with sampled shift locations, or under a fitted Hansen model (optionally with resampled optima)
● Data Source:
CranContrib
● Keywords: datagen
● Alias: surfaceSimulate
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Generate a model to start a SURFACE analysis, or fit specific Hansen or Brownian motion models that can be compared to the models returned by SURFACE
● Data Source:
CranContrib
● Keywords: manip
● Alias: startingModel
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Extracts the time from root of each node in an ouchtree or hansentree formatted phylogenetic tree; used to compute the timing of regime shifts in a Hansen model
● Data Source:
CranContrib
● Keywords: manip
● Alias: getBranchTimes
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Carries out the forward phase of SURFACE's stepwise AIC routine, adding regime shifts to a Hansen model. addRegime performs one step of this analysis, and is called repeatedly by surfaceForward. At each step, the delta-AICc of each possible shift placement (i.e. branch) is calculated, and an updated Hansen model is returned with one shift added. This process is iterated until the model stops improving beyond a threshold delta-AICc
● Data Source:
CranContrib
● Keywords: iteration, models
● Alias: addRegime, surfaceForward
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Carries out the backward phase of SURFACE's stepwise AIC routine. Beginning with a fitted Hansen model produced by surfaceForward, tests pairwise collapses of regimes and identifies collapses that improve the fit. Continues this iterative process until the model stops improving beyond the given AIC threshold
● Data Source:
CranContrib
● Keywords: iteration, models
● Alias: collapseRegimes, surfaceBackward
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convertTreeData converts a phylo-formatted tree and a data frame into formats ready to be analyzed with the ouch functions called by surface. convertBack converts an ouchtree to a data frame including regime information, and is called internally by surfaceTreePlot. nameNodes adds unique node labels to a phylo tree to ensure reliable conversion between formats
● Data Source:
CranContrib
● Keywords: manip
● Alias: convertBack, convertTreeData, nameNodes
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