Initial commit of the project
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385
RawData/Litiere_sample_list.txt
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RawData/Litiere_sample_list.txt
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site_id point_id Latitude Longitude Code.Petit.Plateau Site Habitat Material Replicate Control Control_type
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H20_Al_r1 H20 H20-A 4.083099 -52.682203 70-310 Petit Plateau Terra firme litter r1 sample NA
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H20_Al_r2 H20 H20-A 4.083099 -52.682203 70-310 Petit Plateau Terra firme litter r2 sample NA
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H20_Al_r3 H20 H20-A 4.083099 -52.682203 70-310 Petit Plateau Terra firme litter r3 sample NA
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H20_Al_r4 H20 H20-A 4.083099 -52.682203 70-310 Petit Plateau Terra firme litter r4 sample NA
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H20_As_r1 H20 H20-A 4.083099 -52.682203 70-310 Petit Plateau Terra firme soil r1 sample NA
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H20_As_r2 H20 H20-A 4.083099 -52.682203 70-310 Petit Plateau Terra firme soil r2 sample NA
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H20_As_r3 H20 H20-A 4.083099 -52.682203 70-310 Petit Plateau Terra firme soil r3 sample NA
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H20_As_r4 H20 H20-A 4.083099 -52.682203 70-310 Petit Plateau Terra firme soil r4 sample NA
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H20_Bl_r1 H20 H20-B 4.083029 -52.682266 70-330 Petit Plateau Terra firme litter r1 sample NA
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H20_Bl_r2 H20 H20-B 4.083029 -52.682266 70-330 Petit Plateau Terra firme litter r2 sample NA
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H20_Bl_r3 H20 H20-B 4.083029 -52.682266 70-330 Petit Plateau Terra firme litter r3 sample NA
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H20_Bl_r4 H20 H20-B 4.083029 -52.682266 70-330 Petit Plateau Terra firme litter r4 sample NA
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H20_Bs_r1 H20 H20-B 4.083029 -52.682266 70-330 Petit Plateau Terra firme soil r1 sample NA
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H20_Bs_r2 H20 H20-B 4.083029 -52.682266 70-330 Petit Plateau Terra firme soil r2 sample NA
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H20_Bs_r3 H20 H20-B 4.083029 -52.682266 70-330 Petit Plateau Terra firme soil r3 sample NA
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H20_Bs_r4 H20 H20-B 4.083029 -52.682266 70-330 Petit Plateau Terra firme soil r4 sample NA
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H20_Cl_r1 H20 H20-C 4.082965 -52.620778 70-350 Petit Plateau Terra firme litter r1 sample NA
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H20_Cl_r2 H20 H20-C 4.082965 -52.620778 70-350 Petit Plateau Terra firme litter r2 sample NA
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H20_Cl_r3 H20 H20-C 4.082965 -52.620778 70-350 Petit Plateau Terra firme litter r3 sample NA
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H20_Cl_r4 H20 H20-C 4.082965 -52.620778 70-350 Petit Plateau Terra firme litter r4 sample NA
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H20_Cs_r1 H20 H20-C 4.082965 -52.620778 70-350 Petit Plateau Terra firme soil r1 sample NA
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H20_Cs_r2 H20 H20-C 4.082965 -52.620778 70-350 Petit Plateau Terra firme soil r2 sample NA
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H20_Cs_r3 H20 H20-C 4.082965 -52.620778 70-350 Petit Plateau Terra firme soil r3 sample NA
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H20_Cs_r4 H20 H20-C 4.082965 -52.620778 70-350 Petit Plateau Terra firme soil r4 sample NA
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H20_Dl_r1 H20 H20-D 4.082857 -52.681856 70-370 Petit Plateau Terra firme litter r1 sample NA
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H20_Dl_r2 H20 H20-D 4.082857 -52.681856 70-370 Petit Plateau Terra firme litter r2 sample NA
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H20_Dl_r3 H20 H20-D 4.082857 -52.681856 70-370 Petit Plateau Terra firme litter r3 sample NA
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H20_Dl_r4 H20 H20-D 4.082857 -52.681856 70-370 Petit Plateau Terra firme litter r4 sample NA
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H20_Ds_r1 H20 H20-D 4.082857 -52.681856 70-370 Petit Plateau Terra firme soil r1 sample NA
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H20_Ds_r2 H20 H20-D 4.082857 -52.681856 70-370 Petit Plateau Terra firme soil r2 sample NA
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H20_Ds_r3 H20 H20-D 4.082857 -52.681856 70-370 Petit Plateau Terra firme soil r3 sample NA
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H20_Ds_r4 H20 H20-D 4.082857 -52.681856 70-370 Petit Plateau Terra firme soil r4 sample NA
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H20_El_r1 H20 H20-E 4.082839 -52.681775 50-370 Petit Plateau Terra firme litter r1 sample NA
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H20_El_r2 H20 H20-E 4.082839 -52.681775 50-370 Petit Plateau Terra firme litter r2 sample NA
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H20_El_r3 H20 H20-E 4.082839 -52.681775 50-370 Petit Plateau Terra firme litter r3 sample NA
