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Linear_mixed_effects_order.txt
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Linear_mixed_effects_order.txt
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#mixed effects model
#random effect = plot
#fixed effect = treatment
#fixed effect as categorical variable (here order)
Input = ("
order rank_abundance plot treatment
Cladophorales 1 1 control
Echinosteliales 1 1 control
Geastrales 1 1 control
Entorrhizales 1 1 control
Platygloeales 1 1 control
Helicobasidiales 1 1 control
Agaricostilbales 1 1 control
Coronophorales 1 1 control
Doassansiales 1 1 control
Lagenidiales 1 1 control
Urocystales 1 1 control
Melanosporales 1 1 control
Entylomatales 1 1 control
Mixiales 1 1 control
Phallales 1 1 control
Wallemiales 1 1 control
Dimargaritales 1 1 control
Olpidiopsidales 1 1 control
Leucosporidiales 1 1 control
Acrospermales 1 1 control
Atractiellales 1 1 control
Naohideales 1 1 control
Microthyriales 1 1 control
Mytilinidiales 1 1 control
Septobasidiales 1 1 control
Georgefischeriales 1 1 control
Lichinales 1 1 control
Microbotryales 1 1 control
Trypetheliales 1 1 control
Gomphales 1 1 control
Jahnulales 1 1 control
Thelephorales 1 1 control
Exobasidiales 1 1 control
Microascales 1 1 control
Hysterangiales 1 1 control
Dacrymycetales 2 1 control
Chaetosphaeriales 2 1 control
Erythrobasidiales 2 1 control
Agyriales 2 1 control
Chaetophorales 2 1 control
Sporidiobolales 2 1 control
Archaeosporales 2 1 control
Baeomycetales 2 1 control
Arthoniales 2 1 control
Jaapiales 2 1 control
Tilletiales 3 1 control
Patellariales 3 1 control
Candelariales 3 1 control
Paraglomerales 3 1 control
Filobasidiales 3 1 control
Monoblepharidales 4 1 control
Atheliales 4 1 control
Diversisporales 4 1 control
Kickxellales 4 1 control
Umbilicariales 4 1 control
Neolectales 5 1 control
Harpellales 5 1 control
Microstromatales 5 1 control
Boliniales 5 1 control
Trechisporales 5 1 control
Auriculariales 6 1 control
Sebacinales 6 1 control
Myriangiales 7 1 control
Gloeophyllales 7 1 control
Diaporthales 7 1 control
Xylariales 8 1 control
Malasseziales 8 1 control
Geoglossales 8 1 control
Pertusariales 9 1 control
Blastocladiales 9 1 control
Ustilaginales 9 1 control
Corticiales 12 1 control
Pucciniales 14 1 control
Endogonales 17 1 control
Taphrinales 20 1 control
Phyllachorales 21 1 control
Hysteriales 24 1 control
Orbiliales 26 1 control
Cantharellales 28 1 control
Hymenochaetales 30 1 control
Schizosaccharomycetales 30 1 control
Rhizophydiales 31 1 control
Tremellales 39 1 control
Magnaporthales 39 1 control
Calosphaeriales 42 1 control
Coniochaetales 44 1 control
Pyrenulales 48 1 control
Entomophthorales 55 1 control
Cystofilobasidiales 60 1 control
Polyporales 69 1 control
Sordariales 77 1 control
Mycocaliciales 85 1 control
Pleosporales 89 1 control
Botryosphaeriales 107 1 control
Peltigerales 109 1 control
Agaricales 111 1 control
Dothideales 124 1 control
Eurotiales 125 1 control
Russulales 131 1 control
Chytridiales 148 1 control
Pezizales 149 1 control
Cladochytriales 153 1 control
Hypocreales 156 1 control
Helotiales 189 1 control
Glomerales 189 1 control
Boletales 191 1 control
Neocallimastigales 192 1 control
Lecanorales 202 1 control
Amylocorticiales 219 1 control
Capnodiales 242 1 control
