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.Rhistory
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.Rhistory
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#x.2_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2_), distance_metric = "mord")
new.matrix.1_<-x.1_$distance_matrix[c(1:5),c(1:5)]
new.matrix.2_<-x.2_$distance_matrix[c(6:10),c(6:10)]
xx.1_<-pcoa(new.matrix.1_, correction="none", rn=NULL)
xx.2_<-pcoa(new.matrix.2_, correction="none", rn=NULL)
disparity.1_<-sum(xx.1_$values[,1])
disparity.2_<-sum(xx.2_$values[,1])
print(disparity.1)
print(disparity.1_)
print(disparity.2)
print(disparity.2_)
plot(c(disparity.1, disparity.2) ~c(1,2), xlim=c(0.85,2.5), ylim = c(0,40), frame.plot=FALSE, ylab="Disparity", pch=19, col="#4D7CA8", cex=1.5, xaxt = "n", xlab="")
points(c(disparity.1_, disparity.2_) ~c(1,2),col="#ED5F54", cex=1.5, pch=19,)
lines(c(1,2), c(disparity.1, disparity.2), col="#4D7CA8", lwd=3)
lines(c(1,2), c(disparity.1_, disparity.2_), col="#ED5F54", lwd=3)
text(1,1.17,"Time 1")
text(2,1.17,"Time 2")
# Create random 10-by-50 matrix:
character_taxon_matrix.1 <- matrix(sample(c("0", "1", "2"),40,replace = TRUE),nrow = 10, dimnames =
list(apply(matrix(sample(LETTERS, 40,replace = TRUE), nrow = 10), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.1[c(6:10),]<-""
character_taxon_matrix.2 <- matrix(sample(c("2", "3", "4"),
40,
replace = TRUE
),
nrow = 10, dimnames =
list(apply(matrix(sample(LETTERS, 40,
replace = TRUE
), nrow = 10), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.2[c(1:5),]<-""
# Reformat for use elsewhere in Claddis:
x.1<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "ged", distance_transformation = "none")
x.2<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2), distance_metric = "ged", distance_transformation = "none")
#x.1<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1))
#x.2<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2))
new.matrix.1<-x.1$distance_matrix[c(1:5),c(1:5)]
new.matrix.2<-x.2$distance_matrix[c(6:10),c(6:10)]
xx.1<-pcoa(new.matrix.1, correction="none", rn=NULL)
xx.2<-pcoa(new.matrix.2, correction="none", rn=NULL)
disparity.1<-sum(xx.1$values[,1])
disparity.2<-sum(xx.2$values[,1])
print(disparity.1)
print(disparity.2)
###
character_taxon_matrix.1_<-replace(character_taxon_matrix.1, character_taxon_matrix.1==0, 3)
character_taxon_matrix.1_<-replace(character_taxon_matrix.1, character_taxon_matrix.1==1, 4)
character_taxon_matrix.2_<-replace(character_taxon_matrix.2, character_taxon_matrix.2==3, 1)
character_taxon_matrix.2_<-replace(character_taxon_matrix.2, character_taxon_matrix.2==4, 0)
x.1_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1_), distance_metric = "ged", distance_transformation = "none")
x.2_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2_), distance_metric = "ged", distance_transformation = "none")
#x.1_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1_), distance_metric = "mord")
#x.2_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2_), distance_metric = "mord")
new.matrix.1_<-x.1_$distance_matrix[c(1:5),c(1:5)]
new.matrix.2_<-x.2_$distance_matrix[c(6:10),c(6:10)]
xx.1_<-pcoa(new.matrix.1_, correction="none", rn=NULL)
xx.2_<-pcoa(new.matrix.2_, correction="none", rn=NULL)
disparity.1_<-sum(xx.1_$values[,1])
disparity.2_<-sum(xx.2_$values[,1])
print(disparity.1)
print(disparity.1_)
print(disparity.2)
print(disparity.2_)
