add_tip_states() annotates the tips of a phylo object with state values.
Arguments
- tree
An object of class
phylo.- tip_data
Either a named vector or a
data.frame. If a named vector, the elements of the vector must be the state of each tip and the names must be the labels of those tips. If adata.frame, there must be 2 columns: the first with the tip labels and the second with the tip states.
Details
A tip.states attribute is added to tree based on the tip_data provided by the user.
This function is used within the prepare_tree_for_saasi() function.
See also
drop_tips_by_state() to remove specific traits or prepare_tree_for_saasi() for reformatting phylo objects to be saasi-compatible.
Examples
demo_tree
#> $edge
#> [,1] [,2]
#> [1,] 14 15
#> [2,] 15 16
#> [3,] 16 17
#> [4,] 17 18
#> [5,] 18 3
#> [6,] 18 19
#> [7,] 19 8
#> [8,] 19 9
#> [9,] 17 2
#> [10,] 16 20
#> [11,] 20 21
#> [12,] 21 10
#> [13,] 21 7
#> [14,] 20 6
#> [15,] 15 22
#> [16,] 22 12
#> [17,] 22 11
#> [18,] 14 23
#> [19,] 23 24
#> [20,] 24 25
#> [21,] 25 5
#> [22,] 25 13
#> [23,] 24 4
#> [24,] 23 1
#>
#> $Nnode
#> [1] 12
#>
#> $tip.label
#> [1] "sp2" "sp4" "sp8" "sp9" "sp10" "sp26" "sp27" "sp30" "sp31" "sp59"
#> [11] "sp64" "sp72" "sp75"
#>
#> $node.label
#> [1] "nd1" "nd2" "nd6" "nd22" "nd27" "nd74" "nd32" "nd54" "nd7" "nd8"
#> [11] "nd36" "nd38"
#>
#> $node.state
#> nd1 nd2 nd6 nd22 nd27 nd74 nd32 nd54 nd7 nd8 nd36 nd38
#> 1 1 2 2 2 2 2 2 1 1 1 1
#>
#> $edge.length
#> [1] 0.16467463 0.60776479 0.06123598 0.13756928 0.19052413 0.43829041
#> [7] 0.14919102 0.26797730 0.12387543 0.38247528 0.24214935 0.28936865
#> [13] 0.31255390 0.27670668 0.43629704 1.11293809 1.11550593 0.53064429
#> [19] 0.51423161 0.04706635 0.37366599 0.58693711 0.14126857 0.95898051
#>
#> $orig
#> idx len parent start state extinct split sam idx2 parent2
#> 2 2 0.164674627 1 0.1508471 1 FALSE TRUE FALSE 101 100
#> 3 3 0.095752083 1 0.1508471 1 FALSE TRUE FALSE 102 100
#> 4 4 0.350260185 3 0.2465992 1 FALSE TRUE FALSE 103 102
#> 5 5 0.221791997 3 0.2465992 1 FALSE TRUE FALSE 104 102
#> 6 6 0.607764789 2 0.3155218 2 FALSE TRUE FALSE 105 101
#> 7 7 0.436297042 2 0.3155218 1 FALSE TRUE FALSE 106 101
#> 8 8 0.213100210 5 0.4683912 1 FALSE TRUE FALSE 107 104
#> 9 9 0.178937370 5 0.4683912 1 FALSE TRUE FALSE 108 104
#> 10 10 0.908357264 4 0.5968594 2 FALSE TRUE FALSE 109 103
#> 11 11 0.208011176 4 0.5968594 1 FALSE TRUE FALSE 110 103
#> 12 12 0.958787122 9 0.6473286 3 FALSE TRUE FALSE 111 108
#> 13 13 0.285044132 9 0.6473286 1 FALSE TRUE FALSE 112 108
#> 14 14 0.511629972 8 0.6814914 1 FALSE TRUE FALSE 113 107
#> 15 15 0.187315709 8 0.6814914 1 FALSE TRUE FALSE 114 107
#> 16 16 0.287068808 7 0.7518188 1 FALSE TRUE FALSE 115 106
#> 17 17 0.233292244 7 0.7518188 1 FALSE TRUE FALSE 116 106
#> 18 18 1.121845705 11 0.8048706 1 FALSE FALSE FALSE 1 110
#> 19 19 0.364675377 11 0.8048706 1 FALSE TRUE FALSE 117 110
#> 20 20 0.011876720 15 0.8688071 1 FALSE TRUE FALSE 118 114
#> 21 21 0.771664802 15 0.8688071 1 FALSE FALSE TRUE 2 114
#> 22 22 0.404881489 20 0.8806839 1 FALSE TRUE FALSE 119 118
#> 23 23 0.164910945 20 0.8806839 1 FALSE TRUE FALSE 120 118
#> 24 24 0.061235983 6 0.9232865 2 FALSE TRUE FALSE 121 105
#> 25 25 0.147439207 6 0.9232865 2 FALSE TRUE FALSE 122 105
#> 26 26 0.994343566 13 0.9323727 1 FALSE FALSE FALSE 3 112
#> 27 27 0.718118368 13 0.9323727 3 FALSE TRUE FALSE 123 112
#> 28 28 0.008634727 24 0.9845225 2 FALSE TRUE FALSE 124 121
#> 29 29 0.123875431 24 0.9845225 2 FALSE FALSE TRUE 4 121
#> 30 30 0.941605236 17 0.9851110 1 FALSE FALSE FALSE 5 116
#> 31 31 0.210691558 17 0.9851110 1 FALSE TRUE FALSE 125 116
#> 33 33 0.128934554 28 0.9931573 2 FALSE TRUE FALSE 126 124
#> 34 34 0.196808061 16 1.0388876 1 FALSE TRUE FALSE 127 115
#> 35 35 0.175404690 16 1.0388876 1 FALSE TRUE FALSE 128 115
#> 36 36 0.881121485 23 1.0455948 3 FALSE FALSE FALSE 7 120
#> 37 37 0.523725191 23 1.0455948 1 FALSE TRUE FALSE 129 120
#> 38 38 0.296646520 25 1.0707258 2 FALSE TRUE FALSE 130 122
#> 39 39 0.235036077 25 1.0707258 2 FALSE TRUE FALSE 131 122
#> 40 40 0.190524130 33 1.1220918 2 FALSE FALSE TRUE 8 126
#> 41 41 0.378207392 33 1.1220918 2 FALSE TRUE FALSE 132 126
#> 42 42 0.088889776 19 1.1695460 1 FALSE TRUE FALSE 133 117
#> 43 43 0.084562865 19 1.1695460 3 FALSE TRUE FALSE 134 117
#> 44 44 0.002601639 14 1.1931214 1 FALSE TRUE FALSE 135 113
#> 45 45 0.424346440 14 1.1931214 1 FALSE TRUE FALSE 136 113
#> 46 46 0.047066352 44 1.1957230 1 FALSE TRUE FALSE 137 135
#> 47 47 0.141268574 44 1.1957230 1 FALSE FALSE TRUE 9 135
