Mercurial > repos > ecology > ecology_homogeneity_normality

annotate funct_anomy.r @ 1:3df8937fd6fd draft default tip

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"planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
author ecology
date Fri, 13 Aug 2021 18:16:46 +0000
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3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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1 #Rscript
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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3 ###########################
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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4 ## Anonymization ##
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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5 ###########################
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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7 #####Packages : tangles
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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9 #Load arguments
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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11 args <- commandArgs(trailingOnly = TRUE)
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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13 if (length(args) == 0) {
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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14 stop("This tool needs at least one argument")
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
ecology
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15 }else{
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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16 table <- args[1]
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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17 hr <- args[2]
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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18 latitude <- as.numeric(args[3])
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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19 longitude <- as.numeric(args[4])
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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20 }
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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22 if (hr == "false") {
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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23 hr <- FALSE
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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24 }else{
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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25 hr <- TRUE
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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26 }
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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28 #####Import data
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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29 data <- read.table(table, sep = "\t", dec = ".", header = hr, fill = TRUE, encoding = "UTF-8")
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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31 randomized_data <- tangles::tangles(data = as.matrix(data[, c(latitude, longitude)]), depth = 3, rasterdata = FALSE, raster_object = FALSE, saveTangles = FALSE, path = NULL)
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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33 data[, c(latitude, longitude)] <- NULL
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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35 tab_anon <- data.frame(longitude = randomized_data[[1]]$X, latitude = randomized_data[[1]]$Y)
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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37 tab_anon <- cbind(data, tab_anon)
3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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3df8937fd6fd "planemo upload for repository https://github.com/Marie59/Data_explo_tools commit 60627aba07951226c8fd6bb3115be4bd118edd4e"
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39 write.table(tab_anon, "anonym_data.tabular", row.names = FALSE, quote = FALSE, sep = "\t", dec = ".", fileEncoding = "UTF-8")