extra_download_files/prumetal_heatmap_rosetta.r
In carolinafishes/PhyInformR: Rapid Calculation of Phylogenetic Information Content
##set your wd to match where the below files are
setwd("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness")
###Next read in all the rate vector files
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/loci1_30Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/loci31_62Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/loci63_100Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/loci101_141Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/loci142_197Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/loci200_240Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/242_280Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/281_314Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/314_349Allrates_file.allrates")
##note on the above, we encountered memory limitations getting all the individual rate vectors, so we broke the dataset into stages to save memory. With a better machine you could just estimates all the site rates at once.
##here we are generating PI profiles
L1<-ratesA[1:1594]
L2<-ratesA[1595:3354]
L3<-ratesA[3355:4990]
L4<-ratesA[4991:6483]
L5<-ratesA[6484:8117]
L6<-ratesA[8118:9799]
L7<-ratesA[9800:10831]
L8<-ratesA[10832:12320]
L9<-ratesA[12321:14008]
L10<-ratesA[14009:15201]
L11<-ratesA[15202:16983]
L12<-ratesA[16984:18640]
L21<-ratesA[18641:19530]
L22<-ratesA[19531:21236]
L24<-ratesA[21237:22925]
L27<-ratesA[22926:23933]
L28<-ratesA[23934:25539]
L30<-ratesA[25540:27222]
L31<-ratesB[1:1743]
L32<-ratesB[1744:3155]
L34<-ratesB[3156:4772]
L35<-ratesB[4773:6490]
L36<-ratesB[6491:7839]
L37<-ratesB[7840:9461]
L38<-ratesB[9462:11134]
L39<-ratesB[11135:12773]
L41<-ratesB[12774:14451]
L42<-ratesB[14452:15980]
L43<-ratesB[15981:17635]
L44<-ratesB[17636:19274]
L48<-ratesB[19275:20892]
L49<-ratesB[20893:22501]
L50<-ratesB[22502:24067]
L51<-ratesB[24068:24676]
L53<-ratesB[24677:26336]
L54<-ratesB[26337:27837]
L57<-ratesB[27838:28703]
L58<-ratesB[28704:30437]
L59<-ratesB[30438:32254]
L61<-ratesB[32255:33594]
L62<-ratesB[33595:35320]
L63<-ratesC[1:1639]
L64<-ratesC[1640:3343]
L65<-ratesC[3344:4969]
L67<-ratesC[4970:6692]
L72<-ratesC[6693:8126]
L73<-ratesC[8127:9466]
L74<-ratesC[9467:10561]
L75<-ratesC[10562:12104]
L76<-ratesC[12105:13564]
L77<-ratesC[13565:14900]
L78<-ratesC[14901:16176]
L79<-ratesC[16177:17743]
L80<-ratesC[17744:19041]
L81<-ratesC[19042:20639]
L82<-ratesC[20640:22331]
L85<-ratesC[22332:24059]
L86<-ratesC[24060:25809]
L87<-ratesC[25810:27611]
L88<-ratesC[27612:29278]
L89<-ratesC[29279:30703]
L91<-ratesC[30704:32444]
L94<-ratesC[32445:33290]
L95<-ratesC[33291:34744]
L98<-ratesC[34745:36509]
L99<-ratesC[36510:38221]
L100<-ratesC[38222:39639]
L102<-ratesD[1:1351]
L103<-ratesD[1352:3040]
L104<-ratesD[3041:4772]
L105<-ratesD[4773:6235]
L107<-ratesD[6236:7937]
L108<-ratesD[7938:9637]
L110<-ratesD[9638:11009]
L111<-ratesD[11010:12347]
L113<-ratesD[12348:14304]
L115<-ratesD[14305:15037]
L116<-ratesD[15038:16416]
L118<-ratesD[16417:17430]
L119<-ratesD[17431:19016]
L120<-ratesD[19017:20594]
L121<-ratesD[20595:22531]
L122<-ratesD[22532:24477]
L125<-ratesD[24478:26123]
L126<-ratesD[26124:27793]
L127<-ratesD[27794:29519]
L128<-ratesD[29520:30838]
L129<-ratesD[30839:32483]
L130<-ratesD[32484:34253]
L131<-ratesD[34254:35386]
L133<-ratesD[35387:36951]
L134<-ratesD[36952:38522]
L135<-ratesD[38523:40150]
L136<-ratesD[40151:42208]
L137<-ratesD[42209:43745]
L141<-ratesD[43746:44950]
L142<-ratesE[1:1728]
L143<-ratesE[1729:3316]
L145<-ratesE[3317:5021]
L146<-ratesE[5022:6809]
L147<-ratesE[6810:8445]
L148<-ratesE[8446:9774]
L149<-ratesE[9775:11581]