#> 48 48 0.146166009 31 1.1958026 1 FALSE TRUE FALSE 138 125
#> 49 49 0.067324209 31 1.1958026 1 FALSE TRUE FALSE 139 125
#> 50 50 0.544442729 35 1.2142923 1 FALSE TRUE FALSE 140 128
#> 51 51 0.135830510 35 1.2142923 1 FALSE TRUE FALSE 141 128
#> 52 52 0.054169952 34 1.2356957 1 FALSE TRUE FALSE 142 127
#> 53 53 0.085441542 34 1.2356957 1 FALSE TRUE FALSE 143 127
#> 54 54 0.373665988 46 1.2427894 3 FALSE FALSE TRUE 10 137
#> 55 55 0.005947470 46 1.2427894 1 FALSE TRUE FALSE 144 137
#> 56 56 0.062525080 55 1.2487369 1 FALSE TRUE FALSE 145 144
#> 57 57 0.079893078 55 1.2487369 1 FALSE TRUE FALSE 146 144
#> 58 58 0.672607463 43 1.2541088 3 FALSE FALSE FALSE 11 134
#> 59 59 0.314828098 43 1.2541088 3 FALSE TRUE FALSE 147 134
#> 60 60 0.668280552 42 1.2584357 1 FALSE FALSE FALSE 12 133
#> 61 61 0.668280552 42 1.2584357 1 FALSE FALSE FALSE 13 133
#> 62 62 0.421234449 49 1.2631268 1 FALSE TRUE FALSE 148 139
#> 63 63 0.069066626 49 1.2631268 1 FALSE TRUE FALSE 149 139
#> 64 64 0.369898133 22 1.2855653 1 FALSE TRUE FALSE 150 119
#> 65 65 0.641150941 22 1.2855653 1 FALSE FALSE FALSE 14 119
#> 66 66 0.280602490 52 1.2898656 1 FALSE TRUE FALSE 151 142
#> 67 67 0.320210285 52 1.2898656 1 FALSE TRUE FALSE 152 142
#> 68 68 0.242149352 39 1.3057618 2 FALSE TRUE FALSE 153 131
#> 69 69 0.233226652 39 1.3057618 2 FALSE TRUE FALSE 154 131
#> 70 70 0.570054335 56 1.3112619 1 FALSE TRUE FALSE 155 145
#> 71 71 0.615454346 56 1.3112619 2 FALSE FALSE FALSE 15 145
#> 72 72 0.083934169 53 1.3211372 1 FALSE TRUE FALSE 156 143
#> 73 73 0.593478377 53 1.3211372 1 FALSE TRUE FALSE 157 143
#> 74 74 0.103403746 57 1.3286299 1 FALSE TRUE FALSE 158 146
#> 75 75 0.432689222 57 1.3286299 1 FALSE TRUE FALSE 159 146
#> 76 76 0.288974657 63 1.3321934 1 FALSE TRUE FALSE 160 149
#> 77 77 0.187107326 63 1.3321934 1 FALSE TRUE FALSE 161 149
#> 78 78 0.101989443 48 1.3419686 1 FALSE TRUE FALSE 162 138
#> 79 79 0.358703541 48 1.3419686 1 FALSE TRUE FALSE 163 138
#> 80 80 0.242264625 51 1.3501228 1 FALSE TRUE FALSE 164 141
#> 81 81 0.576593472 51 1.3501228 3 FALSE FALSE FALSE 16 141
#> 82 82 0.043004976 38 1.3673723 2 FALSE TRUE FALSE 165 130
#> 83 83 0.559344007 38 1.3673723 2 FALSE FALSE FALSE 17 130
#> 84 84 0.521644901 72 1.4050714 1 FALSE FALSE FALSE 18 156
#> 85 85 0.521644901 72 1.4050714 1 FALSE FALSE FALSE 19 156
#> 86 86 0.065834152 82 1.4103773 2 FALSE TRUE FALSE 166 165
#> 87 87 0.261437974 82 1.4103773 2 FALSE TRUE FALSE 167 165
#> 88 88 0.296346500 74 1.4320337 1 FALSE TRUE FALSE 168 158
#> 89 89 0.097792699 74 1.4320337 1 FALSE TRUE FALSE 169 158
#> 91 91 0.410609832 78 1.4439581 1 FALSE TRUE FALSE 170 162
#> 92 92 0.293597865 86 1.4762114 2 FALSE TRUE FALSE 171 166
#> 93 93 0.083985009 86 1.4762114 2 FALSE TRUE FALSE 172 166
#> 94 94 0.426417078 41 1.5002992 2 FALSE FALSE FALSE 21 132
#> 95 95 0.060083014 41 1.5002992 2 FALSE TRUE FALSE 173 132
#> 96 96 0.159140297 10 1.5052167 2 FALSE TRUE FALSE 174 109
#> 97 97 0.421499617 10 1.5052167 2 FALSE FALSE FALSE 22 109
#> 98 98 0.407415518 77 1.5193008 1 FALSE FALSE FALSE 23 161
#> 99 99 0.407415518 77 1.5193008 1 FALSE FALSE FALSE 24 161
#> 100 100 0.092729426 89 1.5298264 1 FALSE TRUE FALSE 175 169
#> 101 101 0.274753602 89 1.5298264 3 FALSE TRUE FALSE 176 169
#> 102 102 0.387727798 69 1.5389885 2 FALSE FALSE FALSE 25 154
#> 103 103 0.043480033 69 1.5389885 2 FALSE FALSE TRUE 26 154
#> 104 104 0.175579119 68 1.5479112 2 FALSE TRUE FALSE 177 153
#> 105 105 0.312553900 68 1.5479112 3 FALSE FALSE TRUE 27 153
#> 106 106 0.366519870 93 1.5601964 2 FALSE FALSE FALSE 28 172
#> 107 107 0.366519870 93 1.5601964 2 FALSE FALSE FALSE 29 172
#> 108 108 0.149191016 95 1.5603822 2 FALSE FALSE TRUE 30 173
#> 109 109 0.267977300 95 1.5603822 3 FALSE FALSE TRUE 31 173
#> 110 110 0.357779365 59 1.5689369 3 FALSE FALSE FALSE 32 147
#> 111 111 0.357779365 59 1.5689369 3 FALSE FALSE FALSE 33 147
#> 112 112 0.357396294 37 1.5693200 1 FALSE FALSE FALSE 34 129
#> 113 113 0.357396294 37 1.5693200 1 FALSE FALSE FALSE 35 129
#> 114 114 0.356248170 66 1.5704681 1 FALSE FALSE FALSE 36 151
#> 115 115 0.356248170 66 1.5704681 1 FALSE FALSE FALSE 37 151
#> 116 116 0.334328846 80 1.5923874 3 FALSE FALSE FALSE 38 164
#> 117 117 0.334328846 80 1.5923874 1 FALSE FALSE FALSE 39 164
#> 118 118 0.314805032 12 1.6061157 2 FALSE TRUE FALSE 178 111
#> 119 119 0.222454996 12 1.6061157 3 FALSE TRUE FALSE 179 111
#> 120 120 0.049710495 67 1.6100759 1 FALSE TRUE FALSE 180 152
#> 121 121 0.316640375 67 1.6100759 1 FALSE FALSE FALSE 40 152
#> 122 122 0.309248446 45 1.6174678 1 FALSE FALSE FALSE 41 136
