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 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>.
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
Packaged:	2021-09-12 17:28:26 UTC; gabrielnakamura
Author:	Gabriel Nakamura [aut, cre], 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

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

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

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)

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

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

Function to download species from fishtreeoflife

Description

Function to download species from fishtreeoflife

Usage

filter_rank(order)

Arguments

Value

phylogeny

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

Internal function - auxiliary to interactive procedure

Description

Internal function - auxiliary to interactive procedure

Usage

print_cat(print_cat, spp, family)

Arguments

Value

interactive action in console

Internal function

Description

Internal function

Usage

print_cat2(spp)

Arguments

Value

interactive action in console

Internal function to help in interactive process

Description

Internal function to help in interactive process

Usage

print_cat_family(print_cat, spp, order)

Arguments

Value

interactive action in console

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

Internal function to show the number of species from species pool that lacks in phylogeny

Description

Internal function to show the number of species from species pool that lacks in phylogeny

Usage

treedata_modif(phy, data, sort = FALSE, warnings = TRUE)

Arguments

Value

character vector

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

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)