Nothing
#
# --- Create test data ---
#
weed.com <- read.table(textConnection(
"plot cover taxa
A 5 Centaurea_alba
A 5 Silybum_marianum
A 10 Taraxacum_officinale
A 25 Torilis_arvensis
A 55 Trifolium_repens
B 35 Centaurea_alba
B 35 Silybum_marianum
B 15 Taraxacum_officinale
B 10 Torilis_arvensis
B 5 Trifolium_repens
C 20 Centaurea_alba
C 20 Silybum_marianum
C 20 Taraxacum_officinale
C 20 Torilis_arvensis
C 20 Trifolium_repens"
), header=TRUE)
closeAllConnections()
weed.com2 <- weed.com[c(1:5, 7:10, 13:15),]
weed.tree.notultra <- read.tree(text="(((Taraxacum_officinale:0.058133000000000004,(Silybum_marianum:0.022662,Centaurea_alba:0.02092)0.997000:0.026418999999999998)0.547000:0.075571,Torilis_arvensis:0.105052)0.878000:0.037612,Trifolium_repens:0.25731000000000004)1.000000:0.04059;")
weed.tree <- read.tree(text="(((Taraxacum_officinale:0.2601451047,(Silybum_marianum:0.1088645027,Centaurea_alba:0.1088645027)0.997000:0.151280602)0.547000:0.5232373813,Torilis_arvensis:0.783382486)0.878000:0.216617514,Trifolium_repens:1)1.000000:0.04059;")
#
# --- Test community-level ecoPD functions ---
#
test.phylo4com <- function() {
# Test for error when any supplied taxa are missing from supplied tree
BADTAXA <- weed.com$taxa
levels(BADTAXA) <- paste("Unknown", 1:5, sep="")
checkException(phylo4com(weed.com$plot, BADTAXA, weed.com$cover,
phylo4d(weed.tree)))
}
test.pd.trad <- function() {
DEACTIVATED("no longer calculating pd for ape-based ecophylo objects")
# Create ecophylo objects out of weed community and phylogeny data
ecophydata1 <- ecophylo(weed.com$plot, weed.com$taxa, weed.com$cover,
weed.tree)
ecophydata2 <- ecophylo(weed.com2$plot, weed.com2$taxa,
weed.com2$cover, weed.tree)
ecophydata.notultra <- ecophylo(weed.com$plot, weed.com$taxa,
weed.com$cover, weed.tree.notultra)
ans <- c(3.1523920934, 3.1523920934, 3.1523920934)
checkEqualsNumeric(ans, ecoPD(ecophydata1, method="trad"))
ans <- c(3.1523920934, 3.0435275907, 2.783382486)
checkEqualsNumeric(ans, ecoPD(ecophydata2, method="trad"))
checkException(ecoPD(ecophydata.notultra, method="trad"))
}
test.pd.poly <- function() {
DEACTIVATED("no longer calculating pd for ape-based ecophylo objects")
# Create ecophylo objects out of weed community and phylogeny data
ecophydata1 <- ecophylo(weed.com$plot, weed.com$taxa, weed.com$cover,
weed.tree)
ecophydata2 <- ecophylo(weed.com2$plot, weed.com2$taxa,
weed.com2$cover, weed.tree)
ecophydata.notultra <- ecophylo(weed.com$plot, weed.com$taxa,
weed.com$cover, weed.tree.notultra)
ans <- c(8.26633721124392, 7.05995380972657, 7.54247469939537)
checkEqualsNumeric(ans, ecoPD(ecophydata1, method="poly"))
ans <- c(8.26633721124392, 5.64834888836452, 5.7174610946672)
checkEqualsNumeric(ans, ecoPD(ecophydata2, method="poly"))
checkException(ecoPD(ecophydata.notultra, method="poly"))
}
test.pd.yule <- function() {
DEACTIVATED("no longer calculating pd for ape-based ecophylo objects")
# Create ecophylo objects out of weed community and phylogeny data
ecophydata1 <- ecophylo(weed.com$plot, weed.com$taxa, weed.com$cover,
weed.tree)
ecophydata2 <- ecophylo(weed.com2$plot, weed.com2$taxa,
weed.com2$cover, weed.tree)
ecophydata.notultra <- ecophylo(weed.com$plot, weed.com$taxa,
weed.com$cover, weed.tree.notultra)
ans <- c(4.72177974392577, 4.46454888807077, 4.6275784250289)
checkEqualsNumeric(ans, ecoPD(ecophydata1, method="yule"))
ans <- c(4.72177974392577, 3.97813049106849, 3.76931214789738)
checkEqualsNumeric(ans, ecoPD(ecophydata2, method="yule"))
checkException(ecoPD(ecophydata.notultra, method="yule"))
}
test.siteBySpecies <- function() {
DEACTIVATED("no longer calculating siteBySpecies for ape-based ecophylo objects")
# Create ecophylo objects out of weed community and phylogeny data
ecophydata1 <- ecophylo(weed.com$plot, weed.com$taxa, weed.com$cover,
weed.tree)
ans <- structure(c(5, 5, 10, 25, 55, 35, 35, 15, 10, 5, 20, 20, 20,
20, 20), .Dim = c(5L, 3L), .Dimnames = list(c("Centaurea_alba",
"Silybum_marianum", "Taraxacum_officinale", "Torilis_arvensis",
"Trifolium_repens"), c("A", "B", "C")))
checkEquals(ans, siteBySpecies(ecophydata1))
}
test.richness <- function() {
DEACTIVATED("no longer calculating richness for ape-based ecophylo objects")
# Create ecophylo objects out of weed community and phylogeny data
ecophydata1 <- ecophylo(weed.com$plot, weed.com$taxa, weed.com$cover,
weed.tree)
ecophydata2 <- ecophylo(weed.com2$plot, weed.com2$taxa,
weed.com2$cover, weed.tree)
ans <- structure(c(5L, 5L, 5L), .Names = c("A", "B", "C"))
checkEquals(richness(ecophydata1), ans)
ans <- structure(c(5L, 4L, 3L), .Names = c("A", "B", "C"))
checkEquals(richness(ecophydata2), ans)
}
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