plot(c(disparity.1, disparity.2) ~c(1,2), xlim=c(0.85,2.5), ylim = c(0,40), frame.plot=FALSE, ylab="Disparity", pch=19, col="#4D7CA8", cex=1.5, xaxt = "n", xlab="")
points(c(disparity.1_, disparity.2_) ~c(1,2),col="#ED5F54", cex=1.5, pch=19,)
lines(c(1,2), c(disparity.1, disparity.2), col="#4D7CA8", lwd=3)
lines(c(1,2), c(disparity.1_, disparity.2_), col="#ED5F54", lwd=3)
text(1,1.17,"Time 1")
text(2,1.17,"Time 2")
# Create random 10-by-50 matrix:
character_taxon_matrix.1 <- matrix(sample(c("0", "1", "2"),40,replace = TRUE),nrow = 10, dimnames =
list(apply(matrix(sample(LETTERS, 40,replace = TRUE), nrow = 10), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.1[c(6:10),]<-""
character_taxon_matrix.2 <- matrix(sample(c("2", "3", "4"),
40,
replace = TRUE
),
nrow = 10, dimnames =
list(apply(matrix(sample(LETTERS, 40,
replace = TRUE
), nrow = 10), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.2[c(1:5),]<-""
# Reformat for use elsewhere in Claddis:
x.1<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "ged", distance_transformation = "none")
x.2<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2), distance_metric = "ged", distance_transformation = "none")
#x.1<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1))
#x.2<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2))
new.matrix.1<-x.1$distance_matrix[c(1:5),c(1:5)]
new.matrix.2<-x.2$distance_matrix[c(6:10),c(6:10)]
xx.1<-pcoa(new.matrix.1, correction="none", rn=NULL)
xx.2<-pcoa(new.matrix.2, correction="none", rn=NULL)
disparity.1<-sum(xx.1$values[,1])
disparity.2<-sum(xx.2$values[,1])
print(disparity.1)
print(disparity.2)
###
character_taxon_matrix.1_<-replace(character_taxon_matrix.1, character_taxon_matrix.1==0, 3)
character_taxon_matrix.1_<-replace(character_taxon_matrix.1, character_taxon_matrix.1==1, 4)
character_taxon_matrix.2_<-replace(character_taxon_matrix.2, character_taxon_matrix.2==3, 1)
character_taxon_matrix.2_<-replace(character_taxon_matrix.2, character_taxon_matrix.2==4, 0)
x.1_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1_), distance_metric = "ged", distance_transformation = "none")
x.2_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2_), distance_metric = "ged", distance_transformation = "none")
#x.1_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1_), distance_metric = "mord")
#x.2_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2_), distance_metric = "mord")
new.matrix.1_<-x.1_$distance_matrix[c(1:5),c(1:5)]
new.matrix.2_<-x.2_$distance_matrix[c(6:10),c(6:10)]
xx.1_<-pcoa(new.matrix.1_, correction="none", rn=NULL)
xx.2_<-pcoa(new.matrix.2_, correction="none", rn=NULL)
disparity.1_<-sum(xx.1_$values[,1])
disparity.2_<-sum(xx.2_$values[,1])
print(disparity.1)
print(disparity.1_)
print(disparity.2)
print(disparity.2_)
plot(c(disparity.1, disparity.2) ~c(1,2), xlim=c(0.85,2.5), ylim = c(0,40), frame.plot=FALSE, ylab="Disparity", pch=19, col="#4D7CA8", cex=1.5, xaxt = "n", xlab="")
points(c(disparity.1_, disparity.2_) ~c(1,2),col="#ED5F54", cex=1.5, pch=19,)
lines(c(1,2), c(disparity.1, disparity.2), col="#4D7CA8", lwd=3)
lines(c(1,2), c(disparity.1_, disparity.2_), col="#ED5F54", lwd=3)
text(1,1.17,"Time 1")
text(2,1.17,"Time 2")
# Create random 10-by-50 matrix:
character_taxon_matrix.1 <- matrix(sample(c("0", "1", "2"),40,replace = TRUE),nrow = 10, dimnames =
list(apply(matrix(sample(LETTERS, 40,replace = TRUE), nrow = 10), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.1[c(6:10),]<-""