L150<-ratesE[11582:13436]
L151<-ratesE[13437:15147]
L152<-ratesE[15148:16584]
L153<-ratesE[16585:18687]
L154<-ratesE[18688:20374]
L155<-ratesE[20375:22047]
L157<-ratesE[22048:23581]
L158<-ratesE[23582:25368]
L159<-ratesE[25369:26648]
L161<-ratesE[26649:28612]
L162<-ratesE[28613:30146]
L163<-ratesE[30147:31220]
L165<-ratesE[31221:32704]
L169<-ratesE[32705:34487]
L170<-ratesE[34488:36262]
L171<-ratesE[36263:38252]
L174<-ratesE[38253:39153]
L175<-ratesE[39154:40882]
L176<-ratesE[40883:42794]
L177<-ratesE[42795:44516]
L178<-ratesE[44517:46226]
L180<-ratesE[46227:47912]
L181<-ratesE[47913:49716]
L182<-ratesE[49717:51708]
L183<-ratesE[51709:53072]
L184<-ratesE[53073:54660]
L186<-ratesE[54661:56124]
L187<-ratesE[56125:57793]
L188<-ratesE[57794:59329]
L189<-ratesE[59330:61222]
L190<-ratesE[61223:62883]
L192<-ratesE[62884:64243]
L193<-ratesE[64244:64715]
L194<-ratesE[64716:66490]
L195<-ratesE[66491:68210]
L196<-ratesE[68211:69909]
L197<-ratesE[69910:71170]
L201<-ratesF[1:1060]
L202<-ratesF[1061:2758]
L203<-ratesF[2759:4671]
L204<-ratesF[4672:6700]
L205<-ratesF[6701:8387]
L206<-ratesF[8388:9997]
L207<-ratesF[9998:11414]
L208<-ratesF[11415:11864]
L209<-ratesF[11865:12949]
L210<-ratesF[12950:14353]
L211<-ratesF[14354:16035]
L213<-ratesF[16036:18351]
L214<-ratesF[18352:19979]
L215<-ratesF[19980:21151]
L216<-ratesF[21152:22828]
L217<-ratesF[22829:23765]
L219<-ratesF[23766:24489]
L221<-ratesF[24490:26260]
L222<-ratesF[26261:27927]
L223<-ratesF[27928:28371]
L224<-ratesF[28372:29642]
L225<-ratesF[29643:30613]
L226<-ratesF[30614:32428]
L228<-ratesF[32429:34260]
L229<-ratesF[34261:35864]
L230<-ratesF[35865:37529]
L231<-ratesF[37530:39039]
L232<-ratesF[39040:40783]
L233<-ratesF[40784:41629]
L234<-ratesF[41630:43314]
L235<-ratesF[43315:45010]
L237<-ratesF[45011:45831]
L239<-ratesF[45832:46680]
L240<-ratesF[46681:48146]
L241<-ratesG[1:1737]
L242<-ratesG[1738:3137]
L243<-ratesG[3138:4101]
L244<-ratesG[4102:5203]
L245<-ratesG[5204:6982]
L246<-ratesG[6983:8699]
L247<-ratesG[8700:10305]
L248<-ratesG[10306:11853]
L249<-ratesG[11854:12840]
L250<-ratesG[12841:14367]
L251<-ratesG[14368:16098]
L252<-ratesG[16099:17753]
L253<-ratesG[17754:19097]
L255<-ratesG[19098:20790]
L256<-ratesG[20791:22514]
L257<-ratesG[22515:24232]
L258<-ratesG[24233:26099]
L260<-ratesG[26100:27700]
L261<-ratesG[27701:29447]
L262<-ratesG[29448:31029]
L264<-ratesG[31030:32822]
L265<-ratesG[32823:33361]
L266<-ratesG[33362:35547]
L267<-ratesG[35548:37206]
L269<-ratesG[37207:38604]
L270<-ratesG[38605:40123]
L271<-ratesG[40124:41740]
L272<-ratesG[41741:42304]
L275<-ratesG[42305:43515]
L276<-ratesG[43516:45199]
L277<-ratesG[45200:46347]
L279<-ratesG[46348:47213]
L280<-ratesG[47214:48742]
L281<-ratesH[1:1726]
L282<-ratesH[1727:3670]
L288<-ratesH[3671:5341]
L289<-ratesH[5342:7002]
L290<-ratesH[7003:8661]
L292<-ratesH[8662:10362]
L293<-ratesH[10363:12103]
L294<-ratesH[12104:13576]
L295<-ratesH[13577:15304]
L296<-ratesH[15305:16994]
L297<-ratesH[16995:18550]
L298<-ratesH[18551:20402]
L301<-ratesH[20403:21124]
L302<-ratesH[21125:21990]
L303<-ratesH[21991:23590]
L305<-ratesH[23591:24342]
L306<-ratesH[24343:26134]
L307<-ratesH[26135:27276]
L310<-ratesH[27277:28956]
L311<-ratesH[28957:30731]
L312<-ratesH[30732:32141]
L314<-ratesH[32142:33859]
L315<-ratesI[1:1720]
L316<-ratesI[1721:3516]
L317<-ratesI[3517:4945]
L318<-ratesI[4946:6375]
L319<-ratesI[6376:7991]
L320<-ratesI[7992:9624]
L321<-ratesI[9625:11381]
L322<-ratesI[11382:13087]
L325<-ratesI[13088:14812]
L327<-ratesI[14813:16353]
L328<-ratesI[16354:18028]
L329<-ratesI[18029:19779]
L330<-ratesI[19780:21420]
L331<-ratesI[21421:22620]
L333<-ratesI[22621:24319]
L334<-ratesI[24320:25487]
L335<-ratesI[25488:27171]
