Mercurial > repos > ecology > ecoregion_geonearestneighbor
annotate cluster_ceamarc.R @ 0:5cde56683579 draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
author | ecology |
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date | Thu, 21 Mar 2024 14:05:01 +0000 |
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5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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1 ##13/04/2023 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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2 ##Seguineau Pauline |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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3 ### Clustering with Clara algorithm |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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4 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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5 #load library |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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6 library(cluster) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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7 library(dplyr) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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8 library(tidyverse) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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9 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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10 #load arguments |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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11 args = commandArgs(trailingOnly=TRUE) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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12 if (length(args)==0) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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13 { |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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14 stop("This tool needs at least one argument") |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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15 }else{ |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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16 data <- args[1] |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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17 enviro <- args[2] |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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18 data.bio <- args[3] |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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19 k <- as.numeric(args[4]) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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20 metric <- args[5] |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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21 sample <- as.numeric(args[6]) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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22 } |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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23 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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24 #load data |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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25 env.data <- read.table(enviro, header=TRUE, sep="\t",dec = ".", na.strings = "-9999") |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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26 data.bio <- read.table(data.bio, header=TRUE, sep="\t") |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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27 test3 <- read.table(data, header = TRUE, sep="\t") |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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28 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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29 ###################################################################################################### |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
ecology
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30 #Make clustering |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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31 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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32 k <- k #number of clusters |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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33 test5 <- clara(test3, k, metric = metric, samples = sample, sampsize = min(nrow(test3), (nrow(data.bio)/nrow(test3))+2*k)) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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34 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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35 ####################################################################################################### |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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36 #save results |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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37 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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38 png("sih.png") |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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39 plot(silhouette(test5)) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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40 dev.off() |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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41 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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42 clus <- cbind(data.bio[1:nrow(test3), 1:2],test5$clustering) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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43 names(clus) <- c("lat", "long", "cluster") |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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44 clus <- cbind(clus,test3,env.data[,3:19]) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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45 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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46 write.table(clus[1:3], file = "points_clus.tsv", quote = FALSE, sep="\t", row.names = FALSE) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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47 write.table(clus, file = "clus.tsv", quote = FALSE, sep="\t", row.names = FALSE) |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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48 |
5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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5cde56683579
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/Ecoregionalization_workflow commit 5d48df67919fbc9d77b98a8243d438c397f61a0e
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