distancematrix  R Documentation 
The distancematrix function is used to reformat the input distance matrix
into the format required by the nonbipartite matching Fortran code. The
original matrix should have dimensions NxN
, where N
is the total
number of elements to be matched. The matrix may be created in R and input
into the distancematrix function. Alternately, the matrix may be read in
from a CSV file, i.e. a text file where distances in a given row are
delimited by commas. If a list element is given, it should have a data.frame
element named "dist", preferably generated by the gendistance function.
distancematrix(x, ...)
x 
A matrix, data.frame, list or filename. This should be an

... 
Additional arguments, potentially used when reading in a filename and passed into read.csv. 
The distancematrix function is used to reformat the input distance matrix into the format required by the nonbipartite matching Fortran code.
If an extra column or row is present, it will be converted into row
names. In other words, if the matrix has dimensions (N+1)
xN
, or
N
x(N+1)
, then the function will take the first row, or column, as
an ID column. If both row and column names are present, i.e. a
(N+1)
x(N+1)
matrix, the function cannot identify the names.
If an odd number of elements exist, a ghost element, or sink, will be created whose distance is zero to all of the other elements. For example, when matching 17 elements, the function will create an 18th element that matches every element perfectly. This sink may or not be appropriate for your application. Naturally, you may create sinks as needed in the distance matrix you input to the distancematrix function.
The elements of distancematrix may not be reassigned once created. In other words, you cannot edit the formatted distance matrix. You need to edit the matrix being input into the distancematrix function.
distancematrix S4 object
Cole Beck
nonbimatch gendistance
plainmatrix<as.matrix(dist(sample(1:25, 8, replace=TRUE)))
diag(plainmatrix) < 99999 # setting diagonal to an infinite distance for
# pedagogical reasons (the diagonal may be left
# as zero)
mdm<distancematrix(plainmatrix)
df < data.frame(id=LETTERS[1:25], val1=rnorm(25), val2=rnorm(25))
df[sample(seq_len(nrow(df)), ceiling(nrow(df)*0.1)), 2] < NA
df.dist < gendistance(df, idcol=1, ndiscard=2)
mdm2 < distancematrix(df.dist)
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