Merge branch 'dist-maxdist-attr'

R/avgdist.R

@@ -57,6 +57,6 @@
     }
     output <- as.dist(output, diag = diag, upper = upper)
     attr(output, "call") <- match.call()
-    attr(output, "method") <- "avgdist"
+    attr(output, "method") <- paste("avgdist", dmethod)
     output
 }

R/isomapdist.R

@@ -48,6 +48,7 @@
         attr(dist, "critval") <- epsilon
     }
     attr(dist, "method") <- paste(attr(dist, "method"), "isomap")
+    attr(dist, "maxdist") <- NA
     attr(dist, "net") <- net
     attr(dist, "take") <- take
     attr(dist, "call") <- match.call()

R/taxa2dist.R

@@ -15,7 +15,7 @@
     if (varstep) {
         add <- -diff(c(nrow(x), rich, 1))
         add <- add/c(S, rich)
-        add <- add/sum(add) * 100
+        add <- add/sum(add) * 100 # 100 after Clarke, veganish would be 1
     }
     else {
         add <- rep(100/(ncol(x) + check), ncol(x) + check)
@@ -31,6 +31,7 @@
     out <- as.dist(out)
     attr(out, "method") <- "taxa2dist"
     attr(out, "steps") <- add
+    attr(out, "maxdist") <- 100 # after Clarke, veganish would be 1
     if (missing(labels)) {
         attr(out, "Labels") <- rownames(x)
     } else {

R/treedist.R

@@ -33,5 +33,10 @@
     attr(out, "method") <- if (relative) "treedist" else "raw treeedist"
     attr(out, "call") <- match.call()
     attr(out, "Labels") <- row.names(x)
+    ## if (relative) theoretical maximum is 2, but that is only
+    ## achieved when two zero-height trees (only one species) are
+    ## combined into above zero-height tree (two species), and
+    ## therefore we set here NA (but this can be reconsidered).
+    attr(out, "maxdist") <- NA
     out
 }