A light wrapper around the taxonstand fxn to call Theplantlist.org database.

Usage

tpl_search(taxon, paral = FALSE, ...)

Arguments

taxon

A taxonomic name, or a vector of names.

paral

Paralellize or not (logical). Which back-end package you use depends on your operating system and just general taste. Possibilities include: snow, multicore, parallel, doMC, etc.

...

Further arguments passed on to the TPLck function of Taxonstand. See TPLck for arguments.

Examples

# Regular non-parallel
splist <- c("Heliathus annuus","Abies procera","Poa annua","Platanus occidentalis",
                "Carex abrupta","Arctostaphylos canescens","Ocimum basilicum","Vicia faba",
                "Quercus kelloggii","Lactuca serriola")
tpl_search(taxon = splist)
            Genus      Species Infraspecific Plant.Name.Index Taxonomic.status
1       Heliathus       annuus                          FALSE                 
2           Abies      procera                           TRUE         Accepted
3             Poa        annua                           TRUE         Accepted
4        Platanus occidentalis                           TRUE         Accepted
5           Carex      abrupta                           TRUE         Accepted
6  Arctostaphylos    canescens                           TRUE         Accepted
7          Ocimum    basilicum                           TRUE         Accepted
8           Vicia         faba                           TRUE         Accepted
9         Quercus    kelloggii                           TRUE         Accepted
10        Lactuca     serriola                           TRUE         Accepted
        Family      New.Genus  New.Species New.Infraspecific Authority  Typo WFormat
1                   Heliathus       annuus                             FALSE   FALSE
2     Pinaceae          Abies      procera                      Rehder FALSE   FALSE
3      Poaceae            Poa        annua                          L. FALSE   FALSE
4  Platanaceae       Platanus occidentalis                          L. FALSE   FALSE
5   Cyperaceae          Carex      abrupta                   Mack. FALSE   FALSE
6    Ericaceae Arctostaphylos    canescens                      Eastw. FALSE   FALSE
7    Lamiaceae         Ocimum    basilicum                          L. FALSE   FALSE
8  Leguminosae          Vicia         faba                          L. FALSE   FALSE
9     Fagaceae        Quercus    kelloggii                   Newb. FALSE   FALSE
10  Compositae        Lactuca     serriola                          L. FALSE   FALSE


# In parallel, using package doMC
library(doMC)
Loading required package: iterators
Loading required package: multicore
registerDoMC(cores=4)
tpl_search(taxon = splist, TRUE)
            Genus      Species Infraspecific Plant.Name.Index Taxonomic.status
1       Heliathus       annuus                          FALSE                 
2           Abies      procera                           TRUE         Accepted
3             Poa        annua                           TRUE         Accepted
4        Platanus occidentalis                           TRUE         Accepted
5           Carex      abrupta                           TRUE         Accepted
6  Arctostaphylos    canescens                           TRUE         Accepted
7          Ocimum    basilicum                           TRUE         Accepted
8           Vicia         faba                           TRUE         Accepted
9         Quercus    kelloggii                           TRUE         Accepted
10        Lactuca     serriola                           TRUE         Accepted
        Family      New.Genus  New.Species New.Infraspecific Authority  Typo WFormat
1                   Heliathus       annuus                             FALSE   FALSE
2     Pinaceae          Abies      procera                      Rehder FALSE   FALSE
3      Poaceae            Poa        annua                          L. FALSE   FALSE
4  Platanaceae       Platanus occidentalis                          L. FALSE   FALSE
5   Cyperaceae          Carex      abrupta                   Mack. FALSE   FALSE
6    Ericaceae Arctostaphylos    canescens                      Eastw. FALSE   FALSE
7    Lamiaceae         Ocimum    basilicum                          L. FALSE   FALSE
8  Leguminosae          Vicia         faba                          L. FALSE   FALSE
9     Fagaceae        Quercus    kelloggii                   Newb. FALSE   FALSE
10  Compositae        Lactuca     serriola                          L. FALSE   FALSE


## in parallel is much faster
system.time( out <- tpl_search(taxon = splist) )
   user  system elapsed 
  0.137   0.014   4.289 

registerDoMC(cores=4)
system.time( out2 <- tpl_search(taxon = splist, TRUE) )
   user  system elapsed 
  0.248   0.234   1.509 


# Use more arguments within TPLck
tpl_search(taxon = "Microbryum curvicollum", corr = TRUE)
       Genus     Species Infraspecific Plant.Name.Index Taxonomic.status Family
1 Microbryum curvicollum                          FALSE                        
   New.Genus New.Species New.Infraspecific Authority  Typo WFormat
1 Microbryum curvicollum                             FALSE   FALSE

tpl_search(taxon = "Microbryum curvicollum", corr = TRUE, max.distance=5)
       Genus     Species Infraspecific Plant.Name.Index Taxonomic.status     Family
1 Microbryum curvicollum                           TRUE         Accepted Pottiaceae
   New.Genus New.Species New.Infraspecific           Authority Typo WFormat
1 Microbryum  curvicolle                   (Hedw.) R.H. Zander TRUE   FALSE