checkRd: (-1) export.figtree.Rd:64: Lost braces; missing escapes or markup?
    64 | The tip labels of \code{tree} (accessed via \code{tree$tip.label}) must have the same names (and the same length) as the tip labels in \code{unsorted.pvalues}, but may be in a different order.  The p-values in column 2 of \code{unsorted.pvalues} obviously must be in the [0, 1] range.  \code{p.cutoffs} takes values in the (0, 1) range.  The default value for \code{p.cutoffs} is \code{c(0.01, 0.05, 0.1, 0.9, 0.95, 0.99)} if side is \code{1} and \code{c(0.01, 0.05, 0.1)} if side is \code{2}.  Thus, the ranges (when side is \code{1}) are: [0, .01], (.01, .05], ..., (.99, 1].  These ranges correspond to the colors specified in \code{pal}.  P-values in the [0, .01] range correspond to the left-most color if \code{pal} is a palette (view this via \code{display.brewer.pal(x, pal)} - where \code{x} is the number of colors to be used) or the first value in the vector if \code{pal} is a vector of colors.  If \code{pal} is a vector of colors, then the length of \code{pal} should be one greater than the length of \code{p.cutoffs}.  In other words, its length must be the same as the number of p-value ranges.  In addition, each color in this vector of colors needs to be in hexadecimal format, for example, \code{"#B2182B"}.  Formats of colors other than hexadecimal will likely give unwanted results in the edges of the tree produced in \emph{FigTree}, such as all-black edges or the edges being colored in a meaningless way.  This is because the color conversion assumes hexadecimal colors.  The default value of \code{pal} is \code{"RdBu"} (a divergent palette of reds and blues, with reds corresponding to small p-values) if \code{side} is \code{1} and the reverse of \code{"Reds"} (a sequential palette) if \code{side} is {2}.   The sequential palettes in \code{RColorBrewer} go from light to dark, so \code{"Reds"} is reversed so that the dark red corresponds to small p-values.    It probably makes more sense to use a divergent palette when using 1-sided p-values and a sequential palette (reversed) when using 2-sided p-values.  To create a vector of reversed colors from a palette with \code{x} number of colors and \code{"PaletteName"} as the name of the palette, use \code{rev(brewer.pal(x, "PaletteName"))}.  \code{ignore.edge.length} may be useful to get a more uniformly-shaped tree. \code{export.figtree} assumes that each internal node has exactly two descendants.  It also assumes that each internal node has a lower number than each of its ancestors (excluding tips). 
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checkRd: (-1) plotSigTree.Rd:91: Lost braces; missing escapes or markup?
    91 | The tip labels of \code{tree} (accessed via \code{tree$tip.label}) must have the same names (and the same length) as the tip labels in \code{unsorted.pvalues}, but may be in a different order.  The p-values in column 2 of \code{unsorted.pvalues} obviously must be in the [0, 1] range.  \code{p.cutoffs} takes values in the (0, 1) range.  The default value for \code{p.cutoffs} is \code{c(0.01, 0.05, 0.1, 0.9, 0.95, 0.99)} if \code{side} is \code{1} and \code{c(0.01, 0.05, 0.1)} if side is \code{2}.  Thus, the ranges (when side is \code{1}) are: [0, .01], (.01, .05], ..., (.99, 1].  These ranges correspond to the colors specified in \code{pal}.  P-values in the [0, .01] range correspond to the left-most color if \code{pal} is a palette (view this via \code{display.brewer.pal(x, pal)} - where \code{x} is the number of colors to be used) or the first value in the vector if \code{pal} is a vector of colors.  If \code{pal} is a vector of colors, then the length of \code{pal} should be one greater than the length of \code{p.cutoffs}.  In other words, its length must be the same as the number of p-value ranges.  An example of a color in hexadecimal format is \code{"#B2182B"}. The default value of \code{pal} is \code{"RdBu"} (a divergent palette of reds and blues, with reds corresponding to small p-values) if \code{side} is \code{1} and the reverse of \code{"Reds"} (a sequential palette) if \code{side} is {2}.   The sequential palettes in \code{RColorBrewer} go from light to dark, so \code{"Reds"} is reversed so that the dark red corresponds to small p-values.    It probably makes more sense to use a divergent palette when using 1-sided p-values and a sequential palette (reversed) when using 2-sided p-values.  To create a vector of reversed colors from a palette with \code{x} number of colors and \code{"PaletteName"} as the name of the palette, use \code{rev(brewer.pal(x, "PaletteName"))}.  \code{use.edge.length} may be useful to get a more uniformly-shaped tree.  \code{plotSigTree} assumes that each internal node has exactly two descendants.  It also assumes that each internal node has a lower number than each of its ancestors (excluding tips).
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