I am currently doing Geometric morphometric analysis and I need to know if I can use the covariance matrices generated by Morpho J to do modularity and integration analysis in Geomorph
I see that you have no answers. The functions for analyzing integration and modularity in geomorph do not read in a covariance matrix so it is not as if you can just provide one from MorphoJ to those functions. You might need to rewrite some code as well as provide additional information that the function needs that is not in the covariance matrix. The functions read in shape data, with each landmark in a row (the x-, y- and perhaps z- coordinates are the columns). Hypotheses of modularity are specified by a "partition group" and those refer to the rows of the data. So you would need to find a way to provide that information (and to prevent the function from looking to the data to obtain it). There may be a much simpler way to do what you want to do. Why do you want to read in the covariance matrix from MorphoJ rather than use the one that you'd get from geomorph?
Hello Dr. Miriam, thank you very much for the response. I generated a Gmatrix in quantitative genetics software, I transformed this Gmatrix into landmark coordinates (covariance matrix) in Morpho J, in this program I can do integration and modularity analysis, but I want to work with the CR coefficient. So far I haven't been able to do this in Geomorph.
I think that the only real issue is to write a version of the "partition.gp" that geomorph needs for figuring out which variables belong to which module in the form that is used for partitioning the covariance matrix. But what might be fastest is to ask the geomorph google group. Dean Adams and Michael Collyer answer questions there.
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