L336<-ratesI[27172:28622]
L337<-ratesI[28623:30241]
L338<-ratesI[30242:32164]
L339<-ratesI[32165:33465]
L340<-ratesI[33466:35125]
L341<-ratesI[35126:36853]
L342<-ratesI[36854:38590]
L343<-ratesI[38591:39982]
L344<-ratesI[39983:40942]
L346<-ratesI[40943:42519]
L347<-ratesI[42520:44188]
L348<-ratesI[44189:45275]
L349<-ratesI[45276:45636]
##signal noise functions require matrix formatted site rates, so convert first
as.matrix(L1)->L1
as.matrix(L2)->L2
as.matrix(L3)->L3
as.matrix(L4)->L4
as.matrix(L5)->L5
as.matrix(L6)->L6
as.matrix(L7)->L7
as.matrix(L8)->L8
as.matrix(L9)->L9
as.matrix(L10)->L10
as.matrix(L11)->L11
as.matrix(L12)->L12
as.matrix(L21)->L21
as.matrix(L22)->L22
as.matrix(L24)->L24
as.matrix(L27)->L27
as.matrix(L28)->L28
as.matrix(L30)->L30
as.matrix(L31)->L31
as.matrix(L32)->L32
as.matrix(L34)->L34
as.matrix(L35)->L35
as.matrix(L36)->L36
as.matrix(L37)->L37
as.matrix(L38)->L38
as.matrix(L39)->L39
as.matrix(L41)->L41
as.matrix(L42)->L42
as.matrix(L43)->L43
as.matrix(L44)->L44
as.matrix(L48)->L48
as.matrix(L49)->L49
as.matrix(L50)->L50
as.matrix(L51)->L51
as.matrix(L53)->L53
as.matrix(L54)->L54
as.matrix(L57)->L57
as.matrix(L58)->L58
as.matrix(L59)->L59
as.matrix(L61)->L61
as.matrix(L62)->L62
as.matrix(L63)->L63
as.matrix(L64)->L64
as.matrix(L65)->L65
as.matrix(L67)->L67
as.matrix(L72)->L72
as.matrix(L73)->L73
as.matrix(L74)->L74
as.matrix(L75)->L75
as.matrix(L76)->L76
as.matrix(L77)->L77
as.matrix(L78)->L78
as.matrix(L79)->L79
as.matrix(L80)->L80
as.matrix(L81)->L81
as.matrix(L82)->L82
as.matrix(L85)->L85
as.matrix(L86)->L86
as.matrix(L87)->L87
as.matrix(L88)->L88
as.matrix(L89)->L89
as.matrix(L91)->L91
as.matrix(L94)->L94
as.matrix(L95)->L95
as.matrix(L98)->L98
as.matrix(L99)->L99
as.matrix(L100)->L100
as.matrix(L102)->L102
as.matrix(L103)->L103
as.matrix(L104)->L104
as.matrix(L105)->L105
as.matrix(L107)->L107
as.matrix(L108)->L108
as.matrix(L110)->L110
as.matrix(L111)->L111
as.matrix(L113)->L113
as.matrix(L115)->L115
as.matrix(L116)->L116
as.matrix(L118)->L118
as.matrix(L119)->L119
as.matrix(L120)->L120
as.matrix(L121)->L121
as.matrix(L122)->L122
as.matrix(L125)->L125
as.matrix(L126)->L126
as.matrix(L127)->L127
as.matrix(L128)->L128
as.matrix(L129)->L129
as.matrix(L130)->L130
as.matrix(L131)->L131
as.matrix(L133)->L133
as.matrix(L134)->L134
as.matrix(L135)->L135
as.matrix(L136)->L136
as.matrix(L137)->L137
as.matrix(L141)->L141
as.matrix(L142)->L142
as.matrix(L143)->L143
as.matrix(L145)->L145
as.matrix(L146)->L146
as.matrix(L147)->L147
as.matrix(L148)->L148
as.matrix(L149)->L149
as.matrix(L150)->L150
as.matrix(L151)->L151
as.matrix(L152)->L152
as.matrix(L153)->L153
as.matrix(L154)->L154
as.matrix(L155)->L155
as.matrix(L157)->L157
as.matrix(L158)->L158
as.matrix(L159)->L159
as.matrix(L161)->L161
as.matrix(L162)->L162
as.matrix(L163)->L163
as.matrix(L165)->L165
as.matrix(L169)->L169
as.matrix(L170)->L170
as.matrix(L171)->L171
as.matrix(L174)->L174
as.matrix(L175)->L175
as.matrix(L176)->L176
as.matrix(L177)->L177
as.matrix(L178)->L178
as.matrix(L180)->L180
as.matrix(L181)->L181
as.matrix(L182)->L182
as.matrix(L183)->L183
as.matrix(L184)->L184
as.matrix(L186)->L186
as.matrix(L187)->L187
as.matrix(L188)->L188
as.matrix(L189)->L189
as.matrix(L190)->L190
as.matrix(L192)->L192
as.matrix(L193)->L193
as.matrix(L194)->L194
as.matrix(L195)->L195
as.matrix(L196)->L196
as.matrix(L197)->L197
as.matrix(L201)->L201
as.matrix(L202)->L202
as.matrix(L203)->L203
as.matrix(L204)->L204
as.matrix(L205)->L205
as.matrix(L206)->L206
as.matrix(L207)->L207
as.matrix(L208)->L208
as.matrix(L209)->L209
as.matrix(L210)->L210
as.matrix(L211)->L211
as.matrix(L213)->L213
as.matrix(L214)->L214
as.matrix(L215)->L215
