Load packages:

setwd("~/Documents/pyphlawd_local/PyPHLAWD-master_v2/examples/alt_config_oroban2_filtF/Final_SuperMatrix/RAxML_tree/7.3/7.3.2/Tree_dating")

library(phytools)
## Loading required package: ape
## Warning: package 'ape' was built under R version 3.4.2
## Loading required package: maps
library(geiger)
require(phangorn)
## Loading required package: phangorn
## Warning: package 'phangorn' was built under R version 3.4.2
require(ape)

Load Trees:

in_oro_tre <- read.nexus("RAxML_bipartitions.12_gene_7.3.fasta.rtp.nssp.ncorr.tre")
in_oro_tre
## 
## Phylogenetic tree with 923 tips and 922 internal nodes.
## 
## Tip labels:
##  Pedicularis_pygmaea, Pedicularis_debilis, Pedicularis_atuntsiensis, Pedicularis_verbenifolia, Pedicularis_oxyrhyncha, Pedicularis_chenocephala, ...
## 
## Rooted; includes branch lengths.
in_calib_tre <- read.nexus("Orobanchaceae_chronogram_MAP.tre")
in_calib_tre
## 
## Phylogenetic tree with 160 tips and 159 internal nodes.
## 
## Tip labels:
##  Orobanche_owerinii, Orobanche_transcaucasica, Orobanche_picridis, Orobanche_pubescens, Orobanche_crenata, Orobanche_artemisiae-campestris, ...
## 
## Rooted; includes branch lengths.

Point estimate for trees using MAP tree:

