Merge branch 'optspace-decostand-centring'

Author: jarioksa

R/decostand.R

@@ -221,6 +221,11 @@
    if (impute && any(is.na(xx))) {
      xx <- optspace(xx, ropt = ropt, niter = niter, tol = tol,
                     verbose = verbose)$M
+     ## Centring is common operation supporting output visualization
+     ## Centre cols to 0
+     xx <- as.matrix(scale(xx, center = TRUE, scale = FALSE))
+     ## Centre rows to 0
+     xx <- as.matrix(t(scale(t(xx), center = TRUE, scale = FALSE)))
    }
    xx
 }

R/optspace.R

@@ -144,12 +144,6 @@
   # Reconstruct the matrix
   M <- X %*% S %*% t(Y)
 
-  # Centering is common operation supporting output visualization
-  # Center cols to 0
-  M <- as.matrix(scale(M, center = TRUE, scale = FALSE))
-  # Center rows to 0
-  M <- as.matrix(t(scale(t(M), center = TRUE, scale = FALSE)))
-
   dimnames(M) <- dimnames(x)
   # Add imputed matrix to the output
   out$M <- M

man/optspace.Rd

@@ -37,17 +37,17 @@ This implementation removes the trimming step of the original
 \code{Roptspace::OptSpace} code in order to leave feature filtering to the
 user. Some of the defaults have been adjusted to better reflect
 ecological data. The implementation has been adjusted for ecological
-applications as in Martino et al. (2019). The imputed matrix (M) in
-the optspace output includes matrix reconstruction (XSY'), with
-subsequent centering for the columns and rows.
+applications as in Martino et al. (2019). The imputed matrix (\eqn{M}) in
+the optspace output includes matrix reconstruction (\eqn{XSY'}).
 }
 
 \value{Returns a named list containing:
   \item{X}{an \eqn{(n \times r)}{(n x r)} matrix as left singular vectors.}
   \item{S}{an \eqn{(r \times r)}{(r x r)} matrix as singular values.}
   \item{Y}{an \eqn{(m \times r)}{(m x r)} matrix as right singular vectors.}
   \item{dist}{a vector containing reconstruction errors at each successive iteration.}
-  \item{M}{an \eqn{(n \times m)}{(n x m)} imputed matrix, with columns and rows centered to zero.}
+  \item{M}{an \eqn{(n \times m)}{(n x m)} imputed matrix as calculated
+    from \code{X}, \code{S} and \code{Y}.}
 }
 
 \author{Leo Lahti and Cameron Martino, with adaptations of the method

tests/decostand-tests.R

@@ -38,7 +38,7 @@ x[sample(prod(dim(x)), 50)] <- NA # insert some NAs in the data
 all(is.na(decostand(x, "clr", na.rm = FALSE, pseudocount = 1)[is.na(x)])) == TRUE # NAs
 # For the other (non-NA) values, we get non-NA values back
 any(is.na(decostand(x, "clr", na.rm = FALSE, pseudocount = 1)[!is.na(x)])) == FALSE
-any(is.na(decostand(x, "clr", MARGIN = 2, na.rm = FALSE, pseudocount = 1)[!is.na(x)])) == FALSE 
+any(is.na(decostand(x, "clr", MARGIN = 2, na.rm = FALSE, pseudocount = 1)[!is.na(x)])) == FALSE
 # Results match for the non-NA values always (with tolerance 1e-6)
 inds <- !is.na(x) # Non-NA values
 max(abs(decostand(x, "clr", na.rm = FALSE, pseudocount = 1)[inds] -
@@ -76,7 +76,7 @@ decostand(testdata, method = "clr", pseudocount = 1)
 #class(try(decostand(testdata, method = "clr"))) == "try-error"
 #class(try(decostand(testdata, method = "clr", pseudocount = 0))) == "try-error"
 