Chaetothyriales 256 1 control
Onygenales 261 1 control
Spizellomycetales 270 1 control
Saccharomycetales 300 1 control
Mucorales 304 1 control
Mortierellales 306 1 control
Helicobasidiales 1 2 control
Cladophorales 1 2 control
Echinosteliales 1 2 control
Dimargaritales 1 2 control
Naohideales 1 2 control
Hysterangiales 1 2 control
Platygloeales 1 2 control
Agaricostilbales 1 2 control
Mixiales 1 2 control
Candelariales 1 2 control
Lagenidiales 1 2 control
Entorrhizales 1 2 control
Coronophorales 1 2 control
Geastrales 1 2 control
Georgefischeriales 1 2 control
Acrospermales 1 2 control
Atractiellales 1 2 control
Entylomatales 1 2 control
Doassansiales 1 2 control
Olpidiopsidales 1 2 control
Gloeophyllales 1 2 control
Melanosporales 1 2 control
Erythrobasidiales 1 2 control
Wallemiales 1 2 control
Leucosporidiales 1 2 control
Tilletiales 2 2 control
Septobasidiales 2 2 control
Phallales 2 2 control
Urocystales 2 2 control
Chaetophorales 2 2 control
Cystofilobasidiales 2 2 control
Geoglossales 2 2 control
Sporidiobolales 2 2 control
Chaetosphaeriales 2 2 control
Microthyriales 3 2 control
Microbotryales 3 2 control
Neocallimastigales 3 2 control
Jahnulales 4 2 control
Cantharellales 4 2 control
Microstromatales 4 2 control
Auriculariales 5 2 control
Dacrymycetales 5 2 control
Arthoniales 5 2 control
Myriangiales 5 2 control
Pucciniales 5 2 control
Umbilicariales 6 2 control
Baeomycetales 6 2 control
Boliniales 6 2 control
Lichinales 6 2 control
Pertusariales 7 2 control
Trypetheliales 8 2 control
Malasseziales 8 2 control
Patellariales 8 2 control
Filobasidiales 9 2 control
Corticiales 9 2 control
Agyriales 10 2 control
Microascales 10 2 control
Endogonales 10 2 control
Thelephorales 10 2 control
Diaporthales 14 2 control
Jaapiales 16 2 control
Mytilinidiales 16 2 control
Ustilaginales 17 2 control
Harpellales 19 2 control
Paraglomerales 19 2 control
Gomphales 20 2 control
Coniochaetales 23 2 control
Exobasidiales 23 2 control
Rhizophydiales 23 2 control
Amylocorticiales 24 2 control
Neolectales 25 2 control
Kickxellales 27 2 control
Archaeosporales 29 2 control
Calosphaeriales 31 2 control
Xylariales 32 2 control
Schizosaccharomycetales 36 2 control
Monoblepharidales 42 2 control
Magnaporthales 46 2 control
Sordariales 47 2 control
Diversisporales 49 2 control
Dothideales 50 2 control
Trechisporales 52 2 control
Mucorales 54 2 control
Tremellales 60 2 control
Blastocladiales 61 2 control
Chytridiales 61 2 control
Sebacinales 63 2 control
Mycocaliciales 71 2 control
Cladochytriales 78 2 control
Hysteriales 80 2 control
Phyllachorales 81 2 control
Russulales 86 2 control
Spizellomycetales 89 2 control
Peltigerales 92 2 control
Hymenochaetales 92 2 control
Orbiliales 99 2 control
Polyporales 111 2 control
Pyrenulales 117 2 control
Glomerales 130 2 control
Eurotiales 130 2 control
Taphrinales 143 2 control
Pleosporales 150 2 control
Botryosphaeriales 165 2 control
Pezizales 167 2 control
Entomophthorales 177 2 control
Lecanorales 224 2 control
Hypocreales 225 2 control
Mortierellales 234 2 control
Capnodiales 238 2 control
Chaetothyriales 239 2 control
Helotiales 245 2 control
Atheliales 260 2 control
Agaricales 263 2 control
Saccharomycetales 266 2 control
Onygenales 280 2 control
Boletales 287 2 control
Helicobasidiales 1 3 control
Cladophorales 1 3 control
