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Initial commit with analysis files
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Add analysis files for publication record.
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kdyson committed Jun 7, 2023
1 parent 7ce412a commit 49eeafa
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1 change: 1 addition & 0 deletions PilotFarmData/BNA4.All_MOTUs_.csv

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836 changes: 836 additions & 0 deletions PilotFarmData/Gillet_SFX.csv

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1,273 changes: 1,273 additions & 0 deletions PilotFarmData/KeyInvertebrates.csv

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53 changes: 53 additions & 0 deletions PilotFarmData/KeyVertebrates.csv
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id,kingdom,phylum,class,order,family,genus,species,keySpecies,endangered,invasive,domesticated,common,note
RSFX_000000353,Metazoa,Chordata,Aves,Columbiformes,Columbidae,Columbina,Columbina_picui,yes,no,no,no,Picui Ground-Dove,likes heavily degraded forest and shrubland
RSFX_000000100,Metazoa,Chordata,Aves,Cuculiformes,Crotophagidae,Crotophaga,Crotophaga_ani,yes,no,no,no,Smooth-billed Ani,
RSFX_000000512,Metazoa,Chordata,Aves,Galliformes,Phasianidae,Gallus,Gallus_gallus,no,no,no,yes,Red Junglefowl,these are chickens
RSFX_000001030,Metazoa,Chordata,Aves,Passeriformes,Mohoidae,Family_Mohoidae,Family_Mohoidae,no,extinct,no,no,Mohoidae,"uh, this family is extinct. Also from Hawaii"
RSFX_000000242,Metazoa,Chordata,Aves,Passeriformes,Turdidae,Turdus,Turdus_cardis,no,no,yes,no,Japanese Thrush,
RSFX_000000001,Metazoa,Chordata,Mammalia,Artiodactyla,Bovidae,Bos,Bos_taurus,no,no,no,yes,Domestic cow,
RSFX_000000801,Metazoa,Chordata,Mammalia,Artiodactyla,Bovidae,Bos,Genus_Bos,no,no,no,yes,Domestic cow,
RSFX_000015482,Metazoa,Chordata,Mammalia,Artiodactyla,Bovidae,Bos,Bos_taurus,no,no,no,yes,Domestic cow,
RSFX_000002425,Metazoa,Chordata,Mammalia,Artiodactyla,Bovidae,Bos,Genus_Bos,no,no,no,yes,Domestic cow,
RSFX_000018781,Metazoa,Chordata,Mammalia,Artiodactyla,Bovidae,Bos,Genus_Bos,no,no,no,yes,Domestic cow,
RSFX_000003738,Metazoa,Chordata,Mammalia,Artiodactyla,Bovidae,Bos,Genus_Bos,no,no,no,yes,Domestic cow,
RSFX_000012454,Metazoa,Chordata,Mammalia,Artiodactyla,Bovidae,Bos,Genus_Bos,no,no,no,yes,Domestic cow,
RSFX_000017704,Metazoa,Chordata,Mammalia,Artiodactyla,Bovidae,Bos,Genus_Bos,no,no,no,yes,Domestic cow,
RSFX_000021471,Metazoa,Chordata,Mammalia,Artiodactyla,Bovidae,Bos,Genus_Bos,no,no,no,yes,Domestic cow,
RSFX_000059328,Metazoa,Chordata,Mammalia,Artiodactyla,Bovidae,Bos,Genus_Bos,no,no,no,yes,Domestic cow,
RSFX_000006649,Metazoa,Chordata,Mammalia,Artiodactyla,Bovidae,Family_Bovidae,Family_Bovidae,no,no,no,yes,Domestic cow,
RSFX_000028230,Metazoa,Chordata,Mammalia,Artiodactyla,Bovidae,Family_Bovidae,Family_Bovidae,no,no,no,yes,Domestic cow,
RSFX_000039477,Metazoa,Chordata,Mammalia,Artiodactyla,Bovidae,Family_Bovidae,Family_Bovidae,no,no,no,yes,Domestic cow,
RSFX_000028860,Metazoa,Chordata,Mammalia,Artiodactyla,Bovidae,Ovis,Ovis_aries,no,no,no,yes,sheep,sheep
RSFX_000001203,Metazoa,Chordata,Mammalia,Artiodactyla,Cervidae,Family_Cervidae,Family_Cervidae,yes,UNKNOWN,no,no,Native deer,likely native deer
RSFX_000010601,Metazoa,Chordata,Mammalia,Artiodactyla,Cervidae,Family_Cervidae,Family_Cervidae,yes,UNKNOWN,no,no,Native deer,likely native deer
RSFX_000003044,Metazoa,Chordata,Mammalia,Artiodactyla,Suidae,Sus,Sus_scrofa,no,no,yes,no,wild boar,Eurasian species
RSFX_000000117,Metazoa,Chordata,Mammalia,Artiodactyla,Tayassuidae,Pecari,Pecari_tajacu,yes,no,no,no,Collared peccary,Native
RSFX_000000956,Metazoa,Chordata,Mammalia,Artiodactyla,Tayassuidae,Tayassu,Tayassu_pecari,yes,vulnerable,no,no,White-lipped peccary,
RSFX_000001191,Metazoa,Chordata,Mammalia,Carnivora,Canidae,Canis,Canis_lupus,no,no,no,no,Wolf,from domestic dogs?
