example("subscript-package", package = "subscript")
ss(as.dist(pdf$geog), c("b", "d", "a"))
all.equal(dist(pdf$coord), as.dist(pdf$geog))
set.seed(1)
par(mfrow = c(2, 1), mar = rep(0, 4))
plot(pdf$tree)
plot(reOrder(pdf$tree, LETTERS[sample.int(5)]))
regs <- dbDiversityRegression(slist, # species list
as.dist(cophenetic(pdf$tree)), # phylogenetic distances
dist(pdf$traits), # functional distances
setNames(env$x, rownames(env)) # ecosystem function
)
mean(regs)
coef(regs)
a.hpd(regs)
plot(regs)
pdf <- poly.data.frame(env = setDimIds(env, "sites"),
coord = setDimIds(coord, "sites"),
geog = setDimIds(dist(coord), "sites"),
traits = setDimIds(traits, "species"),
coph = setDimIds(as.dist(cophenetic(tree)), "species"),
tree = setDimIds(tree, "species"))
crossprod(summary(pdf))
tcrossprod(summary(pdf))
FPDist(form, pdf, 0)
FPDist(form, pdf, 1)
setDimIds(dist(pdf$traits), dimIds(pdf$traits))
dNames(pdf)
dist(pdf$traits)
pdf <- list(env = setDimIds(env, NULL),
coord = setDimIds(coord, NULL),
geog = setDimIds(dist(coord), NULL),
traits = setDimIds(traits, NULL),
coph = setDimIds(as.dist(cophenetic(tree)), NULL),
tree = setDimIds(tree, NULL),
comm = setDimIds(slist, NULL))
summary(pdf)
dNamesNested(pdf)
pdf <- as.poly.data.frame(pdf, 2)
summary(pdf)
Reduce("union", dNamesConcat(pdf))
library(subscript)
l <- list(env = env,
coord = coord,
geog = dist(coord),
traits = traits,
coph = as.dist(cophenetic(tree)),
tree = tree,
comm = slist)
pdf2 <- as.poly.data.frame(l, 2)
summary(pdf)
summary(pdf2)
dNames(pdf)
dNames(pdf2)
dNames(pdf00)
pdf00 <- ss(pdf, list(species = c("D","C","A"), sites = c("a","e","f")))
ii <- list(sites = c("a","e","f"), species = c("D","C","A"))
attributes(pdf$slist)
attributes(ss(pdf$slist, ii))
with(pdf, coph)
pdf <- within(pdf, coph <- coph/max(coph))
pdf <- within(pdf, {
fdist <- dist(traits)/max(dist(traits))
dimIds(fdist) <- dimIds(traits)
})
with(pdf, plot(coph, ss(fdist, dNames(coph))))
pdf <- within(pdf, {
fpdist <- combineDists(coph, fdist, 0.5)
dimIds(fpdist) <- "species"
})
with(pdf, meanPairwiseDist(slist, fpdist))
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