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zdk123 / SpiecEasi

Sparse InversE Covariance estimation for Ecological Association and Statistical Inference
GNU General Public License v3.0
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Reproducing Result in the Publication #15

Closed leimao closed 7 years ago

leimao commented 7 years ago

Hi Zach,

I am recently practicing Spiec-Easi, and trying to reproduce the figure 4 i and j in your science paper "Helminth infection promotes colonization resistance via type 2 immunity" using your published method in the supplemental materials. However, the data I obtained for the plot using my own codes is slightly different to the data shown on your published figures. I was actually using the data downloaded from https://github.com/biocore/American-Gut, and I found these data are different to the data you claimed in your published paper. That might be one of the reasons why I got different results. I wondered whether you can kindly send me the biom-formatted data you used in the paper? I may use these data to see whether I can reproduce the published result and further use Spiec-Easi in other projects. My email is dukeleimao@gmail.com. Thank you very much.

Best regards, Lei Mao

ParamjitGill commented 7 years ago

I tried to install the package 'SpiecEasi' in R3.3.3 using

library(devtools) install_github("zdk123/SpiecEasi", force=TRUE) but got the error message

  • installing source package 'SpiecEasi' ... R data * moving datasets to lazyload DB inst tests preparing package for lazy loading Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : there is no package called 'phyloseq' ERROR: lazy loading failed for package 'SpiecEasi'
  • removing 'C:/Program Files/R/R-3.3.3/library/SpiecEasi' Error: Command failed (1)
ParamjitGill commented 7 years ago

Solved by source('http://bioconductor.org/biocLite.R') biocLite('phyloseq')