res=congruify.phylo(reference=in_calib_tre, target=in_oro_tre, scale=NA)
## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.
class(res)
## [1] "list"
res[2]
## $calibrations
##                                 MRCA    MaxAge    MinAge
## 1   3be5642378a9b6697a3330fe1b40afec 31.392036 31.392036
## 2   96f4b98259d5785033bb9a54cdfc054e 30.230328 30.230328
## 3   a7dd8ed89aef0dce36d08473786129dd 29.178399 29.178399
## 4   f487d6e3df169044053746ec1e569b0e 27.723483 27.723483
## 5   65d0ce2a773d837342ec6465b26d6cf0 26.576600 26.576600
## 7   ba8aabe3bc803d2913cdb6ce870d3b6a 24.143421 24.143421
## 8   524c99119d58f43c63628856f7293766 21.904891 21.904891
## 10  7856320c2b1a60bc0ce25140bdf44911 12.472683 12.472683
## 14  4cd20afdd9f0de11d327ae6e24dd53ae  3.586328  3.586328
## 143 9b89e63e5bf6d9131d95b99b6517af2e  1.597123  1.597123
## 375 a2eb9d984f3cd50a6c5bc7460fec72a9 10.945603 10.945603
## 475 6b175c673fe62dd3b62d0eb317fcabe9  4.885254  4.885254
## 482 f84f1d7805274718199b770b86652009  5.811030  5.811030
## 528 0be7edb870c40468eed3ca6841a7786f 10.932643 10.932643
## 551 b8fc3b0e91c8274e5850cf4584c17df8  6.069928  6.069928
## 584 e50136c92546d14fcef34c7e35ab5373  5.131019  5.131019
## 585 a6413c2c146a6f4e2ef3bf90192cc74b  1.858037  1.858037
## 589 71219186235c52ad4e56d5f429cd3600  1.671235  1.671235
## 597 51b4bfe91c3361840bca928912955c8d  3.129314  3.129314
## 613 f4c33ff16845cbd6fd1722c4e50a599f 12.200906 12.200906
## 614 1b53f8dd74bb1e5071a55cf786f88702  9.019463  9.019463
## 616 08584d3612b4ad8ce595a2544bb9b7cd  7.866207  7.866207
## 753 b1ee62a543be5aec6d5d30b3bbabd775  6.703529  6.703529
## 778 1fad308bc661fc503faac1cb37251786  2.850805  2.850805
## 790 3aeadd1ad60ac0a16e3a75faeb11c03e 16.480198 16.480198
## 791 5dbf889066cb16a585229609868e2e54 15.620983 15.620983
## 793 fb690ce6f8e8053f6e258d1fbda21129 13.900829 13.900829
## 794 bfb79890ceff48b163bfe7f8372a551c 13.202029 13.202029
## 797 1046b8257efe7c7980ac4769f38c6dd9 11.954068 11.954068
## 798 cd9815714b7874284d7437149f255281 11.218206 11.218206
## 801 87eee2f71e37862fc25475c9b8f26276  3.629006  3.629006
## 802 03ffe8289e60b2d53c775dfe7be2f225  3.232844  3.232844
## 803 2508aa2dfde8a154a977def095fec181  2.780412  2.780412
## 808 97ec7ea7b0d7b6b1077451c06c8f2713  1.538403  1.538403
## 810 b775222c2dd8b3ff69e6f871228142b6  0.809449  0.809449
## 820 464cd302ad36b4c7a5ea09ffb6b32e0e  0.055861  0.055861
## 829 63de3939917d80a7454dbff9a4e33992  0.352206  0.352206
## 832 7371abc451464cd8dfd60e265173c731  0.041497  0.041497
## 834 cff514640e0083d867e7c158a7a6aa3e  0.536520  0.536520
## 837 3ddcc2413aa30253111f8578df8b9f71  0.481796  0.481796
## 842 c6ac2040f609df86f8b78562e8101041  1.700774  1.700774
## 843 0f562776889cde8ed3e4329b42799cf8  0.196176  0.196176
## 845 ecf4a5c39c8ab655a8f2625b17606b13  0.451804  0.451804
## 847 c6f5d9b95719f196c311e8722ec7fc59  1.236919  1.236919
## 848 48e7e1c267f180decad3c384a792b193  3.082356  3.082356
## 849 c7c066c4bcab65b01b61103475c4a48b  3.170879  3.170879
## 854 667b7075b3bc06bfc49f56a4bb5daff5  0.415397  0.415397
## 859 706d6cb30691f25afb130dc1fe104575  0.062680  0.062680
## 860 9683cb90d2b9a966c30af2149109644a  0.222591  0.222591
## 868 5898d474c32c8b42f9dfcc9e25132cf3  7.294102  7.294102
## 869 0e66e329071b5198189c55e672eb3f03  2.915883  2.915883
## 874 50be8e8fe83656654b47e6e54204fea2  0.808775  0.808775
## 880 76e1a79214542ec2729f5e6c8d37b198  0.567669  0.567669
## 886 f4245ec022b4cd02ca027029111adaf0  3.058435  3.058435
## 888 1123ff442da7eb5a8e4ef9d6cfec96e0  7.279179  7.279179
## 889 ff9e64e6a51191c6b298a81843ee86eb  1.532344  1.532344
## 892 226aca05732a55df453f9a900f142ccc  0.438941  0.438941
## 893 