Package 'rphylotastic'

Title: An R Interface to 'Phylotastic' Web Services
Description: This wraps the 'Phylotastic' services APIs described on Web Services at <www.phylotastic.org>. The main use case is to return a phylogenetic tree for a set of species, but the services also include ways to extract species names from web pages, perform taxonomic name resolution, retrieve a list of all descendant species of a taxon, find images of a species, and more.
Authors: Brian O'Meara [aut, cre], Abu Saleh Md Tayeen [aut], Luna L. Sanchez Reyes [aut]
Maintainer: Brian O'Meara <[email protected]>
License: GPL-2
Version: 0.0.8.1
Built: 2024-11-01 03:25:12 UTC
Source: https://github.com/phylotastic/rphylotastic

Help Index


rphylotastic: An R Interface to 'Phylotastic' Web Services

Description

This wraps the 'Phylotastic' services APIs described on Web Services at <www.phylotastic.org>. The main use case is to return a phylogenetic tree for a set of species, but the services also include ways to extract species names from web pages, perform taxonomic name resolution, retrieve a list of all descendant species of a taxon, find images of a species, and more.

Details

See 'vignette("rphylotastic", package = "rphylotastic")' for an overview of the package and its utilities.

Author(s)

Maintainer: Brian O'Meara [email protected]

Authors:

See Also

Useful links:


Add arc labels to tips of a phylogeny; works for non-monophyletic groups and single tip lineages.

Description

Add arc labels to tips of a phylogeny; works for non-monophyletic groups and single tip lineages.

Usage

arclabels(phy, tips, ...)

## Default S3 method:
arclabels(
  phy = NULL,
  tips,
  text,
  plot_singletons = TRUE,
  ln.offset = 1.02,
  lab.offset = 1.06,
  cex = 1,
  orientation = "horizontal",
  ...
)

Arguments

phy

An object of class phylo.

tips

A character vector (or a list ?) with the names of the tips that belong to the clade or group. If multiple groups are going to be plotted, tips must be given in the form of a list.

...

optional arguments for arc.cladelabels.

text

A character vector indicating the desired text to label the arcs.

plot_singletons

Boolean. If TRUE (default), it will add arcs (and labels) to single tip lineages too. If FALSE, no arc or labels will be plotted over that tip..

ln.offset

line offset (as a function of total tree height) for arc.cladelabels.

lab.offset

label offset for arc.cladelabels.

cex

character expansion factor.

orientation

orientation of the text. Can be orientation = "vertical" (the default) or "horizontal".

Value

NULL


Function to pull scientific names from file

Description

This uploads a file (a PDF, Microsoft Word document, plain text file, etc.) and extracts all scientific names from it. For example, you can input a PDF of a scientific article and it will return all the scientific names in that article.

Usage

file_get_scientific_names(file_name, search_engine = 0, above_species = FALSE)

Arguments

file_name

The file path and name to extract names from

search_engine

1 to use TaxonFinder, 2 to use NetiNeti, 0 to use both

above_species

Boolean. Default to FALSE. If TRUE it will only return scientific names above the species level.

Details

It requires that curl is installed on your system.

Value

A vector of scientific names

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription


Function to pull scientific names from file using GNRD

Description

This uploads a file (a PDF, Microsoft Word document, plain text file, etc.) and extracts all scientific names from it. For example, you can input a PDF of a scientific article and it will return all the scientific names in that article.

Usage

file_get_scientific_names_from_GNRD(
  file_name,
  search_engine = 0,
  above_species = FALSE
)

Arguments

file_name

The file path and name to extract names from

search_engine

1 to use TaxonFinder, 2 to use NetiNeti, 0 to use both

above_species

Boolean. Default to FALSE. If TRUE it will only return scientific names above the species level.

Details

It requires that curl is installed on your system.

Value

A vector of scientific names

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription


Flowering plants families from Open Tree Taxonomy

Description

Flowering plants families from Open Tree Taxonomy

Usage

flower_plant_fams

Format

A character vector

Details

flower_plant_fams <- datelife::get_ott_children(ott_ids = 99252, ott_rank = "family") flower_plant_fams <- flower_plant_fams[[1]] flower_plant_fams <- rownames(flower_plant_fams)[as.character(flower_plant_fams[,"rank"]) == "family"] usethis::use_data(flower_plant_fams, overwrite = TRUE)

Author(s)

Luna L. Sanchez-Reyes [email protected] Brian O'Meara [email protected]

Source

https://tree.opentreeoflife.org/about/taxonomy-version/ott3.0


Get Phylotastic base URL return The URL for the phylotastic server

Description

Get Phylotastic base URL return The URL for the phylotastic server

Usage

get_base_url()

Return Species List server URL

Description

Return Species List server URL

Usage

get_list_server_url()