RSFX_000001603,Metazoa,Chordata,Mammalia,Carnivora,Canidae,Canis,Canis_lupus,no,no,no,no,Wolf,from domestic dogs?
RSFX_000000411,Metazoa,Chordata,Mammalia,Carnivora,Felidae,Felis,Felis_catus,no,no,yes,yes,Domestic cat,
RSFX_000011166,Metazoa,Chordata,Mammalia,Carnivora,Procyonidae,Nasua,Nasua_nasua,yes,decreasing,no,no,South American coati,
RSFX_000002791,Metazoa,Chordata,Mammalia,Chiroptera,Phyllostomidae,Phyllostomus,Phyllostomus_discolor,yes,no,no,no,Pale spear-nosed bat,ag areas and forests
RSFX_000017716,Metazoa,Chordata,Mammalia,Chiroptera,Phyllostomidae,Uroderma,Uroderma_magnirostrum,yes,no,no,no,Brown tent-making bat,
RSFX_000002822,Metazoa,Chordata,Mammalia,Cingulata,Chlamyphoridae,Family_Chlamyphoridae,Family_Chlamyphoridae,yes,UNKNOWN,no,no,Armadillo,
RSFX_000002238,Metazoa,Chordata,Mammalia,Cingulata,Dasypodidae,Dasypus,Dasypus_yepesi,yes,UNKNOWN,no,no,Yungas lesser long-nosed armadillo,Range is unknown but likely Argentina.
RSFX_000000307,Metazoa,Chordata,Mammalia,Didelphimorphia,Didelphidae,Marmosa,Marmosa_demerarae,yes,no,no,no,Woolly Mouse Opossum,
RSFX_000000933,Metazoa,Chordata,Mammalia,Didelphimorphia,Didelphidae,Philander,Philander_opossum,yes,no,no,no,gray four-eyed opossum,"likes forest, rainforest, scrub forest"
RSFX_000003498,Metazoa,Chordata,Mammalia,Perissodactyla,Equidae,Equus,Equus_caballus,no,no,no,yes,domestic horse,
RSFX_000003809,Metazoa,Chordata,Mammalia,Perissodactyla,Equidae,Equus,Equus_caballus,no,no,no,yes,domestic horse,
RSFX_000000087,Metazoa,Chordata,Mammalia,Primates,Atelidae,Alouatta,Genus_Alouatta,yes,decreasing,no,no,Howler monkeys,
RSFX_000000187,Metazoa,Chordata,Mammalia,Primates,Pitheciidae,Plecturocebus,Plecturocebus_cupreus,yes,no,no,no,Coppery titi,
RSFX_000006460,Metazoa,Chordata,Mammalia,Rodentia,Muridae,Rattus,Rattus_norvegicus,no,no,yes,no,Norway rat,
RSFX_000070484,Metazoa,Chordata,Mammalia,Rodentia,Muridae,Rattus,Rattus_norvegicus,no,no,yes,no,Norway rat,
GSFX_000173026,Metazoa,Chordata,Amphibia,Class_Amphibia,Class_Amphibia,Class_Amphibia,Class_Amphibia,no,no,no,no,amphibians,
GSFX_000053322,Metazoa,Chordata,Aves,Class_Aves,Class_Aves,Class_Aves,Class_Aves,no,no,no,no,birds,
GSFX_000000460,Metazoa,Chordata,Mammalia,Artiodactyla,Bovidae,Bos,Bos_taurus,no,no,yes,no,cows,
GSFX_000055237,Metazoa,Chordata,Mammalia,Artiodactyla,Tayassuidae,Pecari,Pecari_tajacu,no,no,no,no,collared peccary,
GSFX_000319164,Metazoa,Chordata,Mammalia,Cingulata,Dasypodidae,Dasypus,Dasypus_beniensis,no,no,no,no,greater long-nosed armadillo,
