Commit f96cd20c authored by Eric Coissac's avatar Eric Coissac

Initial commit...

parents
.Rproj.user
.Rhistory
.RData
.Ruserdata
Version: 1.0
RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default
EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: ISO-8859-1
RnwWeave: knitr
LaTeX: pdfLaTeX
AutoAppendNewline: Yes
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"","Aspect","TempSeasonality","MaxMonTemp","Elevation","KLg","pH","AlLg","FeLg","Total.C","PLg","SLg","MeanMonTempRange","CaLg","Total.N","AnnMeanTemp","Latitude","Longitude","MgLg","MnLg","Isothemality","CNratio","CLg","NLg","SurfaceGeology","BiogegraphicalRegion","Location","Altitude"
"AA1.1",103.6505,0.9665,30.71,410,2.336459734,5.51,4.752824104,5.123854906,8.623,3.152594078,2.995196292,9.62,2.80140371,0.6445,22.5,-17.609964,145.766577,2.923244019,3.127428778,0.5483,2.59371350857308,2.15443305197019,-0.439280456602895,"Basalt","WT","Tchupala","MEDIUM"
"AA1.2",99.7398,0.9665,30.71,410,2.292256071,5.74,4.764930447,5.214846496,7.667,3.240798771,2.944482672,9.62,3.10754913,0.6065,22.5,-17.609964,145.766577,2.926856709,3.283527365,0.5483,2.53697595517479,2.03692540457676,-0.500050550598032,"Basalt","WT","Tchupala","MEDIUM"
"AA1.3",308.2145,0.9665,30.71,410,2.23299611,5.94,4.773062017,5.264820183,7.966,3.245759356,2.958563883,9.62,2.976349979,0.6591,22.5,-17.609964,145.766577,2.864511081,3.574147064,0.5483,2.49206249568292,2.07518248475945,-0.416880010923463,"Basalt","WT","Tchupala","MEDIUM"
"AA2.1",187.3814,0.9971,27.14,1050,2.225309282,5.38,5.021193435,5.206828574,7.842,3.238297068,2.902546779,8.64,2.26245109,0.6247,19.13,-17.68226,145.53411,2.99343623,3.187802639,0.5107,2.52997764835275,2.05949390387014,-0.470483744482613,"Basalt","WT","Coochimbeerum","HIGH"
"AA2.2",152.8623,0.9971,27.14,1050,2.012837225,5.26,4.804827486,4.818892005,6.31,2.662757832,2.72427587,8.64,2.184691431,0.4403,19.13,-17.68226,145.53411,2.536558443,2.315970345,0.5107,2.66243464277355,1.84213567655312,-0.820298966220429,"Basalt","WT","Coochimbeerum","HIGH"
"AA2.3",139.7832,0.9971,27.14,1050,2.290034611,5.24,4.761935352,4.62014647,6.569,2.460897843,2.77524626,8.64,2.392696953,0.4586,19.13,-17.68226,145.53411,2.495544338,1.923761961,0.5107,2.66193852246867,1.88236161391034,-0.779576908558333,"Basalt","WT","Coochimbeerum","HIGH"
"AA3.1",87.605,0.8224,31.9,70,2.600972896,5.59,4.442495447,4.212214247,2.369,1.883661435,2.499687083,9.12,1.996511672,0.147,24.46,-16.167472,145.404203,2.178976947,1.824125834,0.5699,2.77979061738005,0.862467925176648,-1.9173226922034,"Mudstone","WT","Turpentine","LOW"
"AA3.2",98.0973,0.8224,31.9,70,3.290257269,5.63,4.383833312,4.173215415,3.503,2.220108088,2.631443769,9.12,2.50242712,0.2488,24.46,-16.167472,145.404203,3.090258053,2.511883361,0.5699,2.64472566233246,1.25361974421535,-1.39110591811711,"Mudstone","WT","Turpentine","LOW"