Mixiales 1 3 control
Coronophorales 1 3 control
Melanosporales 1 3 control
Agaricostilbales 1 3 control
Phallales 1 3 control
Acrospermales 1 3 control
Lagenidiales 1 3 control
Platygloeales 1 3 control
Echinosteliales 1 3 control
Boliniales 1 3 control
Dimargaritales 2 3 control
Chaetosphaeriales 2 3 control
Doassansiales 2 3 control
Atractiellales 2 3 control
Naohideales 2 3 control
Jahnulales 2 3 control
Microthyriales 2 3 control
Urocystales 2 3 control
Wallemiales 2 3 control
Entylomatales 2 3 control
Hysterangiales 3 3 control
Leucosporidiales 3 3 control
Trypetheliales 3 3 control
Gloeophyllales 3 3 control
Tilletiales 4 3 control
Microbotryales 4 3 control
Geastrales 4 3 control
Trechisporales 4 3 control
Olpidiopsidales 4 3 control
Chaetophorales 6 3 control
Neocallimastigales 6 3 control
Agyriales 6 3 control
Erythrobasidiales 6 3 control
Georgefischeriales 6 3 control
Lichinales 7 3 control
Calosphaeriales 7 3 control
Mycocaliciales 8 3 control
Cystofilobasidiales 8 3 control
Pucciniales 9 3 control
Candelariales 10 3 control
Malasseziales 11 3 control
Microascales 11 3 control
Baeomycetales 12 3 control
Kickxellales 12 3 control
Umbilicariales 12 3 control
Microstromatales 14 3 control
Pyrenulales 14 3 control
Sporidiobolales 14 3 control
Hysteriales 15 3 control
Gomphales 16 3 control
Arthoniales 17 3 control
Geoglossales 18 3 control
Exobasidiales 19 3 control
Mytilinidiales 19 3 control
Entorrhizales 20 3 control
Paraglomerales 20 3 control
Cantharellales 20 3 control
Auriculariales 20 3 control
Atheliales 22 3 control
Myriangiales 24 3 control
Orbiliales 28 3 control
Peltigerales 29 3 control
Neolectales 31 3 control
Jaapiales 32 3 control
Amylocorticiales 32 3 control
Corticiales 32 3 control
Diaporthales 32 3 control
Rhizophydiales 32 3 control
Dacrymycetales 33 3 control
Schizosaccharomycetales 37 3 control
Pertusariales 37 3 control
Patellariales 38 3 control
Archaeosporales 40 3 control
Ustilaginales 42 3 control
Taphrinales 44 3 control
Monoblepharidales 50 3 control
Magnaporthales 52 3 control
Chytridiales 53 3 control
Hymenochaetales 55 3 control
Septobasidiales 57 3 control
Xylariales 59 3 control
Blastocladiales 61 3 control
Mucorales 62 3 control
Harpellales 66 3 control
Tremellales 67 3 control
Diversisporales 71 3 control
Dothideales 87 3 control
Russulales 96 3 control
Cladochytriales 97 3 control
Phyllachorales 98 3 control
Sordariales 103 3 control
Lecanorales 109 3 control
Sebacinales 109 3 control
Filobasidiales 113 3 control
Glomerales 114 3 control
Hypocreales 116 3 control
Botryosphaeriales 118 3 control
Coniochaetales 121 3 control
Endogonales 123 3 control
Eurotiales 134 3 control
Boletales 140 3 control
Chaetothyriales 152 3 control
Mortierellales 155 3 control
Spizellomycetales 162 3 control
Entomophthorales 163 3 control
Pezizales 175 3 control
Polyporales 176 3 control
Capnodiales 192 3 control
Thelephorales 199 3 control
Pleosporales 215 3 control
Agaricales 222 3 control
Saccharomycetales 229 3 control
Onygenales 253 3 control
Helotiales 284 3 control
Echinosteliales 1 4 control
Dimargaritales 1 4 control
Cladophorales 1 4 control
Mixiales 1 4 control
Phallales 1 4 control
Helicobasidiales 1 4 control
Hysterangiales 1 4 control
Coronophorales 1 4 control
Platygloeales 1 4 control
Lagenidiales 1 4 control
