Latest version of the manuscript

data-raw/Soil_litter/prepare_data.R

 library(vegan)
 library(ROBITools)
+library(ProcMod)
 
 litere_col_clean <- readRDS("litere_col_clean.rds")
 litere_col_clean <- metabarcoding.data(reads = litere_col_clean$reads,
@@ -27,7 +28,27 @@ litere_euk_clean <- metabarcoding.data(reads = litere_euk_clean$reads,
 
 # Remove rare motus
 
-litere_col_norare <- litere_col_clean[,apply(decostand(litere_col_clean$reads,method = "total"),MARGIN = 2,max) >= 0.01]
-litere_euk_norare <- litere_euk_clean[,apply(decostand(litere_euk_clean$reads,method = "total"),MARGIN = 2,max) >= 0.01]
-litere_ins_norare <- litere_ins_clean[,apply(decostand(litere_ins_clean$reads,method = "total"),MARGIN = 2,max) >= 0.01]
-litere_bac_norare <- litere_bac_clean[,apply(decostand(litere_bac_clean$reads,method = "total"),MARGIN = 2,max) >= 0.01]
+litere_col_norare <- litere_col_clean[,apply(decostand(litere_col_clean$reads,method = "total"),MARGIN = 2,max) >= 0.001]
+litere_euk_norare <- litere_euk_clean[,apply(decostand(litere_euk_clean$reads,method = "total"),MARGIN = 2,max) >= 0.001]
+litere_ins_norare <- litere_ins_clean[,apply(decostand(litere_ins_clean$reads,method = "total"),MARGIN = 2,max) >= 0.001]
+litere_bac_norare <- litere_bac_clean[,apply(decostand(litere_bac_clean$reads,method = "total"),MARGIN = 2,max) >= 0.001]
+
+
+litere_euk_classes <- lapply(levels(litere_euk_norare$motus$class_name),
+                             function(x) litere_euk_norare[,which(litere_euk_norare$motus$class_name == x)])
+names(litere_euk_classes)=levels(litere_euk_norare$motus$class_name)
+
+litere_euk_classes <- litere_euk_classes[! sapply(litere_euk_classes, is.numeric)]
+litere_euk_classes.diverse = litere_euk_classes[sapply(litere_euk_classes,ncol) >=30]
+
+litere_euk_dist <- lapply(litere_euk_classes.diverse,
+                          function(metabar)
+                            vegdist(decostand(metabar@reads,"hellinger"),"euclidean"))
+
+litere_euk_dist <- as.procmod.frame(litere_euk_dist)
+
+litere_euk_cor <- corls(litere_euk_dist)
+ilitere_euk_cor <- solve(litere_euk_cor)
+litere_euk_cor.partial = ilitere_euk_cor/sqrt(diag(ilitere_euk_cor) %*% t(diag(ilitere_euk_cor)))
+
+plot(hclust(as.dist(1- ilitere_euk_cor.partial^2)))

manuscript/main.bbl

@@ -96,4 +96,10 @@ Sz{\'e}kely, G.~J., Rizzo, M.~L., and Bakirov, N.~K. (2007).
 \newblock Measuring and testing dependence by correlation of distances.
 \newblock {\em Ann. Stat.}, {\bf 35}(6), 2769--2794.
 
+\bibitem[Theil {\em et~al.}(1958)Theil, Cramer, Moerman, and
+  Russchen]{Theil:58:00}
+Theil, H., Cramer, J.~S., Moerman, H., and Russchen, A. (1958).
+\newblock {\em Economic forecasts and policy\/}, page 213.
+\newblock North-Holland Publishing Company, Amsterdam.
+
 \end{thebibliography}