7f9452c84987c59863ceaaf42c793151  9.468062  9.468062
## 894 8dde6bcaac61315f64f458a98db08a32  7.321506  7.321506
## 895 c844fa000c0b1300bdfc0469fe6d073c  3.989683  3.989683
## 896 8af8dc40c58f7d5534fe7e45f7a61f74  0.638443  0.638443
## 897 a1e59eef9ee34de5abf4c36cb383b0fe  0.281082  0.281082
## 898 5a0c8c64b9b8734cbac44bb43b42e0ac  4.025178  4.025178
## 899 f4195f70bc9140a15e6581e17eb8a0da 15.562020 15.562020
## 903 c96cc9bf9b727f0fff7e51ed9c74c048  3.718098  3.718098
## 904 1a53e0398867127943c6f9af7bf76a5c  2.979752  2.979752
## 906 b43ac1be9d0231468d7c0799b79362b9 15.585488 15.585488
## 909 9c0121cadffdedeb9b90a90522bc25a5  0.558164  0.558164
## 912 00f33d24a1fc93c9ca16af76155b3de4  1.663119  1.663119
## 915 16a18572a7d18b897030c5d6e8430be6  0.142506  0.142506
## 921 a078df13c46b1a918db37719f4397e5e  1.917775  1.917775
##                          taxonA                    taxonB
## 1           Pedicularis_pygmaea        Paulownia_fortunei
## 2           Pedicularis_pygmaea        Rehmannia_angulata
## 3           Pedicularis_pygmaea       Lindenbergia_indica
## 4           Pedicularis_pygmaea        Cymbaria_mongolica
## 5           Pedicularis_pygmaea           Orobanche_minor
## 7           Pedicularis_pygmaea    Euphrasia_marchesettii
## 8           Pedicularis_pygmaea         Harveya_silvatica
## 10          Pedicularis_pygmaea        Castilleja_yukonis
## 14          Pedicularis_pygmaea   Pedicularis_trichocymba
## 143        Pedicularis_elongata      Pedicularis_racemosa
## 375          Castilleja_yukonis          Agalinis_tenella
## 475   Orthocarpus_pachystachyus   Orthocarpus_tenuifolius
## 482            Agalinis_tenella      Aureolaria_pectinata
## 528           Harveya_silvatica        Buchnera_floridana
## 551             Hyobanche_rubra       Hyobanche_sanguinea
## 584         Striga_gesnerioides            Striga_elegans
## 585         Striga_gesnerioides          Striga_bilabiata
## 589              Striga_elegans           Striga_asiatica
## 597          Xylocalyx_carterae           Xylocalyx_asper
## 613      Euphrasia_marchesettii       Melampyrum_italicum
## 614      Euphrasia_marchesettii      Rhinanthus_serotinus
## 616      Euphrasia_marchesettii       Odontites_sillettii
## 753        Rhinanthus_serotinus         Lathraea_japonica
## 778       Melampyrum_carstiense        Melampyrum_arvense
## 790             Orobanche_minor      Conopholis_americana
## 791             Orobanche_minor       Cistanche_phelypaea
## 793             Orobanche_minor     Mannagettaea_hummelii
## 794             Orobanche_minor        Aphyllon_chilensis
## 797             Orobanche_minor  Diphelypaea_tournefortii
## 798             Orobanche_minor       Orobanche_anatolica
## 801             Orobanche_minor        Orobanche_grenieri
## 802             Orobanche_minor      Orobanche_boninsimae
## 803             Orobanche_minor         Orobanche_foetida
## 808             Orobanche_minor        Orobanche_alsatica
## 810             Orobanche_minor         Orobanche_hederae
## 820           Orobanche_hederae      Orobanche_amethystea
## 829             Orobanche_flava         Orobanche_lucorum
## 832           Orobanche_lucorum         Orobanche_salviae
## 834      Orobanche_pallidiflora        Orobanche_pancicii
## 837    Orobanche_caryophyllacea         Orobanche_teucrii
## 842           Orobanche_foetida Orobanche_austrohispanica
## 843           Orobanche_foetida      Orobanche_densiflora
## 845   Orobanche_austrohispanica        Orobanche_gracilis
## 847         Orobanche_anatolica        Orobanche_colorata
## 848    Diphelypaea_tournefortii      Diphelypaea_coccinea
## 849 Phelipanche_georgii_reuteri        