Package flora August 29, 2013 Type Package Title flora: taxonomical information on flowering species that occur in Brazil Version 0.1 Date 2013-07-03 Author Gustavo Carvalho Maintainer Gustavo Carvalho <gustavo.bio@gmail.com> Depends R (>= 2.10), RCurl, XML, rjson Retrieve taxonomical information of botanical names from the Flora do Brasil website License GPL NeedsCompilation yes Repository CRAN Date/Publication 2013-07-04 21:48:47 R topics documented: flora-package........................................ 2 Botanical-info........................................ 2 fmt.taxa........................................... 4 get.taxon.info........................................ 5 suggest.names........................................ 6 Index 8 1
2 Botanical-info flora-package Taxonomic information from the Flora do Brasil website Details Functions to retrieve taxonomical information on flowering plants from the Flora do Brasil website and suggest valid botanical names in place of misspeled ones. Package: flora Type: Package Version: 0.1 Date: 2013-07-03 License: GPL Gustavo Carvalho <gustavo.bio@gmail.com> http://floradobrasil.jbrj.gov.br/ ## Not run: taxon.author("coffea arabica") taxon.citation("coffea") taxon.family("coffea arabica") taxon.synonyms("myrcia guianensis") suggest.names("fabaceaea") ## End(Not run) Botanical-info Retrieve the taxonomical information of a botanical name. Retrieve the taxonomical information of a botanical name from the Flora do Brasil website.
Botanical-info 3 Usage taxon.author(spp) taxon.citation(spp) taxon.family(spp) lower.taxa(spp) taxon.synonyms(spp) Arguments spp A character string containing a botanical name to be looked up on Flora do Brasil. Value A character string or logical value. Note Please note that the purpose of these functions is to make it easier to gather taxonomical information in bulk. It s highly recommended that you always verify the results on Flora do Brasil. Gustavo Carvalho (gustavo.bio@gmail.com) http://floradobrasil.jbrj.gov.br/jabot/ See Also is.accepted suggest.names get.taxon.info ## Not run: taxon.author("miconia albicans") taxon.author("myrcia") taxon.citation("myrcia") taxon.family("coffea arabica") taxon.family("anadenanthera") lower.taxa("melastomataceae") lower.taxa("ouratea") taxon.synonyms("myrcia guianensis") ## End(Not run)
4 fmt.taxa fmt.taxa Present taxonomical information in a more readable way This function converts a flora object to a data frame Usage fmt.taxa(taxa) Arguments taxa A taxa object as returned by get.taxon.info. Value A data frame. Gustavo Carvalho (gustavo.bio@gmail.com) http://floradobrasil.jbrj.gov.br/ See Also get.taxon.info ## Not run: species <- get.taxon.info(c("myrcia bella", "Myrcia lingua", "Myconia")) fmt.taxa(species) ## End(Not run)
get.taxon.info 5 get.taxon.info Retrieve information of a list of botanical names. Usage Retrieve taxonomical information on flowering plants that occur in Brazil from the Flora do Brasil website. get.taxon.info(taxa, verbose = FALSE, pbar = TRUE) Arguments taxa verbose pbar A character string containing one or more botanical names. A logical value indicating whether R detailed information on the data requests to Flora do Brasil should be shown. A logical value indicating if a progress bar should be shown. Details Value This function gets the status, family, author, and synonyms of a botanical name. It can also suggest a valid name if the one used as input is misspelled. You must have a working connection to the internet for it to work properly. If either your connection or Flora do Brasil crash whilst processing a list of botanical names, get.taxon.info will try to return an object with your unfinished list. You can use this object later as input in get.taxon.info to resume the search. This process can be repeated as many times as needed. Since get.taxon.info relies heavily on data scrapped from a website, changes upstream can lead to broken functions in flora. Always check if you have the latest version of the package. An invisible list with the following fields: tax.rank id accepted accepted.name family name author lower.taxa synonyms A character string of the taxonomical rank of the botanical name or a flora object with unprocessed names. It can contain, families, genera, species, varieties (var.), subspecies (subsp.), and hybrids. A characther string of the identification of the botanical name on Flora do Brasil A logical value indicating the status of the botanical name A character string of the accepted name A character string of the family A character string of the searched botanical name A character string of the author A character string of all accepted taxa of a lower rank A character string containing all the synonyms of a botanical name
6 suggest.names found suggestion citation processed A logical value indicating whether the name was found or not A character string of a name suggestion A character string indicating how to cite Flora do Brasil A logical value indicating whether the botanical name was processed Note Please note that the purpose of these functions is to make it easier to gather information in bulk. It is still highly recommended that you always verify the results on Flora do Brasil. Please cite them accordingly. Gustavo Carvalho (gustavo.bio@gmail.com) http://floradobrasil.jbrj.gov.br/ ## Not run: get.taxon.info(c("myrcia lingua", "Myrcia bella", "Miconia", "Rubiaceae")) ## End(Not run) suggest.names Suggest valid botanical names This function suggest valid botanical names using data from the Flora do Brasil website. Usage suggest.names(spp) Arguments spp A character string containing botanical name. Value Either a character string of a valid name suggestion or NA. Note The code for this function was borrowed from the RecordLinkage package.
suggest.names 7 Gustavo Carvalho http://floradobrasil.jbrj.gov.br/ suggest.names("mircia lingua")
Index Topic author Topic autor Topic citar Topic citation Topic cite Topic familia Topic family Topic flora flora-package, 2 Topic format fmt.taxa, 4 Topic lower.taxa Topic sinonimia Topic sinonimo Topic suggestion suggest.names, 6 Topic synonyms Topic synonymy Topic taxa get.taxon.info, 5 Topic taxon get.taxon.info, 5 get.taxon.info, 3, 4, 5 is.accepted, 3 is.accepted (Botanical-info), 2 lower.taxa (Botanical-info), 2 suggest.names, 3, 6 taxon.author (Botanical-info), 2 taxon.citation (Botanical-info), 2 taxon.family (Botanical-info), 2 taxon.synonyms (Botanical-info), 2 flora (flora-package), 2 flora-package, 2 fmt.taxa, 4 8