character_taxon_matrix.2 <- matrix(sample(c("2", "3", "4"),
40,
replace = TRUE
),
nrow = 10, dimnames =
list(apply(matrix(sample(LETTERS, 40,
replace = TRUE
), nrow = 10), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.2[c(1:5),]<-""
# Reformat for use elsewhere in Claddis:
x.1<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "ged", distance_transformation = "none")
x.2<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2), distance_metric = "ged", distance_transformation = "none")
#x.1<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1))
#x.2<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2))
new.matrix.1<-x.1$distance_matrix[c(1:5),c(1:5)]
new.matrix.2<-x.2$distance_matrix[c(6:10),c(6:10)]
xx.1<-pcoa(new.matrix.1, correction="none", rn=NULL)
xx.2<-pcoa(new.matrix.2, correction="none", rn=NULL)
disparity.1<-sum(xx.1$values[,1])
disparity.2<-sum(xx.2$values[,1])
print(disparity.1)
print(disparity.2)
###
character_taxon_matrix.1_<-replace(character_taxon_matrix.1, character_taxon_matrix.1==0, 3)
character_taxon_matrix.1_<-replace(character_taxon_matrix.1, character_taxon_matrix.1==1, 4)
character_taxon_matrix.2_<-replace(character_taxon_matrix.2, character_taxon_matrix.2==3, 1)
character_taxon_matrix.2_<-replace(character_taxon_matrix.2, character_taxon_matrix.2==4, 0)
x.1_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1_), distance_metric = "ged", distance_transformation = "none")
x.2_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2_), distance_metric = "ged", distance_transformation = "none")
#x.1_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1_), distance_metric = "mord")
#x.2_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2_), distance_metric = "mord")
new.matrix.1_<-x.1_$distance_matrix[c(1:5),c(1:5)]
new.matrix.2_<-x.2_$distance_matrix[c(6:10),c(6:10)]
xx.1_<-pcoa(new.matrix.1_, correction="none", rn=NULL)
xx.2_<-pcoa(new.matrix.2_, correction="none", rn=NULL)
disparity.1_<-sum(xx.1_$values[,1])
disparity.2_<-sum(xx.2_$values[,1])
print(disparity.1)
print(disparity.1_)
print(disparity.2)
print(disparity.2_)
plot(c(disparity.1, disparity.2) ~c(1,2), xlim=c(0.85,2.5), ylim = c(0,40), frame.plot=FALSE, ylab="Disparity", pch=19, col="#4D7CA8", cex=1.5, xaxt = "n", xlab="")
points(c(disparity.1_, disparity.2_) ~c(1,2),col="#ED5F54", cex=1.5, pch=19,)
lines(c(1,2), c(disparity.1, disparity.2), col="#4D7CA8", lwd=3)
lines(c(1,2), c(disparity.1_, disparity.2_), col="#ED5F54", lwd=3)
text(1,1.17,"Time 1")
text(2,1.17,"Time 2")
# Create random 10-by-50 matrix:
character_taxon_matrix.1 <- matrix(sample(c("0", "1", "2"),40,replace = TRUE),nrow = 10, dimnames =
list(apply(matrix(sample(LETTERS, 40,replace = TRUE), nrow = 10), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.1[c(6:10),]<-""
character_taxon_matrix.2 <- matrix(sample(c("2", "3", "4"),
40,
replace = TRUE
),
nrow = 10, dimnames =
list(apply(matrix(sample(LETTERS, 40,
replace = TRUE
), nrow = 10), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.2[c(1:5),]<-""
# Reformat for use elsewhere in Claddis:
x.1<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "ged", distance_transformation = "none")
x.2<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2), distance_metric = "ged", distance_transformation = "none")
#x.1<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1))
