Help for package flora (original) (raw)
| Type: | Package |
|---|---|
| Title: | Tools for Interacting with the Brazilian Flora 2020 |
| Version: | 0.3.4 |
| Author: | Gustavo Carvalho |
| Maintainer: | Gustavo Carvalho gustavo.bio@gmail.com |
| Depends: | R (≥ 3.0.0) |
| Imports: | httr, dplyr, utils, jsonlite, stringdist |
| Suggests: | testthat, shiny |
| Description: | Tools to quickly compile taxonomic and distribution data from the Brazilian Flora 2020. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| URL: | http://www.github.com/gustavobio/flora |
| BugReports: | http://www.github.com/gustavobio/flora/issues |
| RoxygenNote: | 6.1.1 |
| NeedsCompilation: | no |
| Packaged: | 2020-04-27 22:22:23 UTC; gustavo |
| Repository: | CRAN |
| Date/Publication: | 2020-04-28 05:00:03 UTC |
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
| taxa | A data frame with columns named family, genus, and species. |
|---|---|
| uppercase | logical. Should the function capitalize first letters? |
Fix the name case of a taxon
Description
Fix the name case of a taxon
Usage
fixCase(x)
Arguments
| x | a unit character vector with a taxon |
|---|
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
| taxon | a character vector containing a name. |
|---|---|
| fix | should the function fix issues (synonyms, mispelled names) in taxon? |
| relationship | return the kind of relationship? |
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
| taxa | a character vector containing one or more taxa, without authors see remove.authors if you have a list with authorities |
|---|---|
| replace.synonyms | should the function automatically replace synonyms? |
| suggest.names | should the function try to correct misspelled names? |
| life.form | include the life form of the taxon? |
| habitat | include the habitat of the taxon? |
| vegetation.type | include the listed vegetation types? |
| vernacular | include vernacular names and localities? |
| states | include occurrence data? |
| establishment | include the establishment type (native, cultivated or naturalized)? |
| domain | return phytogeographyc domains? |
| endemism | is the taxon endemic to Brazil? |
| drop | NULL or character vector with names of columns with taxonomic information to be removed from the returned data frame. Available names: "id", "scientific.name", "accepted.name", "family", "genus", "specific.epiteth", "infra.epiteth", "taxon.rank", "authorship", "taxon.status", "name.status", "threat.status", and "search.str". |
| suggestion.distance | a value between 0 and 1 indicanting how conservative the name suggestion algorithm should be. Values closer to 1 are very conservative. Be very careful, lower values can give wrong suggestions. |
| parse | Parse names through the GBIF parser to remove authors? |
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
| taxa | A data frame with taxon names as returned by get.taxa() |
|---|
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
| taxa | A data frame with taxon names as returned by get.taxa() |
|---|
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
| taxa | A data frame with taxon names as returned by get.taxa() |
|---|
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
| taxa | A data frame with taxon names as returned by get.taxa() |
|---|
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
| taxon | a character vector with either a family or genus name |
|---|---|
| accepted | list only accepted names? |
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
| states | a character vector with one or more state abbreviations following. See notes for abbreviations. |
|---|---|
| type | type of matching to be used. any will return the taxa that occur in any of the passed states. only matches taxa that occur only in all provided (no more, no less) states and all matches taxa that occur at least in all states passed. See examples. |
| taxa | optional character vector to match against the states |
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
Description
This attempts to remove the authorities of a taxonomic name.
Usage
remove.authors(taxon)
Arguments
| taxon | a character vector containing a single taxon |
|---|
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
| taxon | a character vector containing a single name |
|---|
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
| taxon | a character vector containing a single name |
|---|---|
| max.distance | a numeric value indicating how conservative the function should be when searching for suggestions. Values close to 1 are very conservative |
| return.na | a logical indicating whether to return a NA or the original input when no suggestion is found |
| ignore.words | NULL or a character vector with words to be ignored by the function. Useful if you are automatizing a workflow and wants the function to ignore words or phrases such as "not found", "dead", "undetermined", and so on |
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
| taxon | a character vector with a single taxon name |
|---|
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
| name | a vernacular name |
|---|---|
| exact | approximate or exact match? |
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()