- Author: Hong Xu, Hilmar Lapp, John Bradley
- Maintainer: Hilmar Lapp
Most of the services provided with the Phenoscape Knowledgebase API return data in JSON format, plain text (usually tab-delimited), and NeXML. This package facilitates interfacing with the Phenoscape Knowledgebase for searching ontology terms, retrieving term info, and querying data matrices.
The development version of RPhenoscape is available on
Github. It has not yet been
released to CRAN. To install RPhenoscape
from Github, use the install_github()
function in the remotes
package (which can be installed from CRAN using install.packages()
):
remotes::install_github("phenoscape/rphenoscape")
By default, this will skip building the package vignettes. To build and
install package vignettes as well, you must have recent versions of the
knitr
and rmarkdown
packages installed, and use additional
parameters, depending on the version of the remotes
package you have
installed, to request building vignettes.
packageVersion("remotes")
## [1] '2.4.2'
If the version is 2.1.0 or higher, use the build_vignettes
parameter
(which by default is FALSE):
remotes::install_github("phenoscape/rphenoscape", build_vignettes = TRUE)
If the version of remotes
is lower, use the build_opts
parameter:
remotes::install_github("phenoscape/rphenoscape", build_opts=c("--no-manual"))
Once installed, the package can be loaded (“attached”) as any other R package:
library(rphenoscape)
Until v1.x is released, upgrades from one minor (patch) release to another, i.e., from v0.x.n to v0.x.m where m > n, can be expected to be fully backwards compatible. Upgrading to a new major release, i.e., from v0.n.x to v0.m.y, where m > n, should be expected to be at least in part backwards incompatible.
A backwards incompatible change may result in deprecation warnings being issued, or errors when using a no longer supported function. Whenever possible, we will try to provide a deprecation path. Function or arguments that are deprecated in one major release may be dropped and thus result in an error in the next major release.
Specifically, upgrading from v0.2.x to v0.3.y includes a number of backwards incompatible changes, including a large-scale streamlining and restructuring of the function API.
The functionality and operations of the RPhenoscape package can be viewed on the dedicated package website: http://rphenoscape.phenoscape.org/
Use cases described there include the following:
- Using OntoTrace to obtain a character matrix
- Obtaining the character matrices for studies published for a taxonomic clade
- Subsetting matrices by taxonomic subgroup or anatomical part
- Searching for details for a given taxon
By definition, most functions in this package connect to the Phenoscape
Knowledgebase API. The base URL
path to the API endpoints can changed from the default by setting the
PHENOSCAPE_API
environment variable. (See R
Startup
and RStudio support on
.Renviron
on how to control environment variables at R session startup.)