#x.2<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2))
new.matrix.1<-x.1$distance_matrix[c(1:5),c(1:5)]
new.matrix.2<-x.2$distance_matrix[c(6:10),c(6:10)]
xx.1<-pcoa(new.matrix.1, correction="none", rn=NULL)
xx.2<-pcoa(new.matrix.2, correction="none", rn=NULL)
disparity.1<-sum(xx.1$values[,1])
disparity.2<-sum(xx.2$values[,1])
print(disparity.1)
print(disparity.2)
###
character_taxon_matrix.1_<-replace(character_taxon_matrix.1, character_taxon_matrix.1==0, 3)
character_taxon_matrix.1_<-replace(character_taxon_matrix.1, character_taxon_matrix.1==1, 4)
character_taxon_matrix.2_<-replace(character_taxon_matrix.2, character_taxon_matrix.2==3, 1)
character_taxon_matrix.2_<-replace(character_taxon_matrix.2, character_taxon_matrix.2==4, 0)
x.1_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1_), distance_metric = "ged", distance_transformation = "none")
x.2_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2_), distance_metric = "ged", distance_transformation = "none")
#x.1_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1_), distance_metric = "mord")
#x.2_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2_), distance_metric = "mord")
new.matrix.1_<-x.1_$distance_matrix[c(1:5),c(1:5)]
new.matrix.2_<-x.2_$distance_matrix[c(6:10),c(6:10)]
xx.1_<-pcoa(new.matrix.1_, correction="none", rn=NULL)
xx.2_<-pcoa(new.matrix.2_, correction="none", rn=NULL)
disparity.1_<-sum(xx.1_$values[,1])
disparity.2_<-sum(xx.2_$values[,1])
print(disparity.1)
print(disparity.1_)
print(disparity.2)
print(disparity.2_)
plot(c(disparity.1, disparity.2) ~c(1,2), xlim=c(0.85,2.5), ylim = c(0,40), frame.plot=FALSE, ylab="Disparity", pch=19, col="#4D7CA8", cex=1.5, xaxt = "n", xlab="")
points(c(disparity.1_, disparity.2_) ~c(1,2),col="#ED5F54", cex=1.5, pch=19,)
lines(c(1,2), c(disparity.1, disparity.2), col="#4D7CA8", lwd=3)
lines(c(1,2), c(disparity.1_, disparity.2_), col="#ED5F54", lwd=3)
text(1,1.17,"Time 1")
text(2,1.17,"Time 2")
# Create random 10-by-50 matrix:
character_taxon_matrix.1 <- matrix(sample(c("0", "1", "2"),40,replace = TRUE),nrow = 10, dimnames =
list(apply(matrix(sample(LETTERS, 40,replace = TRUE), nrow = 10), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.1[c(6:10),]<-""
character_taxon_matrix.2 <- matrix(sample(c("2", "3", "4"),
40,
replace = TRUE
),
nrow = 10, dimnames =
list(apply(matrix(sample(LETTERS, 40,
replace = TRUE
), nrow = 10), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.2[c(1:5),]<-""
# Reformat for use elsewhere in Claddis:
x.1<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "ged", distance_transformation = "none")
x.2<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2), distance_metric = "ged", distance_transformation = "none")
#x.1<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1))
#x.2<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2))
new.matrix.1<-x.1$distance_matrix[c(1:5),c(1:5)]
new.matrix.2<-x.2$distance_matrix[c(6:10),c(6:10)]
xx.1<-pcoa(new.matrix.1, correction="none", rn=NULL)
xx.2<-pcoa(new.matrix.2, correction="none", rn=NULL)
disparity.1<-sum(xx.1$values[,1])
disparity.2<-sum(xx.2$values[,1])
print(disparity.1)
print(disparity.2)
###
character_taxon_matrix.1_<-replace(character_taxon_matrix.1, character_taxon_matrix.1==0, 3)
character_taxon_matrix.1_<-replace(character_taxon_matrix.1, character_taxon_matrix.1==1, 4)
character_taxon_matrix.2_<-replace(character_taxon_matrix.2, character_taxon_matrix.2==3, 1)