"AA3.3",86.0931,0.8224,31.9,70,2.555094449,5.32,4.214870329,3.952840857,2.438,1.662757832,2.376576957,9.12,1.707570176,0.138,24.46,-16.167472,145.404203,2.348304863,1.668385917,0.5699,2.87167962488401,0.89117803105908,-1.98050159382493,"Mudstone","WT","Turpentine","LOW"
"AA4.1",270.3022,0.8563,26.97,940,2.491361694,4.79,4.136752266,3.532881719,2.663,2.371067862,2.444044796,7.92,2.136720567,0.1865,19.8,-16.594605,145.281487,2.257678575,1.959041392,0.5285,2.65877734673006,0.979453306831795,-1.67932403989827,"Granite","WT","Mt Lewis","HIGH"
"AA4.2",175.3886,0.8563,26.97,940,2.285557309,5.11,4.350267406,4.03746634,4.858,2.436162647,2.558708571,7.92,2.285557309,0.3197,19.8,-16.594605,145.281487,2.195899652,1.824125834,0.5285,2.72099905349632,1.58062683057998,-1.14037222291634,"Granite","WT","Mt Lewis","HIGH"
"AA4.3",130.0218,0.8563,26.97,940,2.710117365,4.65,4.574042849,4.198684573,4.64,2.5132176,2.701567985,7.92,2.093421685,0.3333,19.8,-16.594605,145.281487,2.596597096,1.698100546,0.5285,2.63342665990661,1.53471436623816,-1.09871229366844,"Granite","WT","Mt Lewis","HIGH"
"ABR.1",142.1181,1.4235,24.98,950,3.130655349,4.4,4.60853673,4.399691024,12.85,2.825426118,2.933993164,9.5,3.374931554,0.8239,14.01,-32.122698,151.681657,2.98721923,2.835690571,0.4607,2.74704992700182,2.55334381134123,-0.193706115660593,"sediments","BR","Barrington Tops","HIGH"
"ABR.3",121.1986,1.4235,24.98,950,3.013258665,4.7,4.679436982,4.383833312,9.823,2.872738827,2.847572659,9.5,3.426673888,0.7293,14.01,-32.122698,151.681657,3.021602716,3.083144143,0.4607,2.60039668368468,2.28472657469273,-0.31567010899195,"sediments","BR","Barrington Tops","HIGH"
"ADR.1",105.0941,1.4423,26.4,720,2.760422483,4.5,4.860343997,4.916985305,13.59,3.633569443,3.053462605,11.94,3.742803658,1.024,15.92,-30.36654,152.730009,3.385784959,3.124178055,0.5151,2.58561770154574,2.60933422816305,0.0237165266173161,"Granodiorite","BR","Dorrigo1","HIGH"
"ADR.2",96.8626,1.4423,26.4,720,2.927370363,5.1,4.788882177,4.917510761,11.67,3.576456532,3.057285644,11.94,3.963835031,0.971,15.92,-30.36654,152.730009,3.532881719,3.350441857,0.5151,2.48645025698928,2.45702144629846,-0.0294288106908122,"Basalt.rich Volcanics","BR","Dorrigo1","HIGH"
"ADR.3",64.8861,1.4423,26.4,720,2.770115295,4.9,4.761935352,4.902008334,12.3,3.568319085,3.049605613,11.94,3.849480837,1.03,15.92,-30.36654,152.730009,3.450403086,3.173477643,0.5151,2.48004046013683,2.50959926237837,0.0295588022415444,"Basalt.rich Volcanics","BR","Dorrigo1","HIGH"
"AE1.2",302.2543,1.2487,27.89,880,2.579783597,5.74,4.950369723,5.053082287,9.751,3.429913698,2.996073654,9.16,3.158663981,0.7758,19.21,-21.25014,148.54388,2.700703717,3.265053789,0.4793,2.53123036782925,2.27736984385298,-0.25386052397627,"Mafic volcanics","CQ","Crediton","HIGH"