#> 123 123 0.309248446 45 1.6174678 1 FALSE FALSE FALSE 42 136
#> 124 124 0.102119268 76 1.6211681 1 FALSE TRUE FALSE 181 160
#> 125 125 0.305548186 76 1.6211681 3 FALSE FALSE FALSE 43 160
#> 126 126 0.052236063 100 1.6225558 1 FALSE TRUE FALSE 182 175
#> 127 127 0.304160477 100 1.6225558 3 FALSE FALSE FALSE 44 175
#> 128 128 0.276225198 27 1.6504911 3 FALSE FALSE FALSE 45 123
#> 129 129 0.016622859 27 1.6504911 3 FALSE TRUE FALSE 183 123
#> 130 130 0.147642260 64 1.6554635 1 FALSE TRUE FALSE 184 150
#> 131 131 0.271252808 64 1.6554635 1 FALSE FALSE FALSE 46 150
#> 132 132 0.266929879 120 1.6597864 1 FALSE FALSE FALSE 47 180
#> 133 133 0.266929879 120 1.6597864 1 FALSE FALSE FALSE 48 180
#> 134 134 0.191284415 96 1.6643570 2 FALSE TRUE FALSE 185 174
#> 135 135 0.093227680 96 1.6643570 2 FALSE TRUE FALSE 186 174
#> 136 136 0.259602339 129 1.6671139 3 FALSE FALSE FALSE 49 183
#> 137 137 0.259602339 129 1.6671139 1 FALSE FALSE FALSE 50 183
#> 139 139 0.254901057 87 1.6718152 2 FALSE FALSE FALSE 52 167
#> 140 140 0.054001298 126 1.6747919 1 FALSE TRUE FALSE 187 182
#> 141 141 0.006521519 126 1.6747919 1 FALSE TRUE FALSE 188 182
#> 142 142 0.245402895 141 1.6813134 1 FALSE FALSE FALSE 53 188
#> 143 143 0.245402895 141 1.6813134 1 FALSE FALSE FALSE 54 188
#> 144 144 0.242355020 62 1.6843613 1 FALSE FALSE FALSE 55 148
#> 146 146 0.226044128 79 1.7006722 1 FALSE FALSE FALSE 57 163
#> 147 147 0.197537764 79 1.7006722 1 FALSE TRUE FALSE 189 163
#> 148 148 0.203428919 124 1.7232874 1 FALSE FALSE FALSE 58 181
#> 149 149 0.034087869 124 1.7232874 1 FALSE TRUE FALSE 190 181
#> 150 150 0.113789534 104 1.7234903 2 FALSE FALSE TRUE 59 177
#> 151 151 0.203225979 104 1.7234903 2 FALSE FALSE FALSE 60 177
#> 152 152 0.198336103 88 1.7283802 1 FALSE FALSE FALSE 61 168
#> 153 153 0.198336103 88 1.7283802 1 FALSE FALSE FALSE 62 168
#> 154 154 0.197923116 140 1.7287932 1 FALSE FALSE FALSE 63 187
#> 155 155 0.166374148 140 1.7287932 1 FALSE TRUE FALSE 191 187
#> 156 156 0.014147720 149 1.7573752 1 FALSE TRUE FALSE 192 190
#> 157 157 0.109949497 149 1.7573752 3 FALSE FALSE TRUE 64 190
#> 158 158 0.169131640 135 1.7575846 3 FALSE FALSE FALSE 65 186
#> 159 159 0.169131640 135 1.7575846 2 FALSE FALSE FALSE 66 186
#> 160 160 0.157153882 50 1.7587350 1 FALSE TRUE FALSE 193 140
#> 161 161 0.041193647 50 1.7587350 2 FALSE TRUE FALSE 194 140
#> 162 162 0.121493122 75 1.7613192 1 FALSE TRUE FALSE 195 159
#> 163 163 0.141347666 75 1.7613192 1 FALSE TRUE FALSE 196 159
#> 164 164 0.156907014 92 1.7698093 2 FALSE FALSE FALSE 67 171
#> 165 165 0.156907014 92 1.7698093 2 FALSE FALSE FALSE 68 171
#> 166 166 0.155193329 156 1.7715230 1 FALSE FALSE FALSE 69 192
#> 167 167 0.155193329 156 1.7715230 1 FALSE FALSE FALSE 70 192
#> 168 168 0.126787606 161 1.7999287 2 FALSE FALSE FALSE 71 194
#> 169 169 0.064828216 161 1.7999287 2 FALSE FALSE TRUE 72 194
#> 170 170 0.123610548 130 1.8031057 1 FALSE FALSE FALSE 73 184
#> 171 171 0.123610548 130 1.8031057 1 FALSE FALSE FALSE 74 184
#> 172 172 0.058918845 101 1.8045800 3 FALSE TRUE FALSE 197 176
#> 173 173 0.025146519 101 1.8045800 3 FALSE FALSE TRUE 75 176
#> 174 174 0.098145581 119 1.8285707 3 FALSE FALSE FALSE 76 179
#> 176 176 0.072148394 91 1.8545679 1 FALSE FALSE FALSE 78 170
#> 177 177 0.072148394 91 1.8545679 1 FALSE FALSE FALSE 79 170
#> 178 178 0.071074905 134 1.8556414 2 FALSE FALSE FALSE 80 185
#> 179 179 0.071074905 134 1.8556414 2 FALSE FALSE FALSE 81 185
#> 180 180 0.063217456 172 1.8634988 3 FALSE FALSE FALSE 82 197
#> 181 181 0.063217456 172 1.8634988 3 FALSE FALSE FALSE 83 197
#> 182 182 0.045400011 70 1.8813163 1 FALSE FALSE FALSE 84 155
#> 183 183 0.045400011 70 1.8813163 1 FALSE FALSE FALSE 85 155
#> 184 184 0.043904005 162 1.8828123 1 FALSE FALSE FALSE 86 195
#> 185 185 0.043904005 162 1.8828123 1 FALSE FALSE FALSE 87 195
#> 186 186 0.031548968 155 1.8951673 1 FALSE FALSE FALSE 88 191
#> 187 187 0.031548968 155 1.8951673 1 FALSE FALSE FALSE 89 191
#> 188 188 0.028506365 147 1.8982099 1 FALSE FALSE FALSE 90 189
#> 190 190 0.024049461 163 1.9026668 1 FALSE FALSE FALSE 92 196
#> 191 191 0.024049461 163 1.9026668 1 FALSE FALSE FALSE 93 196
#> 192 192 0.012100693 73 1.9146156 1 FALSE FALSE FALSE 94 157
#> 193 193 0.012100693 73 1.9146156 1 FALSE FALSE FALSE 95 157
#> 194 194 0.010827371 160 1.9158889 1 FALSE FALSE FALSE 96 193
#> 195 195 0.010827371 160 1.9158889 1 FALSE FALSE FALSE 97 193
#> 196 196 0.005795544 118 1.9209207 2 FALSE FALSE FALSE 98 178
#> 197 197 0.005795544 118 1.9209207 2 FALSE FALSE FALSE 99 178
