this one is the Yang and Chen SimMSeq simulation method.

R/helper_yang_chen.R

@@ -0,0 +1,62 @@
+#!/usr/bin/Rscript
+### SIMBA
+### Simulation of Microbiome data with Biological Accuracy
+### Morgan Essex - MDC Berlin
+### Jakob Wirbel - EMBL Heidelberg
+### 2020 GNU GPL 3.0
+
+# Helper functions to simulate data according to Yang and Chen
+# Based on the SimulateMSeq function in the GUniFrac package
+
+#' # wrapper for the Yang and Chen 
+#' @keywords internal
+simulate.SimMSeq <- function(feat, meta, sim.out, sim.params){
+
+  test.package("GUniFrac")
+
+  ab.scale <- sim.params$ab.scale
+  prop.markers <- sim.params$prop.markers
+  class.balance <- sim.params$class.balance
+  repeats <- sim.params$repeats
+
+  no.marker.feat <- round(prop.markers * nrow(feat))
+  el.feat.names <- rownames(feat)
+  num.sample <- ncol(feat)
+
+  libSizesOrig <- colSums(feat)
+
+  pb <- progress_bar$new(total = length(ab.scale)*repeats)
+  for (a in seq_along(ab.scale)){
+    for (r in seq_len(repeats)){
+
+      # create new dataset with their function
+      sim.chen <- SimulateMSeq(feat,
+                               nSam=ncol(feat), nOTU=nrow(feat),
+                               diff.otu.pct = prop.markers, 
+                               diff.otu.mode = 'mix', 
+                               diff.otu.direct = 'balanced',
+                               covariate.type = 'binary', 
+                               grp.ratio = 0.5/class.balance,
+                               covariate.eff.mean = a,
+                               depth.mu = mean(libSizesOrig))
+      # get the info out of sim.chen
+      sim.feat <- sim.chen$otu.tab.sim[rownames(feat),]
+      marker.idx <- sim.chen$otu.names[which(sim.chen$diff.otu.ind)]
+      label <- sim.chen$covariate[,1]
+      label <- label[colnames(sim.feat)]
+      label[label==0] <- -1
+
+      # save data in H5-file
+      h5.subdir <- paste0('ab', a, '_rep', r)
+      stopifnot(h5createGroup(sim.out, h5.subdir))
+      h5write(label, sim.out, paste0(h5.subdir, '/labels'))
+      h5write(sim.feat, sim.out, paste0(h5.subdir, '/features'))
+      h5write(marker.idx, sim.out, paste0(h5.subdir, '/marker_idx'))
+      h5write(colnames(sim.feat), sim.out,
+              paste(h5.subdir, '/sample_names', sep=''))
+      h5write(rownames(sim.feat), sim.out,
+              paste(h5.subdir, '/feature_names', sep=''))
+      pb$tick()
+    }
+  }
+}