character_taxon_matrix.2_<-replace(character_taxon_matrix.2, character_taxon_matrix.2==4, 0)
x.1_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1_), distance_metric = "ged", distance_transformation = "none")
x.2_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2_), distance_metric = "ged", distance_transformation = "none")
#x.1_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1_), distance_metric = "mord")
#x.2_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2_), distance_metric = "mord")
new.matrix.1_<-x.1_$distance_matrix[c(1:5),c(1:5)]
new.matrix.2_<-x.2_$distance_matrix[c(6:10),c(6:10)]
xx.1_<-pcoa(new.matrix.1_, correction="none", rn=NULL)
xx.2_<-pcoa(new.matrix.2_, correction="none", rn=NULL)
disparity.1_<-sum(xx.1_$values[,1])
disparity.2_<-sum(xx.2_$values[,1])
print(disparity.1)
print(disparity.1_)
print(disparity.2)
print(disparity.2_)
plot(c(disparity.1, disparity.2) ~c(1,2), xlim=c(0.85,2.5), ylim = c(0,40), frame.plot=FALSE, ylab="Disparity", pch=19, col="#4D7CA8", cex=1.5, xaxt = "n", xlab="")
points(c(disparity.1_, disparity.2_) ~c(1,2),col="#ED5F54", cex=1.5, pch=19,)
lines(c(1,2), c(disparity.1, disparity.2), col="#4D7CA8", lwd=3)
lines(c(1,2), c(disparity.1_, disparity.2_), col="#ED5F54", lwd=3)
text(1,1.17,"Time 1")
text(2,1.17,"Time 2")
# Create random 10-by-50 matrix:
character_taxon_matrix.1 <- matrix(sample(c("0", "1", "2"),40,replace = TRUE),nrow = 10, dimnames =
list(apply(matrix(sample(LETTERS, 40,replace = TRUE), nrow = 10), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.1[c(6:10),]<-""
character_taxon_matrix.2 <- matrix(sample(c("2", "3", "4"),
40,
replace = TRUE
),
nrow = 10, dimnames =
list(apply(matrix(sample(LETTERS, 40,
replace = TRUE
), nrow = 10), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.2[c(1:5),]<-""
# Reformat for use elsewhere in Claddis:
x.1<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "ged", distance_transformation = "none")
x.2<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2), distance_metric = "ged", distance_transformation = "none")
#x.1<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1))
#x.2<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2))
new.matrix.1<-x.1$distance_matrix[c(1:5),c(1:5)]
new.matrix.2<-x.2$distance_matrix[c(6:10),c(6:10)]
xx.1<-pcoa(new.matrix.1, correction="none", rn=NULL)
xx.2<-pcoa(new.matrix.2, correction="none", rn=NULL)
disparity.1<-sum(xx.1$values[,1])
disparity.2<-sum(xx.2$values[,1])
print(disparity.1)
print(disparity.2)
###
character_taxon_matrix.1_<-replace(character_taxon_matrix.1, character_taxon_matrix.1==0, 3)
character_taxon_matrix.1_<-replace(character_taxon_matrix.1, character_taxon_matrix.1==1, 4)
character_taxon_matrix.2_<-replace(character_taxon_matrix.2, character_taxon_matrix.2==3, 1)
character_taxon_matrix.2_<-replace(character_taxon_matrix.2, character_taxon_matrix.2==4, 0)
x.1_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1_), distance_metric = "ged", distance_transformation = "none")
x.2_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2_), distance_metric = "ged", distance_transformation = "none")
#x.1_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1_), distance_metric = "mord")
#x.2_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2_), distance_metric = "mord")
new.matrix.1_<-x.1_$distance_matrix[c(1:5),c(1:5)]
new.matrix.2_<-x.2_$distance_matrix[c(6:10),c(6:10)]