GSFX_000000096,Metazoa,Chordata,Mammalia,Primates,Hominidae,Homo,Homo_sapiens,no,no,yes,no,humans,
GSFX_000002654,Metazoa,Chordata,Mammalia,Primates,Hominidae,Homo,Homo_sapiens,no,no,yes,no,humans,
GSFX_000004995,Metazoa,Chordata,Mammalia,Primates,Hominidae,Homo,Homo_sapiens,no,no,yes,no,humans,
GSFX_000000538,Metazoa,Chordata,Mammalia,Primates,Hominidae,Homo,Homo_sapiens,no,no,yes,no,humans,
GSFX_000009166,Metazoa,Chordata,Mammalia,Primates,Hominidae,Homo,Homo_sapiens,no,no,yes,no,humans,
GSFX_000003879,Metazoa,Chordata,Mammalia,Primates,Hominidae,Homo,Homo_sapiens,no,no,yes,no,humans,
GSFX_000018818,Metazoa,Chordata,Mammalia,Primates,Hominidae,Homo,Homo_sapiens,no,no,yes,no,humans,
39 changes: 39 additions & 0 deletions PilotFarmData/Lookup_SFX.csv
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system,site,siteEasy,recievedPlot,updatedPlot,labCode,labCode2,labCode20,riazCode2,riazCode20,cluster
COCOA,SFX006-02C,Cocoa 5,SFX006-02C-01,SFX006-02C-01,SFX32,SFX32_2,SFX32_20,SFX32_2g,SFX32_20g,Cluster 1
COCOA,SFX006-02C,Cocoa 5,SFX006-02C-02,SFX006-02C-02,SFX33,SFX33_2,SFX33_20,SFX33_2g,SFX33_20g,Cluster 1
COCOA,SFX006-02C,Cocoa 5,SFX006-02C-03,SFX006-02C-03,SFX34,SFX34_2,SFX34_20,SFX34_2g,SFX34_20g,Cluster 1
COCOA,SFX006-02C,Cocoa 5,SFX006-02C-04,SFX006-02C-04,SFX35,SFX35_2,SFX35_20,SFX35_2g,SFX35_20g,Cluster 1
COCOA,SFX217-03C,Cocoa 2,SFX217-03-01,SFX217-03C-01,SFX21,SFX21_2,SFX21_20,SFX21_2g,SFX21_20g,Cluster 1
COCOA,SFX217-03C,Cocoa 2,SFX217-03-02,SFX217-03C-02,SFX22,SFX22_2,SFX22_20,SFX22_2g,SFX22_20g,Cluster 1
COCOA,SFX217-03C,Cocoa 2,SFX217-03-03,SFX217-03C-03,SFX23,SFX23_2,SFX23_20,SFX23_2g,SFX23_20g,Cluster 1
COCOA,SFX217-03C,Cocoa 2,SFX217-03-04,SFX217-03C-04,SFX24,SFX24_2,SFX24_20,SFX24_2g,SFX24_20g,Cluster 1
COCOA,SFX188-05C,Cocoa 4,SFX188-05C-01,SFX188-05C-01,SFX28,SFX28_2,SFX28_20,SFX28_2g,SFX28_20g,Cluster 2
COCOA,SFX188-05C,Cocoa 4,SFX188-05C-02,SFX188-05C-02,SFX29,SFX29_2,SFX29_20,SFX29_2g,SFX29_20g,Cluster 2
COCOA,SFX188-05C,Cocoa 4,SFX188-05C-03,SFX188-05C-03,SFX30,SFX30_2,SFX30_20,SFX30_2g,SFX30_20g,Cluster 2
COCOA,SFX188-05C,Cocoa 4,SFX188-05C-04,SFX188-05C-04,SFX31,SFX31_2,SFX31_20,SFX31_2g,SFX31_20g,Cluster 2
COCOA,SFX204-07C,Cocoa 1,SFX204-07C-01,SFX204-07C-01,SFX18,SFX18_2,SFX18_20,SFX18_2g,SFX18_20g,Cluster 1
COCOA,SFX204-07C,Cocoa 1,SFX204-07C-02,SFX204-07C-02,SFX19,SFX19_2,SFX19_20,SFX19_2g,SFX19_20g,Cluster 1
COCOA,SFX204-07C,Cocoa 1,SFX204-07C-03,SFX204-07C-03,SFX20,SFX20_2,SFX20_20,SFX20_2g,SFX20_20g,Cluster 1