"AE1.3",309.0598,1.2487,27.89,880,2.571708832,5.76,4.900918524,5.004325674,10.24,3.228143608,3.009025742,9.16,3.38039216,0.7488,19.21,-21.25014,148.54388,2.818225894,2.758154622,0.4793,2.61558497343012,2.32630161961136,-0.289283353818755,"Mafic volcanics","CQ","Crediton","HIGH"
"AE1.1",310.0796,1.2487,27.89,880,2.59439255,5.82,4.964264346,5.075550611,8.555,3.456517858,2.963787827,9.16,3.045714059,0.7114,19.21,-21.25014,148.54388,2.617000341,3.320354033,0.4793,2.48703632681194,2.14651590734416,-0.340520419467782,"Mafic volcanics","CQ","Crediton","HIGH"
"AE2.1",203.875,1.2345,27.62,880,2.481442629,6.12,4.754355982,4.594403601,4.912,2.963787827,2.816903839,8.91,3.01745073,0.4271,19.11,-21.118972,148.508602,2.610660163,3.285782274,0.4752,2.44241829197956,1.59168119084484,-0.850737101134716,"Granodiorite","CQ","Eungella","HIGH"
"AE2.2",67.0991,1.2345,27.62,880,2.521138084,6.02,4.76716329,4.683056048,6.361,2.952792443,2.853698212,8.91,3.14332713,0.514,19.11,-21.118972,148.508602,2.749736316,3.288025535,0.4752,2.51571761122364,1.85018559769667,-0.665532013526972,"Granodiorite","CQ","Eungella","HIGH"
"AE2.3",257.348,1.2345,27.62,880,2.338456494,5.92,4.380229337,4.198684573,4.382,2.686636269,2.745074792,8.91,2.948901761,0.3747,19.11,-21.118972,148.508602,2.656098202,2.667452953,0.4752,2.45913481435577,1.47750524117327,-0.981629573182495,"Granodiorite","CQ","Eungella","HIGH"
"AI1.1",170.3255,0.5761,32.52,55,2.588831726,6,3.893817224,4.348324338,2.833,2.342422681,2.484299839,8.41,3.243286146,0.212,25.95,-12.714988,143.319181,2.803457116,2.562292864,0.6182,2.5925052251585,1.04133622084838,-1.55116900431012,"Metamorphics","CY","Iron Range","LOW"
"AI1.2",318.9783,0.5761,32.52,55,2.217483944,6.01,3.9263939,4.382035063,2.158,2.176091259,2.444044796,8.41,3.090258053,0.1729,25.95,-12.714988,143.319181,2.598790507,2.761175813,0.6182,2.52422375312883,0.769181866835943,-1.75504188629289,"Metamorphics","CY","Iron Range","LOW"
"AI1.3",145.3618,0.5761,32.52,55,2.522444234,5.6,3.879153246,4.294488271,2.423,2.225309282,2.457881897,8.41,2.957128198,0.2013,25.95,-12.714988,143.319181,2.536558443,2.51054501,0.6182,2.48796538817078,0.885006441834389,-1.60295894633639,"Metamorphics","CY","Iron Range","LOW"
"AI2.1",344.4032,0.5752,32.9,50,3.086715664,4.76,3.894371454,4.113976758,3.174,2.178976947,2.460897843,8.84,2.696356389,0.228,26.12,-12.739328,143.241397,2.693726949,2.002597981,0.6285,2.63340227213191,1.15499262210422,-1.4784096500277,"Granite","CY","Iron Range2","LOW"
"AI2.2",344.4032,0.5752,32.9,50,3.075911761,4.6,3.838912027,4.233021507,2.805,2.365487985,2.394451681,8.84,2.380211242,0.194,26.12,-12.739328,143.241397,2.709269961,2.064457989,0.6285,2.67130065889347,1.03140353897466,-1.63989711991881,"Granite","CY","Iron Range2","LOW"
"AI2.3",31.9254,0.5752,32.9,50,2.71432976,5.15,3.683137131,3.770189023,1.734,1.895422546,2.238046103,8.84,2.307496038,0.1315,26.12,-12.739328,143.241397,2.346352974,1.992995098,0.6285,2.57917930572267,0.55043087835835,-2.02874842736432,"Granite","CY","Iron Range2","LOW"
