[Vegan-commits] r378 - pkg/R

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2008-05-30 11:03:13 +0200 (Fri, 30 May 2008)
New Revision: 378

Removed:
   pkg/R/plot.mso.R
Log:
removed plot.mso that duplicates msoplot and shadows plot.cca

Deleted: pkg/R/plot.mso.R
===================================================================
--- pkg/R/plot.mso.R	2008-05-29 16:35:44 UTC (rev 377)
+++ pkg/R/plot.mso.R	2008-05-30 09:03:13 UTC (rev 378)
@@ -1,97 +0,0 @@
-`plot.mso` <-
-    function (x, alpha = 0.05, explained = FALSE, ...) 
-{
-    object.cca <- x
-    if (is.data.frame(object.cca$vario)) {
-        object <- object.cca
-        vario <- object$vario
-        grain <- object$grain
-        z <- qnorm(alpha/2)
-        if (is.numeric(vario$CA.signif)) {
-            vario <- vario[, -ncol(vario)]
-        }
-        ymax <- max(vario[, -1:-3], na.rm = TRUE)
-        b <- ncol(vario) - 3
-        label <- c("", "", "", "Total variance", "Explained plus residual", 
-                   "Residual variance", "Explained variance", "Conditioned variance")
-        ## You should not change par, or at least you must put
-        ## back the old values when exiting:
-        ## op <- par(omi = c(0.5, 0.5, 0, 0))
-        ## on.exit(par(op))
-        ##par(omi = c(0.5, 0.5, 0, 0))
-        if (is.numeric(object$CCA$rank)) {
-            if (!explained) 
-                b <- b - 1
-            if (is.numeric(object$vario$se)) 
-                b <- b - 1
-            plot(vario$Dist, vario$All, type = "n", lty = 1, 
-                 pch = 3, xlab = "Distance", ylab = "Variance", 
-                 ylim = c(0, ymax), cex.lab = 1.2, ...)
-            lines(vario$Dist, vario$All + z * vario$se, lty = 1, ...)
-            lines(vario$Dist, vario$All - z * vario$se, lty = 1, ...)
-            lines(vario$Dist, vario$Sum, type = "b", lty = 2, 
-                  pch = 3, ...)
-            for (i in 6:(b + 3)) {
-                lines(vario$Dist, vario[, i], type = "b", lty = 1, 
-                      pch = i - 6, ...)
-                points(x = 1.2 * grain,
-                       y = ymax - ymax * (b + 6 - i)/20, pch = i - 6, ...)
-            }
-            text(x = rep(2 * grain, b - 1), y = ymax - ymax * 
-                 c(2:b)/20, label = label[c(2, b:3) + 3], pos = 4, 
-                 cex = 1.2, ...)
-            points(x = 1.2 * grain, y = ymax - ymax * 2/20, pch = 3, ...)
-            for (i in 2:b) {
-                lines(x = c(0.7, 1.1) * grain,
-                      y = rep(ymax -  ymax * i/20, 2),
-                      lty = c(1, 2, 1, 1, 1)[i])
-                lines(x = c(1.3, 1.7) * grain,
-                      y = rep(ymax -  ymax * i/20, 2), lty = c(1, 2, 1, 1, 1)[i])
-            }
-            text(x = c(vario$Dist), y = rep(0, length(vario$Dist)), 
-                 label = c(vario$n), cex = 0.8, ...)
-            lines(x = rep(max(object$H)/2, 2), y = c(-10, ymax + 
-                                               10), lty = 3, ...)
-            text(x = 2 * grain, y = ymax - ymax/20, label = "C.I. for total variance", 
-                 pos = 4, cex = 1.2, ...)
-            lines(x = c(0.7, 1.7) * grain, y = rep(ymax - ymax/20, 2),
-                  lty = 1, ...)
-        }
-        else {
-            plot(vario$Dist, vario$All, type = "b", lty = 1, 
-                 pch = 0, xlab = "Distance", ylab = "Variance", 
-                 ylim = c(0, ymax), cex.lab = 1.2, ...)
-            lines(c(0, 10), rep(object$tot.chi, 2), lty = 5, ...)
-            lines(x = c(0.7, 1.7) * grain, y = rep(ymax - ymax * 
-                                           b/20, 2), lty = 5, ...)
-            text(x = 2 * grain, y = ymax - ymax * b/20, label = "Global variance estimate", 
-                 pos = 4, cex = 1.2, ...)
-            text(x = c(vario$Dist), y = rep(0, length(vario$Dist)), 
-                 label = c(vario$n), cex = 0.8)
-            lines(x = rep(max(object$H)/2, 2), y = c(-10, ymax + 
-                                               10), lty = 3, ...)
-            text(x = 2 * grain, y = ymax - ymax/20, label = "Total variance", 
-                 pos = 4, cex = 1.2, ...)
-            lines(x = c(0.7, 1.7) * grain, y = rep(ymax - ymax/20, 
-                                           2), lty = 1, ...)
-        }
-    }
-    if (is.numeric(object$vario$CA.signif)) {
-        a <- c(1:nrow(object$vario))[object$vario$CA.signif < 
-                                     alpha]
-        points(vario$Dist[a], object$vario$CA[a], pch = 15, ...)
-        points(x = 1.2 * grain, y = ymax - ymax * (b + 1)/20, 
-               pch = 15, ...)
-        text(x = 2 * grain, y = ymax - ymax * (b + 1)/20, pos = 4, 
-             cex = 1.2, label = c("Sign. autocorrelation"), ...)
-        if (is.numeric(object$CCA$rank)) {
-            inflation <- 1 - weighted.mean(object$vario$CA, object$vario$n)/
-                weighted.mean(object$vario$CA[-a], 
-                              object$vario$n[-a])
-            cat("Error variance of regression model underestimated by", 
-                round(inflation * 100, 1), "percent", "\n")
-        }
-    }
-    invisible()
-}
-