Nothing

```
checkcost <- function(sma, seqdata, with.missing, indel, tol = NULL) {
msg("checking 'sm' (size and triangle inequality)")
if (is.null(tol)) {
tol <- 1e-07 * max(sma)
}
alphabet <- attr(seqdata, "alphabet")
## Gaps in sequences
if (with.missing) {
alphabet <- c(alphabet, attr(seqdata, "nr"))
}
alphsize <- length(alphabet)
if (length(dim(sma)) == 2) {
dim(sma) <- c(dim(sma), 1)
} else {
if (ncol(seqdata) != dim(sma)[3]) {
stop(" [!] size of substitution cost matrix must be ", alphsize, "x",
alphsize, "x", ncol(seqdata), call. = FALSE)
}
}
if (!missing(indel) && any(indel <= 0)) {
stop(" [!] indel cost should be positive")
}
for (i in 1:dim(sma)[3]) {
sm <- sma[, , i]
if (nrow(sm) != alphsize | ncol(sm) != alphsize) {
stop(" [!] size of substitution cost matrix must be ", alphsize, "x",
alphsize, call. = FALSE)
}
if (any(sm < 0)) {
stop(" [!] Negative substitution costs are not allowed", call. = FALSE)
}
if (any(diag(sm) != 0)) {
stop(" [!] All element on the diagonal of sm (substitution cost) should be equal to zero")
}
triangleineq <- checktriangleineq(sm, warn = FALSE, indices = TRUE, tol = tol)
## triangleineq contains a vector of problematic indices.
if (!is.logical(triangleineq)) {
message(" [!!] at least, one substitution cost doesn't respect the triangle inequality.\n",
" [!!] replacing ", alphabet[triangleineq[1]], " with ", alphabet[triangleineq[3]],
" (cost=", format(sm[triangleineq[1], triangleineq[3]]), ") and then ",
alphabet[triangleineq[3]], " with ", alphabet[triangleineq[2]], " (cost=",
format(sm[triangleineq[3], triangleineq[2]]), ")\n [!] costs less than replacing directly ",
alphabet[triangleineq[1]], " with ", alphabet[triangleineq[2]], " (cost=",
format(sm[triangleineq[1], triangleineq[2]]), ")\n", " [!] total difference ([",
alphabet[triangleineq[1]], "=>", alphabet[triangleineq[3]], "] + [",
alphabet[triangleineq[3]], "=>", alphabet[triangleineq[2]], "] - [",
alphabet[triangleineq[1]], "=>", alphabet[triangleineq[2]], "]): ",
format(sm[triangleineq[1], triangleineq[3]] + sm[triangleineq[3],
triangleineq[2]] - sm[triangleineq[1], triangleineq[2]]))
}
if (!missing(indel)) {
if (length(indel) > 1) {
if (length(indel) != alphsize) {
stop(" [!] You should specify either one global indel or one indel per state.")
}
sm2 <- cbind(sm, indel)
sm2 <- rbind(sm2, c(indel, 0))
triangleineq <- checktriangleineq(sm2, warn = FALSE, indices = TRUE, tol = tol)
## triangleineq contains a vector of problematic indices.
if (!is.logical(triangleineq)) {
warning(" [!] at least, one indel cost does not respect the triangle inequality.\n",
call. = FALSE)
}
} else if (any(sm > 2 * indel)) {
warning("At least one substitution cost greater than twice the indel cost.",
" Such substitution costs will never be used.", call. = FALSE)
}
}
## Testing for symmetric matrix
if (any((sm - t(sm)) > tol)) {
warning("The substitution cost matrix is not symmetric.", call. = FALSE)
}
}
}
```

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