"AML.1",152.9057,1.1795,27.71,270,2.933487288,5.3,4.499700826,4.638499241,10.32,3.193402903,2.98721923,9.93,3.854366778,0.9038,19,-26.735437,152.89289,3.706803097,3.360025089,0.5164,2.43523094205837,2.33408376005342,-0.101147182004958,"Landsborough Sandstone","BR","Maleny Range","LOW"
"AML.2",141.3304,1.1795,27.71,270,2.790988475,5.3,4.481456961,4.826081285,6.066,3.161667412,2.784617293,9.93,3.767230098,0.5519,19,-26.735437,152.89289,3.848250715,3.20709554,0.5164,2.39708781780307,1.80269940926639,-0.594388408536682,"Sandstone","BR","Maleny Range","LOW"
"AML.3",148.1982,1.1795,27.71,270,2.829946696,5.5,4.511896724,4.717678823,11.88,3.290257269,3.037824751,9.93,4.004364371,1.002,19,-26.735437,152.89289,3.867526411,3.546666025,0.5164,2.47285831127183,2.4748563139345,0.00199800266267306,"Landsborough Sandstone","BR","Maleny Range","LOW"
"AN1.1",137.0323,1.2401,28.53,200,2.641474111,5.4,4.849425557,5.029387836,7.865,3.363799945,2.951337519,10.81,3.817631467,0.7196,19.05,-28.64008,153.332294,3.083144143,3.416806872,0.5231,2.391482313416,2.06242253651024,-0.329059776905759,"Basalt.rich Volcanics","BR","Big Scrub","LOW"
"AN1.2",148.5239,1.2401,28.53,200,2.709269961,5.1,4.810239241,5.0492219,8.79,3.352375495,2.951337519,10.81,3.782544284,0.7729,19.05,-28.64008,153.332294,3.167612673,3.250663919,0.5231,2.4312203165664,2.17361471169709,-0.257605604869312,"Basalt.rich Volcanics","BR","Big Scrub","LOW"
"AN1.3",117.2708,1.2401,28.53,200,2.718501689,5,4.812920038,5.012841441,8.612,3.316180099,2.95616843,10.81,3.722716167,0.7591,19.05,-28.64008,153.332294,3.086715664,3.276691529,0.5231,2.42877833746153,2.15315657950212,-0.275621757959415,"Basalt.rich Volcanics","BR","Big Scrub","LOW"
"AN2.1",188.1505,1.1367,25.76,500,2.547774705,4.4,4.61910377,4.187548921,9.3,2.190331698,2.799340549,8.84,3.262688344,0.5854,17.3,-28.581605,153.375615,2.618048097,1.703291378,0.495,2.76547430488356,2.23001440015921,-0.535459904724352,"Felsic volcanics","BR","Peates Mountain","MEDIUM"
"AN2.2",211.9075,1.1367,25.76,500,2.593286067,4.9,4.578650669,4.173215415,12.17,2.123851641,2.800717078,8.84,3.193402903,0.6304,17.3,-28.581605,153.375615,2.641474111,1.640481437,0.495,2.9603746474379,2.49897390699944,-0.461400740438468,"Felsic volcanics","BR","Peates Mountain","MEDIUM"
"AN2.3",197.685,1.1367,25.76,500,2.661812686,5,4.409950022,3.988603543,13.41,2.285557309,2.874481818,8.84,3.228143608,0.7795,17.3,-28.581605,153.375615,2.6599162,2.1430148,0.495,2.84510328777789,2.59600069729359,-0.249102590484306,"Felsic volcanics","BR","Peate's Mountain","MEDIUM"
"AN3.1",189.0312,1.1072,24.35,570,2.51054501,4.7,4.57635287,4.243062865,8.057,2.214843848,2.773786445,8,3.100715087,0.5383,16.26,-28.568607,153.344726,2.563481085,1.631443769,0.478,2.70588053221028,2.08654127879506,-0.619339253415225,"Felsic volcanics","BR","Tungun Range","MEDIUM"
