unsolved problem

[WeichuanLin6688]

bin.size.limit = 12 sig.index="Confidence" # see other options in help document of icamp.big. icres=iCAMP::icamp.big(comm=comm, pd.desc = pd.big$pd.file, pd.spname=pd.big$tip.label,

• pd.wd = pd.big$pd.wd, rand = rand.time, tree=tree,
• prefix = prefix, ds = 0.2, pd.cut = NA, sp.check = TRUE,
• phylo.rand.scale = "within.bin", taxa.rand.scale = "across.all",
• phylo.metric = "bMPD", sig.index=sig.index, 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(comm), special.method = "depend",
• ses.cut = 1.96, rc.cut = 0.95, conf.cut=0.975, omit.option = "no",meta.ab = NULL) The names are re-ranked. Now calculating max phylogenetic distance. ----------Now binning-----------------Sun Apr 17 13:30:44 2022 Now computing path. begin at Sun Apr 17 13:30:45 2022. Please wait... Now computing path. begin at Sun Apr 17 17:37:25 2022. Please wait... Now computing dist to root. begin at Sun Apr 17 21:43:29 2022. Please wait... ----------Now binning com and sp without omitting small bins-----------------Sun Apr 17 21:45:58 2022 ----bMPD bin i=1 in 471 ---- Sun Apr 17 21:45:59 2022 Now calculating observed betaMPD. Begin at Sun Apr 17 21:46:00 2022. Please wait... Now randomizing by parallel computing. Begin at Sun Apr 17 21:46:03 2022. Please wait... Now fixing special cases. Begin at Sun Apr 17 22:13:18 2022. Please wait... ----bMPD bin i=2 in 471 ---- Sun Apr 17 22:13:18 2022 Now calculating observed betaMPD. Begin at Sun Apr 17 22:13:19 2022. Please wait... Now randomizing by parallel computing. Begin at Sun Apr 17 22:13:19 2022. Please wait... Now fixing special cases. Begin at Sun Apr 17 22:14:25 2022. Please wait... ----bMPD bin i=3 in 471 ---- Sun Apr 17 22:14:26 2022 Now calculating observed betaMPD. Begin at Sun Apr 17 22:14:26 2022. Please wait... Now randomizing by parallel computing. Begin at Sun Apr 17 22:14:27 2022. Please wait... Now fixing special cases. Begin at Sun Apr 17 22:15:34 2022. Please wait... ----bMPD bin i=4 in 471 ---- Sun Apr 17 22:15:35 2022 Now calculating observed betaMPD. Begin at Sun Apr 17 22:15:35 2022. Please wait... Now randomizing by parallel computing. Begin at Sun Apr 17 22:15:35 2022. Please wait... Now fixing special cases. Begin at Sun Apr 17 22:16:40 2022. Please wait... ----bMPD bin i=5 in 471 ---- Sun Apr 17 22:16:41 2022 Now calculating observed betaMPD. Begin at Sun Apr 17 22:16:41 2022. Please wait... Now randomizing by parallel computing. Begin at Sun Apr 17 22:16:42 2022. Please wait... Now fixing special cases. Begin at Sun Apr 17 22:17:45 2022. Please wait... All match very well. Now calculating observed MPD. Begin at Sun Apr 17 22:17:46 2022. Please wait... Now randomizing by parallel computing. Begin at Sun Apr 17 22:17:47 2022. Please wait... Error in checkForRemoteErrors(val) : 2 nodes produced errors; first error: 'size'参数不对 Dear professor how we solve this problem?

[DaliangNing]

I need to test your dataset to figure out the reason. You may send me (ningdaliang@ou.edu) the input files and your R code : )

[DaliangNing]

Has your problem been solved?

[WeichuanLin6688]

Yeah！I have solved this problem！Thank your for that！

林维钏weichuanlin @.***

------------------ Original ------------------ From: Daliang Ning @.> Date: Fri,Jun 3,2022 11:08 PM To: DaliangNing/iCAMP1 @.> Cc: WeichuanLin6688 @.>, Author @.> Subject: Re: [DaliangNing/iCAMP1] unsolved problem (Issue #23)

Has your problem been solved?

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[WeichuanLin6688]

Dear Ning By the way，may I ask your a question about bacterial network construction？ which the methods could be used if a bacterial community is dominated by stochastic processes （my data nst >70%）.Please do not hesitate to give advise.

------------------ 原始邮件 ------------------ 发件人: "DaliangNing/iCAMP1" @.>; 发送时间: 2022年6月3日(星期五) 晚上11:11 @.>; @.**@.>; 主题: Re: [DaliangNing/iCAMP1] unsolved problem (Issue #23)

Closed #23 as completed.

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[DaliangNing]

How to integrate the stochasticity results into network analysis is still under development. Currently, you may still use any network methods to explore the associations among taxa, which generally does not conflict with the stochasticity results. Species controlled by stochastic processes (e.g., neutral dispersal) can show strong associations if they travel together due to a strong flood or thrive together due to general resources increase.