Get existing list/lists of species

Description

Get existing list/lists of species

Usage

get_species_from_list(
  userid,
  access_token,
  list_id,
  verbose = FALSE,
  content = TRUE
)

Arguments

userid

A valid gmail address of the user

access_token

Access token of the gmail address

list_id

An integer id of the list to retrieve

verbose

(optional)By default FALSE and shows minimal meta-data of the list.

content

(optional)By default TRUE and shows the species collection of the list

Value

An existing list with metadata and content based on parameters

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription

Examples

# This gives you the syntax, but since the access token expires after one hour,
  # this particular example will not work.
  ## Not run: 
  userid = "[email protected]"
  access_token = "ya29..zQLmLjbyujJjwV6RVSM2sy-mkeaKu-9"
  list_id = 12
  verbose = TRUE
  content = FALSE
  get_species_from_list(userid, access_token, list_id, verbose, content)
  
## End(Not run)

Insert list of species

Description

Insert list of species

Usage

insert_species_in_list(userid, listObj)

Arguments

userid

A valid gmail address of the user

listObj

A list object

Value

A list with the id of the new list created

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription

Examples

userid = "[email protected]"
  listObj = list(list_extra_info="", list_description="A sublist on the bird species added",
      list_keywords=c("bird", "endangered species", "Everglades"),
      list_curator="HD Laughinghouse", list_origin="webapp",
      list_curation_date="02-24-2016", list_source="des", list_focal_clade="Aves",
      list_title="Bird Species List",list_author=c("Bass", "O. & Cunningham", "R."),
      list_date_published="01-01-2017", is_list_public=TRUE,
      list_species=list(list(family="",scientific_name="Aix sponsa",
          scientific_name_authorship="", vernacular_name="Wood Duck",
          phylum="",nomenclature_code="ICZN",order="Anseriformes",class=""),
          list(family="",scientific_name="Anas strepera",
          scientific_name_authorship="", vernacular_name="Gadwall",
          phylum="",nomenclature_code="ICZN",
          order="Anseriformes",class="") ))
  insert_species_in_list(userid, listObj)

Remove an existing list of species

Description

Remove an existing list of species

Usage

remove_species_from_list(userid, access_token, list_id)

Arguments

userid

A valid gmail address of the user

access_token

Access token of the gmail address

list_id

An integer id of the list to retrieve

Value

A list with the id of the list removed

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription

Examples

# This gives you the syntax, but since the access token expires after one hour,
  # this particular example will not work.
  ## Not run: 
  userid = "[email protected]"
  access_token = "ya29..zQLmLjbyujJjwV6RVSM2sy-mkeaKu-9"
  list_id = 12
  remove_species_from_list(userid, access_token, list_id)
  
## End(Not run)

Replace a list of species

Description

Replace a list of species

Usage

replace_species_in_list(userid, access_token, list_id, speciesObj)

Arguments

userid

A valid gmail address of the user

access_token

Access token of the gmail address

list_id

An integer id of the list to be modified

speciesObj

A species object to replace with

Value

A list with the old species and new species list

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription

Examples

# This gives you the syntax, but since the access token expires after one hour,
  # this particular example will not work.
  ## Not run: 
  userid = "[email protected]"
  access_token = "ya29..zQLmLjbyujJjwV6RVSM2sy-mkeaKu-9"
  list_id = 12
  speciesObj = list( list(family="",scientific_name="Aix sponsa",scientific_name_authorship="",
  vernacular_name="Wood Duck",phylum="",nomenclature_code="ICZN",order="Anseriformes",class=""))
  replace_species_in_list(userid, access_token, list_id, speciesObj)
  
## End(Not run)

Get image metadata of a list of species

Description

Get image metadata of a list of species

Usage

species_get_image_data(species)

Arguments

species

A vector of names

Value

A data frame of image metadata(image urls, license info etc.) of species

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription or https://eol.org/api/


Get information from Encyclopedia of Life of a list of species

Description

Get information from Encyclopedia of Life of a list of species

Usage

species_get_info(species)

Arguments

species

A vector of names

Value

A data frame of species information from Encyclopedia of Life. Type of information available varies among species.

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription or https://eol.org/api/


Convert common names to scientific names.

Description

Convert common names to scientific names.

Usage

taxa_common_to_scientific(taxa, service = "NCBI", multiple = FALSE)

Arguments

taxa

A character vector of common names. Binomials can be spaced with underscore or white space.

service

Which service to use: NCBI, ITIS, or TROPICOS

multiple

If TRUE, then the service will return multiple matches (if available) for each common name in the input list.

Value

A vector of scientific names. Output order may not correspond to input order.

See Also

taxize package for name resolution in general and its sci2comm function.

