| Title: | Interface to USDA Databases |
|---|---|
| Description: | An interface to the web service methods provided by the United States Department of Agriculture (USDA). The Agricultural Research Service (ARS) provides a large set of databases. The current version of the package holds interfaces to the Systematic Mycology and Microbiology Laboratory (SMML), which consists of four databases: Fungus-Host Distributions, Specimens, Literature and the Nomenclature database. It provides functions for querying these databases. The main function is \code{associations}, which allows searching for fungus-host combinations. |
| Authors: | Franz-Sebastian Krah |
| Maintainer: | Franz-Sebastian Krah <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.0.8 |
| Built: | 2024-08-29 22:59:02 UTC |
| Source: | https://github.com/ropensci/rusda |
An interface to the web service methods provided by the United States Department of Agriculture (USDA). The Agricultural Research Service (ARS) provides a large set of databases. The current version of the package holds interfaces to the Systematic Mycology and Microbiology Laboratory (SMML), which consists of four databases: Fungus-Host Distributions, Specimens, Literature and the Nomenclature database. It provides functions for querying these databases. The main function is associations, which allows searching for fungus-host combinations.
| Package: | rusda |
| Type: | Package |
| Version: | 1.0.7 |
| Date: | 2016-01-20 |
Franz-Sebastian Krah
Maintainer: Franz-Sebastian Krah <[email protected]>
Farr, D.F., & Rossman, A.Y. Fungal Databases, Systematic Mycology and Microbiology Laboratory, ARS, USDA
http://nt.ars-grin.gov/sbmlweb/fungi/databases.cfm, http://www.usda.gov/wps/portal/usda/usdahome
Searches and downloads associations from SMML Fungus-Hosts Distributions and Specimens database for fungus or plant species input vector
associations(x, database = c("FH", "SP", "both"), spec_type = c("plant", "fungus"), clean = TRUE, syn_include = TRUE, process = TRUE, db = "ncbi")associations(x, database = c("FH", "SP", "both"), spec_type = c("plant", "fungus"), clean = TRUE, syn_include = TRUE, process = TRUE, db = "ncbi")
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 |
db |
if x is higher than species level, all species for the higher taxon are retrived using the function taxize::downstream. Here one of ITIS (itis), Catalogue of Life (col), GBIF (gbif), or NCBI (ncbi) has to be selected. NCBI is default. |
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.
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
Franz-Sebastian Krah
## 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)## 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)
Downloads specimens records for input study BPI accession number
getBPI(BPI, sep = "; ")getBPI(BPI, sep = "; ")
BPI |
a single study BPI or a vector of study BPIs |
sep |
seperator how to collapse output literature references |
an object of class data.frame with studies
Franz-Sebastian Krah
Downloads studies for study IDs which are output of associations
getStudy(id, sep = "; ")getStudy(id, sep = "; ")
id |
a single study id or a vector of study ids |
sep |
seperator how to collapse output literature references |
an object of class data.frame with studies
Franz-Sebastian Krah
Searches and downloads literature entries from the SMML Literature database
literature(x, spec_type = c("plant", "fungus"), process = TRUE)literature(x, spec_type = c("plant", "fungus"), process = TRUE)
x |
a vector of class |
spec_type |
a character string specifying the type of |
process |
logical, if an object of class |
a vector of mode list with literature entries for x
Franz-Sebastian Krah
## Not run: x <- "Polyporus badius" lit <- literature(x, process = TRUE, spec_type = "fungus") lit ## End(Not run)## Not run: x <- "Polyporus badius" lit <- literature(x, process = TRUE, spec_type = "fungus") lit ## End(Not run)
Searches, downloads and evaluates presence/absence of data in the SMML databases
meta_smml(x, spec_type = c("plant", "fungus"), process = TRUE)meta_smml(x, spec_type = c("plant", "fungus"), process = TRUE)
x |
a vector of class |
spec_type |
a character string specifying the type of |
process |
logical, if |
Use this function before deriving data from one of the databases in order to prune your
input species vector. With pruned species vectors the functions will run faster. This is important
if x is some hundred species long.
an object of class data.frame: presence/absence
Franz-Sebastian Krah
## Not run: fungus.meta <- meta_smml(x = "Picea abies", process = TRUE, spec_type = "plant") fungus.meta hosts.meta <- meta_smml(x = "Antrodiella citrinella", process = TRUE, spec_type = "fungus") hosts.meta ## End(Not run)## Not run: fungus.meta <- meta_smml(x = "Picea abies", process = TRUE, spec_type = "plant") fungus.meta hosts.meta <- meta_smml(x = "Antrodiella citrinella", process = TRUE, spec_type = "fungus") hosts.meta ## End(Not run)
Searches and downloads substrate data from SMML Nomenclature database
substrate(x, process = TRUE)substrate(x, process = TRUE)
x |
a vector of class |
process |
logical, if |
Don't be disappointed. Not much data there. But depends on the study group, so give it try.
an object of mode list containing substrate for fungus species
Franz-Sebastian Krah
## Not run: x <- c("Polyporus_rhizophilus", "Polyporus_squamosus") subs.poly <- substrate(x, process=TRUE) subs.poly ## End(Not run)## Not run: x <- c("Polyporus_rhizophilus", "Polyporus_squamosus") subs.poly <- substrate(x, process=TRUE) subs.poly ## End(Not run)
Searches and downloads synonym data from SMML Nomenclature database
synonyms_smml(x, spec_type = c("plant", "fungus"), clean = TRUE, process = TRUE)synonyms_smml(x, spec_type = c("plant", "fungus"), clean = TRUE, process = TRUE)
x |
a vector of class |
spec_type |
a character string specifying the type of |
clean |
logical, if |
process |
logical, if |
an object of class list containing synonyms for x
Franz-Sebastian Krah
## Not run: x <- "Solanum tuberosum" synonyms_usda(x, spec_type = "plant", process = TRUE, clean = TRUE) x <- c("Phytophthora infestans", "Polyporus badius") synonyms_usda(x, spec_type = "fungus", process = TRUE, clean = TRUE) ## End(Not run)## Not run: x <- "Solanum tuberosum" synonyms_usda(x, spec_type = "plant", process = TRUE, clean = TRUE) x <- c("Phytophthora infestans", "Polyporus badius") synonyms_usda(x, spec_type = "fungus", process = TRUE, clean = TRUE) ## End(Not run)