maybe comment out some long running things

It was recently pointed out to us that some README.html files (generated
from the corresponding README.md ones) on the CRAN package web pages are
incomplete, missing 'local' images not available from the web page and
in most cases actually not even shipped with the package. This clearly
should be changed, so we will move to using '--self-contained' for the
pandoc conversion to ensure that the README.html files are "complete".

Of course, this implies that all 'local' images used in README.md are
needed in the package sources.

If the images are also used for vignettes or Rd files, you can put them
in the 'vignettes' or 'man/figures' directories. Otherwise, please put
them in the top-level 'tools' directory, or a subdirectory of it.

The CRAN incoming checks in r-devel were changed to perform the pandoc
conversion checks with '--self-contained', and hence will warn about
missing images.

Pls ensure completeness in the next regular update of your package.

$`/data/rsync/PKGS/brranching/README.md`
[1] "inst/img/unnamed-chunk-5-1.png" "inst/img/unnamed-chunk-6-1.png"

in inst/ignore in taxize right now https://github.com/ropensci/taxize/blob/4f1eb5201db95dfb837100c4091cda1100c48335/inst/ignore/rbladj.r

could be too much of a headache - i imagine it's also written in awk, but not sure

utf-8 encoding and parse manually

with the new package https://github.com/ropenscilabs/conditionz working on - could test out here to see if it's useful, and not too slow, not too burdensome

This package was removed from CRAN back in February due to its dependence on the 'phylocomr' package. That package has since been fixed and restored on CRAN, but it looks like you'll need to either reach out to CRAN or push a new version of 'brranching' to get it restored on CRAN as well.

don't know of a way to get the entire tree...

brranching::phylomatic does not accept a list of taxon other than species for the binindaemonds2007 stored tree. For example, if I input a list of genus of mammals, The error No taxa in common is produced.

Would you know why?

Thank you,

Christophe

Code example

taxa<-c("Canis", "Vulpes","Lycaon", "Nyctereutes", "Otocyon" )
phylomatic(taxa = taxa, get = "POST", storedtree = "binindaemonds2007", clean = T, db="ncbi")

missing from the datset in taxize, see also ropensci/taxize#478

heard this is the latest plant tree, show example of using,

👋 @LunaSare!

Do you still intend to become this package's maintainer?

If so do you need any help? For instance an aspect where you'd appreciate some tips, contributions, a PR review? Do you need an invitation to our friendly Slack workspace?

from #13

My name is Aelton Giroldo, and I am PhD student in Ecology.

I am trying to build a phylogenetic tree using brranching.

My data set had 11438 species.

I wrote the code as below:

>tax<- read.delim("taxa.txt")
>taxa1k<-unique(as.character(tax$Taxa[1:1000]))#Same format as example in brranching - 200 spp
>tree1k<-phylomatic(taxa=taxa1k,  get = "POST",method = "phylomatic", storedtree = "R20120829")
No encoding supplied: defaulting to UTF-8.
NOTE: 9 taxa not matched: ....
>tree1k#Returns
Phylogenetic tree with 991 tips and 190 internal nodes.

Tip labels:
    abarema_cochliacarpos, abarema_langsdorffii, abarema_villosa, albizia_inundata, albizia_niopoides, albizia_pedicellaris, ...
Node labels:
    magnoliales_to_asterales, poales_to_asterales, eudicots, , , , ...
Rooted; no branch lengths.

I did more 3 trees just increasing the species number (taxa).

>taxa4k<-unique(as.character(tax$Taxa[1:4000]))#Just increasing to 4000 the number of species.
>tree4k<-phylomatic(taxa=taxa4k,  get = "POST",method = "phylomatic", storedtree = "R20120829")#Until here ok, I had the tree.
No encoding supplied: defaulting to UTF-8.
NOTE: 73 taxa not matched: .....
> tree4k

Phylogenetic tree with 3927 tips and 552 internal nodes.

Tip labels:
    bulbostylis_brevifolia, bulbostylis_capillaris, bulbostylis_carajana, bulbostylis_circinata, bulbostylis_conifera, bulbostylis_conostachya, ...
Node labels:
    magnoliales_to_asterales, poales_to_asterales, eudicots, , , , ...