#> name name2
#> 2 <NA> nd2
#> 3 <NA> nd3
#> 4 <NA> nd4
#> 5 <NA> nd5
#> 6 <NA> nd6
#> 7 <NA> nd7
#> 8 <NA> nd8
#> 9 <NA> nd9
#> 10 <NA> nd10
#> 11 <NA> nd11
#> 12 <NA> nd12
#> 13 <NA> nd13
#> 14 <NA> nd14
#> 15 <NA> nd15
#> 16 <NA> nd16
#> 17 <NA> nd17
#> 18 sp1 sp1
#> 19 <NA> nd18
#> 20 <NA> nd19
#> 21 sp2 sp2
#> 22 <NA> nd20
#> 23 <NA> nd21
#> 24 <NA> nd22
#> 25 <NA> nd23
#> 26 sp3 sp3
#> 27 <NA> nd24
#> 28 <NA> nd25
#> 29 sp4 sp4
#> 30 sp5 sp5
#> 31 <NA> nd26
#> 33 <NA> nd27
#> 34 <NA> nd28
#> 35 <NA> nd29
#> 36 sp7 sp7
#> 37 <NA> nd30
#> 38 <NA> nd31
#> 39 <NA> nd32
#> 40 sp8 sp8
#> 41 <NA> nd33
#> 42 <NA> nd34
#> 43 <NA> nd35
#> 44 <NA> nd36
#> 45 <NA> nd37
#> 46 <NA> nd38
#> 47 sp9 sp9
#> 48 <NA> nd39
#> 49 <NA> nd40
#> 50 <NA> nd41
#> 51 <NA> nd42
#> 52 <NA> nd43
#> 53 <NA> nd44
#> 54 sp10 sp10
#> 55 <NA> nd45
#> 56 <NA> nd46
#> 57 <NA> nd47
#> 58 sp11 sp11
#> 59 <NA> nd48
#> 60 sp12 sp12
#> 61 sp13 sp13
#> 62 <NA> nd49
#> 63 <NA> nd50
#> 64 <NA> nd51
#> 65 sp14 sp14
#> 66 <NA> nd52
#> 67 <NA> nd53
#> 68 <NA> nd54
#> 69 <NA> nd55
#> 70 <NA> nd56
#> 71 sp15 sp15
#> 72 <NA> nd57
#> 73 <NA> nd58
#> 74 <NA> nd59
#> 75 <NA> nd60
#> 76 <NA> nd61
#> 77 <NA> nd62
#> 78 <NA> nd63
#> 79 <NA> nd64
#> 80 <NA> nd65
#> 81 sp16 sp16
#> 82 <NA> nd66
#> 83 sp17 sp17
#> 84 sp18 sp18
#> 85 sp19 sp19
#> 86 <NA> nd67
#> 87 <NA> nd68
#> 88 <NA> nd69
#> 89 <NA> nd70
#> 91 <NA> nd71
#> 92 <NA> nd72
#> 93 <NA> nd73
#> 94 sp21 sp21
#> 95 <NA> nd74
#> 96 <NA> nd75
#> 97 sp22 sp22
#> 98 sp23 sp23
#> 99 sp24 sp24
#> 100 <NA> nd76
#> 101 <NA> nd77
#> 102 sp25 sp25
#> 103 sp26 sp26
#> 104 <NA> nd78
#> 105 sp27 sp27
#> 106 sp28 sp28
#> 107 sp29 sp29
#> 108 sp30 sp30
#> 109 sp31 sp31
#> 110 sp32 sp32
#> 111 sp33 sp33
#> 112 sp34 sp34
#> 113 sp35 sp35
#> 114 sp36 sp36
#> 115 sp37 sp37
#> 116 sp38 sp38
#> 117 sp39 sp39
#> 118 <NA> nd79
#> 119 <NA> nd80
#> 120 <NA> nd81
#> 121 sp40 sp40
#> 122 sp41 sp41
#> 123 sp42 sp42
#> 124 <NA> nd82
#> 125 sp43 sp43
#> 126 <NA> nd83
#> 127 sp44 sp44
#> 128 sp45 sp45
#> 129 <NA> nd84
#> 130 <NA> nd85
#> 131 sp46 sp46
#> 132 sp47 sp47
#> 133 sp48 sp48
#> 134 <NA> nd86
#> 135 <NA> nd87
#> 136 sp49 sp49
#> 137 sp50 sp50
#> 139 sp52 sp52
#> 140 <NA> nd88
#> 141 <NA> nd89
#> 142 sp53 sp53
#> 143 sp54 sp54
#> 144 sp55 sp55
#> 146 sp57 sp57
#> 147 <NA> nd90
#> 148 sp58 sp58
#> 149 <NA> nd91
#> 150 sp59 sp59
#> 151 sp60 sp60
#> 152 sp61 sp61
#> 153 sp62 sp62
#> 154 sp63 sp63
#> 155 <NA> nd92
#> 156 <NA> nd93
#> 157 sp64 sp64
#> 158 sp65 sp65
#> 159 sp66 sp66
#> 160 <NA> nd94
#> 161 <NA> nd95
#> 162 <NA> nd96
#> 163 <NA> nd97
#> 164 sp67 sp67
#> 165 sp68 sp68
#> 166 sp69 sp69
#> 167 sp70 sp70
#> 168 sp71 sp71
#> 169 sp72 sp72
#> 170 sp73 sp73
#> 171 sp74 sp74
#> 172 <NA> nd98
#> 173 sp75 sp75
#> 174 sp76 sp76
#> 176 sp78 sp78
#> 177 sp79 sp79
#> 178 sp80 sp80
#> 179 sp81 sp81
#> 180 sp82 sp82
#> 181 sp83 sp83
#> 182 sp84 sp84
#> 183 sp85 sp85
#> 184 sp86 sp86
#> 185 sp87 sp87
#> 186 sp88 sp88
#> 187 sp89 sp89
#> 188 sp90 sp90
#> 190 sp92 sp92
#> 191 sp93 sp93
#> 192 sp94 sp94
#> 193 sp95 sp95
#> 194 sp96 sp96
#> 195 sp97 sp97
#> 196 sp98 sp98
#> 197 sp99 sp99
#>
#> $hist
#> idx t from to x0 tc idx2 name2
#> 13 36 1.7712115 1 3 1.0455948 0.72561669 6 sp7
#> 7 54 1.4714900 1 3 1.2427894 0.22870062 9 sp10
#> 11 71 1.7523062 1 2 1.3112619 0.44104431 14 sp15
#> 6 81 1.3637622 1 3 1.3501228 0.01363937 15 sp16
#> 12 105 1.7655396 2 3 1.5479112 0.21762839 25 sp27
#> 9 109 1.6938940 2 3 1.5603822 0.13351183 29 sp31
#> 17 116 1.8579434 1 3 1.5923874 0.26555601 36 sp38
#> 20 125 1.9110279 1 3 1.6211681 0.28985983 41 sp43
#> 15 127 1.8226049 1 3 1.6225558 0.20004911 42 sp44
#> 10 137 1.7423445 3 1 1.6671139 0.07523055 48 sp50
#> 16 157 1.8506348 1 3 1.7573752 0.09325955 60 sp64
#> 19 158 1.9005004 2 3 1.7575846 0.14291580 61 sp65
#> 2 6 0.7937786 1 2 0.3155218 0.47825687 96 nd6
#> 14 161 1.7896296 1 2 1.7587350 0.03089453 124 nd95
#> 1 10 0.7664957 1 2 0.5968594 0.16963631 141 nd10
#> 5 43 1.2514209 1 3 1.1695460 0.08187492 148 nd35
#> 8 101 1.6656791 1 3 1.5298264 0.13585273 167 nd77
#> 4 12 1.1409286 1 3 0.6473286 0.49360002 181 nd12
#> 18 118 1.8697629 3 2 1.6061157 0.26364715 182 nd79
#> 3 27 1.1014641 1 3 0.9323727 0.16909142 184 nd24
#>
#> $edge.state
#> [1] 1 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 1
#> [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 1 1 3 1 3 1 1 1 1 1 1
#> [75] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 3 1 1 1 1 1 2 2 2 2 2 2 3 2 2 1