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H20_El_r4 H20 H20-E 4.082839 -52.681775 50-370 Petit Plateau Terra firme litter r4 sample NA
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H20_Es_r1 H20 H20-E 4.082839 -52.681775 50-370 Petit Plateau Terra firme soil r1 sample NA
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H20_Es_r2 H20 H20-E 4.082839 -52.681775 50-370 Petit Plateau Terra firme soil r2 sample NA
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H20_Es_r3 H20 H20-E 4.082839 -52.681775 50-370 Petit Plateau Terra firme soil r3 sample NA
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H20_Es_r4 H20 H20-E 4.082839 -52.681775 50-370 Petit Plateau Terra firme soil r4 sample NA
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H20_Fl_r1 H20 H20-F 4.08304 -52.618758 50-350 Petit Plateau Terra firme litter r1 sample NA
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H20_Fl_r2 H20 H20-F 4.08304 -52.618758 50-350 Petit Plateau Terra firme litter r2 sample NA
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H20_Fl_r3 H20 H20-F 4.08304 -52.618758 50-350 Petit Plateau Terra firme litter r3 sample NA
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H20_Fl_r4 H20 H20-F 4.08304 -52.618758 50-350 Petit Plateau Terra firme litter r4 sample NA
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H20_Fs_r1 H20 H20-F 4.08304 -52.618758 50-350 Petit Plateau Terra firme soil r1 sample NA
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H20_Fs_r2 H20 H20-F 4.08304 -52.618758 50-350 Petit Plateau Terra firme soil r2 sample NA
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H20_Fs_r3 H20 H20-F 4.08304 -52.618758 50-350 Petit Plateau Terra firme soil r3 sample NA
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H20_Fs_r4 H20 H20-F 4.08304 -52.618758 50-350 Petit Plateau Terra firme soil r4 sample NA
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H20_Gl_r1 H20 H20-G 4.083078 -52.681965 50-330 Petit Plateau Terra firme litter r1 sample NA
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H20_Gl_r2 H20 H20-G 4.083078 -52.681965 50-330 Petit Plateau Terra firme litter r2 sample NA
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H20_Gl_r3 H20 H20-G 4.083078 -52.681965 50-330 Petit Plateau Terra firme litter r3 sample NA
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H20_Gl_r4 H20 H20-G 4.083078 -52.681965 50-330 Petit Plateau Terra firme litter r4 sample NA
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H20_Gs_r1 H20 H20-G 4.083078 -52.681965 50-330 Petit Plateau Terra firme soil r1 sample NA
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H20_Gs_r2 H20 H20-G 4.083078 -52.681965 50-330 Petit Plateau Terra firme soil r2 sample NA
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H20_Gs_r3 H20 H20-G 4.083078 -52.681965 50-330 Petit Plateau Terra firme soil r3 sample NA
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H20_Gs_r4 H20 H20-G 4.083078 -52.681965 50-330 Petit Plateau Terra firme soil r4 sample NA
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H20_Hl_r1 H20 H20-H 4.031718 -52.682164 50-310 Petit Plateau Terra firme litter r1 sample NA
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H20_Hl_r2 H20 H20-H 4.031718 -52.682164 50-310 Petit Plateau Terra firme litter r2 sample NA
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||||
H20_Hl_r3 H20 H20-H 4.031718 -52.682164 50-310 Petit Plateau Terra firme litter r3 sample NA
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H20_Hl_r4 H20 H20-H 4.031718 -52.682164 50-310 Petit Plateau Terra firme litter r4 sample NA
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H20_Hs_r1 H20 H20-H 4.031718 -52.682164 50-310 Petit Plateau Terra firme soil r1 sample NA
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H20_Hs_r2 H20 H20-H 4.031718 -52.682164 50-310 Petit Plateau Terra firme soil r2 sample NA
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||||
H20_Hs_r3 H20 H20-H 4.031718 -52.682164 50-310 Petit Plateau Terra firme soil r3 sample NA
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H20_Hs_r4 H20 H20-H 4.031718 -52.682164 50-310 Petit Plateau Terra firme soil r4 sample NA
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H20_Il_r1 H20 H20-I 4.083272 -52.682151 30-310 Petit Plateau Terra firme litter r1 sample NA
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||||
H20_Il_r2 H20 H20-I 4.083272 -52.682151 30-310 Petit Plateau Terra firme litter r2 sample NA
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H20_Il_r3 H20 H20-I 4.083272 -52.682151 30-310 Petit Plateau Terra firme litter r3 sample NA
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H20_Il_r4 H20 H20-I 4.083272 -52.682151 30-310 Petit Plateau Terra firme litter r4 sample NA
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H20_Is_r1 H20 H20-I 4.083272 -52.682151 30-310 Petit Plateau Terra firme soil r1 sample NA
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H20_Is_r2 H20 H20-I 4.083272 -52.682151 30-310 Petit Plateau Terra firme soil r2 sample NA
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H20_Is_r3 H20 H20-I 4.083272 -52.682151 30-310 Petit Plateau Terra firme soil r3 sample NA
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H20_Is_r4 H20 H20-I 4.083272 -52.682151 30-310 Petit Plateau Terra firme soil r4 sample NA
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H20_Jl_r1 H20 H20-J 4.083411 -52.682034 30-330 Petit Plateau Terra firme litter r1 sample NA