Phelipanche_ramosa
## 854 Phelipanche_georgii_reuteri          Phelipanche_nana
## 859  Phelipanche_portoilicitana     Phelipanche_pulchella
## 860         Phelipanche_mutelii  Phelipanche_lavandulacea
## 868          Aphyllon_chilensis     Aphyllon_fasciculatum
## 869          Aphyllon_chilensis        Aphyllon_tuberosum
## 874          Aphyllon_chilensis      Aphyllon_multiflorum
## 880           Aphyllon_riparium       Aphyllon_arizonicum
## 886       Aphyllon_fasciculatum        Aphyllon_uniflorum
## 888         Cistanche_phelypaea     Cistanche_deserticola
## 889         Cistanche_phelypaea        Cistanche_violacea
## 892       Cistanche_deserticola           Cistanche_salsa
## 893        Conopholis_americana       Boschniakia_rossica
## 894        Conopholis_americana        Kopsiopsis_hookeri
## 895        Conopholis_americana       Epifagus_virginiana
## 896        Conopholis_americana         Conopholis_alpina
## 897          Kopsiopsis_hookeri    Kopsiopsis_strobilacea
## 898         Boschniakia_rossica     Boschniakia_himalaica
## 899          Cymbaria_mongolica       Siphonostegia_laeta
## 903         Siphonostegia_laeta       Schwalbea_americana
## 904         Siphonostegia_laeta   Siphonostegia_chinensis
## 906         Lindenbergia_indica Lindenbergia_philippensis
## 909         Lindenbergia_indica      Lindenbergia_muraria
## 912          Rehmannia_angulata        Rehmannia_japonica
## 915          Rehmannia_angulata       Rehmannia_piasezkii
## 921          Paulownia_fortunei       Paulownia_tomentosa
res$calibrations
##                                 MRCA    MaxAge    MinAge
## 1   3be5642378a9b6697a3330fe1b40afec 31.392036 31.392036
## 2   96f4b98259d5785033bb9a54cdfc054e 30.230328 30.230328
## 3   a7dd8ed89aef0dce36d08473786129dd 29.178399 29.178399
## 4   f487d6e3df169044053746ec1e569b0e 27.723483 27.723483
## 5   65d0ce2a773d837342ec6465b26d6cf0 26.576600 26.576600
## 7   ba8aabe3bc803d2913cdb6ce870d3b6a 24.143421 24.143421
## 8   524c99119d58f43c63628856f7293766 21.904891 21.904891
## 10  7856320c2b1a60bc0ce25140bdf44911 12.472683 12.472683
## 14  4cd20afdd9f0de11d327ae6e24dd53ae  3.586328  3.586328
## 143 9b89e63e5bf6d9131d95b99b6517af2e  1.597123  1.597123
## 375 a2eb9d984f3cd50a6c5bc7460fec72a9 10.945603 10.945603
## 475 6b175c673fe62dd3b62d0eb317fcabe9  4.885254  4.885254
## 482 f84f1d7805274718199b770b86652009  5.811030  5.811030
## 528 0be7edb870c40468eed3ca6841a7786f 10.932643 10.932643
## 551 b8fc3b0e91c8274e5850cf4584c17df8  6.069928  6.069928
## 584 e50136c92546d14fcef34c7e35ab5373  5.131019  5.131019
## 585 a6413c2c146a6f4e2ef3bf90192cc74b  1.858037  1.858037
## 589 71219186235c52ad4e56d5f429cd3600  1.671235  1.671235
## 597 51b4bfe91c3361840bca928912955c8d  3.129314  3.129314
## 613 f4c33ff16845cbd6fd1722c4e50a599f 12.200906 12.200906
## 614 1b53f8dd74bb1e5071a55cf786f88702  9.019463  9.019463
## 616 08584d3612b4ad8ce595a2544bb9b7cd  7.866207  7.866207
## 753 b1ee62a543be5aec6d5d30b3bbabd775  6.703529  6.703529
## 778 1fad308bc661fc503faac1cb37251786  2.850805  2.850805
## 790 3aeadd1ad60ac0a16e3a75faeb11c03e 16.480198 16.480198
## 791 5dbf889066cb16a585229609868e2e54 15.620983 15.620983
## 793 fb690ce6f8e8053f6e258d1fbda21129 13.900829 13.900829
## 794 bfb79890ceff48b163bfe7f8372a551c 13.202029 13.202029
## 797 1046b8257efe7c7980ac4769f38c6dd9 11.954068 11.954068
## 798 cd9815714b7874284d7437149f255281 11.218206 11.218206
## 801 87eee2f71e37862fc25475c9b8f26276  3.629006  3.629006
## 802 03ffe8289e60b2d53c775dfe7be2f225  3.232844  3.232844
## 803 2508aa2dfde8a154a977def095fec181  2.780412  2.780412
## 808 97ec7ea7b0d7b6b1077451c06c8f2713  1.538403  1.538403
## 810 