Agaricostilbales 1 4 control
Entylomatales 1 4 control
Acrospermales 1 4 control
Doassansiales 1 4 control
Mytilinidiales 1 4 control
Melanosporales 1 4 control
Trypetheliales 1 4 control
Septobasidiales 1 4 control
Georgefischeriales 1 4 control
Entorrhizales 2 4 control
Olpidiopsidales 2 4 control
Atractiellales 2 4 control
Urocystales 2 4 control
Chaetophorales 2 4 control
Naohideales 2 4 control
Geoglossales 2 4 control
Microascales 2 4 control
Wallemiales 2 4 control
Candelariales 3 4 control
Jaapiales 3 4 control
Leucosporidiales 3 4 control
Trechisporales 3 4 control
Microthyriales 3 4 control
Erythrobasidiales 3 4 control
Microbotryales 3 4 control
Geastrales 3 4 control
Jahnulales 4 4 control
Exobasidiales 4 4 control
Gomphales 4 4 control
Lichinales 4 4 control
Boliniales 5 4 control
Thelephorales 5 4 control
Archaeosporales 6 4 control
Neolectales 6 4 control
Tilletiales 6 4 control
Microstromatales 7 4 control
Sporidiobolales 8 4 control
Ustilaginales 8 4 control
Paraglomerales 10 4 control
Pucciniales 10 4 control
Monoblepharidales 11 4 control
Malasseziales 12 4 control
Arthoniales 12 4 control
Dacrymycetales 12 4 control
Myriangiales 12 4 control
Patellariales 14 4 control
Harpellales 15 4 control
Agyriales 15 4 control
Chaetosphaeriales 17 4 control
Diversisporales 18 4 control
Pertusariales 19 4 control
Gloeophyllales 21 4 control
Diaporthales 26 4 control
Filobasidiales 26 4 control
Schizosaccharomycetales 27 4 control
Hymenochaetales 28 4 control
Neocallimastigales 29 4 control
Atheliales 30 4 control
Russulales 30 4 control
Baeomycetales 30 4 control
Auriculariales 36 4 control
Magnaporthales 37 4 control
Calosphaeriales 39 4 control
Chytridiales 40 4 control
Phyllachorales 43 4 control
Umbilicariales 46 4 control
Corticiales 51 4 control
Cladochytriales 53 4 control
Xylariales 54 4 control
Endogonales 66 4 control
Hysteriales 70 4 control
Blastocladiales 70 4 control
Rhizophydiales 70 4 control
Orbiliales 72 4 control
Polyporales 80 4 control
Peltigerales 81 4 control
Mycocaliciales 82 4 control
Pyrenulales 83 4 control
Sebacinales 83 4 control
Taphrinales 88 4 control
Tremellales 90 4 control
Dothideales 91 4 control
Cantharellales 125 4 control
Botryosphaeriales 128 4 control
Pleosporales 143 4 control
Amylocorticiales 152 4 control
Entomophthorales 159 4 control
Sordariales 160 4 control
Boletales 164 4 control
Cystofilobasidiales 167 4 control
Pezizales 173 4 control
Coniochaetales 176 4 control
Kickxellales 194 4 control
Lecanorales 210 4 control
Eurotiales 213 4 control
Helotiales 227 4 control
Glomerales 235 4 control
Chaetothyriales 247 4 control
Capnodiales 251 4 control
Agaricales 254 4 control
Hypocreales 257 4 control
Saccharomycetales 265 4 control
Spizellomycetales 275 4 control
Onygenales 276 4 control
Mucorales 303 4 control
Mortierellales 305 4 control
Helicobasidiales 1 1 warmed
Coronophorales 1 1 warmed
Lagenidiales 1 1 warmed
Dimargaritales 1 1 warmed
Platygloeales 1 1 warmed
Candelariales 1 1 warmed
Hysterangiales 1 1 warmed
Cladophorales 1 1 warmed
Doassansiales 1 1 warmed
Trypetheliales 2 1 warmed
Echinosteliales 2 1 warmed
Melanosporales 2 1 warmed
Wallemiales 2 1 warmed
Mytilinidiales 2 1 warmed
Acrospermales 3 1 warmed
Phallales 3 1 warmed
Tilletiales 3 1 warmed
Geoglossales 3 1 warmed