as.matrix(L216)->L216
as.matrix(L217)->L217
as.matrix(L219)->L219
as.matrix(L221)->L221
as.matrix(L222)->L222
as.matrix(L223)->L223
as.matrix(L224)->L224
as.matrix(L225)->L225
as.matrix(L226)->L226
as.matrix(L228)->L228
as.matrix(L229)->L229
as.matrix(L230)->L230
as.matrix(L231)->L231
as.matrix(L232)->L232
as.matrix(L233)->L233
as.matrix(L234)->L234
as.matrix(L235)->L235
as.matrix(L237)->L237
as.matrix(L239)->L239
as.matrix(L240)->L240
as.matrix(L241)->L241
as.matrix(L242)->L242
as.matrix(L243)->L243
as.matrix(L244)->L244
as.matrix(L245)->L245
as.matrix(L246)->L246
as.matrix(L247)->L247
as.matrix(L248)->L248
as.matrix(L249)->L249
as.matrix(L250)->L250
as.matrix(L251)->L251
as.matrix(L252)->L252
as.matrix(L253)->L253
as.matrix(L255)->L255
as.matrix(L256)->L256
as.matrix(L257)->L257
as.matrix(L258)->L258
as.matrix(L260)->L260
as.matrix(L261)->L261
as.matrix(L262)->L262
as.matrix(L264)->L264
as.matrix(L265)->L265
as.matrix(L266)->L266
as.matrix(L267)->L267
as.matrix(L269)->L269
as.matrix(L270)->L270
as.matrix(L271)->L271
as.matrix(L272)->L272
as.matrix(L275)->L275
as.matrix(L276)->L276
as.matrix(L277)->L277
as.matrix(L279)->L279
as.matrix(L280)->L280
as.matrix(L281)->L281
as.matrix(L282)->L282
as.matrix(L288)->L288
as.matrix(L289)->L289
as.matrix(L290)->L290
as.matrix(L292)->L292
as.matrix(L293)->L293
as.matrix(L294)->L294
as.matrix(L295)->L295
as.matrix(L296)->L296
as.matrix(L297)->L297
as.matrix(L298)->L298
as.matrix(L301)->L301
as.matrix(L302)->L302
as.matrix(L303)->L303
as.matrix(L305)->L305
as.matrix(L306)->L306
as.matrix(L307)->L307
as.matrix(L310)->L310
as.matrix(L311)->L311
as.matrix(L312)->L312
as.matrix(L314)->L314
as.matrix(L315)->L315
as.matrix(L316)->L316
as.matrix(L317)->L317
as.matrix(L318)->L318
as.matrix(L319)->L319
as.matrix(L320)->L320
as.matrix(L321)->L321
as.matrix(L322)->L322
as.matrix(L325)->L325
as.matrix(L327)->L327
as.matrix(L328)->L328
as.matrix(L329)->L329
as.matrix(L330)->L330
as.matrix(L331)->L331
as.matrix(L333)->L333
as.matrix(L334)->L334
as.matrix(L335)->L335
as.matrix(L336)->L336
as.matrix(L337)->L337
as.matrix(L338)->L338
as.matrix(L339)->L339
as.matrix(L340)->L340
as.matrix(L341)->L341
as.matrix(L342)->L342
as.matrix(L343)->L343
as.matrix(L344)->L344
as.matrix(L346)->L346
as.matrix(L347)->L347
as.matrix(L348)->L348
as.matrix(L349)->L349
allrates<- c(L1,L2,L3,L4,L5,L6,L7,L8,L9,L10,L11,L12,L21,L22,L24,L27,L28,L30,L31,L32,L34,L35,L3 6,L37,L38,L39,L41,L42,L43,L44,L48,L49,L50,L51,L53,L54,L57,L58,L59,L61,L62,L63,L64,L 65,L67,L72,L73,L74,L75,L76,L77,L78,L79,L80,L81,L82,L85,L86,L87,L88,L89,L91,L94,L95, L98,L99,L100,L102,L103,L104,L105,L107,L108,L110,L111,L113,L115,L116,L118,L119,L12 0,L121,L122,L125,L126,L127,L128,L129,L130,L131,L133,L134,L135,L136,L137,L141,L142, L143,L145,L146,L147,L148,L149,L150,L151,L152,L153,L154,L155,L157,L158,L159,L161,L 162,L163,L165,L169,L170,L171,L174,L175,L176,L177,L178,L180,L181,L182,L183,L184,L1 86,L187,L188,L189,L190,L192,L193,L194,L195,L196,L197,L201,L202,L203,L204,L205,L209,L207,L208,L209,L210,L211,L213,L214,L215,L216,L217,L219,L221,L222,L223,L224,L225, L226,L228,L229,L230,L231,L232,L233,L234,L235,L237,L239,L240,L241,L242,L243,L244,L 245,L246,L247,L248,L249,L250,L251,L252,L253,L255,L256,L257,L258,L260,L261,L262,L2 64,L265,L266,L267,L269,L270,L271,L272,L275,L276,L277,L279,L280,L281,L282,L288,L28 9,L290,L292,L293,L294,L295,L296,L297,L298,L301,L302,L303,L305,L306,L307,L310,L311, L312,L314,L315,L316,L317,L318,L319,L320,L321,L322,L325,L327,L328,L329,L330,L331,L 333,L334,L335,L336,L337,L338,L339,L340,L341,L342,L343,L344,L346,L347,L348,L349)
as.matrix(allrates)->allrates
carolinafishes/PhyInformR documentation built on May 13, 2019, 12:50 p.m.
