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Commit 1b6761f1 authored by Amine GHOZLANE's avatar Amine GHOZLANE
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Solved issue with missing data in diversities

parent d82b7044
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Rfunctions/VisuPlot.R
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......@@ -446,32 +446,36 @@ Plot_Visu_Diversity <- function(input,resDiff,ForScatter=FALSE, alpha_transparen
#save(counts_tmp_combined,targetInt,file = "testDiv.RData")
alpha <- tapply(TaxoNumber(counts_tmp_combined), targetInt$AllVar, mean)
alpha=alpha[!is.na(alpha)]
alpha_selected = !is.na(alpha)
alpha=alpha[alpha_selected]
alpha_sd = tapply(TaxoNumber(counts_tmp_combined), targetInt$AllVar, sd)
alpha_sd=alpha_sd[!is.na(alpha_sd)]
ci.alpha.down = pmax(alpha - 1.96*alpha_sd/sqrt.nb,0)
ci.alpha.up = alpha + 1.96*alpha_sd/sqrt.nb
alpha_sd=alpha_sd[alpha_selected]
ci.alpha.down = pmax(alpha - 1.96*alpha_sd/sqrt.nb[alpha_selected],0)
ci.alpha.up = alpha + 1.96*alpha_sd/sqrt.nb[alpha_selected]
shan <- tapply(vegan::diversity(counts_tmp_combined, index = "shannon"), targetInt$AllVar, mean)
shan = shan[!is.na(shan)]
shan_selected = !is.na(shan)
shan = shan[shan_selected]
shan_sd = tapply(vegan::diversity(counts_tmp_combined, index = "shannon"), targetInt$AllVar, sd)
shan_sd = shan_sd[!is.na(shan_sd)]
ci.shan.down = pmax(shan - 1.96*shan_sd/sqrt.nb,0)
ci.shan.up = shan + 1.96*shan_sd/sqrt.nb
shan_sd = shan_sd[shan_selected]
ci.shan.down = pmax(shan - 1.96*shan_sd/sqrt.nb[shan_selected],0)
ci.shan.up = shan + 1.96*shan_sd/sqrt.nb[shan_selected]
simpson <- tapply(vegan::diversity(counts_tmp_combined, index = "simpson"), targetInt$AllVar, mean)
simpson = simpson[!is.na(simpson)]
simpson_selected = !is.na(simpson)
simpson = simpson[simpson_selected]
simpson_sd = tapply(vegan::diversity(counts_tmp_combined, index = "simpson"), targetInt$AllVar, sd)
simpson_sd = simpson_sd[!is.na(simpson_sd)]
ci.simpson.down = pmax(simpson - 1.96*simpson_sd/sqrt.nb,0)
ci.simpson.up = simpson + 1.96*simpson_sd/sqrt.nb
simpson_sd = simpson_sd[simpson_selected]
ci.simpson.down = pmax(simpson - 1.96*simpson_sd/sqrt.nb[simpson_selected],0)
ci.simpson.up = simpson + 1.96*simpson_sd/sqrt.nb[simpson_selected]
invsimpson <- tapply(vegan::diversity(counts_tmp_combined, index = "invsimpson"), targetInt$AllVar, mean)
invsimpson = invsimpson[!is.na(invsimpson)]
invsimpson_selected = !is.na(invsimpson)
invsimpson = invsimpson[invsimpson_selected]
invsimpson_sd = tapply(vegan::diversity(counts_tmp_combined, index = "invsimpson"), targetInt$AllVar, sd)
invsimpson_sd = invsimpson_sd[!is.na(invsimpson_sd)]
ci.invsimpson.down = pmax(invsimpson - 1.96*invsimpson_sd/sqrt.nb,0)
ci.invsimpson.up = invsimpson + 1.96*invsimpson_sd/sqrt.nb
invsimpson_sd = invsimpson_sd[invsimpson_selected]
ci.invsimpson.down = pmax(invsimpson - 1.96*invsimpson_sd/sqrt.nb[invsimpson_selected],0)
ci.invsimpson.up = invsimpson + 1.96*invsimpson_sd/sqrt.nb[invsimpson_selected]
gamma <- TaxoNumber(counts_tmp_combined, targetInt$AllVar)
gamma = gamma[!is.na(gamma)]
......
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