Merge branch 'sppscores'

NAMESPACE

@@ -500,6 +500,8 @@ S3method(specslope, fitspecaccum)
 S3method("sppscores<-", capscale)
 S3method("sppscores<-", dbrda)
 S3method("sppscores<-", metaMDS)
+S3method("sppscores<-", monoMDS)
+S3method("sppscores<-", wcmdscale)
 # SSD: stats
 S3method(SSD, cca)
 # str: utils

R/print.monoMDS.R

@@ -40,20 +40,16 @@
 }
 
 `scores.monoMDS` <-
-    function(x, choices = NA, ...)
+    function(x, display = "sites",  shrink = FALSE, choices, tidy = FALSE, ...)
 {
-    if (any(is.na(choices)))
-        x$points
-    else {
-        choices <- choices[choices <= x$ndim]
-        x$points[, choices, drop = FALSE]
-    }
+    scores.metaMDS(x, display = display, shrink = shrink, choices, tidy = tidy,
+                   ...)
 }
 
 `plot.monoMDS` <-
-    function(x, choices = c(1,2), type = "t",  ...)
+    function(x, display = "sites", choices = c(1,2), type = "t",  ...)
 {
-    ordiplot(x, display = "sites", choices = choices, type = type, ...)
+    ordiplot(x, display = display, choices = choices, type = type, ...)
 }
 
 `points.monoMDS` <-

R/print.wcmdscale.R

@@ -46,26 +46,43 @@
 }
 
 `scores.wcmdscale` <-
-    function(x, choices = NA, tidy = FALSE, ...)
+    function(x, choices = NA, display = "sites", tidy = FALSE, ...)
 {
-    p <-
-        if (any(is.na(choices))) {
-            x$points
-        } else {
-            choices <- choices[choices <= NCOL(x$points)]
-            x$points[, choices, drop = FALSE]
+    if ("species" %in% names(x))
+        display <- match.arg(display, c("sites", "species"), several.ok = TRUE)
+    else
+        display <- match.arg(display, "sites")
+    p <- list()
+    for (sco in display) {
+        if (sco == "sites")
+            p[[sco]] <- x$points
+        else
+            p[[sco]] <- x[[sco]]
+        if (!anyNA(choices)) {
+            choices <- choices[choices <= NCOL(p[[sco]])]
+            p[[sco]] <- p[[sco]][, choices, drop = FALSE]
         }
-    if (is.null(rownames(p)))
-        rownames(p) <- as.character(seq_len(nrow(p)))
-    if (tidy) {
-        p <- data.frame(p, "scores" = "sites", "label" = rownames(p),
-                        "weight" = weights(x))
+        if (is.null(rownames(p[[sco]])))
+            rownames(sco) <- as.character(seq_len(nrow(p[[sco]])))
+        if (tidy) {
+            wts <- if(sco == "sites") weights(x) else NA
+            p[[sco]] <- data.frame(p[[sco]], "score" = sco,
+                                   "label" = rownames(p[[sco]]),
+                                   weights = wts)
+        }
+    }
+    if (tidy && length(display) > 1) {
+        p <- do.call("rbind", p)
+        rownames(p) <- p$label
     }
-    p
+    if (length(p) == 1)
+        p[[1]]
+    else
+        p
 }
 
 `plot.wcmdscale` <-
-    function(x, choices = c(1,2), type = "t", ...)
+    function(x, choices = c(1,2), display = "sites", type = "t", ...)
 {
-    ordiplot(x, display = "sites", choices = choices, type = type, ...)
+    ordiplot(x, display = display, choices = choices, type = type, ...)
 }

R/scores.metaMDS.R

@@ -13,7 +13,9 @@
         colnames(sites) <- paste0("NMDS", choices)
         out$sites <- sites
     }
-    if ("species" %in% display && !is.null(x$species) && !all(is.na(x$species))) {
+    if ("species" %in% display) {
+        if (is.null(x$species) || all(is.na(x$species)))
+            stop("ordination object has no 'species' scores")
         species <- x$species[, choices, drop=FALSE]
         colnames(species) <- paste0("NMDS", choices)
         if (shrink) {

