                      Package ‘FishPhyloMaker’
                                            October 12, 2022
Type Package
Title Phylogenies for a List of Finned-Ray Fishes
Version 0.2.0
Description Provides an alternative to facilitate the construction of a phy-
      logeny for fish species from a list of species
      or a community matrix using as a backbone the phylogenetic tree proposed by Ra-
      bosky et al. (2018) <doi:10.1038/s41586-018-0273-1>.
License MIT + file LICENSE
Encoding UTF-8
LazyData true
RoxygenNote 7.1.1
Imports ape, fishtree, geiger, knitr, phytools, progress, rfishbase,
      rmarkdown, utils
VignetteBuilder knitr, rmarkdown
Depends R (>= 2.10)
Suggests markdown, gh
NeedsCompilation no
Author Gabriel Nakamura [aut, cre] (<https://orcid.org/0000-0002-5144-5312>),
      Aline Richter [aut],
      Bruno Soares [aut]
Maintainer Gabriel Nakamura <gabriel.nakamura.souza@gmail.com>
Repository CRAN
Date/Publication 2021-09-15 08:00:10 UTC
R topics documented:
         FishPhyloMaker . .     . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
         FishTaxaMaker . .      . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
         neotropical_comm       . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
         PD_defict . . . . .    . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
                                                      1
2                                                                                          FishPhyloMaker
          spp_afrotropic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
          taxon_data_PhyloMaker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .      6
          whichFishAdd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .   7
Index                                                                                                    8
  FishPhyloMaker                Obtaining fish phylogeny according to a local pool of species
Description
    Obtaining fish phylogeny according to a local pool of species
Usage
    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 Fam-
                        ily (f) and the Order (o). This data frame can be generated with tab_function
                        function.
    insert.base.node
                        Logical argument indicating if the species must be added automatically in the
                        family and order (when needed) nodes. Default is FALSE
    return.insertions
                        Logical, if TRUE (default) the output is a list of length two containing the phy-
                        logeny and a dataframe with a column indicating at which level each species
                        was inserted.
    progress.bar        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.
FishTaxaMaker                                                                                            3
Examples
          data("taxon_data_PhyloMaker")
          res_phylo <- FishPhyloMaker(data = taxon_data_PhyloMaker,
          insert.base.node = TRUE,
          return.insertions = TRUE,
          progress.bar = TRUE)
   FishTaxaMaker                 Generate a list of species Auxiliary function to obtain taxonomic clas-
                                 sification and check the names of species present in species pool
Description
     Generate a list of species Auxiliary function to obtain taxonomic classification and check the names
     of species present in species pool
Usage
     FishTaxaMaker(data, allow.manual.insert = TRUE)
Arguments
     data                 A character vector with species names or a community matrix with species
                          names in columns
     allow.manual.insert
                          Logical, if TRUE (default), the user must type the names of Family and Order
                          of species not found in Fishbase
Value
     List with three elements.
     - A data frame containing the taxonomic classification of valid species accordingy to Fishbase
     - A data frame with three columns containing the name of species (s), the Family (f) and Order (o) that ca
         FishPhyloMaker function
     - A character vector containing all names of species that was not find in Fishbase
4                                                                                 neotropical_comm
Examples
     ## Not run:
     data(neotropical_comm)
     data_comm <- neotropical_comm[, -c(1, 2)]
     taxon_data <- FishTaxaMaker(data_comm, allow.manual.insert = TRUE)
     Characidae
     Characiformes
     Characidae
     Characiformes
     Characidae
     Characiformes
     Loricariidae
     Siluriformes
     Characidae
     Characiformes
     Cichlidae
     Cichliformes
     Crenuchidae
     Characiformes
     Gymnotidae
     Gymnotiformes
     Loricariidae
     Siluriformes
     Loricariidae
     Siluriformes
     Loricariidae
     Siluriformes
     Loricariidae
     Siluriformes
     Heptapteridae
     Siluriformes
     Characidae
     Characiformes
     Loricariidae
     Siluriformes
     Characidae
     Characiformes
    ## End(Not run)
  neotropical_comm           Abundance of stream fish species in Parana and Paraguay streams
Description
    A dataset containing the abundance of stream fish species distributed in streams of Parana and
    Paraguay river Basins
PD_defict                                                                                                5
Usage
    neotropical_comm
Format
    A data frame with 20 rows and 61 variables:
Source
    Article published in Neotropical Ichthyology doi: 10.1590/1982022420200126
  PD_defict                     Title Calculate the amount of phylogenetic deficit in assemblages
Description
    Title Calculate the amount of phylogenetic deficit in assemblages
Usage
    PD_defict(phylo, data, level = "Congeneric_insertion")
Arguments
    phylo               Phylogenetic tree in newick format, can be an object from FishPhyloMaker
                        function
    data                A data frame containing the classification informing the level of insertions. This
                        can be obtained from FishPhyloMaker function
    level               Character indicating which level must be considered in the calculation of PD
                        deficit. default is "Congeneric_insertion"
Value
    A scalar containing the value of PD deficit for the level chosen
See Also
    FishPhyloMaker for phylogeny and data frame containing the classification of insertions
6                                                                                 taxon_data_PhyloMaker
  spp_afrotropic                List of fish species with occurrence in Afrotropical ecoregion
Description
    A list of species that occur in basins of Afrotropical ecoregion
Usage
    spp_afrotropic
Format
    A character vector with 767 species names:
References
    https://www.nature.com/articles/sdata2017141
  taxon_data_PhyloMaker Data frame with species names needed to assemble the phylogenetic
                                tree
Description
    A data frame that can be directly used in FishPhyloMaker to obtain a phylogenetic tree
Usage
    taxon_data_PhyloMaker
Format
    A data frame with taxonomic classification (species, family and order) of 45 species
References
    Species that make up the dataset in the paper published in Neotropical Ichthyology doi: 10.1590/
    1982022420200126
whichFishAdd                                                                                         7
  whichFishAdd                 Function to inform which species must be added to the mega-tree phy-
                               logeny in the insertion process.
Description
    Function to inform which species must be added to the mega-tree phylogeny in the insertion process.
Usage
    whichFishAdd(data)
Arguments
    data               A data frame with three column containing the name of species (s), the Family
                       (f) and Order (o). This can be generated with function FishTaxaMaker
Details
    This function can be used in order to known which species that must be added in the insertion
    process made by FishPhyloMaker.
Value
    A data frame containing a column informing at which level the species in data must be added.
Examples
        data("taxon_data_PhyloMaker")
        res_test <- whichFishAdd(data = taxon_data_PhyloMaker)
Index
∗ datasets
     neotropical_comm, 4
     spp_afrotropic, 6
     taxon_data_PhyloMaker, 6
FishPhyloMaker, 2, 5, 7
FishTaxaMaker, 3, 7
neotropical_comm, 4
PD_defict, 5
spp_afrotropic, 6
taxon_data_PhyloMaker, 6
whichFishAdd, 7
                              8