Rooted; no branch lengths.

So, the next tree is stucked, I don't know if there is a limit of taxa, I hope not!

taxa5k<-unique(as.character(tax$Taxa[1:5000]))#Just increasing to 5000 the number of species.
tree5k<-phylomatic(taxa=taxa5k,  get = "POST",method = "phylomatic", storedtree = "R20120829")
No encoding supplied: defaulting to UTF-8.
> tree5#Problem... return the error!

Phylogenetic tree with 0 tips and  internal nodes.

Tip labels:
NULL
Error in tabulate(phy$edge[, 1]) : 'bin' need to be numeric or factor.

Could anyone tell me what I am doing wrong in the code? Or really is there taxa limit in brranching?

Thanks! Regards

see discussion in ropensci/taxize#29

@sckott I'm going to shut down phylodiversity.net in a year (it's been over twenty years!). Phylomatic has phylodiversity.net/phylomatic as its front-end, but the code actually runs elsewhere, on a cloud server I also manage. I know phylomatic is still used heavily: ~300 POSTs to pmws a week, most from r-curl which I assume are generated from taxize/brranching. Can you suggest a clean way to transition to a sustainable, long-term cloud solution for phylomatic? Does it have to be a cloud solution? If we could package it right, the script engine (gawk) and data files are only a few MB.

Also, there are many requests from 128.123.63.10 (Mesilla Park, NM) via python-requests. Any idea who is running this interface?

Thanks, Cam

http://phylomedb.org/web_api

• it prints out the missing taxa, but ideally we can collect those
• and would be nice to be able to suppress the printed out missing taxa

Hi, my name is Karl and I am a PhD in Ecology.

I am currently doing a plant trait analysis for gymnosperm species and wanted to correct for phylogeny using the function phylomatic.
Unfortunately, I recieved an error message when trying to run:

phylo.data <- phylomatic(Data$gymno.phylogeny, taxnames = FALSE, get="POST", storedtree="zanne2014")
Error in curl::curl_fetch_memory(x$url$url, handle = x$url$handle) :
Recv failure: Connection was reset

Here is my original species list:

Data$gymno.phylogeny
[1] "cupressaceae/chamaecyparis/Chamaecyparis_obtusa"
[2] "cupressaceae/chamaecyparis/Chamaecyparis_pisifera"
[3] "cupressaceae/juniperus/Juniperus_chinensis"
[4] "cupressaceae/juniperus/Juniperus_monosperma"
[5] "cupressaceae/juniperus/Juniperus_sabina"
[6] "cupressaceae/metasequoia/Metasequoia_glyptostroboides"
[7] "cupressaceae/taxodium/Taxodium_distichum"
[8] "cupressaceae/thuja/Thuja_occidentalis"
[9] "cupressaceae/cunninghamia/Cunninghamia_lanceolata"
[10] "cupressaceae/cryptomeria/Cryptomeria_japonica"
[11] "cupressaceae/cupressus/Cupressus_funebris"
[12] "cupressaceae/platycladus/Platycladus_orientalis"
[13] "ephedraceae/ephedra/Ephedra_distachya"
[14] "ginkgoaceae/ginkgo/Ginkgo_biloba"
[15] "pinaceae/larix/Larix_decidua"
[16] "pinaceae/larix/Larix_gmelinii"
[17] "pinaceae/larix/Larix_kaempferi"
[18] "pinaceae/picea/Picea_abies"
[19] "pinaceae/picea/Picea_glauca"
[20] "pinaceae/picea/Picea_koraiensis"
[21] "pinaceae/picea/Picea_meyeri"
[22] "pinaceae/picea/Picea_rubens"
[23] "pinaceae/picea/Picea_wilsonii"
[24] "pinaceae/pinus/Pinus_armandii"
[25] "pinaceae/pinus/Pinus_edulis"
[26] "pinaceae/pinus/Pinus_elliottii"
[27] "pinaceae/pinus/Pinus_koraiensis"
[28] "pinaceae/pinus/Pinus_massoniana"
[29] "pinaceae/pinus/Pinus_palustris"
[30] "pinaceae/pinus/Pinus_pumila"
[31] "pinaceae/pinus/Pinus_resinosa"
[32] "pinaceae/pinus/Pinus_strobus"
[33] "pinaceae/pinus/Pinus_sylvestris"
[34] "pinaceae/pinus/Pinus_tabuliformis"
[35] "pinaceae/pinus/Pinus_taeda"
[36] "pinaceae/pinus/Pinus_virginiana"
[37] "pinaceae/tsuga/Tsuga_canadensis"
[38] "pinaceae/abies/Abies_alba"
[39] "pinaceae/abies/Abies_nephrolepis"
[40] "podocarpaceae/dacrycarpus/Dacrycarpus_imbricatus"
[41] "podocarpaceae/podocarpus/Podocarpus_neriifolius"
[42] "sciadopityaceae/sciadopitys/Sciadopitys_verticillata"
[43] "taxaceae/cephalotaxus/Cephalotaxus_harringtonii"
[44] "taxaceae/taxus/Taxus_chinensis"
[45] "taxaceae/taxus/Taxus_cuspidata"