Microthyriales 4 1 warmed
Gloeophyllales 4 1 warmed
Boliniales 6 1 warmed
Urocystales 6 1 warmed
Georgefischeriales 7 1 warmed
Gomphales 7 1 warmed
Umbilicariales 7 1 warmed
Chaetophorales 7 1 warmed
Lichinales 8 1 warmed
Olpidiopsidales 8 1 warmed
Jahnulales 8 1 warmed
Neocallimastigales 9 1 warmed
Chaetosphaeriales 9 1 warmed
Trechisporales 9 1 warmed
Geastrales 10 1 warmed
Entylomatales 11 1 warmed
Hysteriales 14 1 warmed
Coniochaetales 17 1 warmed
Arthoniales 23 1 warmed
Thelephorales 24 1 warmed
Paraglomerales 24 1 warmed
Baeomycetales 27 1 warmed
Patellariales 28 1 warmed
Calosphaeriales 29 1 warmed
Jaapiales 31 1 warmed
Atractiellales 35 1 warmed
Malasseziales 38 1 warmed
Diaporthales 40 1 warmed
Myriangiales 40 1 warmed
Mycocaliciales 40 1 warmed
Mixiales 42 1 warmed
Atheliales 43 1 warmed
Filobasidiales 47 1 warmed
Microascales 47 1 warmed
Cystofilobasidiales 50 1 warmed
Ustilaginales 57 1 warmed
Microstromatales 59 1 warmed
Chytridiales 67 1 warmed
Pyrenulales 68 1 warmed
Agyriales 73 1 warmed
Agaricostilbales 75 1 warmed
Pertusariales 76 1 warmed
Entorrhizales 82 1 warmed
Orbiliales 86 1 warmed
Auriculariales 93 1 warmed
Peltigerales 96 1 warmed
Magnaporthales 99 1 warmed
Amylocorticiales 102 1 warmed
Naohideales 102 1 warmed
Exobasidiales 104 1 warmed
Corticiales 112 1 warmed
Dothideales 119 1 warmed
Archaeosporales 120 1 warmed
Endogonales 121 1 warmed
Russulales 122 1 warmed
Microbotryales 123 1 warmed
Xylariales 124 1 warmed
Sporidiobolales 129 1 warmed
Cantharellales 137 1 warmed
Harpellales 142 1 warmed
Leucosporidiales 145 1 warmed
Botryosphaeriales 150 1 warmed
Rhizophydiales 151 1 warmed
Septobasidiales 168 1 warmed
Sordariales 171 1 warmed
Monoblepharidales 178 1 warmed
Pucciniales 181 1 warmed
Schizosaccharomycetales 182 1 warmed
Taphrinales 183 1 warmed
Mucorales 184 1 warmed
Kickxellales 185 1 warmed
Blastocladiales 188 1 warmed
Sebacinales 196 1 warmed
Polyporales 200 1 warmed
Tremellales 204 1 warmed
Diversisporales 206 1 warmed
Cladochytriales 208 1 warmed
Phyllachorales 214 1 warmed
Eurotiales 217 1 warmed
Hymenochaetales 218 1 warmed
Erythrobasidiales 221 1 warmed
Capnodiales 223 1 warmed
Dacrymycetales 226 1 warmed
Lecanorales 228 1 warmed
Pleosporales 237 1 warmed
Boletales 241 1 warmed
Pezizales 246 1 warmed
Glomerales 250 1 warmed
Neolectales 259 1 warmed
Chaetothyriales 264 1 warmed
Mortierellales 269 1 warmed
Spizellomycetales 272 1 warmed
Helotiales 281 1 warmed
Entomophthorales 282 1 warmed
Saccharomycetales 288 1 warmed
Onygenales 289 1 warmed
Agaricales 293 1 warmed
Hypocreales 296 1 warmed
Helicobasidiales 1 2 warmed
Echinosteliales 1 2 warmed
Mixiales 1 2 warmed
Melanosporales 1 2 warmed
Dimargaritales 1 2 warmed
Cladophorales 1 2 warmed
Lagenidiales 1 2 warmed
Naohideales 1 2 warmed
Agaricostilbales 1 2 warmed
Coronophorales 1 2 warmed
Phallales 2 2 warmed
Entorrhizales 2 2 warmed
Georgefischeriales 2 2 warmed
Septobasidiales 2 2 warmed
Wallemiales 2 2 warmed
Olpidiopsidales 2 2 warmed
Platygloeales 3 2 warmed
Doassansiales 3 2 warmed
Geastrales 3 2 warmed
Candelariales 3 2 warmed
Atractiellales 3 2 warmed
Boliniales 4 2 warmed
Entylomatales 4 2 warmed
Tilletiales 4 2 warmed
Geoglossales 4 2 warmed
Acrospermales 5 2 warmed
Mytilinidiales 6 2 warmed
Hysterangiales 6 2 warmed
Cystofilobasidiales 6 2 warmed
