#' @title Download test microbiome data
#' @description Test microbiome data in phyloseq format.
#' @details You can download few example datasets in phyloseq format from Duvallet et al 2017 https://www.nature.com/articles/s41467-017-01973-8.pdf?origin=ppub. The source file for these data is the microbiomedatarepo https://github.com/microsud/microbiomedatarepo.
#' @param studynumber A numerical value corresponsing to the one given by list_microbiome_data()
#' @return \code{\link{phyloseq-class}} object.
#' @import microbiome
#' @import phyloseq
#' @export
#' @examples \dontrun{
#' # Example data
#' library(microbiome)
#' library(microbiomeUtilities)
#' list_microbiome_data()
#' ps1 <- get_microbiome_data(studynumber = 1)
#' # this will download the first study listed in list_microbiome_data() function
#' print(p)
#' }
#' @keywords utilities
get_microbiome_data <- function(studynumber = 1) {
if (studynumber == 1) {
ps1 <- readRDS(url("https://github.com/microsud/microbiomedatarepo/blob/master/datasets/microbiomeDB/cdi_schubert.rds?raw=true"))
} else if (studynumber == 2) {
ps1 <- readRDS(url("https://github.com/microsud/microbiomedatarepo/blob/master/datasets/microbiomeDB/cdi_youngster.rds?raw=true"))
} else if (studynumber == 3) {
ps1 <- readRDS(url("https://github.com/microsud/microbiomedatarepo/blob/master/datasets/microbiomeDB/ob_goodrich.rds?raw=true"))
} else if (studynumber == 4) {
ps1 <- readRDS(url("https://github.com/microsud/microbiomedatarepo/blob/master/datasets/microbiomeDB/hiv_dinh.rds?raw=true"))
} else if (studynumber == 5) {
ps1 <- readRDS(url("https://github.com/microsud/microbiomedatarepo/blob/master/datasets/microbiomeDB/crc_zeller.rds?raw=true"))
} else if (studynumber == 6) {
print("Use the following link and use the read_phyloseq function from microbiome package")
message("consensus taxonomy file link https://raw.githubusercontent.com/microsud/microbiomedatarepo/master/datasets/Baxter_FITs_Microbiome_2016/baxter_con.taxonomy")
message("shared otu file link https://raw.githubusercontent.com/microsud/microbiomedatarepo/master/datasets/Baxter_FITs_Microbiome_2016/baxter_shared.shared")
message("metadata file link https://raw.githubusercontent.com/microsud/microbiomedatarepo/master/datasets/Baxter_FITs_Microbiome_2016/baxter_metadat.csv")
}
}
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