-# Tests that clr robust gives values that are approximately same if only 
+# Tests that clr robust gives values that are approximately same if only
 # one value per sample are changed to zero
 # Adds pseudocount
 test <- testdata + 1
@@ -103,9 +103,8 @@ x2 <- decostand(varespec, method = "rclr", impute = FALSE)
 
 # Matrix completion
 x2c <- optspace(x2, ropt = 3, niter = 5, tol = 1e-5, verbose = FALSE)$M
-all(as.matrix(x1) == as.matrix(x2c))
-
-x2c <- optspace(x2, niter = 5, tol = 1e-5, verbose = FALSE)$M
+x2c <- scale(x2c, center = TRUE, scale = FALSE)
+x2c <- t(scale(t(x2c), center = TRUE, scale = FALSE))
 all(as.matrix(x1) == as.matrix(x2c))
 
 ############################# NAMES ####################################

tests/decostand-tests.Rout.save

@@ -60,7 +60,7 @@ Type 'q()' to quit R.
 > # For the other (non-NA) values, we get non-NA values back
 > any(is.na(decostand(x, "clr", na.rm = FALSE, pseudocount = 1)[!is.na(x)])) == FALSE
 [1] TRUE
-> any(is.na(decostand(x, "clr", MARGIN = 2, na.rm = FALSE, pseudocount = 1)[!is.na(x)])) == FALSE 
+> any(is.na(decostand(x, "clr", MARGIN = 2, na.rm = FALSE, pseudocount = 1)[!is.na(x)])) == FALSE
 [1] TRUE
 > # Results match for the non-NA values always (with tolerance 1e-6)
 > inds <- !is.na(x) # Non-NA values
@@ -334,10 +334,14 @@ row18 -0.14885299
 row19  0.91755915
 row20  0.33766080
 attr(,"scaled:center")
- [1] -0.0031079619 -0.0463480942 -0.0267762284  0.0089869339  0.0380073003
- [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
+         row1          row2          row3          row4          row5 
+-0.0031079619 -0.0463480942 -0.0267762284  0.0089869339  0.0380073003 
+         row6          row7          row8          row9         row10 
+-0.0216677154 -0.0095070243 -0.0129853877 -0.0151765084  0.0739366224 
+        row11         row12         row13         row14         row15 
+ 0.0813752690  0.0153170116 -0.0001358339 -0.0203385433 -0.0102092705 
+        row16         row17         row18         row19         row20 
+-0.0133788389  0.0543704488 -0.0876478093  0.0272043261 -0.0319186959 
 attr(,"decostand")
 [1] "rclr"
 > decostand(testdata, method = "clr", pseudocount = 1)
@@ -551,7 +555,7 @@ attr(,"decostand")
 > #class(try(decostand(testdata, method = "clr"))) == "try-error"
 > #class(try(decostand(testdata, method = "clr", pseudocount = 0))) == "try-error"
 > 
-> # Tests that clr robust gives values that are approximately same if only 
+> # Tests that clr robust gives values that are approximately same if only
 > # one value per sample are changed to zero
 > # Adds pseudocount
 > test <- testdata + 1
@@ -828,10 +832,8 @@ col50 FALSE
 > 
 > # Matrix completion
 > x2c <- optspace(x2, ropt = 3, niter = 5, tol = 1e-5, verbose = FALSE)$M
-> all(as.matrix(x1) == as.matrix(x2c))
-[1] TRUE
-> 
-> x2c <- optspace(x2, niter = 5, tol = 1e-5, verbose = FALSE)$M
+> x2c <- scale(x2c, center = TRUE, scale = FALSE)
+> x2c <- t(scale(t(x2c), center = TRUE, scale = FALSE))
 > all(as.matrix(x1) == as.matrix(x2c))
 [1] TRUE
 > 
@@ -875,4 +877,4 @@ col50 FALSE
 > 
 > proc.time()
    user  system elapsed 
-  0.438   0.048   0.485 
+  0.436   0.048   0.481