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H20_Jl_r2 H20 H20-J 4.083411 -52.682034 30-330 Petit Plateau Terra firme litter r2 sample NA
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H20_Jl_r3 H20 H20-J 4.083411 -52.682034 30-330 Petit Plateau Terra firme litter r3 sample NA
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H20_Jl_r4 H20 H20-J 4.083411 -52.682034 30-330 Petit Plateau Terra firme litter r4 sample NA
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H20_Js_r1 H20 H20-J 4.083411 -52.682034 30-330 Petit Plateau Terra firme soil r1 sample NA
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H20_Js_r2 H20 H20-J 4.083411 -52.682034 30-330 Petit Plateau Terra firme soil r2 sample NA
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H20_Js_r3 H20 H20-J 4.083411 -52.682034 30-330 Petit Plateau Terra firme soil r3 sample NA
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H20_Js_r4 H20 H20-J 4.083411 -52.682034 30-330 Petit Plateau Terra firme soil r4 sample NA
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H20_Kl_r1 H20 H20-K 4.08325 -52.681894 30-350 Petit Plateau Terra firme litter r1 sample NA
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H20_Kl_r2 H20 H20-K 4.08325 -52.681894 30-350 Petit Plateau Terra firme litter r2 sample NA
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H20_Kl_r3 H20 H20-K 4.08325 -52.681894 30-350 Petit Plateau Terra firme litter r3 sample NA
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H20_Kl_r4 H20 H20-K 4.08325 -52.681894 30-350 Petit Plateau Terra firme litter r4 sample NA
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H20_Ks_r1 H20 H20-K 4.08325 -52.681894 30-350 Petit Plateau Terra firme soil r1 sample NA
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||||
H20_Ks_r2 H20 H20-K 4.08325 -52.681894 30-350 Petit Plateau Terra firme soil r2 sample NA
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H20_Ks_r3 H20 H20-K 4.08325 -52.681894 30-350 Petit Plateau Terra firme soil r3 sample NA
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||||
H20_Ks_r4 H20 H20-K 4.08325 -52.681894 30-350 Petit Plateau Terra firme soil r4 sample NA
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||||
H20_Ll_r1 H20 H20-L 4.083155 -52.681725 30-370 Petit Plateau Terra firme litter r1 sample NA
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||||
H20_Ll_r2 H20 H20-L 4.083155 -52.681725 30-370 Petit Plateau Terra firme litter r2 sample NA
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||||
H20_Ll_r3 H20 H20-L 4.083155 -52.681725 30-370 Petit Plateau Terra firme litter r3 sample NA
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||||
H20_Ll_r4 H20 H20-L 4.083155 -52.681725 30-370 Petit Plateau Terra firme litter r4 sample NA
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H20_Ls_r1 H20 H20-L 4.083155 -52.681725 30-370 Petit Plateau Terra firme soil r1 sample NA
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H20_Ls_r2 H20 H20-L 4.083155 -52.681725 30-370 Petit Plateau Terra firme soil r2 sample NA
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H20_Ls_r3 H20 H20-L 4.083155 -52.681725 30-370 Petit Plateau Terra firme soil r3 sample NA
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||||
H20_Ls_r4 H20 H20-L 4.083155 -52.681725 30-370 Petit Plateau Terra firme soil r4 sample NA
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||||
H20_Ml_r1 H20 H20-M 4.083161 -52.681634 10-370 Petit Plateau Terra firme litter r1 sample NA
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H20_Ml_r2 H20 H20-M 4.083161 -52.681634 10-370 Petit Plateau Terra firme litter r2 sample NA
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||||
H20_Ml_r3 H20 H20-M 4.083161 -52.681634 10-370 Petit Plateau Terra firme litter r3 sample NA
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||||
H20_Ml_r4 H20 H20-M 4.083161 -52.681634 10-370 Petit Plateau Terra firme litter r4 sample NA
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||||
H20_Ms_r1 H20 H20-M 4.083161 -52.681634 10-370 Petit Plateau Terra firme soil r1 sample NA
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H20_Ms_r2 H20 H20-M 4.083161 -52.681634 10-370 Petit Plateau Terra firme soil r2 sample NA
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H20_Ms_r3 H20 H20-M 4.083161 -52.681634 10-370 Petit Plateau Terra firme soil r3 sample NA
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||||
H20_Ms_r4 H20 H20-M 4.083161 -52.681634 10-370 Petit Plateau Terra firme soil r4 sample NA
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H20_Nl_r1 H20 H20-N 4.083266 -52.681616 10-350 Petit Plateau Terra firme litter r1 sample NA
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H20_Nl_r2 H20 H20-N 4.083266 -52.681616 10-350 Petit Plateau Terra firme litter r2 sample NA
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||||
H20_Nl_r3 H20 H20-N 4.083266 -52.681616 10-350 Petit Plateau Terra firme litter r3 sample NA
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||||
H20_Nl_r4 H20 H20-N 4.083266 -52.681616 10-350 Petit Plateau Terra firme litter r4 sample NA
|
||||
H20_Ns_r1 H20 H20-N 4.083266 -52.681616 10-350 Petit Plateau Terra firme soil r1 sample NA
|
||||
H20_Ns_r2 H20 H20-N 4.083266 -52.681616 10-350 Petit Plateau Terra firme soil r2 sample NA
|
||||
H20_Ns_r3 H20 H20-N 4.083266 -52.681616 10-350 Petit Plateau Terra firme soil r3 sample NA
|
||||
H20_Ns_r4 H20 H20-N 4.083266 -52.681616 10-350 Petit Plateau Terra firme soil r4 sample NA
|
||||
