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rtrees: an R package to assemble phylogenetic trees from mega-trees

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# rtrees

The goal of `rtrees` is to remove the barriers to derive phylogenies for
a list of species from mega-trees. Basically, `Phylomatic` and more.

**`rtrees` just got an important update to speed it up! Please try to
install the latest version. If you see any problem, please file a GitHub
issue. Thanks!**

# Installation

``` r
options(repos = c(
  rtrees = 'https://daijiang.r-universe.dev',
  CRAN = 'https://cloud.r-project.org'))
install.packages("rtrees")
```

The above code will also install one dependency
[{megatrees}](https://github.com/daijiang/megatrees), an R data package
that hosts the megatrees used here.

## Shinny app

There is also a [Shinny app](https://djli.shinyapps.io/rtrees_shiny/) to
get phylogenies without using R. However, given that I can only afford
the free plan, the number of species to be inserted to the megatrees
here will be limited to 1,000.

# Mega-trees

Currently, `rtrees` provides mega-trees for the following taxonomic
groups: amphibian, bird, fish, mammal, plant, reptile, and shark_ray.
The mega-trees (or subset of 100 posterior phylogenies; 50 for fish to
reduce the package size) are stored as GitHub release assets in the data
package [{megatrees}](https://github.com/daijiang/megatrees) and
downloaded on demand via getter functions.

| Taxon | \# of species | \# of trees | How to load (in `{megatrees}`) | Reference |
|----|----|----|----|----|
| Amphibian | 7238 | 100 | `get_tree_amphibian_n100()` | Jetz and Pyron 2018 |
| Bee | 4651 | 1 | `tree_bee` | Henríquez-Piskulich et al. 2023 |
|  | 4651 | 100 | `get_tree_bee_n100()` | Henríquez-Piskulich et al. 2023 |
| Butterfly | 2244 | 1 | `tree_butterfly` | Kawahara et al. 2023 |
| Bird | 9993 | 100 | `get_tree_bird_n100()` | Jetz et al. 2012 |
|  | 11017 | 1 | `tree_bird_McTavish` | McTavish et al. 2025 |
| Fish | 11638 | 1 | `tree_fish_12k` | Rabosky et al. 2018 |
|  | 31516 | 50 | `get_tree_fish_32k_n50()` | Rabosky et al. 2018 |
| Mammal | 5831 | 100 | `get_tree_mammal_n100_phylacine()` | Faurby et al. 2018 |
|  | 5911 | 100 | `get_tree_mammal_n100_vertlife()` | Upham et al. 2019 |
| Plant | 74531 | 1 | `tree_plant_otl` (default) | Smith and Brown 2018 |
|  | 123182 | 1 | `tree_plant_Carruthers` | Carruthers et al. 2026 |
|  | 123182 | 100 | `get_tree_plant_n100_Carruthers()` | Carruthers et al. 2026 |
| Reptile (Squamate) | 9755 | 100 | `get_tree_reptile_n100()` | Tonini et al. 2016 |
| Shark, Ray, and Chimaera | 1192 | 100 | `get_tree_shark_ray_n100()` | Stein et al. 2018 |