#> [112] 1 1 1 1 1 3 3 3 3 3 1 1 1 1 1 3 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#> [149] 1 3 3 3 3 3 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 1 1 3 2 2
#> [186] 2 3 3 3 1 1 3 3 3 3 1
#>
#> attr(,"class")
#> [1] "phylo"
#> attr(,"order")
#> [1] "cladewise"
head(demo_metadata)
#> node state
#> 1 sp2 1
#> 2 sp4 2
#> 3 sp8 2
#> 4 sp9 1
#> 5 sp10 3
#> 6 sp26 2
add_tip_states(demo_tree, demo_metadata)
#> $edge
#> [,1] [,2]
#> [1,] 14 15
#> [2,] 15 16
#> [3,] 16 17
#> [4,] 17 18
#> [5,] 18 3
#> [6,] 18 19
#> [7,] 19 8
#> [8,] 19 9
#> [9,] 17 2
#> [10,] 16 20
#> [11,] 20 21
#> [12,] 21 10
#> [13,] 21 7
#> [14,] 20 6
#> [15,] 15 22
#> [16,] 22 12
#> [17,] 22 11
#> [18,] 14 23
#> [19,] 23 24
#> [20,] 24 25
#> [21,] 25 5
#> [22,] 25 13
#> [23,] 24 4
#> [24,] 23 1
#>
#> $Nnode
#> [1] 12
#>
#> $tip.label
#> [1] "sp2" "sp4" "sp8" "sp9" "sp10" "sp26" "sp27" "sp30" "sp31" "sp59"
#> [11] "sp64" "sp72" "sp75"
#>
#> $node.label
#> [1] "nd1" "nd2" "nd6" "nd22" "nd27" "nd74" "nd32" "nd54" "nd7" "nd8"
#> [11] "nd36" "nd38"
#>
#> $node.state
#> nd1 nd2 nd6 nd22 nd27 nd74 nd32 nd54 nd7 nd8 nd36 nd38
#> 1 1 2 2 2 2 2 2 1 1 1 1
#>
#> $edge.length
#> [1] 0.16467463 0.60776479 0.06123598 0.13756928 0.19052413 0.43829041
#> [7] 0.14919102 0.26797730 0.12387543 0.38247528 0.24214935 0.28936865
#> [13] 0.31255390 0.27670668 0.43629704 1.11293809 1.11550593 0.53064429
#> [19] 0.51423161 0.04706635 0.37366599 0.58693711 0.14126857 0.95898051
#>
#> $orig
#> idx len parent start state extinct split sam idx2 parent2
#> 2 2 0.164674627 1 0.1508471 1 FALSE TRUE FALSE 101 100
#> 3 3 0.095752083 1 0.1508471 1 FALSE TRUE FALSE 102 100
#> 4 4 0.350260185 3 0.2465992 1 FALSE TRUE FALSE 103 102
#> 5 5 0.221791997 3 0.2465992 1 FALSE TRUE FALSE 104 102
#> 6 6 0.607764789 2 0.3155218 2 FALSE TRUE FALSE 105 101
#> 7 7 0.436297042 2 0.3155218 1 FALSE TRUE FALSE 106 101
#> 8 8 0.213100210 5 0.4683912 1 FALSE TRUE FALSE 107 104
#> 9 9 0.178937370 5 0.4683912 1 FALSE TRUE FALSE 108 104
#> 10 10 0.908357264 4 0.5968594 2 FALSE TRUE FALSE 109 103
#> 11 11 0.208011176 4 0.5968594 1 FALSE TRUE FALSE 110 103
#> 12 12 0.958787122 9 0.6473286 3 FALSE TRUE FALSE 111 108
#> 13 13 0.285044132 9 0.6473286 1 FALSE TRUE FALSE 112 108
#> 14 14 0.511629972 8 0.6814914 1 FALSE TRUE FALSE 113 107
#> 15 15 0.187315709 8 0.6814914 1 FALSE TRUE FALSE 114 107
#> 16 16 0.287068808 7 0.7518188 1 FALSE TRUE FALSE 115 106
#> 17 17 0.233292244 7 0.7518188 1 FALSE TRUE FALSE 116 106
#> 18 18 1.121845705 11 0.8048706 1 FALSE FALSE FALSE 1 110
#> 19 19 0.364675377 11 0.8048706 1 FALSE TRUE FALSE 117 110
#> 20 20 0.011876720 15 0.8688071 1 FALSE TRUE FALSE 118 114
#> 21 21 0.771664802 15 0.8688071 1 FALSE FALSE TRUE 2 114
#> 22 22 0.404881489 20 0.8806839 1 FALSE TRUE FALSE 119 118
#> 23 23 0.164910945 20 0.8806839 1 FALSE TRUE FALSE 120 118
#> 24 24 0.061235983 6 0.9232865 2 FALSE TRUE FALSE 121 105
#> 25 25 0.147439207 6 0.9232865 2 FALSE TRUE FALSE 122 105
#> 26 26 0.994343566 13 0.9323727 1 FALSE FALSE FALSE 3 112
#> 27 27 0.718118368 13 0.9323727 3 FALSE TRUE FALSE 123 112
#> 28 28 0.008634727 24 0.9845225 2 FALSE TRUE FALSE 124 121
#> 29 29 0.123875431 24 0.9845225 2 FALSE FALSE TRUE 4 121
#> 30 30 0.941605236 17 0.9851110 1 FALSE FALSE FALSE 5 116
#> 31 31 0.210691558 17 0.9851110 1 FALSE TRUE FALSE 125 116
#> 33 33 0.128934554 28 0.9931573 2 FALSE TRUE FALSE 126 124
#> 34 34 0.196808061 16 1.0388876 1 FALSE TRUE FALSE 127 115
#> 35 35 0.175404690 16 1.0388876 1 FALSE TRUE FALSE 128 115
#> 36 36 0.881121485 23 1.0455948 3 FALSE FALSE FALSE 7 120
#> 37 37 0.523725191 23 1.0455948 1 FALSE TRUE FALSE 129 120
#> 38 38 0.296646520 25 1.0707258 2 FALSE TRUE FALSE 130 122
#> 39 39 0.235036077 25 1.0707258 2 FALSE TRUE FALSE 131 122
#> 40 40 0.190524130 33 1.1220918 2 FALSE FALSE TRUE 8 126
#> 41 41 0.378207392 33 1.1220918 2 FALSE TRUE FALSE 132 126
#> 42 42 0.088889776 19 1.1695460 1 FALSE TRUE FALSE 133 117
#> 43 43 0.084562865 19 1.1695460 3 FALSE TRUE FALSE 134 117
#> 44 44 0.002601639 14 1.1931214 1 FALSE TRUE FALSE 135 113
#> 45 45 0.424346440 14 1.1931214 1 FALSE TRUE FALSE 136 113
#> 46 46 0.047066352 44 1.1957230 1 FALSE TRUE FALSE 137 135
#> 47 47 0.141268574 44 1.1957230 1 FALSE FALSE TRUE 9 135
#> 48 48 0.146166009 31 1.1958026 1 FALSE TRUE FALSE 138 125
#> 49 49 0.067324209 31 1.1958026 1 FALSE TRUE FALSE 139 125
#> 50 50 0.544442729 35 1.2142923 1 FALSE TRUE FALSE 140 128
#> 51 51 0.135830510 35 1.2142923 1 FALSE TRUE FALSE 141 128
#> 52 52 0.054169952 34 1.2356957 1 FALSE TRUE FALSE 142 127
#> 53 53 0.085441542 34 1.2356957 1 FALSE TRUE FALSE 143 127
