MicrobiomeStat

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Wiki Example Code Seems Outdated

4

In [Feature-level Analysis](https://www.microbiomestat.wiki/single-point-analysis/cross-sectional-investigation-taxa-analysis-with-microbiomestat), I see `generate_taxa_volcano_single` example but function is not present in version 1.2 on CRAN. ```r > library(MicrobiomeStat) > generate_taxa_volcano_single Error: object 'generate_taxa_volcano_single' not found ``` Also, is...

DarioS

LinDA Unusual p-value Distribution

2

Using the data set shared previously via e-mail and fitting ```r adjNormalCancerFit

DarioS

Linear model strategy, post hoc tests, and modeling specific taxa in MicrobiomeStat

3

Hello, Thank you for developing MicrobiomeStat — it's a very helpful and well-designed tool! I'm new to applying linear models to microbiome data and would appreciate your advice on a...

lauraflows

! task 1 failed - "number of levels of each grouping factor must be < number of observations (problems: ID)"

1

When I try to use the mStat_generate_report_long() or generate_taxa_per_time_test_long() I get the error, "! task 1 failed - "number of levels of each grouping factor must be < number of...

carolyndoty

Missing Adj Variable Term in Coefficient Table from "generate_beta_change_test_pair" function

1

Hello, Thank you for the development of such a great package. I have been testing your package functions for beta diversity analysis of paired samples. When I used "generate_beta_change_test_pair" function...

eray-sahin

Too big figures in the report

3

Hi, I’ve been using your very helpful MicrobiomeStat package and wanted to generate a report. However, in the PDF version, the figures appear too large and don’t fit on the...

scilexenko

Count normalization for generate_taxa_trend_test_long()

1

I was wondering why options for original LinDa count normalization ("count") as well as possibility to use data as it is ("other") are not options anymore in generate_taxa_trend_test_long()? Are there...

AlexanderUm

Different beta diversity calculation results between microViz and microbiomeStat

1

Dear Chen, Thank you for developing such a useful package. I am working with temporal series data and have been using your package for beta diversity analysis. To better understand...

scilexenko

Could LinDA have a survival time analysis (event indicator, follow-up days) mode?

DarioS

!System command 'Rcmd.exe' failed

6

**Describe the Installation Issue** I am facing the following installation issue **Error Messages** ── R CMD build ───────────────────────────────────────────────────────────────────────────────────────────────────────── ✔ checking for file 'C:\Users\LENOVO\AppData\Local\Temp\RtmpOOzPsy\remotes94546abe4490\cafferychen777-MicrobiomeStat-0ccb605/DESCRIPTION' Warning in file.copy(pkgname, Tdir, recursive = TRUE,...

chongchunwie