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stefpeschel / NetCoMi

Network construction, analysis, and comparison for microbial compositional data
GNU General Public License v3.0
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Issue during netConstruct #53

Closed tsantiagoro closed 2 years ago

tsantiagoro commented 2 years ago

Hi, I'm just learning how to use NetCoMi, and after finally being able to install it because I had a couple of issues with some of the dependencies, I now have this issue after using the American Gut dataset and typing the same line of code for netConstruct as the tutorial. It seems like it's working and then I get the error message below. Has anyone experienced this or has this issue been brought before? Thanks

Data filtering ... 27 taxa removed. 100 taxa and 289 samples remaining.

Calculate 'spring' associations ... Error in hatRupper[-ind_cutoff] <- bridgeInv(Kupper[-ind_cutoff], zratio1 = zratio1vec[-ind_cutoff], : replacement has length zero

stefpeschel commented 2 years ago

Hey, This error is caused by a current issue with the fast latent correlation computation in mixedCCA, which is used by the SPRING package (a dependency of mixedCCA needed for the fast approach is no longer available). The SPRING parameter Rmethod must be set to "original" until the issue is solved:

measurePar = list(nlambda=10, 
                  rep.num=10,
                  Rmethod = "original")

In the latest NetCoMi version, this is done internally to avoid this error. Please update NetCoMi as well as mixedCCA to the latest version to solve the problem. Best, Stefanie