b775222c2dd8b3ff69e6f871228142b6  0.809449  0.809449
## 820 464cd302ad36b4c7a5ea09ffb6b32e0e  0.055861  0.055861
## 829 63de3939917d80a7454dbff9a4e33992  0.352206  0.352206
## 832 7371abc451464cd8dfd60e265173c731  0.041497  0.041497
## 834 cff514640e0083d867e7c158a7a6aa3e  0.536520  0.536520
## 837 3ddcc2413aa30253111f8578df8b9f71  0.481796  0.481796
## 842 c6ac2040f609df86f8b78562e8101041  1.700774  1.700774
## 843 0f562776889cde8ed3e4329b42799cf8  0.196176  0.196176
## 845 ecf4a5c39c8ab655a8f2625b17606b13  0.451804  0.451804
## 847 c6f5d9b95719f196c311e8722ec7fc59  1.236919  1.236919
## 848 48e7e1c267f180decad3c384a792b193  3.082356  3.082356
## 849 c7c066c4bcab65b01b61103475c4a48b  3.170879  3.170879
## 854 667b7075b3bc06bfc49f56a4bb5daff5  0.415397  0.415397
## 859 706d6cb30691f25afb130dc1fe104575  0.062680  0.062680
## 860 9683cb90d2b9a966c30af2149109644a  0.222591  0.222591
## 868 5898d474c32c8b42f9dfcc9e25132cf3  7.294102  7.294102
## 869 0e66e329071b5198189c55e672eb3f03  2.915883  2.915883
## 874 50be8e8fe83656654b47e6e54204fea2  0.808775  0.808775
## 880 76e1a79214542ec2729f5e6c8d37b198  0.567669  0.567669
## 886 f4245ec022b4cd02ca027029111adaf0  3.058435  3.058435
## 888 1123ff442da7eb5a8e4ef9d6cfec96e0  7.279179  7.279179
## 889 ff9e64e6a51191c6b298a81843ee86eb  1.532344  1.532344
## 892 226aca05732a55df453f9a900f142ccc  0.438941  0.438941
## 893 7f9452c84987c59863ceaaf42c793151  9.468062  9.468062
## 894 8dde6bcaac61315f64f458a98db08a32  7.321506  7.321506
## 895 c844fa000c0b1300bdfc0469fe6d073c  3.989683  3.989683
## 896 8af8dc40c58f7d5534fe7e45f7a61f74  0.638443  0.638443
## 897 a1e59eef9ee34de5abf4c36cb383b0fe  0.281082  0.281082
## 898 5a0c8c64b9b8734cbac44bb43b42e0ac  4.025178  4.025178
## 899 f4195f70bc9140a15e6581e17eb8a0da 15.562020 15.562020
## 903 c96cc9bf9b727f0fff7e51ed9c74c048  3.718098  3.718098
## 904 1a53e0398867127943c6f9af7bf76a5c  2.979752  2.979752
## 906 b43ac1be9d0231468d7c0799b79362b9 15.585488 15.585488
## 909 9c0121cadffdedeb9b90a90522bc25a5  0.558164  0.558164
## 912 00f33d24a1fc93c9ca16af76155b3de4  1.663119  1.663119
## 915 16a18572a7d18b897030c5d6e8430be6  0.142506  0.142506
## 921 a078df13c46b1a918db37719f4397e5e  1.917775  1.917775
##                          taxonA                    taxonB
## 1           Pedicularis_pygmaea        Paulownia_fortunei
## 2           Pedicularis_pygmaea        Rehmannia_angulata
## 3           Pedicularis_pygmaea       Lindenbergia_indica
## 4           Pedicularis_pygmaea        Cymbaria_mongolica
## 5           Pedicularis_pygmaea           Orobanche_minor
## 7           Pedicularis_pygmaea    Euphrasia_marchesettii
## 8           Pedicularis_pygmaea         Harveya_silvatica
## 10          Pedicularis_pygmaea        Castilleja_yukonis
## 14          Pedicularis_pygmaea   Pedicularis_trichocymba
## 143        Pedicularis_elongata      Pedicularis_racemosa
## 375          Castilleja_yukonis          Agalinis_tenella
## 475   Orthocarpus_pachystachyus   Orthocarpus_tenuifolius
## 482            Agalinis_tenella      Aureolaria_pectinata
## 528           Harveya_silvatica        Buchnera_floridana
## 551             Hyobanche_rubra       Hyobanche_sanguinea
## 584         Striga_gesnerioides            Striga_elegans
## 585         Striga_gesnerioides          Striga_bilabiata
## 589              Striga_elegans           Striga_asiatica
## 597          Xylocalyx_carterae           Xylocalyx_asper
## 613      Euphrasia_marchesettii       Melampyrum_italicum
## 614      Euphrasia_marchesettii      Rhinanthus_serotinus
## 616      Euphrasia_marchesettii       Odontites_sillettii
## 753        Rhinanthus_serotinus         Lathraea_japonica
## 778       