I also tried to set get = "GET", but then R takes ages to run without any result.

Could anyone help me here?

Thank you very much for your help!!

sessionInfo:

R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] taxize_0.9.99 rentrez_1.2.3 brranching_0.7.0 ape_5.6-1 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4 readr_2.0.1 tidyr_1.1.3 tibble_3.1.4 ggplot2_3.3.5
[13] tidyverse_1.3.1 here_1.0.1

loaded via a namespace (and not attached):
[1] colorspace_2.0-2 phylocomr_0.3.2 ellipsis_0.3.2 rprojroot_2.0.2 htmlTable_2.4.0 base64enc_0.1-3 fs_1.5.0 httpcode_0.3.0
[9] rstudioapi_0.13 urltools_1.7.3 fansi_0.5.0 lubridate_1.7.10 xml2_1.3.2 ritis_1.0.0 codetools_0.2-18 splines_4.1.2
[17] mnormt_2.0.2 bold_1.2.0 knitr_1.34 Formula_1.2-4 jsonlite_1.7.2 broom_0.7.9 cluster_2.1.2 dbplyr_2.1.1
[25] png_0.1-7 compiler_4.1.2 httr_1.4.2 backports_1.2.1 assertthat_0.2.1 Matrix_1.3-4 fastmap_1.1.0 cli_3.0.1
[33] htmltools_0.5.2 tools_4.1.2 igraph_1.2.11 coda_0.19-4 gtable_0.3.0 glue_1.4.2 clusterGeneration_1.3.7 maps_3.4.0
[41] fastmatch_1.1-3 Rcpp_1.0.7 cellranger_1.1.0 vctrs_0.3.8 crul_1.2.0 nlme_3.1-153 conditionz_0.1.0 iterators_1.0.14
[49] xfun_0.26 rvest_1.0.1 lifecycle_1.0.0 phangorn_2.8.1 XML_3.99-0.8 zoo_1.8-9 MASS_7.3-54 scales_1.1.1
[57] hms_1.1.0 parallel_4.1.2 expm_0.999-6 RColorBrewer_1.1-2 curl_4.3.2 gridExtra_2.3 triebeard_0.3.0 rpart_4.1-15
[65] reshape_0.8.8 latticeExtra_0.6-29 stringi_1.7.4 foreach_1.5.2 plotrix_3.8-2 checkmate_2.0.0 phytools_1.0-1 rlang_0.4.11
[73] pkgconfig_2.0.3 lattice_0.20-45 htmlwidgets_1.5.4 tidyselect_1.1.1 plyr_1.8.6 magrittr_2.0.1 R6_2.5.1 generics_0.1.0
[81] Hmisc_4.6-0 combinat_0.0-8 DBI_1.1.1 pillar_1.6.2 haven_2.4.3 foreign_0.8-81 withr_2.4.3 survival_3.2-13
[89] scatterplot3d_0.3-41 nnet_7.3-16 modelr_0.1.8 crayon_1.4.1 uuid_0.1-4 utf8_1.2.2 solrium_1.2.0 tmvnsim_1.0-2
[97] tzdb_0.1.2 jpeg_0.1-9 grid_4.1.2 readxl_1.3.1 data.table_1.14.0 reprex_2.0.1 digest_0.6.27 numDeriv_2016.8-1.1
[105] munsell_0.5.0 quadprog_1.5-8

or move here? probably not, but something

I think using phytools::read.newick(text = "<tree>") will work

Hi,
I have an abundance table (each row corresponds to a taxa). I would like to get the tree (newick default format) of the table.
The table contains bacteria, archeae and fungi.

