I want to relate geographical distance to biochemical parameters (variation in chemical content) of a plant. I came across papers where they used a Mahalanobis distance matrix to relate these parameters. I also found out that it can be deduced using PASSAGE (http://www.passagesoftware.net/).
Can anybody explain how I this programme (stepwise advice)?
"Biometrical Methods in quantitative genetic anlaysis" by Sing and Chaudhry (1979) is a good reference for Mahalanobis distance measures. They have given the calculation procedures in details. SPSS/Statistica could be used for the purpose.
As is true of most statistical questions, the quick answer is to look for the appropriate package in R. It turns out that the Mahalanobis distance is in the stats package (in core R).
According to the help menu:
Returns the squared Mahalanobis distance of all rows in x and the vector mu = center with respect to Sigma = cov. This is (for vector x) defined as
D^2 = (x - μ)' Σ^-1 (x - μ)
Given your question, you seem interested in various geographical questions. You might want to consult http://www.social-statistics.org/?p=354 which seems to summarize a book on using R for geographical and environmental statistics.
Also go to the cran.r-project.org web page and look for the task view on Analysis of ecological and environmental data.
There a very easy way to do it using R Package "biotools". In this case you will get a Squared Distance Mahalanobis Matrix.
#Manly (2004, p.65-66)
x1
Dineshreddy Vemula ·there is no range to Mahalanobis Distance...
check:
https://en.wikipedia.org/wiki/Mahalanobis_distance
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