sidtraits

sidtraits is a package to scrape the Royal Botanical Gardens Kew's Seed Information Database (SID, http://data.kew.org/sid/) using plant binomial names.

Currently sidtraits fetches information related to seed weight and dispersal.

sidtraits is still very much a work in progress.

Author: Konsta Happonen

Installing

Install sidtraits with devtools:

install.packages("devtools")
library(devtools)
install_github("sidtraits", "Koalha")
library(sidtraits)

Functions

sidtraits has one function: sidseeds(sciname, sepa = " ", single = FALSE), which scrapes seed trait information from SID.

sciname is a vector of one or more plant binomial names, eg. c("Betula pendula", "Betula pubescens").

sepa is the separator between genus and species names. For example: sidseeds(sciname = "Betula_pendula", sepa = "_").

single is a logical vector indicating, if the results of sidseeds() should be restricted to one species per entry in the sciname. If single = FALSE, sidseeds() returns traits for all taxons that partially match the queried binomial name, including variations and subspecies.

With single = TRUE it will return only one result per binomial name queried. In this case all subspecies and variations are ignored unless there is no seed trait information for a higher taxon.

Examples

A normal call returns a data frame for all matches to the specified species.

species = c("Betula pendula", "Impatiens parviflora", "Carex nigra")
sidseeds(species)

##                   call                 speciesname seed1000 zoochory
## 1       Betula pendula Betula pendula var. pendula     0.49       NA
## 2       Betula pendula         Betula pendula Roth     0.27       NA
## 3 Impatiens parviflora    Impatiens parviflora DC.     8.00       NA
## 4          Carex nigra   Carex nigra (L.) Reichard     0.69       NA
##   anemochory hydrochory autochory barochory atelochory other_dispersal
## 1         NA         NA        NA        NA         NA              NA
## 2          1         NA        NA        NA         NA              NA
## 3         NA         NA         1        NA         NA              NA
## 4         NA         NA        NA        NA         NA              NA
##   desc_dispersal
## 1             NA
## 2   Wind; Di....
## 3   Methods ....
## 4             NA

The dispersal categories are Principal Dispersal Agents (PDAs). If the PDA is other than animal, wind, water, self-assisted, unassisted or prevented dispersal (for example a combination of some of the above), it is marked as other_disperal. desc_dispersal is a list of Kew's description of the PDA's, such as which animal disperses a zoochorous plant's seeds. It also lists references to literature. For more detailed info, visit Kew's webpage.

Specifying single = TRUE tries to skip all subspecies and variations, and returns only one result per species queried.

result = sidseeds(species, single = TRUE)
result

##                   call               speciesname seed1000 zoochory
## 1       Betula pendula       Betula pendula Roth     0.27       NA
## 2 Impatiens parviflora  Impatiens parviflora DC.     8.00       NA
## 3          Carex nigra Carex nigra (L.) Reichard     0.69       NA
##   anemochory hydrochory autochory barochory atelochory other_dispersal
## 1          1         NA        NA        NA         NA              NA
## 2         NA         NA         1        NA         NA              NA
## 3         NA         NA        NA        NA         NA              NA
##   desc_dispersal
## 1   Wind; Di....
## 2   Methods ....
## 3             NA

result$desc_dispersal[2]

## [[1]]
## [1] "Methods originating from parent plant or diaspore; Explosive mechanism; Direct or experimental observation; (Kozlowski, 1972); Diaspore=seed. Seeds are expelled from the fruit via a turgor mechanism."
## [2] "Methods originating from parent plant or diaspore; Method not stated; (Bouman et al., 2000)"

The second species Impatiens parviflora has 2 sources for its PDA. These are included in a list in the column desc_dispersal