H20_Ol_r1 H20 H20-O 4.083373 -52.681861 10-330 Petit Plateau Terra firme litter r1 sample NA
|
||||
H20_Ol_r2 H20 H20-O 4.083373 -52.681861 10-330 Petit Plateau Terra firme litter r2 sample NA
|
||||
H20_Ol_r3 H20 H20-O 4.083373 -52.681861 10-330 Petit Plateau Terra firme litter r3 sample NA
|
||||
H20_Ol_r4 H20 H20-O 4.083373 -52.681861 10-330 Petit Plateau Terra firme litter r4 sample NA
|
||||
H20_Os_r1 H20 H20-O 4.083373 -52.681861 10-330 Petit Plateau Terra firme soil r1 sample NA
|
||||
H20_Os_r2 H20 H20-O 4.083373 -52.681861 10-330 Petit Plateau Terra firme soil r2 sample NA
|
||||
H20_Os_r3 H20 H20-O 4.083373 -52.681861 10-330 Petit Plateau Terra firme soil r3 sample NA
|
||||
H20_Os_r4 H20 H20-O 4.083373 -52.681861 10-330 Petit Plateau Terra firme soil r4 sample NA
|
||||
H20_Pl_r1 H20 H20-P 4.083477 -52.682032 10-310 Petit Plateau Terra firme litter r1 sample NA
|
||||
H20_Pl_r2 H20 H20-P 4.083477 -52.682032 10-310 Petit Plateau Terra firme litter r2 sample NA
|
||||
H20_Pl_r3 H20 H20-P 4.083477 -52.682032 10-310 Petit Plateau Terra firme litter r3 sample NA
|
||||
H20_Pl_r4 H20 H20-P 4.083477 -52.682032 10-310 Petit Plateau Terra firme litter r4 sample NA
|
||||
H20_Ps_r1 H20 H20-P 4.083477 -52.682032 10-310 Petit Plateau Terra firme soil r1 sample NA
|
||||
H20_Ps_r2 H20 H20-P 4.083477 -52.682032 10-310 Petit Plateau Terra firme soil r2 sample NA
|
||||
H20_Ps_r3 H20 H20-P 4.083477 -52.682032 10-310 Petit Plateau Terra firme soil r3 sample NA
|
||||
H20_Ps_r4 H20 H20-P 4.083477 -52.682032 10-310 Petit Plateau Terra firme soil r4 sample NA
|
||||
MAN_Al_r1 MAN MAN-A 5.407813 -53.64559 NA Mana White sands litter r1 sample NA
|
||||
MAN_Al_r2 MAN MAN-A 5.407813 -53.64559 NA Mana White sands litter r2 sample NA
|
||||
MAN_Al_r3 MAN MAN-A 5.407813 -53.64559 NA Mana White sands litter r3 sample NA
|
||||
MAN_Al_r4 MAN MAN-A 5.407813 -53.64559 NA Mana White sands litter r4 sample NA
|
||||
MAN_As_r1 MAN MAN-A 5.407813 -53.64559 NA Mana White sands soil r1 sample NA
|
||||
MAN_As_r2 MAN MAN-A 5.407813 -53.64559 NA Mana White sands soil r2 sample NA
|
||||
MAN_As_r3 MAN MAN-A 5.407813 -53.64559 NA Mana White sands soil r3 sample NA
|
||||
MAN_As_r4 MAN MAN-A 5.407813 -53.64559 NA Mana White sands soil r4 sample NA
|
||||
MAN_Bl_r1 MAN MAN-B 5.077534 -53.645498 NA Mana White sands litter r1 sample NA
|
||||
MAN_Bl_r2 MAN MAN-B 5.077534 -53.645498 NA Mana White sands litter r2 sample NA
|
||||
MAN_Bl_r3 MAN MAN-B 5.077534 -53.645498 NA Mana White sands litter r3 sample NA
|
||||
MAN_Bl_r4 MAN MAN-B 5.077534 -53.645498 NA Mana White sands litter r4 sample NA
|
||||
MAN_Bs_r1 MAN MAN-B 5.077534 -53.645498 NA Mana White sands soil r1 sample NA
|
||||
MAN_Bs_r2 MAN MAN-B 5.077534 -53.645498 NA Mana White sands soil r2 sample NA
|
||||
MAN_Bs_r3 MAN MAN-B 5.077534 -53.645498 NA Mana White sands soil r3 sample NA
|
||||
MAN_Bs_r4 MAN MAN-B 5.077534 -53.645498 NA Mana White sands soil r4 sample NA
|
||||
MAN_Cl_r1 MAN MAN-C 5.407747 -53.645317 NA Mana White sands litter r1 sample NA
|
||||
MAN_Cl_r2 MAN MAN-C 5.407747 -53.645317 NA Mana White sands litter r2 sample NA
|
||||
MAN_Cl_r3 MAN MAN-C 5.407747 -53.645317 NA Mana White sands litter r3 sample NA
|
||||
MAN_Cl_r4 MAN MAN-C 5.407747 -53.645317 NA Mana White sands litter r4 sample NA
|
||||
MAN_Cs_r1 MAN MAN-C 5.407747 -53.645317 NA Mana White sands soil r1 sample NA
|
||||
MAN_Cs_r2 MAN MAN-C 5.407747 -53.645317 NA Mana White sands soil r2 sample NA
|
||||
MAN_Cs_r3 MAN MAN-C 5.407747 -53.645317 NA Mana White sands soil r3 sample NA
|
||||
MAN_Cs_r4 MAN MAN-C 5.407747 -53.645317 NA Mana White sands soil r4 sample NA
|
||||
MAN_Dl_r1 MAN MAN-D 5.407685 -53.645156 NA Mana White sands litter r1 sample NA
|
||||
MAN_Dl_r2 MAN MAN-D 5.407685 -53.645156 NA Mana White sands litter r2 sample NA
|
||||
MAN_Dl_r3 MAN MAN-D 5.407685 -53.645156 NA Mana White sands litter r3 sample NA
|
||||
MAN_Dl_r4 MAN MAN-D 5.407685 -53.645156 NA Mana White sands litter r4 sample NA
|
||||
MAN_Ds_r1 MAN MAN-D 5.407685 -53.645156 NA Mana White sands soil r1 sample NA
|
||||
MAN_Ds_r2 MAN MAN-D 5.407685 -53.645156 NA Mana White sands soil r2 sample NA
|
||||
MAN_Ds_r3 MAN MAN-D 5.407685 -53.645156 NA Mana White sands soil r3 sample NA
|
||||
MAN_Ds_r4 MAN MAN-D 5.407685 -53.645156 NA Mana White sands soil r4 sample NA
|
||||
MAN_El_r1 MAN MAN-E 5.407929 -53.64497 NA Mana White sands litter r1 sample NA
|
||||
MAN_El_r2 MAN MAN-E 5.407929 -53.64497 NA Mana White sands litter r2 sample NA
|
||||
MAN_El_r3 MAN MAN-E 5.407929 -53.64497 NA Mana White sands litter r3 sample NA
|
||||
MAN_El_r4 MAN MAN-E 5.407929 -53.64497 NA Mana White sands litter r4 sample NA
|
||||
MAN_Es_r1 MAN MAN-E 5.407929 -53.64497 NA Mana White sands soil r1 sample NA
|
||||
MAN_Es_r2 MAN MAN-E 5.407929 -53.64497 NA Mana White sands soil r2 sample NA
|
||||
MAN_Es_r3 MAN MAN-E 5.407929 -53.64497 NA Mana White sands soil r3 sample NA
|
||||
MAN_Es_r4 MAN MAN-E 5.407929 -53.64497 NA Mana White sands soil r4 sample NA
|
||||
MAN_Fl_r1 MAN MAN-F 5.408024 -53.645137 NA Mana White sands litter r1 sample NA
|
||||
MAN_Fl_r2 MAN MAN-F 5.408024 -53.645137 NA Mana White sands litter r2 sample NA
|
||||
MAN_Fl_r3 MAN MAN-F 5.408024 -53.645137 NA Mana White sands litter r3 sample NA
|
||||
MAN_Fl_r4 MAN MAN-F 5.408024 -53.645137 NA Mana White sands litter r4 sample NA
|
||||
MAN_Fs_r1 MAN MAN-F 5.408024 -53.645137 NA Mana White sands soil r1 sample NA
|
||||
MAN_Fs_r2 MAN MAN-F 5.408024 -53.645137 NA Mana White sands soil r2 sample NA
|
||||
