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############
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##Ordination
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#data format: species matrix
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require(vegan)
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data.ord <- metaMDS(spp_matrix, dustance="bray", trace=TRUE)
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#to extract x and y scores for plotting
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ord.scores <- scores(data.ord, display=c("sites", "species"))
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10
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#adding year column to scores data.frame
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year <- data.frame(spp_matrix$yearColumn)
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colnames(year) <- "year"
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14
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ord.scores.yr <- cbind(ord.scores, year)
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#plotting ordination
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#setting graphical margins
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par(mar=c(bottom, left, top, right), xpd=TRUE)
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plot(data.ord, type = "n",
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xlim = c(xMin, xMax), ylim = c(yMin, yMax))
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points(ord.scores[c(1:25),], cex = 1.2, pch=16, col="#99CC66")
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points(ord.scores[c(26:50),], cex = 1.2, pch=16, col="#990000")
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#labeling points
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require(calibrate)
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textxy(ord.scores.yr$NMDS1, ord.scores.yr$NMDS2, ord.scores.yr$year)
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#legend
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leg.text <- c("x1", "x2")
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leg.col <- c("#99CC66", "#990000")
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legend(xAxisLocation, yAxisLocation, cex = 1.2, leg.text, col=leg.col, pch=16)
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