#> 54 54 0.373665988 46 1.2427894 3 FALSE FALSE TRUE 10 137
#> 55 55 0.005947470 46 1.2427894 1 FALSE TRUE FALSE 144 137
#> 56 56 0.062525080 55 1.2487369 1 FALSE TRUE FALSE 145 144
#> 57 57 0.079893078 55 1.2487369 1 FALSE TRUE FALSE 146 144
#> 58 58 0.672607463 43 1.2541088 3 FALSE FALSE FALSE 11 134
#> 59 59 0.314828098 43 1.2541088 3 FALSE TRUE FALSE 147 134
#> 60 60 0.668280552 42 1.2584357 1 FALSE FALSE FALSE 12 133
#> 61 61 0.668280552 42 1.2584357 1 FALSE FALSE FALSE 13 133
#> 62 62 0.421234449 49 1.2631268 1 FALSE TRUE FALSE 148 139
#> 63 63 0.069066626 49 1.2631268 1 FALSE TRUE FALSE 149 139
#> 64 64 0.369898133 22 1.2855653 1 FALSE TRUE FALSE 150 119
#> 65 65 0.641150941 22 1.2855653 1 FALSE FALSE FALSE 14 119
#> 66 66 0.280602490 52 1.2898656 1 FALSE TRUE FALSE 151 142
#> 67 67 0.320210285 52 1.2898656 1 FALSE TRUE FALSE 152 142
#> 68 68 0.242149352 39 1.3057618 2 FALSE TRUE FALSE 153 131
#> 69 69 0.233226652 39 1.3057618 2 FALSE TRUE FALSE 154 131
#> 70 70 0.570054335 56 1.3112619 1 FALSE TRUE FALSE 155 145
#> 71 71 0.615454346 56 1.3112619 2 FALSE FALSE FALSE 15 145
#> 72 72 0.083934169 53 1.3211372 1 FALSE TRUE FALSE 156 143
#> 73 73 0.593478377 53 1.3211372 1 FALSE TRUE FALSE 157 143
#> 74 74 0.103403746 57 1.3286299 1 FALSE TRUE FALSE 158 146
#> 75 75 0.432689222 57 1.3286299 1 FALSE TRUE FALSE 159 146
#> 76 76 0.288974657 63 1.3321934 1 FALSE TRUE FALSE 160 149
#> 77 77 0.187107326 63 1.3321934 1 FALSE TRUE FALSE 161 149
#> 78 78 0.101989443 48 1.3419686 1 FALSE TRUE FALSE 162 138
#> 79 79 0.358703541 48 1.3419686 1 FALSE TRUE FALSE 163 138
#> 80 80 0.242264625 51 1.3501228 1 FALSE TRUE FALSE 164 141
#> 81 81 0.576593472 51 1.3501228 3 FALSE FALSE FALSE 16 141
#> 82 82 0.043004976 38 1.3673723 2 FALSE TRUE FALSE 165 130
#> 83 83 0.559344007 38 1.3673723 2 FALSE FALSE FALSE 17 130
#> 84 84 0.521644901 72 1.4050714 1 FALSE FALSE FALSE 18 156
#> 85 85 0.521644901 72 1.4050714 1 FALSE FALSE FALSE 19 156
#> 86 86 0.065834152 82 1.4103773 2 FALSE TRUE FALSE 166 165
#> 87 87 0.261437974 82 1.4103773 2 FALSE TRUE FALSE 167 165
#> 88 88 0.296346500 74 1.4320337 1 FALSE TRUE FALSE 168 158
#> 89 89 0.097792699 74 1.4320337 1 FALSE TRUE FALSE 169 158
#> 91 91 0.410609832 78 1.4439581 1 FALSE TRUE FALSE 170 162
#> 92 92 0.293597865 86 1.4762114 2 FALSE TRUE FALSE 171 166
#> 93 93 0.083985009 86 1.4762114 2 FALSE TRUE FALSE 172 166
#> 94 94 0.426417078 41 1.5002992 2 FALSE FALSE FALSE 21 132
#> 95 95 0.060083014 41 1.5002992 2 FALSE TRUE FALSE 173 132
#> 96 96 0.159140297 10 1.5052167 2 FALSE TRUE FALSE 174 109
#> 97 97 0.421499617 10 1.5052167 2 FALSE FALSE FALSE 22 109
#> 98 98 0.407415518 77 1.5193008 1 FALSE FALSE FALSE 23 161
#> 99 99 0.407415518 77 1.5193008 1 FALSE FALSE FALSE 24 161
#> 100 100 0.092729426 89 1.5298264 1 FALSE TRUE FALSE 175 169
#> 101 101 0.274753602 89 1.5298264 3 FALSE TRUE FALSE 176 169
#> 102 102 0.387727798 69 1.5389885 2 FALSE FALSE FALSE 25 154
#> 103 103 0.043480033 69 1.5389885 2 FALSE FALSE TRUE 26 154
#> 104 104 0.175579119 68 1.5479112 2 FALSE TRUE FALSE 177 153
#> 105 105 0.312553900 68 1.5479112 3 FALSE FALSE TRUE 27 153
#> 106 106 0.366519870 93 1.5601964 2 FALSE FALSE FALSE 28 172
#> 107 107 0.366519870 93 1.5601964 2 FALSE FALSE FALSE 29 172
#> 108 108 0.149191016 95 1.5603822 2 FALSE FALSE TRUE 30 173
#> 109 109 0.267977300 95 1.5603822 3 FALSE FALSE TRUE 31 173
#> 110 110 0.357779365 59 1.5689369 3 FALSE FALSE FALSE 32 147
#> 111 111 0.357779365 59 1.5689369 3 FALSE FALSE FALSE 33 147
#> 112 112 0.357396294 37 1.5693200 1 FALSE FALSE FALSE 34 129
#> 113 113 0.357396294 37 1.5693200 1 FALSE FALSE FALSE 35 129
#> 114 114 0.356248170 66 1.5704681 1 FALSE FALSE FALSE 36 151
#> 115 115 0.356248170 66 1.5704681 1 FALSE FALSE FALSE 37 151
#> 116 116 0.334328846 80 1.5923874 3 FALSE FALSE FALSE 38 164
#> 117 117 0.334328846 80 1.5923874 1 FALSE FALSE FALSE 39 164
#> 118 118 0.314805032 12 1.6061157 2 FALSE TRUE FALSE 178 111
#> 119 119 0.222454996 12 1.6061157 3 FALSE TRUE FALSE 179 111
#> 120 120 0.049710495 67 1.6100759 1 FALSE TRUE FALSE 180 152
#> 121 121 0.316640375 67 1.6100759 1 FALSE FALSE FALSE 40 152
#> 122 122 0.309248446 45 1.6174678 1 FALSE FALSE FALSE 41 136
#> 123 123 0.309248446 45 1.6174678 1 FALSE FALSE FALSE 42 136
#> 124 124 0.102119268 76 1.6211681 1 FALSE TRUE FALSE 181 160
#> 125 125 0.305548186 76 1.6211681 3 FALSE FALSE FALSE 43 160
#> 126 126 0.052236063 100 1.6225558 1 FALSE TRUE FALSE 182 175
#> 127 127 0.304160477 100 1.6225558 3 FALSE FALSE FALSE 44 175