# Usage examples

``` r
library(rtrees)
library(ape)
```

## Prepare species data frame (optional)

The species lists which we want to have a phylogeny should be provided
as a data frame with at least 3 columns: `family`, `genus`, and
`species`. Their order does not matter. Here is an example for fish.

``` r
test_fish_list = tibble::tibble(
  species = c("Serrasalmus_geryi", "Careproctus_reinhardti", "Gobiomorphus_coxii", 
              "Periophthalmus_barbarus", "Prognichthys_glaphyrae", "Barathronus_bicolor", 
              "Knipowitschia_croatica", "Rhamphochromis_lucius", "Neolissochilus_tweediei", 
              "Haplochromis_nyanzae", "Astronesthes_micropogon", "Sanopus_reticulatus"),
  genus = c("Serrasalmus", "Careproctus", "Gobiomorphus", "Periophthalmus",
            "Prognichthys", "Barathronus", "Knipowitschia", "Rhamphochromis", 
            "Neolissochilus", "Haplochromis", "Astronesthes", "Sanopus"),
  family = c("Serrasalmidae", "Liparidae", "Eleotridae", "Gobiidae", 
             "Exocoetidae", "Aphyonidae", "Gobiidae", "Cichlidae", 
             "Cyprinidae", "Cichlidae", "Stomiidae", "Batrachoididae")
)
```

``` r
test_fish_list
#> # A tibble: 12 × 3
#>    species                 genus          family        
#>    <chr>                   <chr>          <chr>         
#>  1 Serrasalmus_geryi       Serrasalmus    Serrasalmidae 
#>  2 Careproctus_reinhardti  Careproctus    Liparidae     
#>  3 Gobiomorphus_coxii      Gobiomorphus   Eleotridae    
#>  4 Periophthalmus_barbarus Periophthalmus Gobiidae      
#>  5 Prognichthys_glaphyrae  Prognichthys   Exocoetidae   
#>  6 Barathronus_bicolor     Barathronus    Aphyonidae    
#>  7 Knipowitschia_croatica  Knipowitschia  Gobiidae      
#>  8 Rhamphochromis_lucius   Rhamphochromis Cichlidae     
#>  9 Neolissochilus_tweediei Neolissochilus Cyprinidae    
#> 10 Haplochromis_nyanzae    Haplochromis   Cichlidae     
#> 11 Astronesthes_micropogon Astronesthes   Stomiidae     
#> 12 Sanopus_reticulatus     Sanopus        Batrachoididae
```

For plant, fish, bird, and mammal, it is possible to prepare `sp_list`
with function `sp_list_df()`; though you should check the results. It is
possible to just provide the speices as a character vector for these
taxon groups (or all genus in your species list are presented in the
phylogeny).

``` r
sp_list_df(sp_list = c("Periophthalmus_barbarus", "Barathronus_bicolor"),
           taxon = "fish")
#> # A tibble: 2 × 3
#>   species                 genus          family    
#>   <chr>                   <chr>          <chr>     
#> 1 Periophthalmus_barbarus Periophthalmus Gobiidae  
#> 2 Barathronus_bicolor     Barathronus    Aphyonidae
```

## Get phylogeny from one megatree

Once we have the species list ready, we can then derive a phylogeny from
`tree_fish`.

``` r
test_tree = get_tree(sp_list = test_fish_list,
                     taxon = "fish",
                     scenario = "at_basal_node",
                     show_grafted = TRUE)
#> 
#> 6 species added at genus level (*)
#> 1 species have no co-family species in the mega-tree, skipped
#> (if you know their family, prepare and edit species list with `rtrees::sp_list_df()` may help): 
#> Barathronus_bicolor
plot(test_tree, no.margin = T)
```

No matter whether `show_grafted` is ‘TRUE’ or ‘FALSE’, the grafting
information was saved along with the phylogeny and can be extracted with
the following code:

``` r
# or use rtrees::get_graft_status(test_tree)
test_tree$graft_status
#> # A tibble: 12 × 3
#>    tip_label                species                 status                      
#>    <chr>                    <chr>                   <chr>                       
#>  1 Prognichthys_glaphyrae   Prognichthys_glaphyrae  exisiting species in the me…
#>  2 Periophthalmus_barbarus  Periophthalmus_barbarus exisiting species in the me…
#>  3 Gobiomorphus_coxii       Gobiomorphus_coxii      exisiting species in the me…
#>  4 Careproctus_reinhardti   Careproctus_reinhardti  exisiting species in the me…
#>  5 Sanopus_reticulatus*     Sanopus_reticulatus     grafted at genus level      
#>  6 Serrasalmus_geryi        Serrasalmus_geryi       exisiting species in the me…
#>  7 Knipowitschia_croatica*  Knipowitschia_croatica  grafted at genus level      
#>  8 Rhamphochromis_lucius*   Rhamphochromis_lucius   grafted at genus level      
#>  9 Neolissochilus_tweediei* Neolissochilus_tweediei grafted at genus level      
#> 10 Haplochromis_nyanzae*    Haplochromis_nyanzae    grafted at genus level      
#> 11 Astronesthes_micropogon* Astronesthes_micropogon grafted at genus level      
#> 12 <NA>                     Barathronus_bicolor     skipped as no co-family in …
```