How can i get a phylogenetic tree from this table (the original table has around 600 rows)??
The idea is to use the tree for further analysis using R.

SampleA    Phylum               Class          Order               Family           Genus                 Species
12           Actinobacteria     Actinomycetales Actinobacteria     Actinomycetaceae     Actinomyces Actinomyces neuii
 3             Actinobacteria     Actinomycetales Actinobacteria     Actinomycetaceae     Actinomyces   Unknown
34            Actinobacteria     Corynebacteriales Actinobacteria   Corynebacteriaceae Corynebacterium  Corynebacterium sp. HMSC064E10
59            Actinobacteria     Corynebacteriales Actinobacteria   Corynebacteriaceae Corynebacterium  Corynebacterium aquilae
965          Actinobacteria     Propionibacteriales Actinobacteria Propionibacteriaceae   Tessaracoccus Tessaracoccus sp. NSG39
44           Proteobacteria     Unknown               Unknown              Unknown         Unknown        Unknown

Hi!

I am using the phylomatic function in brranching to prune the Zanne tree for my species set. My code worked well when using brranching 0.5.0 in the beginning of the year. When running it again now with brranching 0.6.0 (sessionInfo below) there are several species from my set that find no match in Zanne anymore:

tree.species.set <- phylomatic(species.set$species_name, get="POST", storedtree="zanne2014")
NOTE: 145 taxa not matched: NA/acacia_crassicarpa/acacia_crassicarpa, NA/acacia_mangium/acacia_mangium, compositae/adenocaulon_himalaicum/adenocaulon_himalaicum, ...

All taxa not matched belong to either compositae or have NA as family.
When entering those species online at http://phylodiversity.net/phylomatic/ I realized that by using Asteraceae instead of Compositae or adding the missing family information, the phylomatic function can still match them with Zanne. Seems to make no difference if the genus is provided alone (fabaceae/acacia/acacia_crassicarpa) or as whole species name (fabaceae/acacia_crassicarpa/acacia_crassicarpa) a far as I see.

My first idea was a classic workaround: reinstalling brranching 0.5.0 or 0.4.0. But I got the following Error:

Unknown or uninitialised column: 'this'. Unknown or uninitialised column: 'that'.Error in if (nchar(as.character(dd$that), keepNA = FALSE) == 0) { :argument is of length zero

Any idea how to solve this problem would be highly appreciated! Thanks in advance!!

R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.5.0     stringr_1.4.0     dplyr_1.0.2       purrr_0.3.4       readr_1.3.1       tidyr_1.1.2      
 [7] tibble_3.0.3      ggplot2_3.3.2     tidyverse_1.3.0   adephylo_1.1-11   ade4_1.7-15       geiger_2.0.7     
[13] caper_1.0.1       mvtnorm_1.1-1     MASS_7.3-51.5     viridis_0.5.1     viridisLite_0.3.0 shape_1.4.4      
[19] phytools_0.7-47   maps_3.3.0        ape_5.4-1         vegan_2.5-6       lattice_0.20-38   permute_0.9-5    
[25] brranching_0.6.0  lme4_1.1-23       Matrix_1.2-18    