#> 128 128 0.276225198 27 1.6504911 3 FALSE FALSE FALSE 45 123
#> 129 129 0.016622859 27 1.6504911 3 FALSE TRUE FALSE 183 123
#> 130 130 0.147642260 64 1.6554635 1 FALSE TRUE FALSE 184 150
#> 131 131 0.271252808 64 1.6554635 1 FALSE FALSE FALSE 46 150
#> 132 132 0.266929879 120 1.6597864 1 FALSE FALSE FALSE 47 180
#> 133 133 0.266929879 120 1.6597864 1 FALSE FALSE FALSE 48 180
#> 134 134 0.191284415 96 1.6643570 2 FALSE TRUE FALSE 185 174
#> 135 135 0.093227680 96 1.6643570 2 FALSE TRUE FALSE 186 174
#> 136 136 0.259602339 129 1.6671139 3 FALSE FALSE FALSE 49 183
#> 137 137 0.259602339 129 1.6671139 1 FALSE FALSE FALSE 50 183
#> 139 139 0.254901057 87 1.6718152 2 FALSE FALSE FALSE 52 167
#> 140 140 0.054001298 126 1.6747919 1 FALSE TRUE FALSE 187 182
#> 141 141 0.006521519 126 1.6747919 1 FALSE TRUE FALSE 188 182
#> 142 142 0.245402895 141 1.6813134 1 FALSE FALSE FALSE 53 188
#> 143 143 0.245402895 141 1.6813134 1 FALSE FALSE FALSE 54 188
#> 144 144 0.242355020 62 1.6843613 1 FALSE FALSE FALSE 55 148
#> 146 146 0.226044128 79 1.7006722 1 FALSE FALSE FALSE 57 163
#> 147 147 0.197537764 79 1.7006722 1 FALSE TRUE FALSE 189 163
#> 148 148 0.203428919 124 1.7232874 1 FALSE FALSE FALSE 58 181
#> 149 149 0.034087869 124 1.7232874 1 FALSE TRUE FALSE 190 181
#> 150 150 0.113789534 104 1.7234903 2 FALSE FALSE TRUE 59 177
#> 151 151 0.203225979 104 1.7234903 2 FALSE FALSE FALSE 60 177
#> 152 152 0.198336103 88 1.7283802 1 FALSE FALSE FALSE 61 168
#> 153 153 0.198336103 88 1.7283802 1 FALSE FALSE FALSE 62 168
#> 154 154 0.197923116 140 1.7287932 1 FALSE FALSE FALSE 63 187
#> 155 155 0.166374148 140 1.7287932 1 FALSE TRUE FALSE 191 187
#> 156 156 0.014147720 149 1.7573752 1 FALSE TRUE FALSE 192 190
#> 157 157 0.109949497 149 1.7573752 3 FALSE FALSE TRUE 64 190
#> 158 158 0.169131640 135 1.7575846 3 FALSE FALSE FALSE 65 186
#> 159 159 0.169131640 135 1.7575846 2 FALSE FALSE FALSE 66 186
#> 160 160 0.157153882 50 1.7587350 1 FALSE TRUE FALSE 193 140
#> 161 161 0.041193647 50 1.7587350 2 FALSE TRUE FALSE 194 140
#> 162 162 0.121493122 75 1.7613192 1 FALSE TRUE FALSE 195 159
#> 163 163 0.141347666 75 1.7613192 1 FALSE TRUE FALSE 196 159
#> 164 164 0.156907014 92 1.7698093 2 FALSE FALSE FALSE 67 171
#> 165 165 0.156907014 92 1.7698093 2 FALSE FALSE FALSE 68 171
#> 166 166 0.155193329 156 1.7715230 1 FALSE FALSE FALSE 69 192
#> 167 167 0.155193329 156 1.7715230 1 FALSE FALSE FALSE 70 192
#> 168 168 0.126787606 161 1.7999287 2 FALSE FALSE FALSE 71 194
#> 169 169 0.064828216 161 1.7999287 2 FALSE FALSE TRUE 72 194
#> 170 170 0.123610548 130 1.8031057 1 FALSE FALSE FALSE 73 184
#> 171 171 0.123610548 130 1.8031057 1 FALSE FALSE FALSE 74 184
#> 172 172 0.058918845 101 1.8045800 3 FALSE TRUE FALSE 197 176
#> 173 173 0.025146519 101 1.8045800 3 FALSE FALSE TRUE 75 176
#> 174 174 0.098145581 119 1.8285707 3 FALSE FALSE FALSE 76 179
#> 176 176 0.072148394 91 1.8545679 1 FALSE FALSE FALSE 78 170
#> 177 177 0.072148394 91 1.8545679 1 FALSE FALSE FALSE 79 170
#> 178 178 0.071074905 134 1.8556414 2 FALSE FALSE FALSE 80 185
#> 179 179 0.071074905 134 1.8556414 2 FALSE FALSE FALSE 81 185
#> 180 180 0.063217456 172 1.8634988 3 FALSE FALSE FALSE 82 197
#> 181 181 0.063217456 172 1.8634988 3 FALSE FALSE FALSE 83 197
#> 182 182 0.045400011 70 1.8813163 1 FALSE FALSE FALSE 84 155
#> 183 183 0.045400011 70 1.8813163 1 FALSE FALSE FALSE 85 155
#> 184 184 0.043904005 162 1.8828123 1 FALSE FALSE FALSE 86 195
#> 185 185 0.043904005 162 1.8828123 1 FALSE FALSE FALSE 87 195
#> 186 186 0.031548968 155 1.8951673 1 FALSE FALSE FALSE 88 191
#> 187 187 0.031548968 155 1.8951673 1 FALSE FALSE FALSE 89 191
#> 188 188 0.028506365 147 1.8982099 1 FALSE FALSE FALSE 90 189
#> 190 190 0.024049461 163 1.9026668 1 FALSE FALSE FALSE 92 196
#> 191 191 0.024049461 163 1.9026668 1 FALSE FALSE FALSE 93 196
#> 192 192 0.012100693 73 1.9146156 1 FALSE FALSE FALSE 94 157
#> 193 193 0.012100693 73 1.9146156 1 FALSE FALSE FALSE 95 157
#> 194 194 0.010827371 160 1.9158889 1 FALSE FALSE FALSE 96 193
#> 195 195 0.010827371 160 1.9158889 1 FALSE FALSE FALSE 97 193
#> 196 196 0.005795544 118 1.9209207 2 FALSE FALSE FALSE 98 178
#> 197 197 0.005795544 118 1.9209207 2 FALSE FALSE FALSE 99 178
#> name name2
#> 2 <NA> nd2
#> 3 <NA> nd3
#> 4 <NA> nd4
#> 5 <NA> nd5
#> 6 <NA> nd6
#> 7 <NA> nd7
#> 8 <NA> nd8
#> 9 <NA> nd9
#> 10 <NA> nd10
#> 11 <NA> nd11
#> 12 <NA> nd12
#> 13 <NA> nd13
#> 14 <NA> nd14
#> 15 <NA> nd15
#> 16 <NA> nd16
#> 17 <NA> nd17
#> 18 sp1 sp1
#> 19 <NA> nd18
#> 20 <NA> nd19
#> 21 sp2 sp2
#> 22 <NA> nd20