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##set your wd to match where the below files are
setwd("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness")
###Next read in all the rate vector files
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/loci1_30Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/loci31_62Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/loci63_100Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/loci101_141Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/loci142_197Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/loci200_240Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/242_280Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/281_314Allrates_file.allrates")
source("~/Dropbox/avian-phylogenomics/Zenodo/Phylogenetic_Informativeness/314_349Allrates_file.allrates")
##note on the above, we encountered memory limitations getting all the individual rate vectors, so we broke the dataset into stages to save memory. With a better machine you could just estimates all the site rates at once.
##here we are generating PI profiles
L1<-ratesA[1:1594]
L2<-ratesA[1595:3354]
L3<-ratesA[3355:4990]
L4<-ratesA[4991:6483]
L5<-ratesA[6484:8117]
L6<-ratesA[8118:9799]
L7<-ratesA[9800:10831]
L8<-ratesA[10832:12320]
L9<-ratesA[12321:14008]
L10<-ratesA[14009:15201]
L11<-ratesA[15202:16983]
L12<-ratesA[16984:18640]
L21<-ratesA[18641:19530]
L22<-ratesA[19531:21236]
L24<-ratesA[21237:22925]
L27<-ratesA[22926:23933]
L28<-ratesA[23934:25539]
L30<-ratesA[25540:27222]
L31<-ratesB[1:1743]
L32<-ratesB[1744:3155]
L34<-ratesB[3156:4772]
L35<-ratesB[4773:6490]
L36<-ratesB[6491:7839]
L37<-ratesB[7840:9461]
L38<-ratesB[9462:11134]
L39<-ratesB[11135:12773]
L41<-ratesB[12774:14451]
L42<-ratesB[14452:15980]
L43<-ratesB[15981:17635]
L44<-ratesB[17636:19274]
L48<-ratesB[19275:20892]
L49<-ratesB[20893:22501]
L50<-ratesB[22502:24067]
L51<-ratesB[24068:24676]
L53<-ratesB[24677:26336]
L54<-ratesB[26337:27837]
L57<-ratesB[27838:28703]
L58<-ratesB[28704:30437]
L59<-ratesB[30438:32254]
L61<-ratesB[32255:33594]
L62<-ratesB[33595:35320]
L63<-ratesC[1:1639]
L64<-ratesC[1640:3343]
L65<-ratesC[3344:4969]
L67<-ratesC[4970:6692]
L72<-ratesC[6693:8126]
L73<-ratesC[8127:9466]
L74<-ratesC[9467:10561]
L75<-ratesC[10562:12104]
L76<-ratesC[12105:13564]
L77<-ratesC[13565:14900]
L78<-ratesC[14901:16176]
L79<-ratesC[16177:17743]
L80<-ratesC[17744:19041]
L81<-ratesC[19042:20639]
L82<-ratesC[20640:22331]
L85<-ratesC[22332:24059]
L86<-ratesC[24060:25809]
L87<-ratesC[25810:27611]
L88<-ratesC[27612:29278]
L89<-ratesC[29279:30703]
L91<-ratesC[30704:32444]
L94<-ratesC[32445:33290]
L95<-ratesC[33291:34744]
L98<-ratesC[34745:36509]
L99<-ratesC[36510:38221]
L100<-ratesC[38222:39639]
L102<-ratesD[1:1351]
L103<-ratesD[1352:3040]
L104<-ratesD[3041:4772]
L105<-ratesD[4773:6235]
L107<-ratesD[6236:7937]
L108<-ratesD[7938:9637]
L110<-ratesD[9638:11009]
L111<-ratesD[11010:12347]
L113<-ratesD[12348:14304]
L115<-ratesD[14305:15037]
L116<-ratesD[15038:16416]
L118<-ratesD[16417:17430]
L119<-ratesD[17431:19016]
L120<-ratesD[19017:20594]
L121<-ratesD[20595:22531]
L122<-ratesD[22532:24477]
L125<-ratesD[24478:26123]
L126<-ratesD[26124:27793]
L127<-ratesD[27794:29519]
L128<-ratesD[29520:30838]
L129<-ratesD[30839:32483]
L130<-ratesD[32484:34253]
L131<-ratesD[34254:35386]
L133<-ratesD[35387:36951]
L134<-ratesD[36952:38522]
L135<-ratesD[38523:40150]
L136<-ratesD[40151:42208]
L137<-ratesD[42209:43745]
L141<-ratesD[43746:44950]
L142<-ratesE[1:1728]
L143<-ratesE[1729:3316]
L145<-ratesE[3317:5021]
L146<-ratesE[5022:6809]
L147<-ratesE[6810:8445]
L148<-ratesE[8446:9774]
L149<-ratesE[9775:11581]
L150<-ratesE[11582:13436]