"AN3.2",174.9317,1.1072,24.35,570,2.598790507,4.7,4.705872261,4.176120211,7.752,2.225309282,2.793790385,8,3.262688344,0.5523,16.26,-28.568607,153.344726,2.72427587,1.72427587,0.478,2.64161477666346,2.04795087458846,-0.593663902074995,"Felsic volcanics","BR","Tungun Range","MEDIUM"
"AN3.3",169.5856,1.1072,24.35,570,2.654176542,4.7,4.451801781,4.041432165,11.92,2.26245109,2.853698212,8,3.110926242,0.7733,16.26,-28.568607,153.344726,2.777426822,1.802773725,0.478,2.73530586900435,2.4782176616372,-0.257088207367147,"Felsic volcanics","BR","Tungun Range","MEDIUM"
"AN4.1",129.9723,1.1237,24.45,750,2.833784375,4.4,4.872744649,4.900372591,10.09,3.114277297,2.993876915,8.23,3.546666025,0.8748,16.19,-28.544691,153.289707,3.25791845,3.255513713,0.4817,2.44530482454504,2.31154483436552,-0.133759990179524,"Basalt.rich Volcanics","BR","Mt Nardi","HIGH"
"AN4.2",127.2769,1.1237,24.45,750,2.95616843,4.8,4.898730665,4.875067054,10.76,3.10754913,2.982723388,8.23,3.669409867,0.8796,16.19,-28.544691,153.289707,3.322426052,3.173477643,0.4817,2.50412357503517,2.37583555473364,-0.128288020301531,"Basalt.rich Volcanics","BR","Mt Nardi","HIGH"
"AN4.3",124.1897,1.1237,24.45,750,2.951337519,4.2,4.877952704,4.87564572,11.28,3.045714059,3.041787319,8.23,3.539201599,0.9258,16.19,-28.544691,153.289707,3.228143608,3.06483222,0.4817,2.50012829645488,2.42303124606991,-0.0770970503849669,"Basalt.rich Volcanics","BR","Mt Nardi","HIGH"
"AN5.1",155.2782,1.1312,23.57,1100,2.790988475,4.2,5.021193435,4.965676671,12.03,3.179264464,3.049605613,7.91,3.563599729,0.8383,15.3,-28.460052,153.133512,3.269746373,2.903632516,0.4715,2.66378277732491,2.48740352998659,-0.176379247338325,"Basalt.rich Volcanics","BR","Bar Mountain","HIGH"
"AN5.2",165.942,1.1312,23.57,1100,2.860936621,4.3,4.978185084,4.922730647,9.937,3.212453961,3.025715384,7.91,3.587823171,0.8239,15.3,-28.460052,153.133512,3.240798771,3.161667412,0.4715,2.48997127990982,2.29626516424923,-0.193706115660593,"Basalt.rich Volcanics","BR","Bar Mountain","HIGH"
"AN5.3",4.7187,1.1312,23.57,1100,2.840733235,4.6,4.84011237,4.712658118,15.31,2.986771734,3.045714059,7.91,3.739651444,0.9534,15.3,-28.460052,153.133512,3.472902652,3.004751156,0.4715,2.776226945881,2.72850620966959,-0.0477207362114117,"Basalt.rich Volcanics","BR","Bar Mountain","HIGH"
"APL.1",179.9313,1.1008,26.66,870,2.170261715,5.44,4.447173542,4.07191881,3.88,2.11058971,2.587710965,7.78,2.198657087,0.2496,19.31,-18.994224,146.164664,2.139879086,1.804139432,0.4675,2.74373079612205,1.35583515363518,-1.38789564248686,"Rhyolite","WT","Paluma","HIGH"
"APL.2",324.8746,1.1008,26.66,870,2.029383778,5.47,4.281056105,4.017075096,4.325,1.971739591,2.547774705,7.78,2.235528447,0.274,19.31,-18.994224,146.164664,2.089905111,1.465382851,0.4675,2.75903931297791,1.46441214038384,-1.29462717259407,"Rhyolite","WT","Paluma","HIGH"
