Tree has no branch lengths, cannot compute pd

[wxy23116]

Hi Dr. Li, I am going to use your rtrees for phylogenetic and diversity analysis, and get the fish phylogenetic tree from taxon=fish, but after PD <- pd(OTU_list_tree, tree), R tells me "Tree has no branch lengths, cannot compute pd", and I would like to make sure that there is no function in rtrees to intercept the branch lengths.Thank you for your help.

[daijiang]

Can you provide a minimal reproducible example so that I can reproduce your error?

[wxy23116]

This is my workflow：
library(picante)
library(rtrees)
species_list_tree <- read.delim("/species_list_tree.txt")
OTU_list_tree <- read.delim("/OTU_list_tree.txt", header=FALSE)
p <- get_tree(species_list_tree,
taxon = "fish",
scenario = c("at_basal_node"),
show_grafted = FALSE,
tree_by_user = FALSE,
mc_cores = future::availableCores() - 2,
.progress = "text",
fish_tree = c("all-taxon"),
dt = TRUE)
PD <- pd(OTU_list_tree, p)
Error in pd(OTU_list_tree, p) :
Tree has no branch lengths, cannot compute pd

The list of species entered (species_list_tree.txt) and the OTU abundance table (OTU_list_tree.txt) I will email to you. Thanks again for your reply!

[wxy23116]

| | wangxiaoyang22919 | | ***@***.*** | ---- Replied Message ---- | From | Daijiang ***@***.***> | | Date | 10/11/2023 11:38 | | To | ***@***.***> | | Cc | ***@***.***> , ***@***.***> | | Subject | Re: [daijiang/rtrees] Tree has no branch lengths, cannot compute pd (Issue #7) | Can you provide a minimal reproducible example so that I can reproduce your error? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***> species genus family species-relative genus-relative Sardinella_zunasi Sardinella Clupeidae Hexagrammos_otakii Hexagrammos Hexagrammidae Engraulis_japonicus Engraulis Engraulidae Konosirus_punctatus Konosirus Clupeidae Acanthogobius_hasta Acanthogobius Gobiidae Thryssa_kammalensis Thryssa Engraulidae Setipinna_tenuifilis Setipinna Engraulidae Eupleurogrammus_muticus Eupleurogrammus Trichiuridae Scophthalmus_maximus Scophthalmus Scophthalmidae Planiliza_haematocheila Planiliza Mugilidae Mugil_cephalus Mugil Mugilidae Trichiurus_japonicus Trichiurus Trichiuridae Scomberomorus_niphonius Scomberomorus Scombridae Cynoglossus_joyneri Cynoglossus Cynoglossidae Auxis_rochei Auxis Scombridae Pampus_echinogaster Pampus Stromateidae Scomber_japonicus Scomber Scombridae Liparis_tanakae Liparis Liparidae Trachidermus_fasciatus Trachidermus Cottidae Ammodytes_personatus Ammodytes Ammodytidae Chelidonichthys_spinosus Chelidonichthys Triglidae Hyporhamphus_sajori Hyporhamphus Hemiramphidae Tridentiger_trigonocephalus Tridentiger Gobiidae Clupea_pallasi Clupea Clupeidae Odontamblyopus_lacepedii Odontamblyopus Gobiidae Sebastes_koreanus Sebastes Scorpaenidae Harpodon_nehereus Harpodon Harpodontidae Pagrus_major Pagrus Sparidae Strongylura_anastomella Strongylura Belonidae Hyporhamphus_intermedius Hyporhamphus Hemiramphidae Thamnaconus_modestus Thamnaconus Monacanthidae Platichthys_stellatus Platichthys Pleuronectidae Cynoglossus_semilaevis Cynoglossus Cynoglossidae Conger_myriaster Conger Congridae Myersina_filifer Myersina Gobiidae Lophius_litulon Lophius Lophiidae Cheilopogon_cyanopterus Cheilopogon Exocoetidae Cynoglossus_abbreviatus Cynoglossus Cynoglossidae Repomucenus_beniteguri Repomucenus Callionymidae Cleisthenes_herzensteini Cleisthenes Pleuronectidae Gadus_macrocephalus Gadus Gadidae Pennahia_argentata Pennahia Sciaenidae Zeus_faber Zeus Zeidae Rhabdosargus_sarba Rhabdosargus Sparidae X13 X14 X15 X16 X17 X18 X19 X20 X21 X22 X23 X24 X25 X26 X27 X28 X29 X3 X30 X34 X36 X37 X38 X4 X40 X44 X46 X5 X6 X7 X9 Sardinella_zunasi 567 963 1846 5677 488 281 2275 6227 6801 8627 6569 3863 3861 92 3635 264 9 8 932 391 1748 5866 8756 1464 1682 2009 0 1217 16 793 7518 Hexagrammos_otakii 3847 459 1346 721 5447 3363 2163 1027 903 216 364 253 205 2084 685 3140 418 22 2451 7861 964 166 176 1043 2483 828 28 3191 2 0 719 Engraulis_japonicus 289 3465 1136 600 388 586 651 376 247 444 1224 2572 3074 20 99 945 2072 6901 303 564 1033 618 213 2054 788 1645 949 1758 2915 2392 378 Konosirus_punctatus 105 1297 760 222 145 155 316 186 55 35 217 2207 626 4 56 37 9 8 925 0 536 1693 212 875 254 210 0 259 1215 3996 52 Acanthogobius_hasta 525 47 72 163 491 3004 544 33 33 7 198 4 66 276 12 984 74 8 1896 4 103 11 13 75 1487 1759 0 913 0 0 132 Thryssa_kammalensis 139 1327 1392 165 131 156 161 353 46 53 132 212 1432 37 36 1351 4174 49 52 1 2653 232 64 105 305 666 342 93 2213 2105 14 Setipinna_tenuifilis 50 67 62 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[daijiang]

Since you used the argument fish_tree = c("all-taxon"), you will get an object with class multiPhylo, which has multiple phylogenies. In your follow up code, you should use something like pd(OTU_list_tree, p[[1]]) to calculate PD.

Or, you can use fish_tree = c("timetree") in get_tree() to just get one phylogeny.

Either way, you should have branch lengths.

Hope this helps.