L151<-ratesE[13437:15147]
L152<-ratesE[15148:16584]
L153<-ratesE[16585:18687]
L154<-ratesE[18688:20374]
L155<-ratesE[20375:22047]
L157<-ratesE[22048:23581]
L158<-ratesE[23582:25368]
L159<-ratesE[25369:26648]
L161<-ratesE[26649:28612]
L162<-ratesE[28613:30146]
L163<-ratesE[30147:31220]
L165<-ratesE[31221:32704]
L169<-ratesE[32705:34487]
L170<-ratesE[34488:36262]
L171<-ratesE[36263:38252]
L174<-ratesE[38253:39153]
L175<-ratesE[39154:40882]
L176<-ratesE[40883:42794]
L177<-ratesE[42795:44516]
L178<-ratesE[44517:46226]
L180<-ratesE[46227:47912]
L181<-ratesE[47913:49716]
L182<-ratesE[49717:51708]
L183<-ratesE[51709:53072]
L184<-ratesE[53073:54660]
L186<-ratesE[54661:56124]
L187<-ratesE[56125:57793]
L188<-ratesE[57794:59329]
L189<-ratesE[59330:61222]
L190<-ratesE[61223:62883]
L192<-ratesE[62884:64243]
L193<-ratesE[64244:64715]
L194<-ratesE[64716:66490]
L195<-ratesE[66491:68210]
L196<-ratesE[68211:69909]
L197<-ratesE[69910:71170]
L201<-ratesF[1:1060]
L202<-ratesF[1061:2758]
L203<-ratesF[2759:4671]
L204<-ratesF[4672:6700]
L205<-ratesF[6701:8387]
L206<-ratesF[8388:9997]
L207<-ratesF[9998:11414]
L208<-ratesF[11415:11864]
L209<-ratesF[11865:12949]
L210<-ratesF[12950:14353]
L211<-ratesF[14354:16035]
L213<-ratesF[16036:18351]
L214<-ratesF[18352:19979]
L215<-ratesF[19980:21151]
L216<-ratesF[21152:22828]
L217<-ratesF[22829:23765]
L219<-ratesF[23766:24489]
L221<-ratesF[24490:26260]
L222<-ratesF[26261:27927]
L223<-ratesF[27928:28371]
L224<-ratesF[28372:29642]
L225<-ratesF[29643:30613]
L226<-ratesF[30614:32428]
L228<-ratesF[32429:34260]
L229<-ratesF[34261:35864]
L230<-ratesF[35865:37529]
L231<-ratesF[37530:39039]
L232<-ratesF[39040:40783]
L233<-ratesF[40784:41629]
L234<-ratesF[41630:43314]
L235<-ratesF[43315:45010]
L237<-ratesF[45011:45831]
L239<-ratesF[45832:46680]
L240<-ratesF[46681:48146]
L241<-ratesG[1:1737]
L242<-ratesG[1738:3137]
L243<-ratesG[3138:4101]
L244<-ratesG[4102:5203]
L245<-ratesG[5204:6982]
L246<-ratesG[6983:8699]
L247<-ratesG[8700:10305]
L248<-ratesG[10306:11853]
L249<-ratesG[11854:12840]
L250<-ratesG[12841:14367]
L251<-ratesG[14368:16098]
L252<-ratesG[16099:17753]
L253<-ratesG[17754:19097]
L255<-ratesG[19098:20790]
L256<-ratesG[20791:22514]
L257<-ratesG[22515:24232]
L258<-ratesG[24233:26099]
L260<-ratesG[26100:27700]
L261<-ratesG[27701:29447]
L262<-ratesG[29448:31029]
L264<-ratesG[31030:32822]
L265<-ratesG[32823:33361]
L266<-ratesG[33362:35547]
L267<-ratesG[35548:37206]
L269<-ratesG[37207:38604]
L270<-ratesG[38605:40123]
L271<-ratesG[40124:41740]
L272<-ratesG[41741:42304]
L275<-ratesG[42305:43515]
L276<-ratesG[43516:45199]
L277<-ratesG[45200:46347]
L279<-ratesG[46348:47213]
L280<-ratesG[47214:48742]
L281<-ratesH[1:1726]
L282<-ratesH[1727:3670]
L288<-ratesH[3671:5341]
L289<-ratesH[5342:7002]
L290<-ratesH[7003:8661]
L292<-ratesH[8662:10362]
L293<-ratesH[10363:12103]
L294<-ratesH[12104:13576]
L295<-ratesH[13577:15304]
L296<-ratesH[15305:16994]
L297<-ratesH[16995:18550]
L298<-ratesH[18551:20402]
L301<-ratesH[20403:21124]
L302<-ratesH[21125:21990]
L303<-ratesH[21991:23590]
L305<-ratesH[23591:24342]
L306<-ratesH[24343:26134]
L307<-ratesH[26135:27276]
L310<-ratesH[27277:28956]
L311<-ratesH[28957:30731]
L312<-ratesH[30732:32141]
L314<-ratesH[32142:33859]
L315<-ratesI[1:1720]
L316<-ratesI[1721:3516]
L317<-ratesI[3517:4945]
L318<-ratesI[4946:6375]
L319<-ratesI[6376:7991]
L320<-ratesI[7992:9624]
L321<-ratesI[9625:11381]
L322<-ratesI[11382:13087]
L325<-ratesI[13088:14812]
L327<-ratesI[14813:16353]
L328<-ratesI[16354:18028]
L329<-ratesI[18029:19779]
L330<-ratesI[19780:21420]
L331<-ratesI[21421:22620]
L333<-ratesI[22621:24319]
L334<-ratesI[24320:25487]
L335<-ratesI[25488:27171]
