himelmallick/benchmarkmicrobiome

Large-scale Benchmarking of Microbial Multivariable Association Methods

benchmarkmicrobiome's Issues

Error in names(simlist) <- simnames

Very cool project!

I had to remove the forward slash in '/Library/sparseDOSSAhelperFunctions.R' from line 106 of the file Load_Simulator.R to remove the error:

Error in file(filename, "r", encoding = encoding) :
  cannot open the connection
Calls: <Anonymous> -> sourceURL -> source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open file '/Library/sparseDOSSAhelperFunctions.R': No such file or directory
Execution halted 

However I get the following error after running the code:
Rscript Codes/Load_Simulator.R --metadataType UVB --nSubjects 5 --nPerSubject 1 --nMicrobes 10 --spikeMicrobes 0.1 --nMetadata 1 --spikeMetadata 1 --effectSize 20 --workingDirectory ~/BenchmarkMicrobiome/

Error in names(simlist) <- simnames :
  'names' attribute [100] must be the same length as the vector [78]
Calls: trigger_sparseDOSSA_Simulator
Execution halted

Enhancesments

• The eval_res_list_repeated function should not return factor values for the numeric entries
• Add a few new methods previously included mgS2, limma2, ZIBBSeq, etc.
• Add a sophisticated summary function per (q, alpha) combination
• Revisit normalizations so that they do not output normalized values (except for TSS, RFA, and CLR)
• Wrap the functionalities into a more streamlined R package