R/covar.rm.R

In metamicrobiomeR: Microbiome Data Analysis & Meta-Analysis with GAMLSS-BEZI & Random Effects

#' Covariate data.
#'
#' Monthly longitudinal clinical data of 50 infants from
#' birth to 2 years of life.
#'
#' @docType data
#'
#' @usage data(covar.rm)
#'
#' @format A dataframe with 996 rows and 32 variables.
#'
#' @keywords datasets
#'
#' @references Subramanian et al. Nature. 2014 Jun 19; 510(7505): 417–421.
#' (\href{https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189846/}{PubMed})
#'
#' @source \href{https://gordonlab.wustl.edu/supplemental-data/supplemental-data-portal/subramanian-et-al-2014/}{Gordon Lab}
#'
#' @examples
#' data(covar.rm)
#' # Load KEGG pathway data
#' data(kegg.12)
#' # Comparison of pathway relative abundances for some first pathways of level 1 only
#' # and assuming crosssectional data (to save running time)
#' path1<-pathway.compare(pathtab=list(kegg.12[[1]][, 1:2]),
#' mapfile=covar.rm,sampleid="sampleid",pathsum="rel", stat.med="gamlss",
#' comvar="gender",adjustvar=c("age.sample","bf"), longitudinal="no",
#' p.adjust.method="fdr", percent.filter=0.05,relabund.filter=0.00005)
#' taxcomtab.show(taxcomtab=path1$l1, sumvar="path",tax.lev="l2",
#' tax.select="none", showvar="genderMale", p.adjust.method="fdr",p.cutoff=1)
"covar.rm"