Merge branch 'issue-#759'

Author: jarioksa

R/decostand.R

@@ -143,7 +143,8 @@
             x <- .calc_rclr(x, na.rm = na.rm, ...)
 	else x <- t(.calc_rclr(t(x), na.rm = na.rm, ...))
         attr <- attr(x, "parameters")
-        attr$margin <- MARGIN
+        if (!is.null(attr)) # no transformation parameters with imputed matrix
+            attr$margin <- MARGIN
     })
     if (any(is.nan(x)))
         warning("result contains NaN, perhaps due to impossible mathematical
@@ -221,13 +222,10 @@
    # Impute NAs if impute=TRUE
    # Otherwise return the transformation with NAs
    if (impute && any(is.na(xx))) {
-
      xx <- optspace(xx, ropt = ropt, niter = niter, tol = tol,
                     verbose = verbose)$M
    }
-
    xx
-
 }
 
 .calc_alr <-
@@ -299,7 +297,7 @@
                               x * para$minpos},
                 "clr" = exp(sweep(x, para$margin, para$means, "+")) -
                     para$pseudocount,
-                "rclr" = { x[x == 0] <- -Inf # x==0 was set: should be safe
+                "rclr" = { x[is.na(x)] <- -Inf # no imputation: 0 |-> NA
                            exp(sweep(x, para$margin, para$means, "+"))},
                 "wisconsin" = { x <- sweep(x, 1, para$total, "*")
                                 sweep(x, 2, para$max, "*") },

tests/decostand-tests.Rout.save

@@ -338,10 +338,6 @@ attr(,"scaled:center")
  [6] -0.0216677154 -0.0095070243 -0.0129853877 -0.0151765084  0.0739366224
 [11]  0.0813752690  0.0153170116 -0.0001358339 -0.0203385433 -0.0102092705
 [16] -0.0133788389  0.0543704488 -0.0876478093  0.0272043261 -0.0319186959
-attr(,"parameters")
-attr(,"parameters")$margin
-[1] 1
-
 attr(,"decostand")
 [1] "rclr"
 > decostand(testdata, method = "clr", pseudocount = 1)
@@ -879,4 +875,4 @@ col50 FALSE
 > 
 > proc.time()
    user  system elapsed 
-  0.437   0.048   0.482 
+  0.438   0.048   0.485