MAN_Fs_r3 MAN MAN-F 5.408024 -53.645137 NA Mana White sands soil r3 sample NA
|
||||
MAN_Fs_r4 MAN MAN-F 5.408024 -53.645137 NA Mana White sands soil r4 sample NA
|
||||
MAN_Gl_r1 MAN MAN-G 5.408052 -53.645306 NA Mana White sands litter r1 sample NA
|
||||
MAN_Gl_r2 MAN MAN-G 5.408052 -53.645306 NA Mana White sands litter r2 sample NA
|
||||
MAN_Gl_r3 MAN MAN-G 5.408052 -53.645306 NA Mana White sands litter r3 sample NA
|
||||
MAN_Gl_r4 MAN MAN-G 5.408052 -53.645306 NA Mana White sands litter r4 sample NA
|
||||
MAN_Gs_r1 MAN MAN-G 5.408052 -53.645306 NA Mana White sands soil r1 sample NA
|
||||
MAN_Gs_r2 MAN MAN-G 5.408052 -53.645306 NA Mana White sands soil r2 sample NA
|
||||
MAN_Gs_r3 MAN MAN-G 5.408052 -53.645306 NA Mana White sands soil r3 sample NA
|
||||
MAN_Gs_r4 MAN MAN-G 5.408052 -53.645306 NA Mana White sands soil r4 sample NA
|
||||
MAN_Hl_r1 MAN MAN-H 5.40807 -53.645468 NA Mana White sands litter r1 sample NA
|
||||
MAN_Hl_r2 MAN MAN-H 5.40807 -53.645468 NA Mana White sands litter r2 sample NA
|
||||
MAN_Hl_r3 MAN MAN-H 5.40807 -53.645468 NA Mana White sands litter r3 sample NA
|
||||
MAN_Hl_r4 MAN MAN-H 5.40807 -53.645468 NA Mana White sands litter r4 sample NA
|
||||
MAN_Hs_r1 MAN MAN-H 5.40807 -53.645468 NA Mana White sands soil r1 sample NA
|
||||
MAN_Hs_r2 MAN MAN-H 5.40807 -53.645468 NA Mana White sands soil r2 sample NA
|
||||
MAN_Hs_r3 MAN MAN-H 5.40807 -53.645468 NA Mana White sands soil r3 sample NA
|
||||
MAN_Hs_r4 MAN MAN-H 5.40807 -53.645468 NA Mana White sands soil r4 sample NA
|
||||
MAN_Il_r1 MAN MAN-I 5.407884 -53.645575 NA Mana White sands litter r1 sample NA
|
||||
MAN_Il_r2 MAN MAN-I 5.407884 -53.645575 NA Mana White sands litter r2 sample NA
|
||||
MAN_Il_r3 MAN MAN-I 5.407884 -53.645575 NA Mana White sands litter r3 sample NA
|
||||
MAN_Il_r4 MAN MAN-I 5.407884 -53.645575 NA Mana White sands litter r4 sample NA
|
||||
MAN_Is_r1 MAN MAN-I 5.407884 -53.645575 NA Mana White sands soil r1 sample NA
|
||||
MAN_Is_r2 MAN MAN-I 5.407884 -53.645575 NA Mana White sands soil r2 sample NA
|
||||
MAN_Is_r3 MAN MAN-I 5.407884 -53.645575 NA Mana White sands soil r3 sample NA
|
||||
MAN_Is_r4 MAN MAN-I 5.407884 -53.645575 NA Mana White sands soil r4 sample NA
|
||||
MAN_Jl_r1 MAN MAN-J 5.407581 -53.645494 NA Mana White sands litter r1 sample NA
|
||||
MAN_Jl_r2 MAN MAN-J 5.407581 -53.645494 NA Mana White sands litter r2 sample NA
|
||||
MAN_Jl_r3 MAN MAN-J 5.407581 -53.645494 NA Mana White sands litter r3 sample NA
|
||||
MAN_Jl_r4 MAN MAN-J 5.407581 -53.645494 NA Mana White sands litter r4 sample NA
|
||||
MAN_Js_r1 MAN MAN-J 5.407581 -53.645494 NA Mana White sands soil r1 sample NA
|
||||
MAN_Js_r2 MAN MAN-J 5.407581 -53.645494 NA Mana White sands soil r2 sample NA
|
||||
MAN_Js_r3 MAN MAN-J 5.407581 -53.645494 NA Mana White sands soil r3 sample NA
|
||||
MAN_Js_r4 MAN MAN-J 5.407581 -53.645494 NA Mana White sands soil r4 sample NA
|
||||
MAN_Kl_r1 MAN MAN-K 5.407512 -53.645234 NA Mana White sands litter r1 sample NA
|
||||
MAN_Kl_r2 MAN MAN-K 5.407512 -53.645234 NA Mana White sands litter r2 sample NA
|
||||
MAN_Kl_r3 MAN MAN-K 5.407512 -53.645234 NA Mana White sands litter r3 sample NA
|
||||
MAN_Kl_r4 MAN MAN-K 5.407512 -53.645234 NA Mana White sands litter r4 sample NA
|
||||
MAN_Ks_r1 MAN MAN-K 5.407512 -53.645234 NA Mana White sands soil r1 sample NA
|
||||
MAN_Ks_r2 MAN MAN-K 5.407512 -53.645234 NA Mana White sands soil r2 sample NA
|
||||
MAN_Ks_r3 MAN MAN-K 5.407512 -53.645234 NA Mana White sands soil r3 sample NA
|
||||
MAN_Ks_r4 MAN MAN-K 5.407512 -53.645234 NA Mana White sands soil r4 sample NA
|
||||
MAN_Ll_r1 MAN MAN-L 5.407444 -53.64503 NA Mana White sands litter r1 sample NA
|
||||
MAN_Ll_r2 MAN MAN-L 5.407444 -53.64503 NA Mana White sands litter r2 sample NA
|
||||
MAN_Ll_r3 MAN MAN-L 5.407444 -53.64503 NA Mana White sands litter r3 sample NA
|
||||
MAN_Ll_r4 MAN MAN-L 5.407444 -53.64503 NA Mana White sands litter r4 sample NA
|
||||
MAN_Ls_r1 MAN MAN-L 5.407444 -53.64503 NA Mana White sands soil r1 sample NA
|
||||
MAN_Ls_r2 MAN MAN-L 5.407444 -53.64503 NA Mana White sands soil r2 sample NA
|
||||
MAN_Ls_r3 MAN MAN-L 5.407444 -53.64503 NA Mana White sands soil r3 sample NA
|
||||
MAN_Ls_r4 MAN MAN-L 5.407444 -53.64503 NA Mana White sands soil r4 sample NA
|
||||
MAN_Ml_r1 MAN MAN-M 5.407247 -53.645045 NA Mana White sands litter r1 sample NA
|
||||
MAN_Ml_r2 MAN MAN-M 5.407247 -53.645045 NA Mana White sands litter r2 sample NA
|
||||
MAN_Ml_r3 MAN MAN-M 5.407247 -53.645045 NA Mana White sands litter r3 sample NA
|
||||
MAN_Ml_r4 MAN MAN-M 5.407247 -53.645045 NA Mana White sands litter r4 sample NA
|
||||
MAN_Ms_r1 MAN MAN-M 5.407247 -53.645045 NA Mana White sands soil r1 sample NA
|
||||
MAN_Ms_r2 MAN MAN-M 5.407247 -53.645045 NA Mana White sands soil r2 sample NA
|
||||
MAN_Ms_r3 MAN MAN-M 5.407247 -53.645045 NA Mana White sands soil r3 sample NA
|
||||
MAN_Ms_r4 MAN MAN-M 5.407247 -53.645045 NA Mana White sands soil r4 sample NA
|
||||
MAN_Nl_r1 MAN MAN-N 5.407318 -53.645405 NA Mana White sands litter r1 sample NA
|
||||
MAN_Nl_r2 MAN MAN-N 5.407318 -53.645405 NA Mana White sands litter r2 sample NA
|
||||
MAN_Nl_r3 MAN MAN-N 5.407318 -53.645405 NA Mana White sands litter r3 sample NA
|
||||
MAN_Nl_r4 MAN MAN-N 5.407318 -53.645405 NA Mana White sands litter r4 sample NA
|
||||
MAN_Ns_r1 MAN MAN-N 5.407318 -53.645405 NA Mana White sands soil r1 sample NA
|
||||
MAN_Ns_r2 MAN MAN-N 5.407318 -53.645405 NA Mana White sands soil r2 sample NA
|
||||
MAN_Ns_r3 MAN MAN-N 5.407318 -53.645405 NA Mana White sands soil r3 sample NA
