# Start with a matrix
mat <- matrix(1:12, ncol = 3)
# Pay attention to the following when
# writing examples that test for identity!
identical(1 * mat, mat) # FALSE
# Create two matrices that are multiples of the first
a <- 1 * mat
b <- 2 * mat
# These both have two dimensions of lengths 4 and 3
dim(a) # 4 3
# Combine them to make an array with three dimensions
x <- list2array(list(a, b))
# The third dimension has length 2
dim(x) # 4 3 2
# The first slice of the third dimension
slice(x, 3) # a
# The second slice of the third dimension
slice(x, 3, 2) # b
# 'slice' works just like the bracket operator
slice(x, 1) # x[1, , ]
slice(x, 1, 2) # x[2, , ]
slice(x, 2, 1) # x[, 1, ]
slice(x, 2, 1:2) # x[, 1:2, ]
# Replace part of the array
y <- slice(x, 3, 2, value = a)
# Now the second slice of the third dimension == a
slice(y, 3, 2) # a
# and the sum across the third dimension == b
dimSums(y, 3) # b
# Taking the sum removes that dimension
dim(y) # 4 3 2
dim(dimSums(y, 1)) # 3 2
dim(dimSums(y, 2)) # 4 2
dim(dimSums(y, 3)) # 4 3
# Working with an 'affinity' object
reset()
basis("CHNOS+")
species("alanine")
a1 <- affinity(O2 = c(-80, -60)) # i.e. pH = 7
a2 <- affinity(O2 = c(-80, -60), pH = c(0, 14, 7))
# In the 2nd dimension (pH) get the 4th slice (pH = 7)
a3 <- slice.affinity(a2, 2, 4)
all.equal(a1$values, a3$values) # TRUE
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