## Get a set of phylogenies from multiple posterior megatrees

The function `rtrees::get_tree()` can also work with a set of posterior
megatrees with the option to use parallel computing for the whole
process. The default number of cores to be used will be the available
number of cores minus 2 (so that users can still perform other tasks on
their computers at the same time). The output will be a set of generated
phylogenies with class `multiPhylo`; the number of derived phylogenies
will be the same as the input megatrees. For this scenario, we can use
exactly the same code described above. For example, if we want to use
the 100 randomly selected posterior phylogenies that have ~32k fish
species, we can add the `fish_tree = "all-taxon`.

``` r
test_tree2 = get_tree(sp_list = test_fish_list,
                     taxon = "fish",
                     scenario = "at_basal_node",
                     show_grafted = TRUE,
                     fish_tree = "all-taxon")
#> Wow, all species are already in the mega-tree!
test_tree2
#> 50 phylogenetic trees
plot(ladderize(test_tree2[[1]]), no.margin = T)
```

## Add tips to user provided trees

It is also possible to derive a phylogeny based on a user provided tree.
This can be particularly useful if we have things like `Acer_spp` that
we want to insert to the basal node of the genus.

``` r
test_tree = ape::read.tree(text = "(((((((((Potentilla_intermedia:1.156097,Potentilla_gracilis:1.156097):9.169741,Potentilla_bipinnatifida:10.325839):10.466967,Potentilla_sterilis:20.792806):11.333216,Fragaria_virginiana:32.126022):6.026567,(((((Rosa_setigera:3.434279,Rosa_arkansana:3.434279):1.991106,Rosa_spinosissima:5.425386):0.993924,Rosa_acicularis:6.419309):6.730804,(Rosa_micrantha:0.188519,Rosa_canina:0.188519):12.961594):23.677485,(Agrimonia_gryposepala:4.730863,Agrimonia_parviflora:4.730863):32.096735):1.324992):6.47604,(Geum_urbanum:11.153303,Geum_rivale:11.153303):33.475326):1.449852,((((((((Rubus_semisetosus:3.10529,Rubus_glandicaulis:3.10529):0.957584,Rubus_steelei:4.062873):0.398394,Rubus_cuneifolius:4.461267):2.271628,Rubus_vagus:6.732895):0.023439,Rubus_superioris:6.756333):0.020104,(Rubus_multifer:4.287114,Rubus_elegantulus:4.287115):2.489323):0.025475,((Rubus_laciniatus:0.125186,Rubus_bifrons:0.125186):0.11903,Rubus_praecox:0.244216):6.557697):11.571849,(Rubus_parviflorus:14.85915,Rubus_odoratus:14.85915):3.514612):27.704718):16.915234,Filipendula_rubra:62.993714):13.354116,((((((((((Crataegus_dissona:0.081863,Crataegus_florifera:0.081863):0.49838,Crataegus_fulleriana:0.580243):1.434261,Crataegus_crus-galli:2.014503):0.177737,Crataegus_chrysocarpa:2.192239):0.051159,Crataegus_uniflora:2.243399):0.438351,Crataegus_persimilis:2.68175):4.697259,((Malus_toringo:6.472694,Malus_ioensis:6.472693):0.772012,Chaenomeles_speciosa:7.244705):0.134305):1.72489,Pyrus_communis:9.1039):0.313393,Amelanchier_spicata:9.417293):40.039557,((((((Prunus_pumila:6.189944,Prunus_nigra:6.189945):0.37487,Prunus_pensylvanica:6.564815):4.856241,(Prunus_padus:4.816999,Prunus_serotina:4.817):6.604057):29.162527,Sorbaria_sorbifolia:40.583584):2.924475,Rhodotypos_scandens:43.50806):2.718224,(Spiraea_X_bumalda:25.921582,Aruncus_dioicus:25.921583):20.304701):3.230567):26.89098);")

test_tree_sp = c("Rosa_sp", "Rubus_sp", "Amelanchier_sp", "Prunus_sp", "Sorbus_sp", "Potentilla_sp",
  "Potentilla_intermedia", "Potentilla_gracilis", "Potentilla_bipinnatifida", "Potentilla_sterilis", "Fragaria_virginiana", "Rosa_setigera", "Rosa_arkansana", "Rosa_spinosissima", "Rosa_acicularis", "Rosa_micrantha", "Rosa_canina", "Agrimonia_gryposepala", "Agrimonia_parviflora", "Geum_urbanum", "Geum_rivale", "Rubus_semisetosus", "Rubus_glandicaulis", "Rubus_steelei", "Rubus_cuneifolius", "Rubus_vagus", "Rubus_superioris", "Rubus_multifer", "Rubus_elegantulus", "Rubus_laciniatus", "Rubus_bifrons", "Rubus_praecox", "Rubus_parviflorus", "Rubus_odoratus", "Filipendula_rubra", "Crataegus_dissona", "Crataegus_florifera", "Crataegus_fulleriana", "Crataegus_crus-galli", "Crataegus_chrysocarpa", "Crataegus_uniflora", "Crataegus_persimilis", "Malus_toringo", "Malus_ioensis", "Chaenomeles_speciosa", "Pyrus_communis", "Amelanchier_spicata", "Prunus_pumila", "Prunus_nigra", "Prunus_pensylvanica", "Prunus_padus", "Prunus_serotina", "Sorbaria_sorbifolia", "Rhodotypos_scandens", "Spiraea_X_bumalda", "Aruncus_dioicus")

plot(get_tree(sp_list = test_tree_sp, tree = test_tree, taxon = "plant",
              show_grafted = T, tree_by_user = T), type = "fan")
#> Not all genus can be found in the phylogeny.
#> Warning: For user provided phylogeny, without a classification for all genus of species in the phylogeny,
#>               it is unlikely to find the most recent ancestor for genus and family; here we proceed the phylogeny
#>               by adding root information for genus and family that can be found in the phylogeny or species list but
#>               we recommend to prepare the phylogeny using `add_root_info()` with a classification
#>               data frame with all tips first.
#> 
#> 5 species added at genus level (*)
#> 1 species added at family level (**)
```