Examples

taxa <- c("blue_whale", "swordfish", "killer whale")
scientific <- taxa_common_to_scientific(taxa)
print(scientific)

Get OToL induced subtree

Description

Get OToL induced subtree

Usage

taxa_get_otol_tree(taxa)

Arguments

taxa

The vector of names, already resolved to match OToL taxa

Value

A phylo object

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription or the rotl package, another interface to Open Tree of Life

Examples

taxa <- c("Crabronidae", "Ophiocordyceps", "Megalyridae",
          "Formica polyctena", "Tetramorium caespitum",
          "Pseudomyrmex", "Carebara diversa", "Formicinae")
phy <- taxa_get_otol_tree(taxa)
plot(phy)

Get phylomatic subtree

Description

Get phylomatic subtree

Usage

taxa_get_phylomatic_tree(taxa)

Arguments

taxa

The vector of names, already resolved

Value

A phylo object

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription or the interface of phylomatic http://phylodiversity.net/phylomatic/

Examples

phy <- taxa_get_phylomatic_tree(c("Panthera leo", "Panthera onca",
         "Panthera tigris", "Panthera uncia"))
plot(phy)

Resolve Scientific Names with GNR TNRS

Description

Resolve Scientific Names with GNR TNRS

Usage

taxa_resolve_names_with_gnr(taxa)

Arguments

taxa

The vector of names

Details

Mispelled or incorrect names will be dropped.

Value

A vector of correct names. THE ORDER MAY NOT CORRESPOND TO YOUR INPUT ORDER.

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription or the rotl package, another interface to Open Tree of Life, or the taxize package for name resolution in general.


Resolve Scientific Names with Open Tree TNRS

Description

Resolve Scientific Names with Open Tree TNRS

Usage

taxa_resolve_names_with_otol(taxa)

Arguments

taxa

The vector of names

Value

A vector of corrected names. THE ORDER MAY NOT CORRESPOND TO YOUR INPUT ORDER.

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription or the rotl package, another interface to Open Tree of Life, or the taxize package for name resolution in general.

Examples

my.species.raw <- c("Formica polyctena", "Formica exsectoides", "Farmica pacifica")
my.species.corrected <- taxa_resolve_names_with_otol(my.species.raw)
print(my.species.corrected)

Keep the first part of the binomial from a vector of taxon names that includes species binomial names

Description

Keep the first part of the binomial from a vector of taxon names that includes species binomial names

Usage

taxa_toss_binomials(taxa)

Arguments

taxa

A character vector of taxon names.

Value

A character vector of lineage names above the species level.

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription or the rotl package, another interface to Open Tree of Life

Examples

taxa_toss_binomials("Vulpes_vulpes")

Get all species from a taxon from Open Tree of Life taxonomy.

Description

Get all species from a taxon from Open Tree of Life taxonomy.

Usage

taxon_get_species(taxon, filters = c("environmental", "sp\\.", "cf\\."))

Arguments

taxon

A character vector of length 1. Specify the taxon name to get all species for. If vector is longer than 1, it will only take the first element and ignore all other names.

filters

A character vector of strings to exclude.

Value

A character vector of species names.

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription or the rotl package, another interface to Open Tree of Life

Examples

print(taxon_get_species("Vulpes"))

Get all species filtered by country from a taxon

Description

Get all species filtered by country from a taxon

Usage

taxon_get_species_from_country(
  taxon,
  country,
  filters = c("environmental", "sp\\.", "cf\\.")
)

Arguments

taxon

A character vector of length 1. Specify the taxon name to get a subset of species that are established in a particular country

country

A country name where species of the input taxon are established.

filters

A character vector of strings to exclude

Value

A vector of names

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription or the rotl package, another interface to Open Tree of Life


Get all species that have genome sequence in NCBI from a taxon

Description

Get all species that have genome sequence in NCBI from a taxon

Usage

taxon_get_species_with_genome(
  taxon,
  filters = c("environmental", "sp\\.", "cf\\.")
)

Arguments

taxon

A character vector of length 1. Specify the taxon name to get a subset of species having genome sequence

filters

A character vector of strings to exclude

Value

A vector of names

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription or the rotl package, another interface to Open Tree of Life


Separate dark from known taxa on another database

Description

Separate dark from known taxa on another database

Usage

taxon_separate_dark_taxa_using_genbank(
  taxon,
  filters = c("environmental", "sp\\.", "cf\\.", "uncultured", "unidentified",
    " clone", " enrichment"),
  verbose = TRUE,
  sleep = 0
)

Arguments

taxon

A taxon to get all species for

filters

A character vector of strings to exclude

verbose

Update on how many are done

sleep

How many seconds to sleep between calls (on top of rentrez's defaults)

Value

A list containing a vector of dark names, a vector of known names, and fraction.dark


