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## Converting a list of characters (ape format) into the Claddis format
convert.to.Claddis <- function(data) {
output <- list()
## Topper
output$topper$head <- "List generated by dispRity::Claddis.ordination"
## Matrix_1
output$matrix_1$block_name <- NA
output$matrix_1$datatype <- "STANDARD"
output$matrix_1$matrix <- do.call(rbind, data)
output$matrix_1$ordering <- rep("unord", length(data[[1]]))
output$matrix_1$character_weights <- rep(1, length(data[[1]]))
op <- options(warn = -1)
output$matrix_1$minimum_values <- unlist(apply(output$matrix_1$matrix, 2, function(x) min(as.numeric(x), na.rm = TRUE)))
is_nas <- is.na(output$matrix_1$minimum_values)
output$matrix_1$maximum_values <- unlist(apply(output$matrix_1$matrix, 2, function(x) max(as.numeric(x), na.rm = TRUE)))
output$matrix_1$characters$symbols <- unique(as.numeric(unlist(data)[-which(is.na(unlist(data)))]))
op <- options(warn = 0)
output$matrix_1$characters$missing <- "?"
output$matrix_1$characters$gap <- "-"
## Transform the missing data into "?"
output$matrix_1$matrix <- ifelse(output$matrix_1$matrix == "?", NA, output$matrix_1$matrix)
## Transform the inapplicables in ""
output$matrix_1$matrix <- ifelse(output$matrix_1$matrix == "-", "", output$matrix_1$matrix)
class(output) <- "cladisticMatrix"
return(output)
}
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