[Vegan-commits] r373 - in pkg: R inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed May 28 09:57:33 CEST 2008
Author: jarioksa
Date: 2008-05-28 09:57:33 +0200 (Wed, 28 May 2008)
New Revision: 373
Modified:
pkg/R/plot.mso.R
pkg/inst/ChangeLog
Log:
plot.mso passes graphical args to grapical functions
Modified: pkg/R/plot.mso.R
===================================================================
--- pkg/R/plot.mso.R 2008-05-27 15:49:32 UTC (rev 372)
+++ pkg/R/plot.mso.R 2008-05-28 07:57:33 UTC (rev 373)
@@ -1,4 +1,5 @@
-plot.mso <- function (x, alpha = 0.05, explained = FALSE, ...)
+`plot.mso` <-
+ function (x, alpha = 0.05, explained = FALSE, ...)
{
object.cca <- x
if (is.data.frame(object.cca$vario)) {
@@ -12,7 +13,7 @@
ymax <- max(vario[, -1:-3], na.rm = TRUE)
b <- ncol(vario) - 3
label <- c("", "", "", "Total variance", "Explained plus residual",
- "Residual variance", "Explained variance", "Conditioned variance")
+ "Residual variance", "Explained variance", "Conditioned variance")
par(omi = c(0.5, 0.5, 0, 0))
if (is.numeric(object$CCA$rank)) {
if (!explained)
@@ -21,21 +22,21 @@
b <- b - 1
plot(vario$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$se, lty = 1)
+ ylim = c(0, ymax), cex.lab = 1.2, ...)
+ lines(vario$Dist, vario$All + z * vario$se, lty = 1, ...)
+ lines(vario$Dist, vario$All - z * vario$se, lty = 1, ...)
lines(vario$Dist, vario$Sum, type = "b", lty = 2,
- pch = 3)
+ pch = 3, ...)
for (i in 6:(b + 3)) {
lines(vario$Dist, vario[, i], type = "b", lty = 1,
- pch = i - 6)
+ pch = i - 6, ...)
points(x = 1.2 * grain,
- y = ymax - ymax * (b + 6 - i)/20, pch = i - 6)
+ 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)
+ 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),
@@ -44,41 +45,41 @@
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$n), cex = 0.8)
+ label = c(vario$n), cex = 0.8, ...)
lines(x = rep(max(object$H)/2, 2), y = c(-10, ymax +
- 10), lty = 3)
+ 10), lty = 3, ...)
text(x = 2 * grain, y = ymax - ymax/20, label = "C.I. for total variance",
- pos = 4, cex = 1.2)
+ pos = 4, cex = 1.2, ...)
lines(x = c(0.7, 1.7) * grain, y = rep(ymax - ymax/20, 2),
- lty = 1)
+ lty = 1, ...)
}
else {
plot(vario$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)
+ ylim = c(0, ymax), cex.lab = 1.2, ...)
+ lines(c(0, 10), rep(object$tot.chi, 2), lty = 5, ...)
lines(x = c(0.7, 1.7) * grain, y = rep(ymax - ymax *
- b/20, 2), lty = 5)
+ b/20, 2), lty = 5, ...)
text(x = 2 * grain, y = ymax - ymax * b/20, label = "Global variance estimate",
- pos = 4, cex = 1.2)
+ pos = 4, cex = 1.2, ...)
text(x = c(vario$Dist), y = rep(0, length(vario$Dist)),
label = c(vario$n), cex = 0.8)
lines(x = rep(max(object$H)/2, 2), y = c(-10, ymax +
- 10), lty = 3)
+ 10), lty = 3, ...)
text(x = 2 * grain, y = ymax - ymax/20, label = "Total variance",
- pos = 4, cex = 1.2)
+ pos = 4, cex = 1.2, ...)
lines(x = c(0.7, 1.7) * grain, y = rep(ymax - ymax/20,
- 2), lty = 1)
+ 2), lty = 1, ...)
}
}
if (is.numeric(object$vario$CA.signif)) {
a <- c(1:nrow(object$vario))[object$vario$CA.signif <
alpha]
- points(vario$Dist[a], object$vario$CA[a], pch = 15)
+ points(vario$Dist[a], object$vario$CA[a], pch = 15, ...)
points(x = 1.2 * grain, y = ymax - ymax * (b + 1)/20,
- pch = 15)
+ pch = 15, ...)
text(x = 2 * grain, y = ymax - ymax * (b + 1)/20, pos = 4,
- cex = 1.2, label = c("Sign. autocorrelation"))
+ 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],
@@ -89,3 +90,4 @@
}
invisible()
}
+
Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog 2008-05-27 15:49:32 UTC (rev 372)
+++ pkg/inst/ChangeLog 2008-05-28 07:57:33 UTC (rev 373)
@@ -4,6 +4,8 @@
Version 1.14-1 (opened May 22, 2008)
+ * plot.mso: passes extra arguments (...) to graphical functions.
+
* mite.xy: new data set with spatial coordinates for the Oribatid
mite data. From Pierre Legendre's web page.
More information about the Vegan-commits
mailing list