Separate dark from known taxa on OpenTree of Life

Description

Separate dark from known taxa on OpenTree of Life

Usage

taxon_separate_dark_taxa_using_otol(
  taxon,
  filters = c("environmental", "sp\\.", "cf\\.", "uncultured", "unidentified",
    " clone", " enrichment")
)

Arguments

taxon

A taxon to get all species for

filters

A character vector of strings to exclude

Value

A list containing a vector of dark names, a vector of known names, and fraction.dark

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription or the rotl package, another interface to Open Tree of Life


Flowering plants families from Open Tree Taxonomy

Description

Flowering plants families from Open Tree Taxonomy

Usage

terrestrial_plant_orders

Format

A character vector

Details

terrestrial_plant_orders <- datelife::get_ott_children(ott_ids = 56610, ott_rank = "order") terrestrial_plant_orders <- terrestrial_plant_orders[[1]] terrestrial_plant_orders <- rownames(terrestrial_plant_orders)[as.character(terrestrial_plant_orders[,"rank"]) == "order"] usethis::use_data(terrestrial_plant_orders, overwrite = TRUE)

Author(s)

Luna L. Sanchez-Reyes [email protected] Brian O'Meara [email protected]

Source

https://tree.opentreeoflife.org/about/taxonomy-version/ott3.0


Function to pull scientific names from text

Description

This takes a string of text and extracts any scientific names in the text. Other words in the text are ignored.

Usage

text_get_scientific_names(text)

Arguments

text

The text string to extract names from

Value

A data.frame of scientific names and other data from GNRD

Examples

text <- "Formica polyctena is a species of European red wood ant in
   the genus Formica. The pavement ant, Tetramorium caespitum
   is an ant native to Europe."
print(text_get_scientific_names(text))

Function to get tree for a traits set.

Description

A common use case is having a set of traits for a set of species and wanting to get a tree for those species. This involves resolving to the same taxonomy, getting a tree for those species, and then (optionally) pruning the traits and tree to the same set of taxa (this is optional: there are approaches to make up traits or phylogenetic placement in the absence of information).

Usage

traits_get_tree(
  traits,
  tnrs_source = "otol",
  tree_source = "otol",
  prune = TRUE,
  summary_format = "phylo_biggest",
  ...
)

Arguments

traits

Data.frame with species names as rownames

tnrs_source

Source for taxonomic name resolution; options are "otol" and "gnr". If set to NULL, assumes names are fine as is

tree_source

Source for tree; options are "otol", "phylomatic", "datelife".

prune

If TRUE, delete taxa to matching sets only

summary_format

What format to return from datelife

...

Other options to pass to datelife::datelife_search

Details

For sources of trees, besides the standard ones (Open Tree of Life, Phylomatic), datelife is also an option. For this, you will have had to install the datelife package (which is only suggested, not required, by this code). It will return the chronogram in the tree store with the most overlap to your set of taxa by default, but you can change options with summary_format; see ?datelife::datelife_search for more info

Value

list with a phy and a traits object, both pruned to the same taxon set, as well as citation information for the sources of the taxonomic resolution and phylogeny (also cite this package and, if you use it, datelife)


Update metadata of a list of species

Description

Update metadata of a list of species

Usage

update_species_in_list(userid, access_token, list_id, listObj)

Arguments

userid

A valid gmail address of the user

access_token

Access token of the gmail address

list_id

An integer id of the list to be modified

listObj

A list object to update with

Value

A list with modified list metadata

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription

Examples

# This gives you the syntax, but since the access token expires after one hour,
  # this particular example will not work.
  ## Not run: 
  userid = "[email protected]"
  access_token = "ya29..zQLmLjbyujJjwV6RVSM2sy-mkeaKu-9"
  list_id = 12
  listObj = list(list_description="A sublist on the bird species",
            list_keywords=c("bird","Everglades"))
  update_species_in_list(userid, access_token, list_id, listObj)

## End(Not run)

Function to pull scientific names from web pages

Description

Function to pull scientific names from web pages

Usage

url_get_scientific_names(URL, search_engine = 0, above_species = FALSE)

Arguments

URL

The URL to extract names from. Can be a pdf url.

search_engine

1 to use TaxonFinder, 2 to use NetiNeti, 0 to use both

above_species

Boolean. Default to FALSE. If TRUE it will only return scientific names above the species level.

Value

A vector of scientific names. It returns unique matches.

See Also

https://github.com/phylotastic/phylo_services_docs/tree/master/ServiceDescription

Examples

# get scientific names from a wikipedia web page:
url_get_scientific_names(URL = "https://en.wikipedia.org/wiki/Plain_pigeon")
# get scientific names from a pdf URL:
url_get_scientific_names(URL =
 "http://darwin-online.org.uk/converted/pdf/1897_Insectivorous_F1229.pdf")