Obtaining fish phylogeny according to a local pool of species

FishPhyloMaker(
data,
insert.base.node = FALSE,
return.insertions = TRUE,
progress.bar = TRUE
)

## Arguments

data A data frame with three columns containing the name of species (s), the Family (f) and the Order (o). This data frame can be generated with tab_function function. Logical argument indicating if the species must be added automatically in the family and order (when needed) nodes. Default is FALSE Logical, if TRUE (default) the output is a list of length two containing the phylogeny and a dataframe with a column indicating at which level each species was inserted. Logical argument. If TRUE (default) a progress bar will be shown in console.

## Value

A newick object containing the phylogeny with the species in data object. If return.insertions = TRUE the output will be a list of length two containing the newick phylogeny and a data frame equal that provided in data plus a column indicating at which level each species was inserted in the tree.

## Examples

# \donttest{
data("taxon_data_PhyloMaker")
res_phylo <- FishPhyloMaker(data = taxon_data_PhyloMaker,
insert.base.node = TRUE,
return.insertions = TRUE,
progress.bar = TRUE)
#> Can't retrieve a chronogram_mrca for family Parodontidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Loricariidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Callichthyidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Cichlidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Crenuchidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Gymnotidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Anostomidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Poeciliidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Serrasalmidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Hemiodontidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Distichodontidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Ctenoluciidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Bryconidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Iguanodectidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Chilodontidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Gasteropelecidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Chalceidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Citharinidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Cynodontidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Erythrinidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Hepsetidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Prochilodontidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Aspredinidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Mochokidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Trichomycteridae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Akysidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Ictaluridae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Anchariidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Plotosidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Astroblepidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Austroglanididae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Clariidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Pseudopimelodidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Siluridae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Cetopsidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Chacidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Cranoglanididae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Diplomystidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Pangasiidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Heteropneustidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Horabagridae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Lacantuniidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Malapteruridae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Nematogenyidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Scoloplacidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Pholidichthyidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Rhamphichthyidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Goodeidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Anablepidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Rivulidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Nothobranchiidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Aplocheilidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Fundulidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Profundulidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for family Valenciidae because the family is monophyletic.#> Can't retrieve a chronogram_mrca for order Characiformes because the family is monophyletic.#> Can't retrieve a chronogram_mrca for order Siluriformes because the family is monophyletic.#> Can't retrieve a chronogram_mrca for order Cichliformes because the family is monophyletic.#> Can't retrieve a chronogram_mrca for order Gymnotiformes because the family is monophyletic.#> Can't retrieve a chronogram_mrca for order Cyprinodontiformes because the family is monophyletic.#> Can't retrieve a chronogram_mrca for order Pholidichthyiformes because the family is monophyletic.#> [1] "Pholidichthyiformes"#> Warning: Requested 3027 but only found 3026 species.
#> * Pholidichthyiformes#> Warning: Astyanax may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Astyanax may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Astyanax may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Astyanax may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Crenicichla may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Hisonotus may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Hypostomus may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Hypostomus may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Hypostomus may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Hypostomus may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Imparfinis may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Imparfinis may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Loricaria may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Loricaria may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Moenkhausia may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Moenkhausia may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus#> Warning: Rineloricaria may not be monophyletic
#>   attaching to the most inclusive group containing members of this genus# }