|
||||
MAN_Ns_r4 MAN MAN-N 5.407318 -53.645405 NA Mana White sands soil r4 sample NA
|
||||
MAN_Ol_r1 MAN MAN-O 5.407461 -53.645487 NA Mana White sands litter r1 sample NA
|
||||
MAN_Ol_r2 MAN MAN-O 5.407461 -53.645487 NA Mana White sands litter r2 sample NA
|
||||
MAN_Ol_r3 MAN MAN-O 5.407461 -53.645487 NA Mana White sands litter r3 sample NA
|
||||
MAN_Ol_r4 MAN MAN-O 5.407461 -53.645487 NA Mana White sands litter r4 sample NA
|
||||
MAN_Os_r1 MAN MAN-O 5.407461 -53.645487 NA Mana White sands soil r1 sample NA
|
||||
MAN_Os_r2 MAN MAN-O 5.407461 -53.645487 NA Mana White sands soil r2 sample NA
|
||||
MAN_Os_r3 MAN MAN-O 5.407461 -53.645487 NA Mana White sands soil r3 sample NA
|
||||
MAN_Os_r4 MAN MAN-O 5.407461 -53.645487 NA Mana White sands soil r4 sample NA
|
||||
MAN_Pl_r1 MAN MAN-P 5.40749 -53.645723 NA Mana White sands litter r1 sample NA
|
||||
MAN_Pl_r2 MAN MAN-P 5.40749 -53.645723 NA Mana White sands litter r2 sample NA
|
||||
MAN_Pl_r3 MAN MAN-P 5.40749 -53.645723 NA Mana White sands litter r3 sample NA
|
||||
MAN_Pl_r4 MAN MAN-P 5.40749 -53.645723 NA Mana White sands litter r4 sample NA
|
||||
MAN_Ps_r1 MAN MAN-P 5.40749 -53.645723 NA Mana White sands soil r1 sample NA
|
||||
MAN_Ps_r2 MAN MAN-P 5.40749 -53.645723 NA Mana White sands soil r2 sample NA
|
||||
MAN_Ps_r3 MAN MAN-P 5.40749 -53.645723 NA Mana White sands soil r3 sample NA
|
||||
MAN_Ps_r4 MAN MAN-P 5.40749 -53.645723 NA Mana White sands soil r4 sample NA
|
||||
H20_Ql_r1 H20 H20-Q NA NA NA Petit Plateau Terra firme litter r1 negative Extraction
|
||||
H20_Ql_r2 H20 H20-Q NA NA NA Petit Plateau Terra firme litter r2 negative Extraction
|
||||
H20_Ql_r3 H20 H20-Q NA NA NA Petit Plateau Terra firme litter r3 negative Extraction
|
||||
H20_Ql_r4 H20 H20-Q NA NA NA Petit Plateau Terra firme litter r4 negative Extraction
|
||||
H20_Qs_r1 H20 H20-Q NA NA NA Petit Plateau Terra firme soil r1 negative Extraction
|
||||
H20_Qs_r2 H20 H20-Q NA NA NA Petit Plateau Terra firme soil r2 negative Extraction
|
||||
H20_Qs_r3 H20 H20-Q NA NA NA Petit Plateau Terra firme soil r3 negative Extraction
|
||||
H20_Qs_r4 H20 H20-Q NA NA NA Petit Plateau Terra firme soil r4 negative Extraction
|
||||
MAN_Ql_r1 MAN MAN-A NA NA NA Mana White sands litter r1 negative Extraction
|
||||
MAN_Ql_r2 MAN MAN-A NA NA NA Mana White sands litter r2 negative Extraction
|
||||
MAN_Ql_r3 MAN MAN-A NA NA NA Mana White sands litter r3 negative Extraction
|
||||
MAN_Ql_r4 MAN MAN-A NA NA NA Mana White sands litter r4 negative Extraction
|
||||
MAN_Qs_r1 MAN MAN-A NA NA NA Mana White sands soil r1 negative Extraction
|
||||
MAN_Qs_r2 MAN MAN-A NA NA NA Mana White sands soil r2 negative Extraction
|
||||
MAN_Qs_r3 MAN MAN-A NA NA NA Mana White sands soil r3 negative Extraction
|
||||
MAN_Qs_r4 MAN MAN-A NA NA NA Mana White sands soil r4 negative Extraction
|
||||
cn_01_r1 NA NA NA NA NA NA NA NA r1 negative PCR
|
||||
cn_01_r2 NA NA NA NA NA NA NA NA r2 negative PCR
|
||||
cn_01_r3 NA NA NA NA NA NA NA NA r3 negative PCR
|
||||
cn_01_r4 NA NA NA NA NA NA NA NA r4 negative PCR
|
||||
cn_02_r1 NA NA NA NA NA NA NA NA r1 negative PCR
|
||||
cn_02_r2 NA NA NA NA NA NA NA NA r2 negative PCR
|
||||
cn_02_r3 NA NA NA NA NA NA NA NA r3 negative PCR
|
||||
cn_02_r4 NA NA NA NA NA NA NA NA r4 negative PCR
|
||||
cn_03_r1 NA NA NA NA NA NA NA NA r1 negative PCR
|
||||
cn_03_r2 NA NA NA NA NA NA NA NA r2 negative PCR
|
||||
cn_03_r3 NA NA NA NA NA NA NA NA r3 negative PCR
|
||||
cn_03_r4 NA NA NA NA NA NA NA NA r4 negative PCR
|
||||
cn_04_r1 NA NA NA NA NA NA NA NA r1 negative PCR
|
||||
cn_04_r2 NA NA NA NA NA NA NA NA r2 negative PCR
|
||||
cn_04_r3 NA NA NA NA NA NA NA NA r3 negative PCR
|
||||
cn_04_r4 NA NA NA NA NA NA NA NA r4 negative PCR
|
||||
cn_05_r1 NA NA NA NA NA NA NA NA r1 negative PCR
|
||||
cn_05_r2 NA NA NA NA NA NA NA NA r2 negative PCR
|
||||
cn_05_r3 NA NA NA NA NA NA NA NA r3 negative PCR
|
||||
cn_05_r4 NA NA NA NA NA NA NA NA r4 negative PCR
|
||||
cn_06_r1 NA NA NA NA NA NA NA NA r1 negative PCR
|
||||
cn_06_r2 NA NA NA NA NA NA NA NA r2 negative PCR
|
||||
cn_06_r3 NA NA NA NA NA NA NA NA r3 negative PCR
|
||||
cn_06_r4 NA NA NA NA NA NA NA NA r4 negative PCR
|
||||
cn_07_r1 NA NA NA NA NA NA NA NA r1 negative PCR
|
||||
cn_07_r2 NA NA NA NA NA NA NA NA r2 negative PCR
|
||||
cn_07_r3 NA NA NA NA NA NA NA NA r3 negative PCR
|
||||
cn_07_r4 NA NA NA NA NA NA NA NA r4 negative PCR
|
||||
cn_08_r1 NA NA NA NA NA NA NA NA r1 negative PCR
|
||||
cn_08_r2 NA NA NA NA NA NA NA NA r2 negative PCR
|
||||
cn_08_r3 NA NA NA NA NA NA NA NA r3 negative PCR
|
||||
cn_08_r4 NA NA NA NA NA NA NA NA r4 negative PCR
|
||||
blk_01_r1 NA NA NA NA NA NA NA NA r1 negative Library/Sequencing
|
||||
blk_01_r2 NA NA NA NA NA NA NA NA r2 negative Library/Sequencing
|
||||
blk_01_r3 NA NA NA NA NA NA NA NA r3 negative Library/Sequencing
|
||||
blk_01_r4 NA NA NA NA NA NA NA NA r4 negative Library/Sequencing
|
||||
blk_02_r1 NA NA NA NA NA NA NA NA r1 negative Library/Sequencing
|
||||
blk_02_r2 NA NA NA NA NA NA NA NA r2 negative Library/Sequencing
|
||||
blk_02_r3 NA NA NA NA NA NA NA NA r3 negative Library/Sequencing
|
||||
blk_02_r4 NA NA NA NA NA NA NA NA r4 negative Library/Sequencing
|
||||
blk_03_r1 NA NA NA NA NA NA NA NA r1 negative Library/Sequencing
|
||||
blk_03_r2 NA NA NA NA NA NA NA NA r2 negative Library/Sequencing
|
||||
blk_03_r3 NA NA NA NA NA NA NA NA r3 negative Library/Sequencing
|
||||
blk_03_r4 NA NA NA NA NA NA NA NA r4 negative Library/Sequencing