Trypetheliales 6 2 warmed
Jahnulales 6 2 warmed
Microthyriales 6 2 warmed
Gloeophyllales 7 2 warmed
Microstromatales 7 2 warmed
Lichinales 7 2 warmed
Chaetophorales 8 2 warmed
Chaetosphaeriales 8 2 warmed
Gomphales 9 2 warmed
Urocystales 11 2 warmed
Microbotryales 11 2 warmed
Corticiales 12 2 warmed
Paraglomerales 12 2 warmed
Leucosporidiales 12 2 warmed
Dacrymycetales 13 2 warmed
Agyriales 13 2 warmed
Neocallimastigales 13 2 warmed
Filobasidiales 13 2 warmed
Arthoniales 13 2 warmed
Jaapiales 14 2 warmed
Cantharellales 14 2 warmed
Mycocaliciales 14 2 warmed
Auriculariales 15 2 warmed
Erythrobasidiales 15 2 warmed
Calosphaeriales 16 2 warmed
Exobasidiales 18 2 warmed
Schizosaccharomycetales 19 2 warmed
Sporidiobolales 19 2 warmed
Baeomycetales 20 2 warmed
Microascales 20 2 warmed
Trechisporales 21 2 warmed
Neolectales 22 2 warmed
Umbilicariales 26 2 warmed
Ustilaginales 29 2 warmed
Pyrenulales 30 2 warmed
Pertusariales 30 2 warmed
Pucciniales 31 2 warmed
Harpellales 31 2 warmed
Monoblepharidales 37 2 warmed
Hysteriales 38 2 warmed
Orbiliales 40 2 warmed
Malasseziales 40 2 warmed
Archaeosporales 44 2 warmed
Endogonales 46 2 warmed
Peltigerales 47 2 warmed
Amylocorticiales 48 2 warmed
Diaporthales 49 2 warmed
Rhizophydiales 52 2 warmed
Thelephorales 52 2 warmed
Phyllachorales 58 2 warmed
Diversisporales 60 2 warmed
Tremellales 61 2 warmed
Patellariales 63 2 warmed
Myriangiales 63 2 warmed
Taphrinales 65 2 warmed
Hymenochaetales 67 2 warmed
Chytridiales 70 2 warmed
Xylariales 78 2 warmed
Blastocladiales 84 2 warmed
Dothideales 89 2 warmed
Sebacinales 91 2 warmed
Cladochytriales 91 2 warmed
Kickxellales 99 2 warmed
Mucorales 105 2 warmed
Magnaporthales 115 2 warmed
Glomerales 124 2 warmed
Botryosphaeriales 127 2 warmed
Lecanorales 132 2 warmed
Atheliales 143 2 warmed
Polyporales 166 2 warmed
Russulales 174 2 warmed
Entomophthorales 180 2 warmed
Spizellomycetales 187 2 warmed
Chaetothyriales 190 2 warmed
Pezizales 198 2 warmed
Hypocreales 211 2 warmed
Boletales 214 2 warmed
Sordariales 215 2 warmed
Coniochaetales 232 2 warmed
Eurotiales 233 2 warmed
Capnodiales 240 2 warmed
Saccharomycetales 255 2 warmed
Onygenales 268 2 warmed
Pleosporales 271 2 warmed
Agaricales 277 2 warmed
Helotiales 291 2 warmed
Mortierellales 292 2 warmed
Cladophorales 1 3 warmed
Helicobasidiales 1 3 warmed
Echinosteliales 1 3 warmed
Naohideales 1 3 warmed
Mixiales 1 3 warmed
Lagenidiales 1 3 warmed
Coronophorales 1 3 warmed
Dimargaritales 1 3 warmed
Platygloeales 1 3 warmed
Melanosporales 2 3 warmed
Agaricostilbales 2 3 warmed
Phallales 2 3 warmed
Acrospermales 2 3 warmed
Candelariales 2 3 warmed
Trypetheliales 3 3 warmed
Atractiellales 3 3 warmed
Microthyriales 4 3 warmed
Trechisporales 4 3 warmed
Entorrhizales 4 3 warmed
Olpidiopsidales 4 3 warmed
Doassansiales 5 3 warmed
Wallemiales 5 3 warmed
Georgefischeriales 7 3 warmed
Atheliales 7 3 warmed
Jahnulales 7 3 warmed
Hysterangiales 7 3 warmed
Entylomatales 8 3 warmed
Gloeophyllales 8 3 warmed
Boliniales 9 3 warmed
Tilletiales 9 3 warmed
Microstromatales 10 3 warmed
Chaetosphaeriales 11 3 warmed
Mytilinidiales 11 3 warmed
Chaetophorales 11 3 warmed
Leucosporidiales 11 3 warmed
Lichinales 11 3 warmed
Corticiales 11 3 warmed
Geoglossales 12 3 warmed
Gomphales 12 3 warmed
Microbotryales 13 3 warmed
Paraglomerales 14 3 warmed