Melampyrum_carstiense        Melampyrum_arvense
## 790             Orobanche_minor      Conopholis_americana
## 791             Orobanche_minor       Cistanche_phelypaea
## 793             Orobanche_minor     Mannagettaea_hummelii
## 794             Orobanche_minor        Aphyllon_chilensis
## 797             Orobanche_minor  Diphelypaea_tournefortii
## 798             Orobanche_minor       Orobanche_anatolica
## 801             Orobanche_minor        Orobanche_grenieri
## 802             Orobanche_minor      Orobanche_boninsimae
## 803             Orobanche_minor         Orobanche_foetida
## 808             Orobanche_minor        Orobanche_alsatica
## 810             Orobanche_minor         Orobanche_hederae
## 820           Orobanche_hederae      Orobanche_amethystea
## 829             Orobanche_flava         Orobanche_lucorum
## 832           Orobanche_lucorum         Orobanche_salviae
## 834      Orobanche_pallidiflora        Orobanche_pancicii
## 837    Orobanche_caryophyllacea         Orobanche_teucrii
## 842           Orobanche_foetida Orobanche_austrohispanica
## 843           Orobanche_foetida      Orobanche_densiflora
## 845   Orobanche_austrohispanica        Orobanche_gracilis
## 847         Orobanche_anatolica        Orobanche_colorata
## 848    Diphelypaea_tournefortii      Diphelypaea_coccinea
## 849 Phelipanche_georgii_reuteri        Phelipanche_ramosa
## 854 Phelipanche_georgii_reuteri          Phelipanche_nana
## 859  Phelipanche_portoilicitana     Phelipanche_pulchella
## 860         Phelipanche_mutelii  Phelipanche_lavandulacea
## 868          Aphyllon_chilensis     Aphyllon_fasciculatum
## 869          Aphyllon_chilensis        Aphyllon_tuberosum
## 874          Aphyllon_chilensis      Aphyllon_multiflorum
## 880           Aphyllon_riparium       Aphyllon_arizonicum
## 886       Aphyllon_fasciculatum        Aphyllon_uniflorum
## 888         Cistanche_phelypaea     Cistanche_deserticola
## 889         Cistanche_phelypaea        Cistanche_violacea
## 892       Cistanche_deserticola           Cistanche_salsa
## 893        Conopholis_americana       Boschniakia_rossica
## 894        Conopholis_americana        Kopsiopsis_hookeri
## 895        Conopholis_americana       Epifagus_virginiana
## 896        Conopholis_americana         Conopholis_alpina
## 897          Kopsiopsis_hookeri    Kopsiopsis_strobilacea
## 898         Boschniakia_rossica     Boschniakia_himalaica
## 899          Cymbaria_mongolica       Siphonostegia_laeta
## 903         Siphonostegia_laeta       Schwalbea_americana
## 904         Siphonostegia_laeta   Siphonostegia_chinensis
## 906         Lindenbergia_indica Lindenbergia_philippensis
## 909         Lindenbergia_indica      Lindenbergia_muraria
## 912          Rehmannia_angulata        Rehmannia_japonica
## 915          Rehmannia_angulata       Rehmannia_piasezkii
## 921          Paulownia_fortunei       Paulownia_tomentosa
length(res$calibrations)
## [1] 5
cal=res$calibrations
write.treePL(in_oro_tre, cal, base="Oro_point_estimation1", nsites=11028, opts=list(nthreads=30, thorough=TRUE, prime=TRUE))
## [1] "Oro_point_estimation1.infile"
## attr(,"method")
## [1] "treePL"
write.treePL(in_oro_tre, cal, base="Oro_point_estimation2", nsites=11028, opts=list(nthreads=30, thorough=TRUE, cv=TRUE, cvoutfile= 'Oro_point_estimation_CVresult.out', opt = 5, optad = 5, optcvad = 3))
## [1] "Oro_point_estimation2.infile"
## attr(,"method")
## [1] "treePL"
write.treePL(in_oro_tre, cal, base="Oro_point_estimation3", nsites=11028, opts=list(nthreads=30, thorough=TRUE, smooth=1000, opt = 5, optad = 5, optcvad = 3))
## [1] "Oro_point_estimation3.infile"
## attr(,"method")
## [1] "treePL"