"APL.3",286.0261,1.1008,26.66,870,1.707570176,5.41,4.436178555,4.079217436,3.479,2.093421685,2.551449998,7.78,1.707570176,0.2342,19.31,-18.994224,146.164664,2.012837225,1.946943271,0.4675,2.69832472398833,1.24674489616981,-1.45157982781852,"Rhyolite","WT","Paluma","HIGH"
"ARY.1",127.4023,1.2902,26.15,180,2.63447727,5.08,4.190359716,4.26009525,5.874,2.622214023,2.640481437,10.07,3.037824751,0.4311,16.02,-34.6369444,150.7208333,2.63447727,2.42975228,0.4965,2.61195103000548,1.77053583277643,-0.841415197229048,"Volcanics with sedimentary bands","SNSW","Minnamurra","LOW"
"ARY.2",138.4965,1.2902,26.15,180,2.873901598,5.03,4.217510264,4.342442421,5.167,2.733197265,2.692846919,10.07,2.989004616,0.3968,16.02,-34.6369444,150.7208333,2.861534411,2.903089987,0.4965,2.56661515287647,1.64229224930505,-0.924322903571419,"Volcanics with sedimentary bands","SNSW","Minnamurra","LOW"
"ARY.3",160.7873,1.2902,26.15,180,2.882524538,5.31,4.257702568,4.36363078,4.608,2.733197265,2.649334859,10.07,3.053462605,0.3868,16.02,-34.6369444,150.7208333,2.859138297,2.889301703,0.4965,2.47764143879659,1.52779392339359,-0.949847515402998,"Volcanics with sedimentary bands","SNSW","Minnamurra","LOW"
"AW1.1",107.2608,1.4214,26.04,720,2.675778342,4.2,4.626350634,4.545319489,10.98,2.5132176,2.916453949,11.57,3.137037455,0.7056,15.82,-30.361,152.795083,2.797959644,1.322219295,0.5108,2.74478221037094,2.39607543608138,-0.348706774289555,"Siltstone","BR","Dorrigo","HIGH"
"AW1.2",244.366,1.4214,26.04,720,2.784617293,4.3,4.846961503,4.663710346,10.07,2.517195898,2.894869657,11.57,3.340642378,0.6454,15.82,-30.361,152.795083,2.7930916,1.322219295,0.5108,2.74744570609475,2.30956070673047,-0.437884999364276,"Siltstone","BR","Dorrigo","HIGH"
"AW1.3",282.7379,1.4214,26.04,720,3.004751156,4.3,4.624292411,4.465397724,13.67,2.523746467,2.953276337,11.57,3.14332713,0.7681,15.82,-30.361,152.795083,2.921686475,1.64738297,0.5108,2.87903899671336,2.61520365073586,-0.263835345977501,"Siltstone","BR","Dorrigo","HIGH"
"AW2.1",53.0343,1.5126,25.57,880,2.607455023,5.3,4.571720475,4.68034458,7.214,2.86332286,2.769377326,11.96,3.632558515,0.5676,14.4,-29.476051,152.335134,2.778874472,3.053462605,0.5039,2.5423619161776,1.97602358248135,-0.566338333696249,"Monzogranite","BR","Washpool","HIGH"
"AW2.2",62.5338,1.5126,25.57,880,2.837588438,5.3,4.831236099,4.684854335,6.622,2.868056362,2.80685803,11.96,3.738859802,0.5453,14.4,-29.476051,152.335134,3.01745073,3.228143608,0.5039,2.49681661617518,1.89039743912505,-0.606419177050121,"Monzogranite","BR","Washpool","HIGH"
"AW2.3",74.534,1.5126,25.57,880,2.889861721,5.5,4.764930447,4.607465746,7.945,2.709269961,2.777426822,11.96,3.7513561,0.5985,14.4,-29.476051,152.335134,3.196176185,3.000434077,0.5039,2.58587155397279,2.07254279998868,-0.513328753984109,"Monzogranite","BR","Washpool","HIGH"