Urocystales 15 3 warmed
Microascales 16 3 warmed
Geastrales 18 3 warmed
Ustilaginales 19 3 warmed
Erythrobasidiales 20 3 warmed
Jaapiales 21 3 warmed
Neolectales 22 3 warmed
Neocallimastigales 23 3 warmed
Thelephorales 25 3 warmed
Exobasidiales 28 3 warmed
Pucciniales 30 3 warmed
Cystofilobasidiales 31 3 warmed
Malasseziales 35 3 warmed
Archaeosporales 37 3 warmed
Sporidiobolales 38 3 warmed
Auriculariales 39 3 warmed
Myriangiales 41 3 warmed
Arthoniales 43 3 warmed
Amylocorticiales 46 3 warmed
Cantharellales 47 3 warmed
Calosphaeriales 48 3 warmed
Schizosaccharomycetales 49 3 warmed
Dacrymycetales 55 3 warmed
Monoblepharidales 56 3 warmed
Harpellales 62 3 warmed
Septobasidiales 64 3 warmed
Diversisporales 66 3 warmed
Patellariales 72 3 warmed
Diaporthales 72 3 warmed
Hymenochaetales 76 3 warmed
Chytridiales 88 3 warmed
Hysteriales 89 3 warmed
Blastocladiales 96 3 warmed
Pertusariales 101 3 warmed
Xylariales 102 3 warmed
Mycocaliciales 106 3 warmed
Endogonales 108 3 warmed
Tremellales 110 3 warmed
Phyllachorales 113 3 warmed
Peltigerales 125 3 warmed
Rhizophydiales 131 3 warmed
Orbiliales 133 3 warmed
Cladochytriales 134 3 warmed
Pyrenulales 135 3 warmed
Boletales 136 3 warmed
Agyriales 138 3 warmed
Magnaporthales 139 3 warmed
Mucorales 146 3 warmed
Kickxellales 147 3 warmed
Polyporales 154 3 warmed
Filobasidiales 158 3 warmed
Taphrinales 161 3 warmed
Russulales 169 3 warmed
Glomerales 172 3 warmed
Baeomycetales 179 3 warmed
Sordariales 193 3 warmed
Dothideales 203 3 warmed
Umbilicariales 207 3 warmed
Entomophthorales 212 3 warmed
Botryosphaeriales 216 3 warmed
Spizellomycetales 220 3 warmed
Coniochaetales 230 3 warmed
Sebacinales 231 3 warmed
Hypocreales 236 3 warmed
Lecanorales 249 3 warmed
Pleosporales 252 3 warmed
Pezizales 258 3 warmed
Agaricales 260 3 warmed
Eurotiales 274 3 warmed
Capnodiales 278 3 warmed
Saccharomycetales 286 3 warmed
Chaetothyriales 294 3 warmed
Mortierellales 297 3 warmed
Helotiales 301 3 warmed
Onygenales 302 3 warmed
Echinosteliales 1 4 warmed
Helicobasidiales 1 4 warmed
Cladophorales 1 4 warmed
Dimargaritales 1 4 warmed
Hysterangiales 1 4 warmed
Coronophorales 1 4 warmed
Mixiales 1 4 warmed
Lagenidiales 1 4 warmed
Phallales 1 4 warmed
Melanosporales 1 4 warmed
Agaricostilbales 1 4 warmed
Naohideales 1 4 warmed
Trypetheliales 2 4 warmed
Geastrales 2 4 warmed
Olpidiopsidales 2 4 warmed
Platygloeales 2 4 warmed
Acrospermales 2 4 warmed
Geoglossales 2 4 warmed
Doassansiales 2 4 warmed
Georgefischeriales 3 4 warmed
Entylomatales 3 4 warmed
Urocystales 3 4 warmed
Thelephorales 3 4 warmed
Wallemiales 4 4 warmed
Trechisporales 4 4 warmed
Candelariales 4 4 warmed
Atractiellales 4 4 warmed
Jaapiales 5 4 warmed
Atheliales 6 4 warmed
Gomphales 6 4 warmed
Erythrobasidiales 6 4 warmed
Microascales 6 4 warmed
Neocallimastigales 7 4 warmed
Entorrhizales 10 4 warmed
Tilletiales 11 4 warmed
Ustilaginales 11 4 warmed
Jahnulales 11 4 warmed
Microthyriales 12 4 warmed
Microstromatales 13 4 warmed
Pucciniales 14 4 warmed
Boliniales 15 4 warmed
Lichinales 16 4 warmed
Chaetophorales 19 4 warmed
Microbotryales 19 4 warmed
Mytilinidiales 20 4 warmed
Gloeophyllales 22 4 warmed
Amylocorticiales 24 4 warmed
Auriculariales 25 4 warmed
Paraglomerales 26 4 warmed
Leucosporidiales 27 4 warmed
Chytridiales 31 4 warmed
Arthoniales 32 4 warmed
