calcEllipseDists: Calculates distance from ellipse and distance from centroid.

In orb16/baselines: Calculates Distance From Desired Baseline

Calculates distance from ellipse and distance from centroid.

Description

Calculates distance from ellipse and distance from centroid.

Usage

calcEllipseDists(
  metadf,
  ord,
  group = "Time_period",
  reflev = "Pre-human",
  ordiType = "sd",
  addConf = TRUE
)

Arguments

metadf	metadata (e.g. groups). Needs to be same length and order as rows that went into ordination.
ord	the ordination object. Currently only works with NMDS
group	the column in the metadata which contains the grouping variable for the baseline
reflev	the value in the column group which is the baseline level
ordiType	what sort of ordiellipse? Options are all those which ordiellipse accepts
addConf	use 95 CI or not? See ordiellipse options.

Value

A named list: "distSF" with the distances from baseline as a spatial point object, "distDF", a data.frame version of the same, and "baseline_polygon" an SF object of the reference baseline polygon

Examples

data("mite")
data("mite.env")
set.seed(999)
met <- metaMDS(mite, "jaccard", try = 50)
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)
with(dlist[["distDF"]][dlist[["distDF"]]$Topo == "Hummock", ],
points(x = NMDS1, y = NMDS2, col = "forestgreen", pch = 16))
with(dlist[["distDF"]][dlist[["distDF"]]$Topo == "Blanket", ],
points(x = NMDS1, y = NMDS2, 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)")

# Example with Boral
## NOTE: As per the boral help, the values below MUST NOT be used in a real application;
## they are only used here to make the examples run quick!!!
example_mcmc_control <- list(n.burnin = 10, n.iteration = 100,
                             n.thin = 1)
data("mite")
data("mite.env")
miteBoral <- boral::boral(mite, family = "negative.binomial",
mcmc.control = example_mcmc_control,
lv.control = list(num.lv = 2),
row.eff = "fixed",
save.model = FALSE, calc.ics = FALSE)

dlist <- calcEllipseDists(metadf = mite.env, ord = miteBoral,
group = "Topo", reflev = "Hummock")
par(mfrow = c(1, 2))
boral::lvsplot(miteBoral, biplot = FALSE,
col = "transparent",
main = "Boral ordination")
plot(dlist[["baseline_polygon"]], add = TRUE,
col = adjustcolor("forestgreen", 0.2),
border = NA)
plot(st_geometry(dlist[["distSF"]][dlist[["distSF"]]$Topo == "Hummock", ],),
add = TRUE,
col = "forestgreen",
pch = 16
)
plot(st_geometry(dlist[["distSF"]][dlist[["distSF"]]$Topo == "Blanket", ],),
     add = TRUE,
     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", main = "NMDS ordination")
plot(dlist[["baseline_polygon"]], add = TRUE,
col = adjustcolor("forestgreen", 0.2),
border = NA)
plot(st_geometry(dlist[["distSF"]][dlist[["distSF"]]$Topo == "Hummock", ],),
add = TRUE,
col = "forestgreen",
pch = 16
)
plot(st_geometry(dlist[["distSF"]][dlist[["distSF"]]$Topo == "Blanket", ],),
     add = TRUE,
     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")

orb16/baselines documentation built on Nov. 20, 2023, 7:56 a.m.