loaded via a namespace (and not attached):
  [1] readxl_1.3.1            uuid_0.1-4              backports_1.1.9         Hmisc_4.4-1            
  [5] fastmatch_1.1-0         plyr_1.8.6              igraph_1.2.5            lazyeval_0.2.2         
  [9] sp_1.4-2                splines_3.6.3           rncl_0.8.4              urltools_1.7.3         
 [13] digest_0.6.25           foreach_1.5.0           htmltools_0.5.0         gdata_2.18.0           
 [17] fansi_0.4.1             magrittr_1.5            checkmate_2.0.0         cluster_2.1.0          
 [21] modelr_0.1.8            gmodels_2.18.1          prettyunits_1.1.1       jpeg_0.1-8.1           
 [25] colorspace_1.4-1        rvest_0.3.6             blob_1.2.1              haven_2.3.1            
 [29] xfun_0.16               crayon_1.3.4            jsonlite_1.7.1          phylobase_0.8.10       
 [33] survival_3.1-8          zoo_1.8-8               phangorn_2.5.5          iterators_1.0.12       
 [37] glue_1.4.2              gtable_0.3.0            seqinr_3.6-1            scales_1.1.1           
 [41] DBI_1.1.0               Rcpp_1.0.5              plotrix_3.7-8           spData_0.3.8           
 [45] xtable_1.8-4            progress_1.2.2          htmlTable_2.0.1         units_0.6-7            
 [49] tmvnsim_1.0-2           spdep_1.1-5             foreign_0.8-75          subplex_1.6            
 [53] bold_1.1.0              deSolve_1.28            Formula_1.2-3           animation_2.6          
 [57] htmlwidgets_1.5.1       httr_1.4.2              RColorBrewer_1.1-2      ellipsis_0.3.1         
 [61] pkgconfig_2.0.3         reshape_0.8.8           XML_3.99-0.3            dbplyr_1.4.4           
 [65] deldir_0.1-28           nnet_7.3-12             conditionz_0.1.0        crul_1.0.0             
 [69] later_1.1.0.1           tidyselect_1.1.0        rlang_0.4.7             reshape2_1.4.4         
 [73] cellranger_1.1.0        munsell_0.5.0           tools_3.6.3             cli_2.0.2              
 [77] generics_0.0.2          broom_0.7.0             fastmap_1.0.1           phylocomr_0.3.2        
 [81] fs_1.5.0                knitr_1.29              nlme_3.1-144            mime_0.9               
 [85] taxize_0.9.97           adegenet_2.1.3          xml2_1.3.2              compiler_3.6.3         
 [89] rstudioapi_0.11         curl_4.3                png_0.1-7               e1071_1.7-3            
 [93] reprex_0.3.0            clusterGeneration_1.3.4 statmod_1.4.34          RNeXML_2.4.5           
 [97] stringi_1.4.6           classInt_0.4-3          nloptr_1.2.2.2          vctrs_0.3.4            
[101] LearnBayes_2.15.1       pillar_1.4.6            lifecycle_0.2.0         triebeard_0.3.0        
[105] combinat_0.0-8          data.table_1.13.0       raster_3.3-13           httpuv_1.5.4           
[109] R6_2.4.1                latticeExtra_0.6-29     promises_1.1.1          KernSmooth_2.23-16     
[113] gridExtra_2.3           codetools_0.2-16        boot_1.3-24             gtools_3.8.2           
[117] assertthat_0.2.1        withr_2.2.0             httpcode_0.3.0          mnormt_2.0.2           
[121] mgcv_1.8-31             expm_0.999-5            parallel_3.6.3          hms_0.5.3              
[125] quadprog_1.5-8          grid_3.6.3              rpart_4.1-15            class_7.3-15           
[129] coda_0.19-3             minqa_1.2.4             sf_0.9-5                lubridate_1.7.9        
[133] numDeriv_2016.8-1.1     scatterplot3d_0.3-41    shiny_1.5.0             base64enc_0.1-3        
[137] tinytex_0.25           

Nice client already for this rotl, so probably remove from here, focusing on phylomatic, and other small phylogeny sources and/or those that don't have clients

This package needs more documentation! Help out the community by contributing a vignette. If you don't know what a vignette is, check out http://r-pkgs.had.co.nz/vignettes.html for an introduction.

If you aren't sure how to contribute on github checkout https://github.com/ropensci/brranching/blob/master/.github/CONTRIBUTING.md

Keep in mind our code of conduct https://github.com/ropensci/brranching/blob/master/CONDUCT.md