Exobasidiales 33 4 warmed
Sebacinales 33 4 warmed
Neolectales 33 4 warmed
Archaeosporales 34 4 warmed
Hymenochaetales 36 4 warmed
Myriangiales 42 4 warmed
Russulales 43 4 warmed
Malasseziales 45 4 warmed
Harpellales 52 4 warmed
Patellariales 52 4 warmed
Monoblepharidales 55 4 warmed
Schizosaccharomycetales 58 4 warmed
Diversisporales 59 4 warmed
Baeomycetales 65 4 warmed
Sporidiobolales 67 4 warmed
Dacrymycetales 67 4 warmed
Kickxellales 71 4 warmed
Blastocladiales 73 4 warmed
Septobasidiales 74 4 warmed
Rhizophydiales 75 4 warmed
Pertusariales 76 4 warmed
Corticiales 76 4 warmed
Endogonales 79 4 warmed
Cystofilobasidiales 83 4 warmed
Agyriales 83 4 warmed
Xylariales 85 4 warmed
Diaporthales 94 4 warmed
Polyporales 95 4 warmed
Cladochytriales 96 4 warmed
Chaetosphaeriales 96 4 warmed
Umbilicariales 100 4 warmed
Tremellales 103 4 warmed
Orbiliales 109 4 warmed
Mycocaliciales 125 4 warmed
Boletales 126 4 warmed
Calosphaeriales 128 4 warmed
Phyllachorales 141 4 warmed
Hysteriales 144 4 warmed
Glomerales 148 4 warmed
Peltigerales 157 4 warmed
Dothideales 170 4 warmed
Pyrenulales 173 4 warmed
Spizellomycetales 175 4 warmed
Magnaporthales 183 4 warmed
Cantharellales 186 4 warmed
Mucorales 195 4 warmed
Taphrinales 197 4 warmed
Filobasidiales 201 4 warmed
Entomophthorales 205 4 warmed
Botryosphaeriales 209 4 warmed
Pezizales 243 4 warmed
Agaricales 244 4 warmed
Coniochaetales 248 4 warmed
Pleosporales 262 4 warmed
Lecanorales 267 4 warmed
Hypocreales 273 4 warmed
Mortierellales 279 4 warmed
Saccharomycetales 283 4 warmed
Sordariales 284 4 warmed
Capnodiales 285 4 warmed
Chaetothyriales 290 4 warmed
Eurotiales 295 4 warmed
Helotiales 298 4 warmed
Onygenales 299 4 warmed
")
Data = read.table(textConnection(Input),header=TRUE)
### Order factors by the order in data frame
### Otherwise, R will alphabetize them
Data$treatment = factor(Data$treatment,
levels=unique(Data$treatment))
Data$plot = factor(Data$plot,
levels=unique(Data$plot))
Data$order = factor(Data$order,
levels=unique(Data$order))
### Check the data frame
library(psych)
headTail(Data)
str(Data)
summary(Data)
### Remove unnecessary objects
rm(Input)
#In this first example, the model will be specified with the lmer function
#in the package lme4. The term (1|Town) in the model formula indicates that
#Town should be treated as a random variable, with each level having its own
#in the model. The anova function in the package lmerTest is used to
#produce p-values for the fixed effects. The rand function in the package
#lmerTest produces p-values for the random effects.
library(lme4)
library(lmerTest)
model = lmer(rank_abundance ~ treatment*order + (1|plot),
data=Data,
REML=TRUE)
anova(model)
Type III Analysis of Variance Table with Satterthwaite's method
Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
treatment 192569 192569 1 693 114.8998 < 2e-16 ***
order 5102330 44368 115 693 26.4730 < 2e-16 ***
treatment:order 239486 2082 115 693 1.2426 0.05509 .
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
rand(model)
ANOVA-like table for random-effects: Single term deletions
Model:
rank_abundance ~ treatment + order + (1 | plot) + treatment:order
npar logLik AIC LRT Df Pr(>Chisq)
<none> 234 -3735.2 7938.4
(1 | plot) 233 -3743.0 7951.9 15.553 1 8.023e-05 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1