R/LCVP.R
LCVP.RdAllow a taxonomic resolution of plant taxa names listed in the "Leipzig Catalogue of Vascular Plants" (LCVP). Connects to the LCVP table and validates the names of a vector of plant taxa, replacing synonyms by accepted names and removing orthographical errors in plant names. The LCVP data package must be installed. It is available from https://github.com/idiv-biodiversity/LCVP.
LCVP( splist, genus_search = FALSE, max_distance = 0, encoding = "UTF-8", family_tab = FALSE, order_tab = FALSE, genus_tab = FALSE, infraspecies_tab = FALSE, status = TRUE, save = FALSE, visualize = FALSE, version = "1.1", max.cores = (detectCores() - 1), out_path = getwd() )
| splist | A character vector specifying the input taxon, each element including genus and specific epithet and, potentially, infraspecific rank, infraspecific name and author name |
|---|---|
| genus_search | Logical. If TRUE, the function will apply the fuzzy match algorithm also for the search of the genus name, otherwise as default the search is applied only to the epithet, the infraspecies and the name author. |
| max_distance | is an integer value. It represents the maximum distance (number of characters) allowed for a match when comparing the submitted name with the closest name matches in the LCVP |
| encoding | character vector. This value will allow the user to set the specific codification of the strings |
| family_tab | Logical. If TRUE, the function will return the list of plant taxa names belonging to the same family name submitted by the user |
| order_tab | Logical. If TRUE, the function will return the list of plant taxa names belonging to the same order name submitted by the user |
| genus_tab | Logical. If TRUE, the function will return the list of plant taxa names belonging to the same genus name submitted by the user |
| infraspecies_tab | Logical. If TRUE, the function will return also all the infraspecies names found for a submitted plant name |
| status | Logical. If FALSE, the function will return not only the valid epithet for a species name but also all the possible synonyms |
| save | Logical. If TRUE, the function will write the output file as comma-separated format (.csv), saving it into the working directory or in the directory already set through the 'out_path' option |
| visualize | If TRUE the function will visualize the output search on the 'Source Tab' of RStudio. This option has to be turned off (FALSE) if the package is execute in a UNIX environment (from the command line) without having a Graphical User Interface |
| version | A character vector indicating the current version of the package. A new version is under development allowing the package to connect the web API that is under construction |
| max.cores | integer value, indicating the number of CPU cores to be used for the parallelization of the plant name search when a list of plant taxa names is submitted. As default, the maximum number of CPU cores available on the working machine menus one is set |
| out_path | a character vector. Defines the path where the output file has to be saved. |
The Leipzig Catalogue of Plants (LCVP) - An improved taxonomic reference list for all known vascular plants
https://idata.idiv.de/ddm/Data/ShowData/1806
LCVP("Hibiscus vitifolius")#>#>#> Time difference of 4.206964 secs#>#>#>#> ID Submitted_Name Order Family Genus Species Infrasp #> 1 1 Hibiscus vitifolius Malvales Malvaceae Hibiscus vitifolius species #> 2 1 Hibiscus vitifolius Malvales Malvaceae Hibiscus vitifolius species #> Infraspecies Authors Status LCVP_Accepted_Taxon PL_Comparison #> 1 L. accepted Hibiscus vitifolius L. identical #> 2 Mill. synonym Hibiscus cannabinus L. identical #> PL_Alternative Score Insertion Deletion Substitution #> 1 matched 0 0 0 #> 2 matched 0 0 0LCVP("Hibiscus abelmoschus var. betulifolius Mast.")#>#>#> Time difference of 1.628659 secs#>#>#>#> ID Submitted_Name Order Family Genus #> 1 1 Hibiscus abelmoschus var. betulifolius Mast. Malvales Malvaceae Hibiscus #> Species Infrasp Infraspecies Authors Status LCVP_Accepted_Taxon #> 1 abelmoschus var. betulifolius Mast. synonym Abelmoschus moschatus Medik. #> PL_Comparison PL_Alternative Score Insertion Deletion Substitution #> 1 identical matched 0 0 0LCVP(c("Hibiscus abelmoschus var. betulifolius Mast.", "Hibiscus abutiloides Willd.", "Hibiscus aculeatus", "Hibiscus acuminatus"), max.cores = 1)#>#> Time difference of 8.229063 secs#>#>#>#> ID Submitted_Name Order Family Genus #> 1 1 Hibiscus abelmoschus var. betulifolius Mast. Malvales Malvaceae Hibiscus #> 2 2 Hibiscus abutiloides Willd. Malvales Malvaceae Hibiscus #> 3 3 Hibiscus aculeatus Malvales Malvaceae Hibiscus #> 4 3 Hibiscus aculeatus Malvales Malvaceae Hibiscus #> 5 3 Hibiscus aculeatus Malvales Malvaceae Hibiscus #> 6 3 Hibiscus aculeatus Malvales Malvaceae Hibiscus #> 7 4 Hibiscus acuminatus Malvales Malvaceae Hibiscus #> Species Infrasp Infraspecies Authors Status #> 1 abelmoschus var. betulifolius Mast. synonym #> 2 abutiloides species Willd. synonym #> 3 aculeatus species F.Dietr. synonym #> 4 aculeatus species G.Don synonym #> 5 aculeatus species Roxb. synonym #> 6 aculeatus species Walter accepted #> 7 acuminatus species Cav. synonym #> LCVP_Accepted_Taxon PL_Comparison #> 1 Abelmoschus moschatus Medik. identical #> 2 Talipariti tiliaceum (L.) Fryxell identical #> 3 Hibiscus heterophyllus Vent. missing #> 4 Hibiscus surattensis L. identical #> 5 Hibiscus furcatus Roxb. other synonym #> 6 Hibiscus aculeatus Walter identical #> 7 Kosteletzkya acuminata (Cav.) Britten other synonym #> PL_Alternative Score Insertion Deletion Substitution #> 1 matched 0 0 0 #> 2 matched 0 0 0 #> 3 matched 0 0 0 #> 4 matched 0 0 0 #> 5 Hibiscus hispidissimus Griff. matched 0 0 0 #> 6 matched 0 0 0 #> 7 Pavonia acuminata (Cav.) Spreng. matched 0 0 0