Package flora

Description

Collect data from the Brazilian Flora checklist (http://floradobrasil.jbrj.gov.br).

Details

This package contains a set of tools solving problems that arise when one has to collect taxonomic and distribution information for large datasets of plants. Interacting with the Brazilian Flora Checklist website from a web browser is often a slow and somewhat cumbersome process, especially if you are not sure about the correct spelling of a name. With flora, however, you can:

• get a suggestion for the correct spelling of a name from an incorrect one

• search for its current taxonomic status

• get its author(s), synonym(s), family, distribution, and lower taxa

• process lists of names and automatically solve synonyms and typing errors

flora now holds all the data it needs. All functions can be used whilst offline.

Phylomatic format

Description

Convert the results of get.taxa() to the phylomatic sample format

Usage

df2phytaxa(taxa, uppercase = TRUE)

Arguments

Fix the name case of a taxon

Description

Fix the name case of a taxon

Usage

fixCase(x)

Arguments

Examples

fixCase("myrcia lingua")
fixCase("Myrcia Lingua")
fixCase("COFFEA ARABICA")

List all synonyms of a given taxa

Description

This function returns all the synonyms of a given taxon according to the Brazilian Flora 2020.

Usage

get.synonyms(taxon, fix = FALSE, relationship = FALSE)

Arguments

Value

a character vector

Examples

## Not run: 
get.synonyms("Myrcia lingua")

## End(Not run)

Get plant taxonomical and distribution data

Description

This function collects taxonomic information and distribution from the Brazilian Flora Checklist. Synonyms and misspelled names are resolved automatically. Results can be combined with life form, habitat, vernacular name, and occurrence data.

Usage

get.taxa(taxa, replace.synonyms = TRUE, suggest.names = TRUE,
  life.form = FALSE, habitat = FALSE, vegetation.type = FALSE,
  vernacular = FALSE, states = FALSE, establishment = FALSE,
  domain = FALSE, endemism = FALSE, drop = c("authorship", "genus",
  "specific.epiteth", "infra.epiteth", "name.status"),
  suggestion.distance = 0.9, parse = FALSE)

Arguments

Details

The returned data frame will contain a variable number of rows and columns depending on how the function was called. For instance, since there might be more than one vernacular name for each taxon, some rows will be duplicated if vernacular is set to TRUE. All misspelled taxa are automatically corrected if the function can come up with a reasonable guess for the name. Conservation status follows the IUCN nomenclature.

Value

a data frame

Examples

## Not run: 
data(plants)
get.taxa(plants)
get.taxa(plants, life.form = TRUE, establishment = TRUE)

## End(Not run)

Get the phytogeographic domain of a list of taxa

Description

Get the phytogeographic domain of a list of taxa

Usage

get_domains(taxa)

Arguments

Value

A data frame as returned by get.taxa with an extra column named domain.

Examples

## Not run: 
taxa <- get.taxa(c("Myrcia guianensis", "bleh", "Xylopia", "Miconia albicans", "bleh", "Poa annua"))
get_domains(taxa)

## End(Not run)

Get the listed endemism for a list of taxa

Description

Get the listed endemism for a list of taxa

Usage

get_endemism(taxa)

Arguments

Value

A data frame as returned by get.taxa with an extra column named vegtype.

Examples

## Not run: 
taxa <- get.taxa(c("Myrcia guianensis", "bleh", "Xylopia", "Miconia albicans", "bleh", "Poa annua"))
get_endemism(taxa)

## End(Not run)

Get the listed vegetation life forms for a list of taxa

Description

Get the listed vegetation life forms for a list of taxa

Usage

get_lifeform(taxa)

Arguments

Value

A data frame as returned by get.taxa with an extra column named life.form

Examples

## Not run: 
taxa <- get.taxa(c("Myrcia guianensis", "bleh", "Xylopia", "Miconia albicans", "bleh", "Poa annua"))
get_lifeform(taxa)

## End(Not run)

Get the listed vegetation types for a list of taxa

Description

Get the listed vegetation types for a list of taxa

Usage

get_vegtype(taxa)

Arguments

Value

A data frame as returned by get.taxa with an extra column named vegtype.

Examples

## Not run: 
taxa <- get.taxa(c("Myrcia guianensis", "bleh", "Xylopia", "Miconia albicans", "bleh", "Poa annua"))
get_vegtype(taxa)

## End(Not run)

Get downstream taxa

Description

Get all downstream taxa from a family or genus name.

Usage

lower.taxa(taxon, accepted = TRUE)

Arguments

Examples

## Not run: 
lower.taxa("Acosmium")
lower.taxa("Zygophyllaceae")

## End(Not run)

Taxa occurrence

Description

Find the taxa that occur in a given state of Brazil.

Usage

occurrence(states, type = c("any", "only", "all"), taxa = NULL)

Arguments

Value

a data frame

Note

List of abbreviations: http://en.wikipedia.org/wiki/States_of_Brazil

Examples

## Not run: 
occ.any <- occurrence(c("SP", "BA", "MG"), type = "any")
occ.only <- occurrence(c("SP", "BA", "MG"), type = "only")
occ.all <- occurrence(c("SP", "BA", "MG"), type = "all")
occ.taxa <- occurrence(c("SP", "BA", "MG"), type = "all", taxa = lower.taxa("Myrcia"))

head(occ.any)
head(occ.only)
head(occ.all)
head(occ.taxa)

## End(Not run)

Plant names

Description

A small character vector containing 16 plant names. Contains accepted names, synonyms, and misspelled taxa.

Format

A character vector with 16 names

Remove the author(s) from a taxon name.

Description

This attempts to remove the authorities of a taxonomic name.

Usage

remove.authors(taxon)

Arguments

Value

a character vector

Examples

## Not run: 
remove.authors("Coffea arabica L.")
remove.authors("Chrysophyllum argenteum subsp. nitidum (G.F.W.Meyer) T.D.Penn.")

## End(Not run)

Standardize taxonomic names

Description

This function standardizes taxa names. It is used mainly internally, but might be helpful to the end user in some situations.

Usage

standardize.names(taxon)

Arguments

Value

a character vector

Examples

## Not run: 
standardize.names("Miconia sp 01")
standardize.names("Miconia Sp 2")
standardize.names("Sp18")

## End(Not run)

Suggest a valid name from a misspelled one

Description

This function tries to suggest a valid name according to the Brazilian Flora Checklist using a possibly incorrect one as a starting point.

Usage

suggest.names(taxon, max.distance = 0.75, return.na = TRUE,
  ignore.words = NULL)

Arguments

Value

A character vector or NA

Examples

## Not run: 
suggest.names("Cofea arabyca")
suggest.names("Myrcia bela")

## End(Not run)

Trim a name and remove duplicate tabs and whitespaces

Description

Remove duplicate and misplaced whitespace characters

Usage

trim(taxon)

Arguments

Value

a character vector

Examples

## Not run: 
trim("   Myrcia  lingua")

## End(Not run)

Vernacular name search

Description

Search for taxa using vernacular names

Usage

vernacular(name, exact = FALSE)

Arguments

Value

a data frame of results or NA

Examples

## Not run: 
vernacular("pimenta", exact = TRUE)
vernacular("pimenta", exact = FALSE)

## End(Not run)

Web front end

Description

This function starts a local webserver to run the shiny app distributed with the package.

Usage

web.flora()