L336<-ratesI[27172:28622]
L337<-ratesI[28623:30241]
L338<-ratesI[30242:32164]
L339<-ratesI[32165:33465]
L340<-ratesI[33466:35125]
L341<-ratesI[35126:36853]
L342<-ratesI[36854:38590]
L343<-ratesI[38591:39982]
L344<-ratesI[39983:40942]
L346<-ratesI[40943:42519]
L347<-ratesI[42520:44188]
L348<-ratesI[44189:45275]
L349<-ratesI[45276:45636]
##signal noise functions require matrix formatted site rates, so convert first
as.matrix(L1)->L1
as.matrix(L2)->L2
as.matrix(L3)->L3
as.matrix(L4)->L4
as.matrix(L5)->L5
as.matrix(L6)->L6
as.matrix(L7)->L7
as.matrix(L8)->L8
as.matrix(L9)->L9
as.matrix(L10)->L10
as.matrix(L11)->L11
as.matrix(L12)->L12
as.matrix(L21)->L21
as.matrix(L22)->L22
as.matrix(L24)->L24
as.matrix(L27)->L27
as.matrix(L28)->L28
as.matrix(L30)->L30
as.matrix(L31)->L31
as.matrix(L32)->L32
as.matrix(L34)->L34
as.matrix(L35)->L35
as.matrix(L36)->L36
as.matrix(L37)->L37
as.matrix(L38)->L38
as.matrix(L39)->L39
as.matrix(L41)->L41
as.matrix(L42)->L42
as.matrix(L43)->L43
as.matrix(L44)->L44
as.matrix(L48)->L48
as.matrix(L49)->L49
as.matrix(L50)->L50
as.matrix(L51)->L51
as.matrix(L53)->L53
as.matrix(L54)->L54
as.matrix(L57)->L57
as.matrix(L58)->L58
as.matrix(L59)->L59
as.matrix(L61)->L61
as.matrix(L62)->L62
as.matrix(L63)->L63
as.matrix(L64)->L64
as.matrix(L65)->L65
as.matrix(L67)->L67
as.matrix(L72)->L72
as.matrix(L73)->L73
as.matrix(L74)->L74
as.matrix(L75)->L75
as.matrix(L76)->L76
as.matrix(L77)->L77
as.matrix(L78)->L78
as.matrix(L79)->L79
as.matrix(L80)->L80
as.matrix(L81)->L81
as.matrix(L82)->L82
as.matrix(L85)->L85
as.matrix(L86)->L86
as.matrix(L87)->L87
as.matrix(L88)->L88
as.matrix(L89)->L89
as.matrix(L91)->L91
as.matrix(L94)->L94
as.matrix(L95)->L95
as.matrix(L98)->L98
as.matrix(L99)->L99
as.matrix(L100)->L100
as.matrix(L102)->L102
as.matrix(L103)->L103
as.matrix(L104)->L104
as.matrix(L105)->L105
as.matrix(L107)->L107
as.matrix(L108)->L108
as.matrix(L110)->L110
as.matrix(L111)->L111
as.matrix(L113)->L113
as.matrix(L115)->L115
as.matrix(L116)->L116
as.matrix(L118)->L118
as.matrix(L119)->L119
as.matrix(L120)->L120
as.matrix(L121)->L121
as.matrix(L122)->L122
as.matrix(L125)->L125
as.matrix(L126)->L126
as.matrix(L127)->L127
as.matrix(L128)->L128
as.matrix(L129)->L129
as.matrix(L130)->L130
as.matrix(L131)->L131
as.matrix(L133)->L133
as.matrix(L134)->L134
as.matrix(L135)->L135
as.matrix(L136)->L136
as.matrix(L137)->L137
as.matrix(L141)->L141
as.matrix(L142)->L142
as.matrix(L143)->L143
as.matrix(L145)->L145
as.matrix(L146)->L146
as.matrix(L147)->L147
as.matrix(L148)->L148
as.matrix(L149)->L149
as.matrix(L150)->L150
as.matrix(L151)->L151
as.matrix(L152)->L152
as.matrix(L153)->L153
as.matrix(L154)->L154
as.matrix(L155)->L155
as.matrix(L157)->L157
as.matrix(L158)->L158
as.matrix(L159)->L159
as.matrix(L161)->L161
as.matrix(L162)->L162
as.matrix(L163)->L163
as.matrix(L165)->L165
as.matrix(L169)->L169
as.matrix(L170)->L170
as.matrix(L171)->L171
as.matrix(L174)->L174
as.matrix(L175)->L175
as.matrix(L176)->L176
as.matrix(L177)->L177
as.matrix(L178)->L178
as.matrix(L180)->L180
as.matrix(L181)->L181
as.matrix(L182)->L182
as.matrix(L183)->L183
as.matrix(L184)->L184
as.matrix(L186)->L186
as.matrix(L187)->L187
as.matrix(L188)->L188
as.matrix(L189)->L189
as.matrix(L190)->L190
as.matrix(L192)->L192
as.matrix(L193)->L193
as.matrix(L194)->L194
as.matrix(L195)->L195
as.matrix(L196)->L196
as.matrix(L197)->L197
as.matrix(L201)->L201
as.matrix(L202)->L202
as.matrix(L203)->L203
as.matrix(L204)->L204
as.matrix(L205)->L205
as.matrix(L206)->L206
as.matrix(L207)->L207
as.matrix(L208)->L208
as.matrix(L209)->L209
as.matrix(L210)->L210
as.matrix(L211)->L211
as.matrix(L213)->L213
as.matrix(L214)->L214
as.matrix(L215)->L215
