rownames-geoR.R

# -----------------------------------------------------------------------------------
# Demo of a function that depends upon matrix rownames
# -----------------------------------------------------------------------------------

rm(list = ls())
graphics.off()

library(geoR) # Tested with geoR_1.7-5.1

# Extract a small matrix for demonstration
x <- as.matrix(cars[1:3, ])
print(x)

# Duplicate rows of coords with duplicate rownames
coords.dup.rownames <- rbind(x, x)

# Duplicate rows of coords with unique rownames
coords.uni.rownames <- rbind(x, x)
rownames(coords.uni.rownames) <- seq_len(nrow(coords.uni.rownames))

# Run the function geoR::jitterDupCoords on both with the same seed
set.seed(64651)
coords.dup.rownames.jit <- jitterDupCoords(coords.dup.rownames, 1)
set.seed(64651)
coords.uni.rownames.jit <- jitterDupCoords(coords.uni.rownames, 1)

# Look at both the results
# Unique rownames in input - expected results
print(coords.uni.rownames.jit)
print(unique(coords.uni.rownames.jit)) # Jitter has been added to all duplicated coords
print(nrow(unique(coords.uni.rownames.jit)) == nrow(coords.uni.rownames.jit))

# Duplicated rownames - unexpected results
print(coords.dup.rownames.jit)
print(unique(coords.dup.rownames.jit)) # Jitter has NOT been added to all duplicated coords
print(nrow(unique(coords.dup.rownames.jit)) == nrow(coords.dup.rownames.jit))

# jitterDupCoords() expects that the rownames be unique for correct working

# ------------------------------------------------------------------------------------
# One level deeper:
# jitterDupCoords() uses geoR::dup.coords() under the hood (See geoR/R/geoRmisc.R)
# dup.coords() identifies which rows are duplicated and stores the rownames not rowindices.
# See ?dup.coords()
# ------------------------------------------------------------------------------------

# In this case, rownames equals rowindices.
# We can see that row named "2" is the same as row named "5",
# Similarly, row named "1" is the same as row named "4".
print(dup.coords(coords.uni.rownames, simplify=FALSE, USE.NAMES=FALSE))

# We get the "correct" answer from dup.coords().
# Row index 2 is the same as row index 5. But both rows have the same row name of "2".
print(dup.coords(coords.dup.rownames, simplify=FALSE, USE.NAMES=FALSE))

# The next step in jitterDupCoords.default() (line 19, geoR/R/geoRmisc.R) uses row names
# to fill in the matrix.
# x[ind[[i]],] <- jitter2d(coords=x[ind[[i]],], ...)
# This causes the unexpected results when the rownames are non-unique.