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README.rmd
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---
output:
md_document:
variant: markdown_github
---
<!-- README.md is generated from README.rmd. Please edit that file -->
# RPhenoscape: Semantically rich phenotypic traits from the Phenoscape Knowledgebase
[](https://app.circleci.com/pipelines/github/phenoscape/rphenoscape)
- 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.
## Installation
The development version of RPhenoscape is available on [Github](https://github.com/phenoscape/rphenoscape). 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()`):
```{r compile-settings, include=FALSE}
## Set the paths for cache and figure
library(knitr)
opts_chunk$set(cache = 1)
basename <- gsub(".Rmd", "", knitr:::knit_concord$get('infile'))
opts_chunk$set(fig.path = paste("figure/", basename, "-", sep=""),
cache.path = paste("cache/", basename, "/", sep=""))
```
```{r, echo=FALSE}
library(knitr)
opts_knit$set(upload.fun = imgur_upload)
opts_chunk$set(tidy=FALSE, warning=FALSE, message=FALSE, comment = NA, verbose = TRUE)
```
```{r eval = FALSE}
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.
```{r}
packageVersion("remotes")
```
If the version is 2.1.0 or higher, use the `build_vignettes` parameter (which by default is FALSE):
```{r, eval = FALSE}
remotes::install_github("phenoscape/rphenoscape", build_vignettes = TRUE)
```
If the version of `remotes` is lower, use the `build_opts` parameter:
```{r, eval = FALSE}
remotes::install_github("phenoscape/rphenoscape", build_opts=c("--no-manual"))
```
Once installed, the package can be loaded ("attached") as any other R package:
```{r}
library(rphenoscape)
```
### Upgrading from an earlier version
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.
## Package Usage Information
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 [.Renviron] on how to control environment variables at R session startup.)
---
[](http://kb.phenoscape.org)
[Use cases]: https://github.com/phenoscape/rphenoscape/wiki/User-Stories
[CRAN]: https://cran.r-project.org
[Phenoscape Knowledgebase API]: https://kb.phenoscape.org/api/v2/docs/
[R Startup]: https://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html
[.Renviron]: https://bookdown.org/csgillespie/efficientR/set-up.html#renviron