Commit 85d25ea3 by Eric Coissac

Delete manuscript and extra data from master branch

parent c560f73f

Too many changes to show.

To preserve performance only 1000 of 1000+ files are displayed.

library(vegan)
library(ROBITools)
library(ProcMod)
litere_col_clean <- readRDS("litere_col_clean.rds")
litere_col_clean <- metabarcoding.data(reads = litere_col_clean$reads,
motus = litere_col_clean$motus,
samples = litere_col_clean$samp)
litere_bac_clean <- readRDS("litere_bac_clean.rds")
litere_bac_clean <- metabarcoding.data(reads = litere_bac_clean$reads,
motus = litere_bac_clean$motus,
samples = litere_bac_clean$samp)
litere_ins_clean <- readRDS("litere_ins_clean.rds")
litere_ins_clean <- metabarcoding.data(reads = litere_ins_clean$reads,
motus = litere_ins_clean$motus,
samples = litere_ins_clean$samp)
litere_euk_clean <- readRDS("litere_euk_clean.rds")
litere_euk_clean <- metabarcoding.data(reads = litere_euk_clean$reads,
motus = litere_euk_clean$motus,
samples = litere_euk_clean$samp)
# Remove rare motus
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)))
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main-concordance.tex
main.blg
main.log
oldsty
SimulationRls.R
main_manuscrit.pdf
bioinfo.log
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