**Pay attention to the warning message there**. Because not all genera
in the species list are presented in the megatree, it is impossible to
find the most recent ancestor for genus and family that are missing from
the megatree. Therefore, **for user-provided phylogenies, here is the
recommended steps**:

1.  Get the classification information (a data frame with two columns:
    genus and family) for all genera presented in the species list and
    the megatree.
2.  Prepare the species list as a data frame with three columns:
    species, genus, and family using the classification information.
3.  Process the megatree using function
    `processed_tree = rtrees::add_root_infor(tree, classification)`.
4.  Pass the processed megatree to
    `rtrees::get_tree(sp_list_data_frame, processed_tree)` to derive the
    phylogeny for your species list.

## Bind missing species to specified places

It is also possible to specify a particular species to bind with by
specifying columns `close_sp` and/or `close_genus`.

``` r
test_tree_sp_df = sp_list_df(test_tree_sp, "plant")
test_tree_sp_df$close_sp = NA
test_tree_sp_df$close_sp[1] = "Rosa_acicularis" # bind Rosa_sp to here
plot(get_tree(sp_list = test_tree_sp_df, tree = test_tree, taxon = "plant",
              show_grafted = T, tree_by_user = T), type = "fan")
#> Not all genus can be found in the phylogeny.
#> Warning: For user provided phylogeny, without a classification for all genus of species in the phylogeny,
#>               it is unlikely to find the most recent ancestor for genus and family; here we proceed the phylogeny
#>               by adding root information for genus and family that can be found in the phylogeny or species list but
#>               we recommend to prepare the phylogeny using `add_root_info()` with a classification
#>               data frame with all tips first.
#> 
#> 5 species added at genus level (*)
#> 1 species added at family level (**)
```

# Some notes

- If `tree` is specified, then `taxon` can be ignored if all genus in
  the species list are presented in the phylogeny.
- If a species does not have a co-family species in the mega-tree, it
  will be skipped.
- If `show_grafted = TRUE`, species that are grafted will have one or
  two `*` at the end of their names.
  - If it is grafted at the genus level, one `*`.
  - If it is grafted at the family level, two `*`s (i.e., `**`).
- The default scenario is `at_basal_node`, which will graft species at
  the genus/family basal node.
  - `random_below_basal` will randomly select a downstream node to
    attach the new tip.
  - If only one species in the mega-tree that is in the same
    genus/family of the new tip, then the new tip will be grafted at the
    middle of this species’ branch for all scenarios.
- The `tree` can be a user provided tree, if so, set
  `tree_by_user = TRUE`.
- See `?get_tree` for more details.

# Contribution

Feel free to test it. Contributions and suggestions are welcome. You can
open an issue or send a pull request.

# Citation

Li Daijiang. (2023). [rtrees: an R package to assemble phylogenetic
trees from
megatrees](https://nsojournals.onlinelibrary.wiley.com/doi/10.1111/ecog.06643).
Ecography. e06643

rtrees

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