"AWO.1",132.1917,1.2578,25.17,330,3.360025089,5.5,3.931508722,4.330434067,5.249,2.971739591,2.671172843,9.29,3.487279816,0.3891,15.85,-34.402028,150.843187,3.009025742,3.120902818,0.483,2.60195648126179,1.65803758227016,-0.943918898991629,"Sandstone","SNSW","Wollongong","LOW"
"AWO.2",136.883,1.2578,25.17,330,3.441066407,5.8,3.995679061,4.406557211,6.572,3.049605613,2.794488047,9.29,3.690284703,0.5054,15.85,-34.402028,150.843187,3.01745073,3.322426052,0.483,2.56522328420306,1.88281820017502,-0.682405084028043,"Sandstone","SNSW","Wollongong","LOW"
"AWO.3",146.9422,1.2578,25.17,330,3.158663981,5.3,4.012879387,4.269536293,6.657,3.025715384,2.775974331,9.29,3.59117595,0.5512,15.85,-34.402028,150.843187,2.85308953,3.48301642,0.483,2.49132649190125,1.89566893261857,-0.595657559282688,"Sandstone","SNSW","Wollongong","LOW"
---
title: "Untitled"
author: "Aurlie & Eric"
date: "27/03/2018"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r}
library(ade4)
library(vegan)
```
```{r}
euk = read.csv("australia.euk.reads.plot.csv",head=TRUE,row.names = 1)
bac = read.csv("australia.bac.reads.plot.csv",head=TRUE,row.names = 1)
env = read.csv("biogegraphy_and_environment.csv",head=TRUE,row.names = 1)
```
```{r}
env=env[,lapply(env,class)=="numeric"]
euk=euk[rownames(env),]
bac=bac[rownames(env),]
```
```{r}
env = sweep(env,MARGIN = 2,colMeans(env),'-')
env = sweep(env,MARGIN = 2,apply(env,2,sd),'/')
```
```{r eval=FALSE, include=FALSE}
euk=sqrt(euk)
euk = sweep(euk,MARGIN = 2,colMeans(euk),'-')
euk = sweep(euk,MARGIN = 2,apply(euk,2,sd),'/')
```
```{r eval=FALSE, include=FALSE}
bac=sqrt(bac)
bac = sweep(bac,MARGIN = 2,colMeans(bac),'-')
bac = sweep(bac,MARGIN = 2,apply(bac,2,sd),'/')
```
```{r}
euk.dist=quasieuclid(vegdist(euk,method = "jaccard"))
euk.pco =dudi.pco(euk.dist,full = TRUE)
euk.pco.li = euk.pco$li
dim(euk.pco.li)
plot(euk.pco.li[,1:2],cex=0)
text(euk.pco.li[,1:2],labels = rownames(euk.pco.li),cex=0.6)
```
```{r}
bac.dist=quasieuclid(vegdist(bac,method = "jaccard"))
bac.pco =dudi.pco(bac.dist,full = TRUE)
bac.pco.li = bac.pco$li
dim(bac.pco.li)
plot(bac.pco.li[,1:2],cex=0)
text(bac.pco.li[,1:2],labels = rownames(bac.pco.li),cex=0.6)
```
```{r}
euk.sct = sum(euk.pco.li**2)
bac.sct = sum(bac.pco.li**2)
```
```{r}
x = procrustes(euk.pco.li,bac.pco.li,scale = TRUE)
```
```{r}
y = procrustes(bac.pco.li,euk.pco.li,scale = TRUE)
```
```{r}
SCR.E.B = sum((euk.pco.li-x$Yrot)^2)
SCT.E = sum((euk.pco.li- colMeans(euk.pco.li))^2)
SCR.E.B/SCT.E
```
```{r}
SCR.B.E = sum((bac.pco.li-y$Yrot)^2)
SCT.B = sum((bac.pco.li- colMeans(bac.pco.li))^2)
SCR.B.E/SCT.B
```
```{r}
x = procrustes(sweep(euk.pco.li,2,colMeans(euk.pco.li),"-"),
sweep(bac.pco.li,2,colMeans(bac.pco.li),"-"),scale = TRUE)
y = procrustes(sweep(bac.pco.li,2,colMeans(bac.pco.li),"-"),
sweep(euk.pco.li,2,colMeans(euk.pco.li),"-"),scale = TRUE)
x$scale
1/y$scale
```
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