as.matrix(L216)->L216
as.matrix(L217)->L217
as.matrix(L219)->L219
as.matrix(L221)->L221
as.matrix(L222)->L222
as.matrix(L223)->L223
as.matrix(L224)->L224
as.matrix(L225)->L225
as.matrix(L226)->L226
as.matrix(L228)->L228
as.matrix(L229)->L229
as.matrix(L230)->L230
as.matrix(L231)->L231
as.matrix(L232)->L232
as.matrix(L233)->L233
as.matrix(L234)->L234
as.matrix(L235)->L235
as.matrix(L237)->L237
as.matrix(L239)->L239
as.matrix(L240)->L240
as.matrix(L241)->L241
as.matrix(L242)->L242
as.matrix(L243)->L243
as.matrix(L244)->L244
as.matrix(L245)->L245
as.matrix(L246)->L246
as.matrix(L247)->L247
as.matrix(L248)->L248
as.matrix(L249)->L249
as.matrix(L250)->L250
as.matrix(L251)->L251
as.matrix(L252)->L252
as.matrix(L253)->L253
as.matrix(L255)->L255
as.matrix(L256)->L256
as.matrix(L257)->L257
as.matrix(L258)->L258
as.matrix(L260)->L260
as.matrix(L261)->L261
as.matrix(L262)->L262
as.matrix(L264)->L264
as.matrix(L265)->L265
as.matrix(L266)->L266
as.matrix(L267)->L267
as.matrix(L269)->L269
as.matrix(L270)->L270
as.matrix(L271)->L271
as.matrix(L272)->L272
as.matrix(L275)->L275
as.matrix(L276)->L276
as.matrix(L277)->L277
as.matrix(L279)->L279
as.matrix(L280)->L280
as.matrix(L281)->L281
as.matrix(L282)->L282
as.matrix(L288)->L288
as.matrix(L289)->L289
as.matrix(L290)->L290
as.matrix(L292)->L292
as.matrix(L293)->L293
as.matrix(L294)->L294
as.matrix(L295)->L295
as.matrix(L296)->L296
as.matrix(L297)->L297
as.matrix(L298)->L298
as.matrix(L301)->L301
as.matrix(L302)->L302
as.matrix(L303)->L303
as.matrix(L305)->L305
as.matrix(L306)->L306
as.matrix(L307)->L307
as.matrix(L310)->L310
as.matrix(L311)->L311
as.matrix(L312)->L312
as.matrix(L314)->L314
as.matrix(L315)->L315
as.matrix(L316)->L316
as.matrix(L317)->L317
as.matrix(L318)->L318
as.matrix(L319)->L319
as.matrix(L320)->L320
as.matrix(L321)->L321
as.matrix(L322)->L322
as.matrix(L325)->L325
as.matrix(L327)->L327
as.matrix(L328)->L328
as.matrix(L329)->L329
as.matrix(L330)->L330
as.matrix(L331)->L331
as.matrix(L333)->L333
as.matrix(L334)->L334
as.matrix(L335)->L335
as.matrix(L336)->L336
as.matrix(L337)->L337
as.matrix(L338)->L338
as.matrix(L339)->L339
as.matrix(L340)->L340
as.matrix(L341)->L341
as.matrix(L342)->L342
as.matrix(L343)->L343
as.matrix(L344)->L344
as.matrix(L346)->L346
as.matrix(L347)->L347
as.matrix(L348)->L348
as.matrix(L349)->L349
allrates<- c(L1,L2,L3,L4,L5,L6,L7,L8,L9,L10,L11,L12,L21,L22,L24,L27,L28,L30,L31,L32,L34,L35,L3 6,L37,L38,L39,L41,L42,L43,L44,L48,L49,L50,L51,L53,L54,L57,L58,L59,L61,L62,L63,L64,L 65,L67,L72,L73,L74,L75,L76,L77,L78,L79,L80,L81,L82,L85,L86,L87,L88,L89,L91,L94,L95, L98,L99,L100,L102,L103,L104,L105,L107,L108,L110,L111,L113,L115,L116,L118,L119,L12 0,L121,L122,L125,L126,L127,L128,L129,L130,L131,L133,L134,L135,L136,L137,L141,L142, L143,L145,L146,L147,L148,L149,L150,L151,L152,L153,L154,L155,L157,L158,L159,L161,L 162,L163,L165,L169,L170,L171,L174,L175,L176,L177,L178,L180,L181,L182,L183,L184,L1 86,L187,L188,L189,L190,L192,L193,L194,L195,L196,L197,L201,L202,L203,L204,L205,L209,L207,L208,L209,L210,L211,L213,L214,L215,L216,L217,L219,L221,L222,L223,L224,L225, L226,L228,L229,L230,L231,L232,L233,L234,L235,L237,L239,L240,L241,L242,L243,L244,L 245,L246,L247,L248,L249,L250,L251,L252,L253,L255,L256,L257,L258,L260,L261,L262,L2 64,L265,L266,L267,L269,L270,L271,L272,L275,L276,L277,L279,L280,L281,L282,L288,L28 9,L290,L292,L293,L294,L295,L296,L297,L298,L301,L302,L303,L305,L306,L307,L310,L311, L312,L314,L315,L316,L317,L318,L319,L320,L321,L322,L325,L327,L328,L329,L330,L331,L 333,L334,L335,L336,L337,L338,L339,L340,L341,L342,L343,L344,L346,L347,L348,L349)
as.matrix(allrates)->allrates
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