search

DaliangNing / iCAMP1

Infer Community Assembly Mechanisms by Phylogenetic bin-based null model analysis (Version 1)
GNU General Public License v2.0
68 stars 25 forks source link

missing values are not allowed with argument 'na.rm = FALSE' #29

Closed liyangyang200112 closed 1 year ago

liyangyang200112 commented 1 year ago

Hi Daliang, When I run

9.5 # input community matrix as relative abundances (values < 1) rather than counts

comra=comm/rowSums(comm) prefixra=paste0(prefix,"RA") bin.size.limit = 24 # For real data, usually use a proper number according to phylogenetic signal test or try some settings then choose the reasonable stochasticity level. our experience is 12, or 24, or 48. but for this example dataset which is too small, have to use 5. icres6=iCAMP::icamp.big(comm=comra,tree=tree,pd.desc=pd.big$pd.file, pd.spname=pd.big$tip.label, pd.wd=pd.big$pd.wd, rand=rand.time,prefix=prefixra,ds=0.2,pd.cut=NA,sp.check=TRUE, phylo.rand.scale="within.bin",taxa.rand.scale="across.all", phylo.metric="bMPD",sig.index="Confidence", bin.size.limit=bin.size.limit,nworker=nworker,memory.G=memory.G, rtree.save=FALSE,detail.save=TRUE,qp.save=FALSE,detail.null=FALSE, ignore.zero=TRUE,output.wd=save.wd,correct.special=TRUE,unit.sum=rowSums(comra), special.method="depend",ses.cut = 1.96,rc.cut = 0.95,conf.cut=0.975, omit.option="no",meta.ab=NULL, taxo.metric="bray", transform.method=NULL, logbase=2, dirichlet=TRUE)

Error shows" 4 nodes produced errors; first error: missing values are not allowed with argument 'na.rm = false' " How can I solve it? Thank you very much!

DaliangNing commented 1 year ago

Did you get this error when using the example dataset or your own dataset? If it happens to your own dataset, please send me (ningdaliang@ou.edu) the input files and your R code for me to debug.

Xiaojie0607 commented 1 year ago

Hi Professor Ning,

I also have the same problem as above when using my own dataset.

When I run"9.5 # input community matrix as relative abundances (values < 1) rather than counts", error shows" 12nodes produced errors; first error: missing values are not allowed with argument 'na.rm = false' ".

I don't know what's wrong with the parameters or dataset. How can I solve it? Thank you very much!

Best regards,

DaliangNing commented 1 year ago

Today's updated version (v1.6.2) may solve this problem. Please download version 1.6.2 or a later version from https://github.com/DaliangNing/iCAMP1/tree/master/RPackage/AllVersions

DaliangNing commented 1 year ago

I hope the problem has been solved. If no more questions, I will close this issue.