addord: Fit new points to an existing NMDS configuration.

In phiala/ecodist: Dissimilarity-Based Functions for Ecological Analysis

Fit new points to an existing NMDS configuration.

Description

Uses a brute force algorithm to find the location for each new point that minimizes overall stress.

Usage

addord(origconf, fulldat, fulldist, isTrain, bfstep = 10, maxit = 50, epsilon = 1e-12)

Arguments

origconf	The original ordination configuration.
fulldat	The dataset containing original and new points.
fulldist	A dissimilarity matrix calculated on fulldat.
isTrain	A boolean vector of length nrow(fulldat) indicating which rows were training data used in determining origconf (TRUE), or are new points (FALSE).
bfstep	A tuning parameter for the brute force algorithm describing the size of grid to use.
maxit	The maximum number of iterations to use.
epsilon	Tolerance value for convergence.

Details

A region comprising the original ordination configuration plus one standard deviation is divided into a grid of bfstep rows and columns. For a new point, the grid cell with the lowest stress is identified. That cell is divided into a finer grid, and the lowest-stress cell identified. This process is repeated up to maxit times, or until stress changes less than epsilon.

Value

fullfitconf	The new ordination configuration containing training and new points.
stress	The stress value for each point.
isTrain	The boolean vector indicating training set membership, for reference.

Author(s)

Sarah Goslee

Examples

data(iris)
iris.d <- dist(iris[,1:4])

### nmds() is timeconsuming, so this was generated
### in advance and saved.
### set.seed(1234)
### iris.nmds <- nmds(iris.d, nits=20, mindim=1, maxdim=4)
### save(iris.nmds, file="ecodist/data/iris.nmds.rda")
data(iris.nmds)

# examine fit by number of dimensions
plot(iris.nmds)

# choose the best two-dimensional solution to work with
iris.nmin <- min(iris.nmds, dims=2)

# rotate the configuration to maximize variance
iris.rot <- princomp(iris.nmin)$scores

# rotation preserves distance apart in ordination space
cor(dist(iris.nmin), dist(iris.rot))

# fit the data to the ordination as vectors
### vf() is timeconsuming, so this was generated
### in advance and saved.
### set.seed(1234)
### iris.vf <- vf(iris.nmin, iris[,1:4], nperm=1000)
### save(iris.vf, file="ecodist/data/iris.vf.rda")
data(iris.vf)

# repeat for the rotated ordination
### vf() is timeconsuming, so this was generated
### in advance and saved.
### set.seed(1234)
### iris.vfrot <- vf(iris.rot, iris[,1:4], nperm=1000)
### save(iris.vfrot, file="ecodist/data/iris.vfrot.rda")
data(iris.vfrot)

par(mfrow=c(1,2))
plot(iris.nmin, col=as.numeric(iris$Species), pch=as.numeric(iris$Species), main="NMDS")
plot(iris.vf)
plot(iris.rot, col=as.numeric(iris$Species), pch=as.numeric(iris$Species), main="Rotated NMDS")
plot(iris.vfrot)

####### addord example

# generate new data points to add to the ordination
# this might be new samples, or a second dataset

iris.new <- structure(list(Sepal.Length = c(4.6, 4.9, 5.4, 5.2, 6, 6.5, 6, 
6.8, 7.3), Sepal.Width = c(3.2, 3.5, 3.6, 2.3, 2.8, 3, 2.7, 3.1, 
3.2), Petal.Length = c(1.2, 1.5, 1.5, 3.5, 4.1, 4.2, 4.8, 5, 
5.7), Petal.Width = c(0.26, 0.26, 0.26, 1.2, 1.3, 1.4, 1.8, 2, 
2), Species = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L), .Label = c("setosa", 
"versicolor", "virginica"), class = "factor")), .Names = c("Sepal.Length", 
"Sepal.Width", "Petal.Length", "Petal.Width", "Species"), class = "data.frame", row.names = c(NA, 
-9L))

# provide a dist object containing original and new data
# provide a logical vector indicating which samples were used to
# construct the original configuration

iris.full <- rbind(iris, iris.new)
all.d <- dist(iris.full[,1:4])
is.orig <- c(rep(TRUE, nrow(iris)), rep(FALSE, nrow(iris.new)))

### addord() is timeconsuming, so this was generated
### in advance and saved.
### set.seed(1234)
### iris.fit <- addord(iris.nmin, iris.full[,1:4], all.d, is.orig, maxit=100)
### save(iris.fit, file="ecodist/data/iris.fit.rda")
data(iris.fit)

plot(iris.fit$conf, col=iris.full$Species, pch=c(18, 4)[is.orig + 1], xlab="NMDS 1", ylab="NMDS 2")
title("Demo: adding points to an ordination")
legend("bottomleft", c("Training set", "Added point"), pch=c(4, 18))
legend("topright", levels(iris$Species), fill=1:3)

phiala/ecodist documentation built on Nov. 5, 2023, 10:47 a.m.