Package 'FishPhyloMaker'

Title: Phylogenies for a List of Finned-Ray Fishes
Description: Provides an alternative to facilitate the construction of a phylogeny for fish species from a list of species or a community matrix using as a backbone the phylogenetic tree proposed by Rabosky et al. (2018) <doi:10.1038/s41586-018-0273-1>.
Authors: Gabriel Nakamura [aut, cre] , Aline Richter [aut], Bruno Soares [aut]
Maintainer: Gabriel Nakamura <[email protected]>
License: MIT + file LICENSE
Version: 0.2.0
Built: 2024-08-25 05:26:53 UTC
Source: https://github.com/GabrielNakamura/FishPhyloMaker

Help Index

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 Family (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 phylogeny 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.

Examples

data("taxon_data_PhyloMaker")
    res_phylo <- FishPhyloMaker(data = taxon_data_PhyloMaker,
    insert.base.node = TRUE, 
    return.insertions = TRUE, 
    progress.bar = TRUE)

Generate a list of species Auxiliary function to obtain taxonomic classification 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 can be used in
   FishPhyloMaker function
   
- A character vector containing all names of species that was not find in Fishbase

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)

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

Usage

neotropical_comm

Format

A data frame with 20 rows and 61 variables:

Source

Article published in Neotropical Ichthyology doi:10.1590/1982-0224-2020-0126

Title Calculate the amount of phylogenetic deficit in assemblages

Description

Title Calculate the amount of phylogenetic deficit in assemblages

Usage

PD_deficit(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. Can be a vector with the levels ("Congeneric_insertion", "Congeneric_Family_level", "Family_insertion", "Order_insertion") which will be considered in the calculation of phylogenetic deficit. default is "Congeneric_insertion".

Value

A vector containing four values: 

- Amount phylogenetic information present in the tree before insertions (PDintree)

- Amount of phylogenetic information inserted in the tree (PDdeficit)

- Total Phylogenetic information of the tree (PDtotal)

- A ratio calculated as PDdeficit/PDtotal (Darwinian_deficit)

See Also

FishPhyloMaker for phylogeny and data frame containing the classification of insertions

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

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:10.1590/1982-0224-2020-0126

Function to inform which species must be added to the mega-tree phylogeny 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)