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nhanhocu / metamicrobiomeR

An R package for analysis of microbiome relative abundance data using zero inflated beta GAMLSS and meta-analysis across microbiome studies using random effects models
https://github.com/nhanhocu/metamicrobiomeR
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format of input data for taxa.compare #5

Open xix017 opened 4 years ago

xix017 commented 4 years ago

Hi, Could you please tell me the format of the input data for taxa.compare ? I formatted my input according to taxtab6.rm[[5]] showed in the example. It is a dataframe with 250 columns: ID(personid), Gender(comvar), Age(adjustvar),and 247 species(relative abundance).

Here is my command: taxa.compare(taxtab=full_data, propmed.rel="lm",personid = "ID",comvar="Gender",adjustvar="Age", longitudinal="yes",p.adjust.method="fdr")

Below is the error: Error in checkFormulaData(formula, data, checkLHS = control$check.formula.LHS == : !checkLHS || length(as.formula(formula, env = denv)) == 3 is not TRUE In addition: Warning message: In lme4::glmer(as.formula(paste(taxname[i], paste(c(comvar, adjustvar, : calling glmer() with family=gaussian (identity link) as a shortcut to lmer() is deprecated; please call lmer() directly Error in model fit, NA introduced.

Could you please tell me what's going on here and how to organize the input format to run this function? Thanks a lot for your time and help, really appreciate it. Best, Min

nhanhocu commented 4 years ago

Hi, Can you try our new version in R cran? If the issue still remains, please let me know. Thanks, Nhan