Make file for CV test

for( i in 1:10){
  write.treePL(in_oro_tre, cal, base=paste("Oro_point_CV_test", i ,sep=""), nsites=11028, opts=list(nthreads=7, thorough=TRUE, cv=TRUE, cvoutfile= 'Oro_point_test_CVresult.out', opt = 5, optad = 5, optcvad = 3))
}

#run all 10 files CV results summarize later.

Function for finding nodes that are calibrated:

mrcaID=function(phy, cal){
    cal=as.matrix(cal)
    res=sapply(1:nrow(cal), function(idx){ ## loop over rows
        tips=cal[idx, c("taxonA", "taxonB")] ## fetch spanning taxa
        return(geiger:::.mrca(tips, phy)) ## MRCA of spanning taxa (node ID)
    })
    N=Ntip(phy)
    n=Nnode(phy)
    nn=integer(N+n) ## create empty vector of same length as branches in tree
    nn[res]=1 ## identify nodes that appear within calibrations
    nn=nn[-c(1:N)] ## exclude tip branches
    return(nn) ## return vector (ordered from first to last internal node in the tree)
}

Where are the calibration points:

vec=mrcaID(in_oro_tre, cal) ## get vector for calibrated nodes
sum(vec)==nrow(cal)
## [1] TRUE
plot.phylo(in_oro_tre, type = 'fan', show.tip=FALSE, edge.width=0.75, cex=0.25)
nodelabels(text=NULL, cex=ifelse(vec==0, NA, 1.0), frame="n", bg="lightskyblue", pch=22)

Multple calibrations from Posterior with 500 trees:

#Switch dirs
setwd("~/Documents/pyphlawd_local/PyPHLAWD-master_v2/examples/alt_config_oroban2_filtF/Final_SuperMatrix/RAxML_tree/7.3/7.3.2/Tree_dating/Schneider_500")

cal_trees <- read.tree('Schneider_post_sample500_clean.trees')
class(cal_trees)
## [1] "multiPhylo"
cal_list<-list(0)
for( i in 1:500){
  calibrations<-congruify.phylo(reference = cal_trees[[i]], target = in_oro_tre, scale = NA)
  cal_list <- c(calibrations[2], cal_list)
  #print(cal_list)
}
## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.

## Warning in smooth_scion(phy, scion, scion_desc, taxa, spp, tol = tol,
## method = method): Supplied 'stock' is non-ultrametric.
#print(cal_list)

length(cal_list)
## [1] 501
#cal_list[1]$calibrations

for( i in 1:500){
  write.treePL(in_oro_tre, cal_list[i]$calibrations, base= paste("oro_multiCalib", i,sep=""), nsites=11028, opts=list(smooth=1000, nthreads=2, opt = 5, optad = 5, optcvad = 3, thorough=TRUE))
}

#This looks like it works pretty well
#Now add the optimized parameters from the point test: specifically the smooth value.