In orb16/baselines: Calculates Distance From Desired Baseline

knitr::opts_chunk$set(
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  fig.path = "man/figures/README-",
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baselines

The goal of baselines is to share code for calculating distance from baselines in ordination space.

Update

Note that baselines has recently been updated to use the sf package. The named output from baselines::calcEllipseDists has changed - please refer to the updated help (including examples).

Installation

You can install this package from github! First you need to have devtools installed. If not, run install.packages("devtools"), before running the code below.

# install.packages("devtools")
devtools::install_github("orb16/baselines")

Example

library(baselines, quietly = TRUE)
library(vegan, quietly = TRUE)

data("mite")
data("mite.env")
met <- metaMDS(mite, "jaccard")
dlist <- calcEllipseDists(metadf = mite.env, ord = met,
group = "Topo", reflev = "Hummock")
par(mfrow = c(2, 2))
plot(met, type = "n")
plot(dlist[["baseline_polygon"]], add = TRUE,
col = adjustcolor("forestgreen", 0.2),
border = NA)
points(dlist[["all_points"]][dlist[["all_points"]]$Topo == "Hummock", ], col = "forestgreen",
pch = 16)
points(dlist[["all_points"]][dlist[["all_points"]]$Topo == "Blanket", ], col = "black",
pch = 16)
legend("topleft", pch = c(16, 16, 15), col = c("forestgreen", "black", adjustcolor("forestgreen", 0.5)),
legend = c("Hummock", "Blanket", "95% CI Ellipse"))
mtext(side = 3, "95% CI around centroid calculated")


plot(met, type = "n")
plot(dlist[["baseline_polygon"]], add = TRUE,
col = adjustcolor("forestgreen", 0.2),
border = NA)
mtext(side = 3, "Points sized by distance from baseline")
with(dlist[["distDF"]][dlist[["distDF"]]$Topo == "Hummock", ],
points(x = NMDS1, y = NMDS2, cex = distEllipse + 0.5, col = "forestgreen"))
with(dlist[["distDF"]][dlist[["distDF"]]$Topo == "Blanket", ],
points(x = NMDS1, y = NMDS2, cex = distEllipse + 0.5, col = "black"))


plot(met, type = "n")
plot(dlist[["baseline_polygon"]], add = TRUE,
col = adjustcolor("forestgreen", 0.2),
border = NA)
mtext(side = 3, "Blanket points by shrub prevalence")
colDF <- data.frame(Shrub = c("None", "Few", "Many"),
cols = I(c("skyblue", "cornflowerblue", "darkblue")))
with(dlist[["distDF"]][dlist[["distDF"]]$Topo == "Hummock", ],
points(x = NMDS1, y = NMDS2,  col = "grey"))
with(dlist[["distDF"]][dlist[["distDF"]]$Topo == "Blanket", ],
points(x = NMDS1, y = NMDS2, col =  colDF[match(Shrub, colDF$Shrub), "cols"]))
legend("topleft", pch = 1, legend = colDF$Shrub, col = colDF$cols)

with(dlist[["distDF"]][dlist[["distDF"]]$Topo == "Blanket", ],
plot(x = Shrub, y = distEllipse, xlab = "Shrub",
ylab = "Distance from baseline"))
mtext(side = 3, "Distance from baseline as a function\nof another col in dataset (shrubs)")