xx.1_<-pcoa(new.matrix.1_, correction="none", rn=NULL)
xx.2_<-pcoa(new.matrix.2_, correction="none", rn=NULL)
disparity.1_<-sum(xx.1_$values[,1])
disparity.2_<-sum(xx.2_$values[,1])
print(disparity.1)
print(disparity.1_)
print(disparity.2)
print(disparity.2_)
plot(c(disparity.1, disparity.2) ~c(1,2), xlim=c(0.85,2.5), ylim = c(0,40), frame.plot=FALSE, ylab="Disparity", pch=19, col="#4D7CA8", cex=1.5, xaxt = "n", xlab="")
points(c(disparity.1_, disparity.2_) ~c(1,2),col="#ED5F54", cex=1.5, pch=19,)
lines(c(1,2), c(disparity.1, disparity.2), col="#4D7CA8", lwd=3)
lines(c(1,2), c(disparity.1_, disparity.2_), col="#ED5F54", lwd=3)
text(1,1.17,"Time 1")
text(2,1.17,"Time 2")
# Create random 10-by-50 matrix:
character_taxon_matrix.1 <- matrix(sample(c("0", "1", "2"),40,replace = TRUE),nrow = 10, dimnames =
list(apply(matrix(sample(LETTERS, 40,replace = TRUE), nrow = 10), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.1[c(6:10),]<-""
character_taxon_matrix.2 <- matrix(sample(c("2", "3", "4"),
40,
replace = TRUE
),
nrow = 10, dimnames =
list(apply(matrix(sample(LETTERS, 40,
replace = TRUE
), nrow = 10), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.2[c(1:5),]<-""
# Reformat for use elsewhere in Claddis:
x.1<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "ged", distance_transformation = "none")
x.2<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2), distance_metric = "ged", distance_transformation = "none")
#x.1<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1))
#x.2<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2))
new.matrix.1<-x.1$distance_matrix[c(1:5),c(1:5)]
new.matrix.2<-x.2$distance_matrix[c(6:10),c(6:10)]
xx.1<-pcoa(new.matrix.1, correction="none", rn=NULL)
xx.2<-pcoa(new.matrix.2, correction="none", rn=NULL)
disparity.1<-sum(xx.1$values[,1])
disparity.2<-sum(xx.2$values[,1])
print(disparity.1)
print(disparity.2)
###
character_taxon_matrix.1_<-replace(character_taxon_matrix.1, character_taxon_matrix.1==0, 3)
character_taxon_matrix.1_<-replace(character_taxon_matrix.1, character_taxon_matrix.1==1, 4)
character_taxon_matrix.2_<-replace(character_taxon_matrix.2, character_taxon_matrix.2==3, 1)
character_taxon_matrix.2_<-replace(character_taxon_matrix.2, character_taxon_matrix.2==4, 0)
x.1_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1_), distance_metric = "ged", distance_transformation = "none")
x.2_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2_), distance_metric = "ged", distance_transformation = "none")
#x.1_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1_), distance_metric = "mord")
#x.2_<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.2_), distance_metric = "mord")
new.matrix.1_<-x.1_$distance_matrix[c(1:5),c(1:5)]
new.matrix.2_<-x.2_$distance_matrix[c(6:10),c(6:10)]
xx.1_<-pcoa(new.matrix.1_, correction="none", rn=NULL)
xx.2_<-pcoa(new.matrix.2_, correction="none", rn=NULL)
disparity.1_<-sum(xx.1_$values[,1])
disparity.2_<-sum(xx.2_$values[,1])
print(disparity.1)
print(disparity.1_)
print(disparity.2)
print(disparity.2_)
plot(c(disparity.1, disparity.2) ~c(1,2), xlim=c(0.85,2.5), ylim = c(0,40), frame.plot=FALSE, ylab="Disparity", pch=19, col="#4D7CA8", cex=1.5, xaxt = "n", xlab="")
points(c(disparity.1_, disparity.2_) ~c(1,2),col="#ED5F54", cex=1.5, pch=19,)
lines(c(1,2), c(disparity.1, disparity.2), col="#4D7CA8", lwd=3)
lines(c(1,2), c(disparity.1_, disparity.2_), col="#ED5F54", lwd=3)
