Codoc mismatches from documentation object 'discrete.gamma':
plot_gamma_plus_inv
  Code: function(shape = 1, inv = 0, k = 4, discrete = TRUE, cdf =
                 TRUE, append = FALSE, xlab = "x", ylab = ifelse(cdf,
                 "F(x)", "f(x)"), xlim = NULL, verticals = FALSE,
                 edge.length = NULL, site.rate = "gamma", ...)
  Docs: function(shape = 1, inv = 0, k = 4, discrete = TRUE, cdf =
                 TRUE, append = FALSE, xlab = "x", ylab = ifelse(cdf,
                 "F(x)", "f(x)"), xlim = NULL, verticals = FALSE, ...)
  Argument names in code not in docs:
    edge.length site.rate
  Mismatches in argument names:
    Position: 11 Code: edge.length Docs: ...

Codoc mismatches from documentation object 'acctran':
parsimony
  Code: function(tree, data, method = "fitch", cost = NULL, site =
                 "pscore")
  Docs: function(tree, data, method = "fitch", ...)
  Argument names in code not in docs:
    cost site
  Argument names in docs not in code:
    ...
  Mismatches in argument names:
    Position: 4 Code: cost Docs: ...

Codoc mismatches from documentation object 'threshStateC':
map_duplicates
  Code: function(x, dist = length(x) < 500, ...)
  Docs: function(x, dist = TRUE, ...)
  Mismatches in argument default values:
    Name: 'dist' Code: length(x) < 500 Docs: TRUE

Codoc mismatches from documentation object 'phyDat':
dna2codon
  Code: function(x, codonstart = 1, code = 1, ambiguity = "---", ...)
  Docs: function(x, codonstart = 1, ambiguity = "---", ...)
  Argument names in code not in docs:
    code
  Mismatches in argument names:
    Position: 3 Code: code Docs: ambiguity
    Position: 4 Code: ambiguity Docs: ...

Codoc mismatches from documentation object 'plot.networx':
plot.networx
  Code: function(x, type = "equal angle", use.edge.length = TRUE,
                 show.tip.label = TRUE, show.edge.label = FALSE,
                 edge.label = NULL, show.node.label = FALSE, node.label
                 = NULL, show.nodes = FALSE, tip.color = "black",
                 edge.color = "black", edge.width = 3, edge.lty = 1,
                 split.color = NULL, split.width = NULL, split.lty =
                 NULL, font = 3, cex = par("cex"), cex.node.label =
                 cex, cex.edge.label = cex, col.node.label = tip.color,
                 col.edge.label = tip.color, font.node.label = font,
                 font.edge.label = font, ...)
  Docs: function(x, type = "3D", use.edge.length = TRUE, show.tip.label
                 = TRUE, show.edge.label = FALSE, edge.label = NULL,
                 show.node.label = FALSE, node.label = NULL, show.nodes
                 = FALSE, tip.color = "black", edge.color = "black",
                 edge.width = 3, edge.lty = 1, split.color = NULL,
                 split.width = NULL, split.lty = NULL, font = 3, cex =
                 par("cex"), cex.node.label = cex, cex.edge.label =
                 cex, col.node.label = tip.color, col.edge.label =
                 tip.color, font.node.label = font, font.edge.label =
                 font, ...)
  Mismatches in argument default values:
    Name: 'type' Code: "equal angle" Docs: "3D"

Codoc mismatches from documentation object 'pml.control':
pml
  Code: function(tree, data, bf = NULL, Q = NULL, inv = 0, k = 1, shape
                 = 1, rate = 1, model = NULL, site.rate = "gamma", ...)
  Docs: function(tree, data, bf = NULL, Q = NULL, inv = 0, k = 1, shape
                 = 1, rate = 1, model = NULL, ...)
  Argument names in code not in docs:
    site.rate
  Mismatches in argument names:
    Position: 10 Code: site.rate Docs: ...

Codoc mismatches from documentation object 'lli':
pml.fit
  Code: function(tree, data, bf = rep(1/length(levels),
                 length(levels)), shape = 1, k = 1, Q = rep(1,
                 length(levels) * (length(levels) - 1)/2), levels =
                 attr(data, "levels"), inv = 0, rate = 1, g = NULL, w =
                 NULL, eig = NULL, INV = NULL, ll.0 = NULL, llMix =
                 NULL, wMix = 0, ..., site = FALSE, Mkv = FALSE,
                 site.rate = "gamma")
  Docs: function(tree, data, bf = rep(1/length(levels),
                 length(levels)), shape = 1, k = 1, Q = rep(1,
                 length(levels) * (length(levels) - 1)/2), levels =
                 attr(data, "levels"), inv = 0, rate = 1, g = NULL, w =
                 NULL, eig = NULL, INV = NULL, ll.0 = NULL, llMix =
                 NULL, wMix = 0, ..., site = FALSE)
  Argument names in code not in docs:
    Mkv site.rate

Codoc mismatches from documentation object 'simSeq':
simSeq.phylo
  Code: function(x, l = 1000, Q = NULL, bf = NULL, rootseq = NULL, type
                 = "DNA", model = NULL, levels = NULL, rate = 1,
                 ancestral = FALSE, code = 1, ...)
  Docs: function(x, l = 1000, Q = NULL, bf = NULL, rootseq = NULL, type
                 = "DNA", model = NULL, levels = NULL, rate = 1,
                 ancestral = FALSE, ...)
  Argument names in code not in docs:
    code
  Mismatches in argument names:
    Position: 11 Code: code Docs: ...