comparison nb_clust_G.R @ 1:e94a25eed489 draft

planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 459ba1277acd7d8d4a02f90dbd7ff444bf8eac92

0:0f6542d0986e

    sample <- as.numeric(args[6])
}

#load data 

env.data <- read.table(enviro, header = TRUE, dec = ".", na.strings = "-9999.00") 

##List of modelled taxa used for clustering
tv <- read.table(taxa_list, dec=".", sep=" ", header=F, na.strings = "NA") 
names(tv) <- c("a")

data_split = str_split(preds,",")
data.bio = NULL

for (i in 1:length(data_split[[1]])) {
data.bio1 <- read.table(data_split[[1]][i], dec=".", sep=" ", header=T, na.strings = "NA")
data.bio <- rbind(data.bio,data.bio1)
remove(data.bio1)
}

names(data.bio) <- c("lat", "long", "pred", "taxon")

  sih_values[k] <- clara_res$silinfo$avg.width
}

# Plot SIH Index Chart by Number of Clusters
png("Indices_SIH.png")
plot(2:max_k, sih_values[2:max_k], type = "b", xlab = "Nombre de clusters", ylab = "Indice SIH")
dev.off()

1:e94a25eed489

    sample <- as.numeric(args[6])
}

#load data 

env.data <- read.table(enviro, sep="\t", header = TRUE, dec = ".", na.strings = "-9999") 

##List of modelled taxa used for clustering
tv <- read.table(taxa_list, dec=".", sep=" ", header=F, na.strings = "NA") 
names(tv) <- c("a")

data_split = str_split(preds,",")
data.bio = NULL

for (i in 1:length(data_split[[1]])) {
data.bio1 <- read.table(data_split[[1]][i], dec=".", sep="\t", header=T, na.strings = "NA")
data.bio <- rbind(data.bio,data.bio1)
remove(data.bio1)
}

names(data.bio) <- c("lat", "long", "pred", "taxon")

  sih_values[k] <- clara_res$silinfo$avg.width
}

# Plot SIH Index Chart by Number of Clusters
png("Indices_SIH.png")
plot(2:max_k, sih_values[2:max_k], type = "b", xlab = "Number of clusters", ylab = "SIH index")
dev.off()