Merge branch 'scores-args'

R/plot.cca.R

@@ -6,7 +6,7 @@
     if (any(display %in% c("c","cn")))
         display <- c(display, "bp")
     g <- scores(x, choices, display, scaling, const, correlation = correlation,
-                hill = hill, tidy = FALSE)
+                hill = hill, tidy = FALSE, droplist = TRUE)
     if (length(g) == 0 || all(is.na(g)))
       stop("nothing to plot: requested scores do not exist")
     if (!is.list(g))

R/points.cca.R

@@ -6,14 +6,16 @@
     if (length(display) > 1)
         stop("only one 'display' item can be added in one command")
     pts <- scores(x, choices = choices, display = display, scaling = scaling,
-                  const, correlation = correlation, hill = hill, tidy=FALSE)
+                  const, correlation = correlation, hill = hill, tidy=FALSE,
+                  droplist = TRUE)
     if (!missing(select))
         pts <- .checkSelect(select, pts)
     if (display == "cn") {
         cnam <- rownames(pts)
         points(pts, ...)
         pts <- scores(x, choices = choices, display = "bp", scaling = scaling,
-                      const, correlation = correlation, hill = hill)
+                      const, correlation = correlation, hill = hill,
+                      droplist = TRUE)
         bnam <- rownames(pts)
         pts <- pts[!(bnam %in% cnam), , drop = FALSE]
         if (nrow(pts) == 0)

R/scores.cca.R

@@ -1,6 +1,6 @@
 `scores.cca` <-
-    function (x, choices = c(1, 2), display = c("sp", "wa", "bp", "cn"),
-              scaling = "species", hill = FALSE, tidy = FALSE, ...)
+    function (x, choices = c(1, 2), display = "all", scaling = "species",
+              hill = FALSE, tidy = FALSE, droplist = TRUE, ...)
 {
     ## Check the na.action, and pad the result with NA or WA if class
     ## "exclude"
@@ -153,5 +153,8 @@
     }
     ## return NULL instead of list(), and matrix instead of a list of
     ## one matrix
-    switch(min(2, length(sol)), sol[[1]], sol)
+    if (droplist)
+        switch(min(2, length(sol)), sol[[1]], sol)
+    else
+        sol
 }

R/scores.rda.R

@@ -2,8 +2,8 @@
 ### latter can have special features which are commented below. cca
 ### results are handled by scores.cca.
 `scores.rda` <-
-    function (x, choices = c(1, 2), display = c("sp", "wa", "bp", "cn"),
-              scaling = "species", const, correlation = FALSE, tidy = FALSE,
+    function (x, choices = c(1, 2), display = "all", scaling = "species",
+              const, correlation = FALSE, tidy = FALSE, droplist = TRUE,
               ...)
 {
     ## Check the na.action, and pad the result with NA or WA if class
@@ -169,7 +169,8 @@
         const <- const[1]
     ## return NULL for list(), matrix for single scores, and a list
     ## for several scores
-    sol <- switch(min(2, length(sol)), sol[[1]], sol)
+    if (droplist)
+        sol <- switch(min(2, length(sol)), sol[[1]], sol)
     if (!is.null(sol))
         attr(sol, "const") <- const
     sol

R/text.cca.R

@@ -6,7 +6,8 @@
     if (length(display) > 1)
         stop("only one 'display' item can be added in one command")
     pts <- scores(x, choices = choices, display = display, scaling = scaling,
-                  const, correlation = correlation, hill = hill, tidy=FALSE)
+                  const, correlation = correlation, hill = hill, tidy=FALSE,
+                  droplist = TRUE)
     ## store rownames of pts for use later, otherwise if user supplies
     ## labels, the checks in "cn" branch fail and "bp" branch will
     ## be entered even if there should be no "bp" plotting
@@ -28,7 +29,7 @@
         }
         pts <- scores(x, choices = choices, display = "bp", scaling = scaling,
                       const, correlation = correlation, hill = hill,
-                      tidy=FALSE)
+                      tidy = FALSE, droplist = TRUE)
         bnam <- rownames(pts)
         pts <- pts[!(bnam %in% cnam), , drop = FALSE]
         if (nrow(pts) == 0)

man/plot.cca.Rd

@@ -25,10 +25,12 @@
 \method{points}{cca}(x, display = "sites", choices = c(1, 2),
        scaling = "species", arrow.mul, head.arrow = 0.05, select, const,
        axis.bp = FALSE, correlation = FALSE, hill = FALSE, ...)
-\method{scores}{cca}(x, choices = c(1,2), display = c("sp","wa","bp","cn"),
-       scaling = "species", hill = FALSE, tidy = FALSE, ...)
-\method{scores}{rda}(x, choices = c(1,2), display = c("sp","wa","bp","cn"),
-       scaling = "species", const, correlation = FALSE, tidy = FALSE, ...)
+\method{scores}{cca}(x, choices = c(1,2), display = "all",
+       scaling = "species", hill = FALSE, tidy = FALSE, droplist = TRUE,
+       ...)
+\method{scores}{rda}(x, choices = c(1,2), display = "all",
+       scaling = "species", const, correlation = FALSE, tidy = FALSE,
+       droplist = TRUE, ...)
 \method{summary}{cca}(object, digits = max(3, getOption("digits") - 3), ...)
 \method{labels}{cca}(object, display, ...)
 }
@@ -105,6 +107,8 @@
     for details and discussion). If \code{const} is a vector of two
     items, the first is used for species, and the second item for site
     scores.}
+  \item{droplist}{Return a matrix instead of a named list when only one
+    kind of scores were requested.}
   \item{axis.bp}{Draw \code{\link{axis}} for biplot arrows.}
   \item{digits}{Number of digits in output.}
   \item{...}{Parameters passed to other functions.}