COCOA,SFX225-08C,Cocoa 3,SFX225-08C-01,SFX225-08C-01,SFX25,SFX25_2,SFX25_20,SFX25_2g,SFX25_20g,Cluster 1
COCOA,SFX225-08C,Cocoa 3,SFX225-08C-03,SFX225-08C-03,SFX26,SFX26_2,SFX26_20,SFX26_2g,SFX26_20g,Cluster 1
COCOA,SFX225-08C,Cocoa 3,SFX225-08C-04,SFX225-08C-04,SFX27,SFX27_2,SFX27_20,SFX27_2g,SFX27_20g,Cluster 1
PASTURE,SFX026-01P,Pasture 3,SFX026-NOVO,SFX026-01P-01,SFX15,SFX15_2,SFX15_20,SFX15_2g,SFX15_20g,Cluster 1
PASTURE,SFX026-01P,Pasture 3,SFX026-01P-03-04 BREJO,SFX026-01P-03,SFX16,SFX16_2,SFX16_20,SFX16_2g,SFX16_20g,Cluster 1
PASTURE,SFX026-01P,Pasture 3,SFX026-01P-04-01,SFX026-01P-04,SFX17,SFX17_2,SFX17_20,SFX17_2g,SFX17_20g,Cluster 1
PASTURE,SFX051-02P,Pasture 2,SFX05-02P-01,SFX051-02P-01,SFX12,SFX12_2,SFX12_20,SFX12_2g,SFX12_20g,Cluster 1
PASTURE,SFX051-02P,Pasture 2,SFX05-02P-02,SFX051-02P-02,SFX13,SFX13_2,SFX13_20,SFX13_2g,SFX13_20g,Cluster 1
PASTURE,SFX051-02P,Pasture 2,SFX05-02P-03,SFX051-02P-03,SFX14,SFX14_2,SFX14_20,SFX14_2g,SFX14_20g,Cluster 1
PASTURE,SFX184-03P,Pasture 5,SFX184-01P.01,SFX184-03P-01,SFX4,SFX4_2,SFX4_20,SFX4_2g,SFX4_20g,Cluster 1
PASTURE,SFX184-03P,Pasture 5,SFX184-03P-02,SFX184-03P-02,SFX6,SFX6_2,SFX6_20,SFX6_2g,SFX6_20g,Cluster 1
PASTURE,SFX184-03P,Pasture 5,SFX184-03P-03,SFX184-03P-03,SFX5,SFX5_2,SFX5_20,SFX5_2g,SFX5_20g,Cluster 1
PASTURE,SFX184-03P,Pasture 5,SFX184-03P-04,SFX184-03P-04,SFX7,SFX7_2,SFX7_20,SFX7_2g,SFX7_20g,Cluster 1
PASTURE,SFX237-04P,Pasture 1,SFX237-04P-01,SFX237-04P-01,SFX8,SFX8_2,SFX8_20,SFX8_2g,SFX8_20g,Cluster 1
PASTURE,SFX237-04P,Pasture 1,SFX237-04P-02,SFX237-04P-02,SFX9,SFX9_2,SFX9_20,SFX9_2g,SFX9_20g,Cluster 1
PASTURE,SFX237-04P,Pasture 1,SFX237-04P-03,SFX237-04P-03,SFX10,SFX10_2,SFX10_20,SFX10_2g,SFX10_20g,Cluster 1
PASTURE,SFX237-04P,Pasture 1,SFX237-04P-04,SFX237-04P-04,SFX11,SFX11_2,SFX11_20,SFX11_2g,SFX11_20g,Cluster 1
PASTURE,SFX128-07P,Pasture 4,SFX128.07P-02,SFX128-07P-02,SFX1,SFX1_2,SFX1_20,SFX1_2g,SFX1_20g,Cluster 1
PASTURE,SFX128-07P,Pasture 4,SFX128.07P-03,SFX128-07P-03,SFX2,SFX2_2,SFX2_20,SFX2_2g,SFX2_20g,Cluster 1
PASTURE,SFX128-07P,Pasture 4,SFX128.07P-04,SFX128-07P-04,SFX3,SFX3_2,SFX3_20,SFX3_2g,SFX3_20g,Cluster 1
FOREST,SFX004-01F,_Forest 1,SFX004-01F,SFX004-01F-99,SFX36,SFX36_2,SFX36_20,SFX36_2g,SFX36_20g,Forest
FOREST,SFX004-01F,_Forest 1,SFX004-01F-03,SFX004-01F-03,SFX37,SFX37_2,SFX37_20,SFX37_2g,SFX37_20g,Forest
FOREST,SFX004-01F,_Forest 1,SFX004-01F-04,SFX004-01F-04,SFX38,SFX38_2,SFX38_20,SFX38_2g,SFX38_20g,Forest
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