|
||||
blk_04_r1 NA NA NA NA NA NA NA NA r1 negative Library/Sequencing
|
||||
blk_04_r2 NA NA NA NA NA NA NA NA r2 negative Library/Sequencing
|
||||
blk_04_r3 NA NA NA NA NA NA NA NA r3 negative Library/Sequencing
|
||||
blk_04_r4 NA NA NA NA NA NA NA NA r4 negative Library/Sequencing
|
||||
blk_05_r1 NA NA NA NA NA NA NA NA r1 negative Library/Sequencing
|
||||
blk_05_r2 NA NA NA NA NA NA NA NA r2 negative Library/Sequencing
|
||||
blk_05_r3 NA NA NA NA NA NA NA NA r3 negative Library/Sequencing
|
||||
blk_05_r4 NA NA NA NA NA NA NA NA r4 negative Library/Sequencing
|
||||
blk_06_r1 NA NA NA NA NA NA NA NA r1 negative Library/Sequencing
|
||||
blk_06_r2 NA NA NA NA NA NA NA NA r2 negative Library/Sequencing
|
||||
blk_06_r3 NA NA NA NA NA NA NA NA r3 negative Library/Sequencing
|
||||
blk_06_r4 NA NA NA NA NA NA NA NA r4 negative Library/Sequencing
|
||||
blk_07_r1 NA NA NA NA NA NA NA NA r1 negative Library/Sequencing
|
||||
blk_07_r2 NA NA NA NA NA NA NA NA r2 negative Library/Sequencing
|
||||
blk_07_r3 NA NA NA NA NA NA NA NA r3 negative Library/Sequencing
|
||||
blk_07_r4 NA NA NA NA NA NA NA NA r4 negative Library/Sequencing
|
||||
blk_08_r1 NA NA NA NA NA NA NA NA r1 negative Library/Sequencing
|
||||
blk_08_r2 NA NA NA NA NA NA NA NA r2 negative Library/Sequencing
|
||||
blk_08_r3 NA NA NA NA NA NA NA NA r3 negative Library/Sequencing
|
||||
blk_08_r4 NA NA NA NA NA NA NA NA r4 negative Library/Sequencing
|
||||
blk_09_r1 NA NA NA NA NA NA NA NA r1 negative Library/Sequencing
|
||||
blk_09_r2 NA NA NA NA NA NA NA NA r2 negative Library/Sequencing
|
||||
blk_09_r3 NA NA NA NA NA NA NA NA r3 negative Library/Sequencing
|
||||
blk_09_r4 NA NA NA NA NA NA NA NA r4 negative Library/Sequencing
|
||||
blk_10_r1 NA NA NA NA NA NA NA NA r1 negative Library/Sequencing
|
||||
blk_10_r2 NA NA NA NA NA NA NA NA r2 negative Library/Sequencing
|
||||
blk_10_r3 NA NA NA NA NA NA NA NA r3 negative Library/Sequencing
|
||||
blk_10_r4 NA NA NA NA NA NA NA NA r4 negative Library/Sequencing
|
||||
blk_11_r1 NA NA NA NA NA NA NA NA r1 negative Library/Sequencing
|
||||
blk_11_r2 NA NA NA NA NA NA NA NA r2 negative Library/Sequencing
|
||||
blk_11_r3 NA NA NA NA NA NA NA NA r3 negative Library/Sequencing
|
||||
blk_11_r4 NA NA NA NA NA NA NA NA r4 negative Library/Sequencing
|
||||
blk_12_r1 NA NA NA NA NA NA NA NA r1 negative Library/Sequencing
|
||||
blk_12_r2 NA NA NA NA NA NA NA NA r2 negative Library/Sequencing
|
||||
blk_12_r3 NA NA NA NA NA NA NA NA r3 negative Library/Sequencing
|
||||
blk_12_r4 NA NA NA NA NA NA NA NA r4 negative Library/Sequencing
|
||||
cp_01_r1 NA NA NA NA NA NA NA NA r1 positive Mock 16 plants
|
||||
cp_01_r2 NA NA NA NA NA NA NA NA r2 positive Mock 16 plants
|
||||
cp_01_r3 NA NA NA NA NA NA NA NA r3 positive Mock 16 plants
|
||||
cp_01_r4 NA NA NA NA NA NA NA NA r4 positive Mock 16 plants
|
||||
cp_02_r1 NA NA NA NA NA NA NA NA r1 positive Mock 16 plants
|
||||
cp_02_r2 NA NA NA NA NA NA NA NA r2 positive Mock 16 plants
|
||||
cp_02_r3 NA NA NA NA NA NA NA NA r3 positive Mock 16 plants
|
||||
cp_02_r4 NA NA NA NA NA NA NA NA r4 positive Mock 16 plants
|
||||
cp_03_r1 NA NA NA NA NA NA NA NA r1 positive Mock 16 plants
|
||||
cp_03_r2 NA NA NA NA NA NA NA NA r2 positive Mock 16 plants
|
||||
cp_03_r3 NA NA NA NA NA NA NA NA r3 positive Mock 16 plants
|
||||
cp_03_r4 NA NA NA NA NA NA NA NA r4 positive Mock 16 plants
|
||||
cp_04_r1 NA NA NA NA NA NA NA NA r1 positive Mock 16 plants
|
||||
cp_04_r2 NA NA NA NA NA NA NA NA r2 positive Mock 16 plants
|
||||
cp_04_r3 NA NA NA NA NA NA NA NA r3 positive Mock 16 plants
|
||||
cp_04_r4 NA NA NA NA NA NA NA NA r4 positive Mock 16 plants
|
||||
cp_05_r1 NA NA NA NA NA NA NA NA r1 positive Mock 16 plants
|
||||
cp_05_r2 NA NA NA NA NA NA NA NA r2 positive Mock 16 plants
|
||||
cp_05_r3 NA NA NA NA NA NA NA NA r3 positive Mock 16 plants
|
||||
cp_05_r4 NA NA NA NA NA NA NA NA r4 positive Mock 16 plants
|
||||
cp_06_r1 NA NA NA NA NA NA NA NA r1 positive Mock 16 plants
|
||||
cp_06_r2 NA NA NA NA NA NA NA NA r2 positive Mock 16 plants
|
||||
cp_06_r3 NA NA NA NA NA NA NA NA r3 positive Mock 16 plants
|
||||
cp_06_r4 NA NA NA NA NA NA NA NA r4 positive Mock 16 plants
|
||||
cp_07_r1 NA NA NA NA NA NA NA NA r1 positive Mock 16 plants
|
||||
cp_07_r2 NA NA NA NA NA NA NA NA r2 positive Mock 16 plants
|
||||
cp_07_r3 NA NA NA NA NA NA NA NA r3 positive Mock 16 plants
|
||||
cp_07_r4 NA NA NA NA NA NA NA NA r4 positive Mock 16 plants
|
||||
cp_08_r1 NA NA NA NA NA NA NA NA r1 positive Mock 16 plants
|
||||
cp_08_r2 NA NA NA NA NA NA NA NA r2 positive Mock 16 plants
|
||||
cp_08_r3 NA NA NA NA NA NA NA NA r3 positive Mock 16 plants
|
||||
cp_08_r4 NA NA NA NA NA NA NA NA r4 positive Mock 16 plants
|
||||
7885
RawData/litiere_ins_cl97_agg_filt_tax.tab
Normal file
7885
RawData/litiere_ins_cl97_agg_filt_tax.tab
Normal file
File diff suppressed because one or more lines are too long
3331
RawData/positifs.uniq.annotated.clean.txt
Normal file
3331
RawData/positifs.uniq.annotated.clean.txt
Normal file
File diff suppressed because one or more lines are too long
24331
RawData/positifs.uniq.annotated.txt
Normal file
24331
RawData/positifs.uniq.annotated.txt
Normal file
File diff suppressed because one or more lines are too long
144
RawData/prepare_data.R
Normal file
144
RawData/prepare_data.R
Normal file
@@ -0,0 +1,144 @@
|
||||
positive = read.delim("RawData/positifs.uniq.annotated.txt",
|
||||
sep="\t",
|
||||
header = TRUE)
|
||||
|
||||
|
||||
