Mercurial > repos > ecology > vigiechiro_idcorrect_2ndlayer

annotate Id_Tidy.R @ 1:89f091a0aa19 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
author ecology
date Fri, 26 Apr 2019 12:14:22 -0400
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89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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diff changeset
1 suppressMessages(library(data.table))
89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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3 args <- commandArgs(trailingOnly = TRUE)
89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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4 #print(args)
89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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5 filename=args[2]
89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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7 DataPar=fread(args[1]) #ids
89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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8 DataPar$participation=substr(filename,nchar(filename)-40,nchar(filename)-17)
89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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9 #DataPar$participation=substr(args[1],nchar(args[1])-40,nchar(args[1])-17)
89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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10 test1=duplicated(cbind(DataPar$'nom du fichier',DataPar$tadarida_taxon))
89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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11 test2=(DataPar$tadarida_taxon=="empty")
89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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12 DataPar=subset(DataPar,(!test1)|(test2))
89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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13 DataPar$tadarida_probabilite[DataPar$tadarida_probabilite==""]="0"
89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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14 DataPar$tadarida_probabilite=as.numeric(DataPar$tadarida_probabilite)
89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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16 #write.table(DataPar,paste0(substr(args[1],nchar(args[1])-40,nchar(args[1])-17),"-DataCorrC2.csv"),row.names=F,sep="\t")
89f091a0aa19 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tools/vigiechiro commit 7ef0e58cbcbf41088e359f00b6c86504c773c271
ecology
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17 write.table(DataPar,"Id_tidy.tabular",row.names=F,sep="\t")