associations {rusda} | R Documentation |
Downloads associations for input species from SMML Fungus-Host DB
Description
Searches and downloads associations from SMML Fungus-Hosts Distributions and Specimens database for fungus or plant species input vector
Usage
associations(x, database = c("FH", "SP", "both"), spec_type = c("plant",
"fungus"), clean = TRUE, syn_include = TRUE, process = TRUE)
Arguments
x |
a vector of class |
database |
a character string specifying the databases that should be queried. Valid are
|
spec_type |
a character string specifying the type of |
clean |
logical, if |
syn_include |
logical, if |
process |
logical, if |
Details
The Fungus-Hosts distributions database 'FH' comprises data compiled from Literature. In the uncleaned output all kinds of unspecified substrates are documented like "submerged wood". Cleanded data displayes Linnean names only and species names with either "subsp.","f. sp." "f.", "var.". The Specimens database comprises entries from field collections.
If genera names are supplied, then species are derived from the NCBI taxonomy.
Value
an object of class list
.
First is synonyms, second is associations. Synonmys is a
vector of mode list
with synonyms for x
. Notice: This is not a
complete list of synonym data in the database. This is the list of synonyms that contain data for
the input x
. For a complete synonyms list check rusda::synonyms
or (if needed) for fungi R package rmycobank.
Associations is a vector of mode list
of associations for x
Author(s)
Franz-Sebastian Krah
Examples
## Not run:
## Example for species name(s) as input
x <- "Fagus sylvatica"
pathogens <- associations(x, database = "both", clean = TRUE, syn_include = TRUE,
spec_type = "plant", process = TRUE)
x <- "Rosellinia ligniaria"
hosts <- associations(x, database = "both", clean = TRUE, syn_include = TRUE,
spec_type = "fungus", process = TRUE)
is.element("Rosellinia ligniaria", pathogens$association[[1]])
is.element("Fagus sylvatica", hosts$association[[1]])
## Example for genus/genera name(s) as input
x <- "Zehneria"
# or
x <- c("Zehneria", "Momordica")
hosts <- associations(x, database = "both", clean = TRUE, syn_include = TRUE,
spec_type = "plant", process = TRUE)
## End(Not run)