columns = names(positive)
|
||||
columns.info = c("id", "dilution", "species_name", "taxid", "true", "sequence")
|
||||
columns.counts= columns[grep("^sample\\.",columns)]
|
||||
|
||||
positive.count = t(positive[,columns.counts])
|
||||
|
||||
motus = as.data.frame(positive[,columns.info])
|
||||
positive.motus = data.frame(dilution = as.numeric(motus$dilution)/2,
|
||||
species = as.character(motus$species_name),
|
||||
taxid = as.integer(motus$taxid),
|
||||
true = motus$true == "True"
|
||||
)
|
||||
|
||||
|
||||
samples.names = rownames(positive.count)
|
||||
|
||||
samples = t(simplify2array(strsplit(samples.names,split="_")))
|
||||
|
||||
# [,1] [,2] [,3] [,4] [,5] [,6]
|
||||
# [1,] "sample.TM" "POS" "d16" "1" "a" "A1"
|
||||
# [2,] "sample.TM" "POS" "d16" "1" "a" "B1"
|
||||
# [3,] "sample.TM" "POS" "d16" "1" "b" "A2"
|
||||
# [4,] "sample.TM" "POS" "d16" "1" "b" "B2"
|
||||
# [5,] "sample.TM" "POS" "d16" "2" "a" "A1"
|
||||
# [6,] "sample.TM" "POS" "d16" "2" "a" "B1"
|
||||
|
||||
samples = as.data.frame(samples[,3:6])
|
||||
names(samples) = c("dilution","repeats","PCR","Plate")
|
||||
|
||||
positive.samples = data.frame(dilution = 32%/%as.integer(substr(as.character(samples$dilution),2,10)),
|
||||
repeats = interaction(samples[,2:4],drop = TRUE)
|
||||
)
|
||||
|
||||
rownames(positive.samples)= samples.names
|
||||
rownames(positive.count) = samples.names
|
||||
|
||||
rownames(positive.motus) = positive$id
|
||||
colnames(positive.count) = positive$id
|
||||
|
||||
plants.16 = positive.motus[positive.motus$true,][,c(2,3,1)]
|
||||
|
||||
plants.16 = plants.16[order(1/plants.16$dilution),]
|
||||
plants.16$log10.dilution = - seq_len(nrow(plants.16)) / log(10)*log(2)
|
||||
plants.16$dilution = 1/(2^seq_len(nrow(plants.16)))
|
||||
usethis::use_data(positive.samples,overwrite = TRUE)
|
||||
usethis::use_data(positive.motus,overwrite = TRUE)
|
||||
usethis::use_data(positive.count,overwrite = TRUE)
|
||||
usethis::use_data(plants.16,overwrite = TRUE)
|
||||
|
||||
positive.clean = read.delim("RawData/positifs.uniq.annotated.clean.txt",
|
||||
sep="\t",
|
||||
header = TRUE)
|
||||
|
||||
columns = names(positive.clean)
|
||||
columns.info = c("id", "dilution", "species_name", "taxid", "true", "sequence")
|
||||
columns.counts= columns[grep("^sample\\.",columns)]
|
||||
|
||||
positive.clean.count = t(positive.clean[,columns.counts])
|
||||
|
||||
motus.clean = as.data.frame(positive.clean[,columns.info])
|
||||
positive.clean.motus = data.frame(dilution = as.numeric(motus.clean$dilution)/2,
|
||||
species = as.character(motus.clean$species_name),
|
||||
taxid = as.integer(motus.clean$taxid),
|
||||
true = motus.clean$true == "True"
|
||||
)
|
||||
|
||||
samples.names = rownames(positive.clean.count)
|
||||
|
||||
samples = t(simplify2array(strsplit(samples.names,split="_")))
|
||||
|
||||
samples = as.data.frame(samples[,3:6])
|
||||
names(samples) = c("dilution","repeats","PCR","Plate")
|
||||
|
||||
positive.clean.samples = data.frame(dilution = 32%/%as.integer(substr(as.character(samples$dilution),2,10)),
|
||||
repeats = interaction(samples[,2:4],drop = TRUE)
|
||||
)
|
||||
|
||||
rownames(positive.clean.samples)= samples.names
|
||||
rownames(positive.clean.count) = samples.names
|
||||
|
||||
rownames(positive.clean.motus) = positive.clean$id
|
||||
colnames(positive.clean.count) = positive.clean$id
|
||||
|
||||
usethis::use_data(positive.clean.samples,overwrite = TRUE)
|
||||
usethis::use_data(positive.clean.motus,overwrite = TRUE)
|
||||
usethis::use_data(positive.clean.count,overwrite = TRUE)
|
||||
|
||||
|
||||
#
|
||||
# Litter/Soil dataset
|
||||
#
|
||||
|
||||
|
||||
guiana = read.delim("RawData/litiere_ins_cl97_agg_filt_tax.tab",
|
||||
header = TRUE,
|
||||
sep="\t")
|
||||
|
||||
columns = names(guiana)
|
||||
|
||||
columns.info = c("id","best_identity.order_filtered_embl_r136_noenv_INS",
|
||||
"taxid",
|
||||
"phylum_name","order_name","class_name","family_name","genus_name","species_name",
|
||||
"sequence")
|
||||
|
||||
columns.counts= columns[grep("^sample\\.",columns)]
|
||||
|
||||
samples.names = gsub(pattern = "sample.",
|
||||
replacement = "",
|
||||
columns.counts)
|
||||
|
||||
guiana.count = t(guiana[,columns.counts])
|
||||
|
||||
motus = as.data.frame(guiana[,columns.info])
|
||||
guiana.motus = data.frame(id = paste("EUK",sprintf("%06d",1:nrow(motus)),sep=""),
|
||||
best_id = motus$best_identity.order_filtered_embl_r136_noenv_INS,
|
||||
taxid = as.integer(motus$taxid),
|
||||
species = factor(as.character(motus$species_name)),
|
||||
genus = factor(as.character(motus$genus_name)),
|
||||
family = factor(as.character(motus$family_name)),
|
||||
class = factor(as.character(motus$class_name)),
|
||||
order = factor(as.character(motus$order_name)),
|
||||
phylum = factor(as.character(motus$phylum_name)),
|
||||
sequence = as.character(motus$sequence),
|
||||
stringsAsFactors = FALSE
|
||||
)
|
||||
|
||||
samples = read.delim("RawData/Litiere_sample_list.txt",header=TRUE)
|
||||
|
||||
guiana.samples = samples[samples.names,]
|
||||
guiana.samples$sample = as.factor(sub("_r.$","",samples.names))
|
||||
|
||||
|
||||
rownames(guiana.count) = samples.names
|
||||
colnames(guiana.count) = guiana.motus$id
|
||||
rownames(guiana.motus) = guiana.motus$id
|
||||
|
||||
usethis::use_data(guiana.samples,overwrite = TRUE)
|
||||
usethis::use_data(guiana.motus,overwrite = TRUE)
|
||||
usethis::use_data(guiana.count,overwrite = TRUE)
|
||||
Reference in New Issue
Block a user