R/sppscores.R

@@ -57,6 +57,51 @@
     object
 }
 
+## monoMDS
+
+`sppscores<-.monoMDS` <-
+    function(object, value)
+{
+    wa <- wascores(object$points, value, expand = TRUE)
+    attr(wa, "data") <- deparse(substitute(value))
+    object$species <- wa
+    object
+}
+
+
+## sppscores<-.wcmdscale works with the simple case of row
+## weights. Verified to give the same result as RDA with duplicated
+## rows when using the number of duplicates as row weights in
+## wcmdscale of Eucliden distances (per sqrt(n-1)). However, does not
+## give the same results as CA in wcmdscale(vegdist(x, "chisq"),
+## w=rowSums(x)/sum(x)).
+
+`sppscores<-.wcmdscale` <-
+    function(object, value)
+{
+    value <- as.matrix(value)
+    w <- weights(object)
+    spp <- crossprod(value, w * object$points)
+    spp <- decostand(spp, "normalize", MARGIN = 2)
+    attr(spp, "vdata") <- deparse(substitute(value))
+    object$species <- spp
+    object
+}
+
+## This code would give CA species scores for
+##    wcmdscale(vegdist(x, "chisq"), w = rowSums(x)/sum(x), eig=TRUE)
+## or CA as weighted PCoA of Chi-square distances
+
+## `sppscores<-.wcmdscale` <-
+##     function(object, value)
+## {
+##     value <- as.matrix(value)
+##     value <- decostand(value, "total", MARGIN=2) # for sum(w) = 1
+##     spp <- crossprod(value, object$points) # wa: sum(w*x) with sum(w)=1
+##     spp <- sweep(spp, 2, object$eig, "/") # for wascores(..., expand=T)
+##     object$species <- spp
+##     object
+## }
 ## the main purpose of accessor function is to provide nicer command
 ## autocompletion and cross-references in help, and of course, to tell
 ## that it is not implemented (and may never be)

man/monoMDS.Rd

@@ -20,8 +20,9 @@ monoMDS(dist, y, k = 2, model = c("global", "local", "linear", "hybrid"),
     threshold = 0.8, maxit = 200, weakties = TRUE, stress = 1,
     scaling = TRUE, pc = TRUE, smin = 1e-4, sfgrmin = 1e-7,
     sratmax=0.999999, ...)
-\method{scores}{monoMDS}(x, choices = NA, ...)
-\method{plot}{monoMDS}(x, choices = c(1,2), type = "t", ...)
+\method{scores}{monoMDS}(x, display = "sites", shrink = FALSE, choices,
+    tidy = FALSE, ...)
+\method{plot}{monoMDS}(x, display = "sites", choices = c(1,2), type = "t", ...)
 \method{points}{monoMDS}(x, choices = c(1,2), select, ...)
 \method{text}{monoMDS}(x, labels, choices = c(1,2), select, ...)
 }
@@ -65,6 +66,20 @@ monoMDS(dist, y, k = 2, model = c("global", "local", "linear", "hybrid"),
 
   \item{x}{A \code{monoMDS} result.}
 
+  \item{display}{Kind of scores. Normally there are only scores for
+    \code{"sites"}, but \code{"species"} scores can be added with
+    \code{\link{sppscores}.}}
+
+  \item{shrink}{Shrink back species scores if they were expanded in
+      \code{\link{wascores}}.}
+
+  \item{tidy}{Return scores that are compatible with \CRANpkg{ggplot2}:
+    all scores are in a single \code{data.frame}, score type is
+    identified by factor variable \code{code} (\code{"sites"} or
+    \code{"species"}), the names by variable \code{label}. These scores
+    are incompatible with conventional \code{plot} functions, but they can
+    be used in \pkg{ggplot2}.}
+
   \item{choices}{Dimensions returned or plotted. The default \code{NA}
     returns all dimensions. }
 
@@ -191,7 +206,8 @@ monoMDS(dist, y, k = 2, model = c("global", "local", "linear", "hybrid"),
   are returned in item \code{points} (function \code{scores} extracts
   these results), and the stress in item \code{stress}. In addition,
   there is a large number of other items (but these may change without
-  notice in the future releases). }
+  notice in the future releases). There are no species scores, but these
+  can be added with \code{\link{sppscores}} function.}
 
 \references{
 

man/sppscores.Rd

@@ -4,6 +4,8 @@
 \alias{sppscores<-.dbrda}
 \alias{sppscores<-.capscale}
 \alias{sppscores<-.metaMDS}
+\alias{sppscores<-.monoMDS}
+\alias{sppscores<-.wcmdscale}
 
 \title{
 Add or Replace Species Scores in Distance-Based Ordination
@@ -12,12 +14,13 @@ Add or Replace Species Scores in Distance-Based Ordination
 \description{
 
   Distance-based ordination (\code{\link{dbrda}},
-  \code{\link{capscale}}, \code{\link{metaMDS}}) have no information
-  on species, but some methods may add species scores if community
-  data were available. However, the species scores may be missing (and
-  they always are in \code{\link{dbrda}}), or they may not have a
-  close relation to used dissimilarity index. This function will add
-  the species scores or replace the existing species scores in
+  \code{\link{capscale}}, \code{\link{metaMDS}}, \code{\link{monoMDS}},
+  \code{\link{wcmdscale}}) has no information on species, but some
+  methods may add species scores if community data were
+  available. However, the species scores may be missing (and they always
+  are in \code{\link{dbrda}} and \code{\link{wcmdscale}}), or they may
+  not have a close relation to used dissimilarity index. This function
+  will add the species scores or replace the existing species scores in
   distance-based methods.
 