#> 23 <NA> nd21
#> 24 <NA> nd22
#> 25 <NA> nd23
#> 26 sp3 sp3
#> 27 <NA> nd24
#> 28 <NA> nd25
#> 29 sp4 sp4
#> 30 sp5 sp5
#> 31 <NA> nd26
#> 33 <NA> nd27
#> 34 <NA> nd28
#> 35 <NA> nd29
#> 36 sp7 sp7
#> 37 <NA> nd30
#> 38 <NA> nd31
#> 39 <NA> nd32
#> 40 sp8 sp8
#> 41 <NA> nd33
#> 42 <NA> nd34
#> 43 <NA> nd35
#> 44 <NA> nd36
#> 45 <NA> nd37
#> 46 <NA> nd38
#> 47 sp9 sp9
#> 48 <NA> nd39
#> 49 <NA> nd40
#> 50 <NA> nd41
#> 51 <NA> nd42
#> 52 <NA> nd43
#> 53 <NA> nd44
#> 54 sp10 sp10
#> 55 <NA> nd45
#> 56 <NA> nd46
#> 57 <NA> nd47
#> 58 sp11 sp11
#> 59 <NA> nd48
#> 60 sp12 sp12
#> 61 sp13 sp13
#> 62 <NA> nd49
#> 63 <NA> nd50
#> 64 <NA> nd51
#> 65 sp14 sp14
#> 66 <NA> nd52
#> 67 <NA> nd53
#> 68 <NA> nd54
#> 69 <NA> nd55
#> 70 <NA> nd56
#> 71 sp15 sp15
#> 72 <NA> nd57
#> 73 <NA> nd58
#> 74 <NA> nd59
#> 75 <NA> nd60
#> 76 <NA> nd61
#> 77 <NA> nd62
#> 78 <NA> nd63
#> 79 <NA> nd64
#> 80 <NA> nd65
#> 81 sp16 sp16
#> 82 <NA> nd66
#> 83 sp17 sp17
#> 84 sp18 sp18
#> 85 sp19 sp19
#> 86 <NA> nd67
#> 87 <NA> nd68
#> 88 <NA> nd69
#> 89 <NA> nd70
#> 91 <NA> nd71
#> 92 <NA> nd72
#> 93 <NA> nd73
#> 94 sp21 sp21
#> 95 <NA> nd74
#> 96 <NA> nd75
#> 97 sp22 sp22
#> 98 sp23 sp23
#> 99 sp24 sp24
#> 100 <NA> nd76
#> 101 <NA> nd77
#> 102 sp25 sp25
#> 103 sp26 sp26
#> 104 <NA> nd78
#> 105 sp27 sp27
#> 106 sp28 sp28
#> 107 sp29 sp29
#> 108 sp30 sp30
#> 109 sp31 sp31
#> 110 sp32 sp32
#> 111 sp33 sp33
#> 112 sp34 sp34
#> 113 sp35 sp35
#> 114 sp36 sp36
#> 115 sp37 sp37
#> 116 sp38 sp38
#> 117 sp39 sp39
#> 118 <NA> nd79
#> 119 <NA> nd80
#> 120 <NA> nd81
#> 121 sp40 sp40
#> 122 sp41 sp41
#> 123 sp42 sp42
#> 124 <NA> nd82
#> 125 sp43 sp43
#> 126 <NA> nd83
#> 127 sp44 sp44
#> 128 sp45 sp45
#> 129 <NA> nd84
#> 130 <NA> nd85
#> 131 sp46 sp46
#> 132 sp47 sp47
#> 133 sp48 sp48
#> 134 <NA> nd86
#> 135 <NA> nd87
#> 136 sp49 sp49
#> 137 sp50 sp50
#> 139 sp52 sp52
#> 140 <NA> nd88
#> 141 <NA> nd89
#> 142 sp53 sp53
#> 143 sp54 sp54
#> 144 sp55 sp55
#> 146 sp57 sp57
#> 147 <NA> nd90
#> 148 sp58 sp58
#> 149 <NA> nd91
#> 150 sp59 sp59
#> 151 sp60 sp60
#> 152 sp61 sp61
#> 153 sp62 sp62
#> 154 sp63 sp63
#> 155 <NA> nd92
#> 156 <NA> nd93
#> 157 sp64 sp64
#> 158 sp65 sp65
#> 159 sp66 sp66
#> 160 <NA> nd94
#> 161 <NA> nd95
#> 162 <NA> nd96
#> 163 <NA> nd97
#> 164 sp67 sp67
#> 165 sp68 sp68
#> 166 sp69 sp69
#> 167 sp70 sp70
#> 168 sp71 sp71
#> 169 sp72 sp72
#> 170 sp73 sp73
#> 171 sp74 sp74
#> 172 <NA> nd98
#> 173 sp75 sp75
#> 174 sp76 sp76
#> 176 sp78 sp78
#> 177 sp79 sp79
#> 178 sp80 sp80
#> 179 sp81 sp81
#> 180 sp82 sp82
#> 181 sp83 sp83
#> 182 sp84 sp84
#> 183 sp85 sp85
#> 184 sp86 sp86
#> 185 sp87 sp87
#> 186 sp88 sp88
#> 187 sp89 sp89
#> 188 sp90 sp90
#> 190 sp92 sp92
#> 191 sp93 sp93
#> 192 sp94 sp94
#> 193 sp95 sp95
#> 194 sp96 sp96
#> 195 sp97 sp97
#> 196 sp98 sp98
#> 197 sp99 sp99
#>
#> $hist
#> idx t from to x0 tc idx2 name2
#> 13 36 1.7712115 1 3 1.0455948 0.72561669 6 sp7
#> 7 54 1.4714900 1 3 1.2427894 0.22870062 9 sp10
#> 11 71 1.7523062 1 2 1.3112619 0.44104431 14 sp15
#> 6 81 1.3637622 1 3 1.3501228 0.01363937 15 sp16
#> 12 105 1.7655396 2 3 1.5479112 0.21762839 25 sp27
#> 9 109 1.6938940 2 3 1.5603822 0.13351183 29 sp31
#> 17 116 1.8579434 1 3 1.5923874 0.26555601 36 sp38
#> 20 125 1.9110279 1 3 1.6211681 0.28985983 41 sp43
#> 15 127 1.8226049 1 3 1.6225558 0.20004911 42 sp44
#> 10 137 1.7423445 3 1 1.6671139 0.07523055 48 sp50
#> 16 157 1.8506348 1 3 1.7573752 0.09325955 60 sp64
#> 19 158 1.9005004 2 3 1.7575846 0.14291580 61 sp65
#> 2 6 0.7937786 1 2 0.3155218 0.47825687 96 nd6
#> 14 161 1.7896296 1 2 1.7587350 0.03089453 124 nd95
#> 1 10 0.7664957 1 2 0.5968594 0.16963631 141 nd10
#> 5 43 1.2514209 1 3 1.1695460 0.08187492 148 nd35
#> 8 101 1.6656791 1 3 1.5298264 0.13585273 167 nd77
#> 4 12 1.1409286 1 3 0.6473286 0.49360002 181 nd12
#> 18 118 1.8697629 3 2 1.6061157 0.26364715 182 nd79
#> 3 27 1.1014641 1 3 0.9323727 0.16909142 184 nd24
#>
#> $edge.state
#> [1] 1 2 2 2 2 2 2 2 2 2 2 3 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 2 2 2 1
#> [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 1 1 3 1 3 1 1 1 1 1 1
#> [75] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 3 1 1 1 1 1 2 2 2 2 2 2 3 2 2 1
#> [112] 1 1 1 1 1 3 3 3 3 3 1 1 1 1 1 3 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
#> [149] 1 3 3 3 3 3 3 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 1 1 1 1 1 3 2 2
#> [186] 2 3 3 3 1 1 3 3 3 3 1
#>
#> $tip.state
#> [1] "1" "2" "2" "1" "3" "2" "3" "2" "3" "2" "3" "2" "3"
#>
#> attr(,"class")
#> [1] "phylo"
#> attr(,"order")
#> [1] "cladewise"