text(1,1.17,"Time 1")
text(2,1.17,"Time 2")
x.1
x.1
# Create random 10-by-50 matrix:
character_taxon_matrix.1 <- matrix(sample(c("0", "1", "2"),40,replace = TRUE),nrow = 10, dimnames =
list(apply(matrix(sample(LETTERS, 40,replace = TRUE), nrow = 10), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.1
# Create random 10-by-50 matrix:
character_taxon_matrix.1 <- matrix(c("0", "1", "2", "0", "1", "2", "0", "1", "2"),nrow = 3, dimnames =
list(apply(matrix(sample(LETTERS, 40,replace = TRUE), nrow = 3), 1, paste,
collapse = ""
), c())
)
# Create random 10-by-50 matrix:
character_taxon_matrix.1 <- matrix(c("0", "1", "2", "0", "1", "2", "0", "1", "2"),nrow = 3, dimnames =
list(apply(matrix(sample(LETTERS, 9,replace = TRUE), nrow = 3), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.1
# Create random 10-by-50 matrix:
character_taxon_matrix.1 <- matrix(c("0", "1", "2", "1", "1", "2", "2", "1", "2"),nrow = 3, dimnames =
list(apply(matrix(sample(LETTERS, 9,replace = TRUE), nrow = 3), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.1
# Create random 10-by-50 matrix:
character_taxon_matrix.1 <- matrix(c("0", "1", "2", "2", "1", "2", "2", "1", "0"),nrow = 3, dimnames =
list(apply(matrix(sample(LETTERS, 9,replace = TRUE), nrow = 3), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.1
# Create random 10-by-50 matrix:
character_taxon_matrix.1 <- matrix(c("0", "2", "2", "2", "1", "2", "2", "1", "0"),nrow = 3, dimnames =
list(apply(matrix(sample(LETTERS, 9,replace = TRUE), nrow = 3), 1, paste,
collapse = ""
), c())
)
character_taxon_matrix.1
x.1<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "red", distance_transformation = "none")
red<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "red", distance_transformation = "none")
ged<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "ged", distance_transformation = "none")
gc<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "gc", distance_transformation = "none")
mord<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "mord", distance_transformation = "none")
red
sqrt((2^2)+1^2+1^2))
sqrt((2^2)+(1^2)+(1^2))
((2^2)/2)+(1^2)+(1^2))
((2^2)/2)+(1^2)+(1^2))
((2^2)/2)+(1^2)+(1^2))
((2^2)/2)+(1^2)+(1^2)
ged<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "ged", distance_transformation = "none")
ged
gc<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "gc", distance_transformation = "none")
gc
character_taxon_matrix.1
mord<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "mord", distance_transformation = "none")
mord
((2^2)/2)+(1^2)+(1^2)
sqrt((2^2)+(1^2)+(1^2))
red
ged
(2/3+(1/3)+(1/3)
(2/3)+(1/3)+(1/3)
gc
character_taxon_matrix.1
character_taxon_matrix.1[1,1]<-NA
character_taxon_matrix.1
red<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "red", distance_transformation = "none")
red
ged<-calculate_morphological_distances(build_cladistic_matrix(character_taxon_matrix.1), distance_metric = "ged", distance_transformation = "none")
ged
character_taxon_matrix.1
sqrt((0)+(1^2)+(1^2))
red
ged
character_taxon_matrix.1
sqrt((1)+(1^2)+(1^2))
sqrt((2)+(1^2)+(1^2))
sqrt((12)+(1^2)+(1^2))
sqrt((1)+(1^2)+(1^2))
sqrt((0.5)+(1^2)+(1^2))
ged
sqrt((0.5^2)+(1^2)+(1^2))
detach("package:evoTS", unload = TRUE)
remove.packages("evoTS")
install.packages("evoTS")
setwd("~/Dropbox/GitHub/evoTS")
### Update website (pkgdown)
pkgdown::build_site()
#When the readme.rmd has been updated, run this:
devtools::build_readme()