 }
@@ -27,7 +30,9 @@ sppscores(object) <- value
 }
 
 \arguments{
-  \item{object}{Ordination result.}
+  \item{object}{Ordination result from \code{\link{capscale}},
+    \code{\link{dbrda}}, \code{\link{metaMDS}}, \code{\link{monoMDS}},
+    \code{\link{pco}} or \code{\link{wcmdscale}}.}
   \item{value}{Community data to find the species scores.}
 }
 
@@ -39,7 +44,7 @@ sppscores(object) <- value
   information after the analysis to help the interpretation of
   results. Some ordination methods (\code{\link{capscale}},
   \code{\link{metaMDS}}) can supplement the species scores during the
-  analysis if community data was available in the analysis.
+  analysis if community data were available in the analysis.
 
   In \code{\link{capscale}} the species scores are found by projecting
   the community data to site ordination (linear combination scores),
@@ -58,16 +63,17 @@ sppscores(object) <- value
   squareroot transformation to damp down the effect of squared
   differences (see Examples).
 
-  Function \code{\link{dbrda}} never finds the species scores, but it
-  is mathematically similar to \code{\link{capscale}}, and similar
-  rules should be followed when supplementing the species scores.
+  Functions \code{\link{dbrda}} and \code{\link{wcmdscale}} never find
+  the species scores, but they mathematically similar to
+  \code{\link{capscale}}, and similar rules should be followed when
+  supplementing the species scores.
 
-  Function \code{\link{metaMDS}} uses weighted averages
-  (\code{\link{wascores}}) to find the species scores. These have a
-  better relationship with most dissimilarities than the projection
-  scores used in metric ordination, but similar transformation of the
-  community data should be used both in dissimilarities and in species
-  scores.
+  Functions for species scores in \code{\link{metaMDS}} and
+  \code{\link{monoMDS}} use weighted averages (\code{\link{wascores}})
+  to find the species scores. These have better relationship with most
+  dissimilarities than the projection scores used in metric ordination,
+  but similar transformation of the community data should be used both
+  in dissimilarities and in species scores.
 
 }
 
@@ -78,7 +84,6 @@ sppscores(object) <- value
 
 }
 
-
 \author{
   Jari Oksanen
 }

man/wcmdscale.Rd

@@ -12,8 +12,8 @@
 \title{Weighted Classical (Metric) Multidimensional Scaling}
 \usage{
 wcmdscale(d, k, eig = FALSE, add = FALSE, x.ret = FALSE, w)
-\method{plot}{wcmdscale}(x, choices = c(1, 2), type = "t", ...)
-\method{scores}{wcmdscale}(x, choices = NA, tidy = FALSE, ...)
+\method{plot}{wcmdscale}(x, choices = c(1, 2), display = "sites", type = "t", ...)
+\method{scores}{wcmdscale}(x, choices = NA, display = "sites", tidy = FALSE, ...)
 }
 \description{
   Weighted classical multidimensional scaling,
@@ -39,6 +39,9 @@ wcmdscale(d, k, eig = FALSE, add = FALSE, x.ret = FALSE, w)
     called with options \code{eig = TRUE} or \code{x.ret = TRUE} (See
     Details).}
   \item{choices}{Axes to be returned; \code{NA} returns all real axes.}
+  \item{display}{Kind of scores. Normally only \code{"sites"} are
+    available, but \code{"species"} can be supplemented with
+    \code{\link{sppscores}}.}
   \item{type}{Type of graph which may be \code{"t"}ext, \code{"p"}oints
     or \code{"n"}one.}
   \item{tidy}{Return scores that are compatible with \CRANpkg{ggplot2}:
@@ -119,7 +122,8 @@ wcmdscale(d, k, eig = FALSE, add = FALSE, x.ret = FALSE, w)
 \seealso{The function is modelled after \code{\link{cmdscale}}, but adds
   weights (hence name) and handles negative eigenvalues differently.
   \code{\link{eigenvals.wcmdscale}} and
-  \code{\link{stressplot.wcmdscale}} are some specific methods. Other
+  \code{\link{stressplot.wcmdscale}} are some specific methods. Species
+  scores can be added to the result with \code{\link{sppscores}}. Other
   multidimensional scaling methods are \code{\link{monoMDS}}, and
   \code{\link[MASS]{isoMDS}} and \code{\link[MASS]{sammon}} in package
   \pkg{MASS}.  }