diff --git a/tests/Examples/vegan-Ex.Rout.save b/tests/Examples/vegan-Ex.Rout.save index b244ad6bb..ece7950c7 100644 --- a/tests/Examples/vegan-Ex.Rout.save +++ b/tests/Examples/vegan-Ex.Rout.save @@ -1785,6 +1785,9 @@ log(N) P K Ca pH Al 6 0.2822 > mod <- rda(dune, scale = TRUE) > biplot(mod, scaling = "symmetric") > +> ## plot.cca can do the same +> plot(mod, scaling = "symmetric", spe.par = list(arrows=TRUE)) +> > ## different type for species and site scores > biplot(mod, scaling = "symmetric", type = c("text", "points")) > @@ -5004,9 +5007,9 @@ Al 1.8804734 -0.3507570 P -0.9168309 -1.6419845 K -0.9931606 -0.3713207 > -> ## draw arrows and text labels +> ## arrows will touch the bounding box of the text > arrows(0, 0, bip.scl[,1], bip.scl[,2], length = 0.1) -> text(bip.lab, labels = labs) +> ordilabel(bip.lab, labels = labs) > > ## Handling of ordination objects directly > mul2 <- ordiArrowMul(ord, display = "bp", fill = 0.8) @@ -6102,18 +6105,19 @@ ungrazed-grazed -0.1219422 -0.2396552 -0.004229243 0.0429502 > data(dune, dune.env) > mod <- cca(dune ~ A1 + Moisture + Management, dune.env) > -> ## better control -- remember to set scaling etc identically -> plot(mod, type="n", scaling="sites", choices = 2:3) -> text(mod, dis="cn", scaling="sites", choices = 2:3) -> points(mod, pch=21, col="red", bg="yellow", cex=1.2, scaling="sites", -+ choices = 2:3) -> text(mod, "species", col="blue", cex=0.8, scaling="sites", choices = 2:3) +> ## default and modified plot +> plot(mod, scaling="sites") +> plot(mod, scaling="sites", type = "text", ++ sit.par = list(type = "points", pch=21, col="red", bg="yellow", cex=1.2), ++ spe.par = list(col="blue", cex=0.8), ++ cen.par = list(bg="white")) > > ## same with pipe -> plot(mod, type="n", scaling="sites", choices = c(2,3)) |> -+ text("centroids") |> -+ points("sites", pch=21, col="red", bg = "yellow", cex=1.2) |> -+ text("species", col="blue", cex=0.8) +> plot(mod, type="n", scaling="sites") |> ++ points("sites", pch=21, col="red", bg = "yellow", cex=1.2) |> ++ text("species", col="blue", cex=0.8) |> ++ text("biplot") |> ++ text("centroids", bg="white") > > ## catch the invisible result and use ordiplot support - the example > ## will make a biplot with arrows for species and correlation scaling @@ -6124,10 +6128,10 @@ ungrazed-grazed -0.1219422 -0.2396552 -0.004229243 0.0429502 > with(dune.env, legend("bottomleft", levels(Management), pch=21, + pt.bg=1:4, bty="n")) > -> ## Configuration with pipes: make an arrow biplot +> ## Pipe > plot(pca, type="n", scaling="sites", correlation=TRUE) |> + points("sites", pch=21, col = 1, cex=1.5, bg = dune.env$Management) |> -+ text("species", col = "blue", arrow = TRUE, xpd = TRUE) ++ text("species", col = "blue", arrows = TRUE, xpd = TRUE, font = 3) > > ## Scaling can be numeric or more user-friendly names > ## e.g. Hill's scaling for (C)CA @@ -8965,7 +8969,7 @@ Procrustes sum of squares: > cleanEx() > options(digits = 7L) > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n") -Time elapsed: 8.574 0.269 8.867 0 0 +Time elapsed: 8.54 0.277 8.841 0 0 > grDevices::dev.off() null device 1