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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | ||
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
| on: | ||
| push: | ||
| branches: [main, master] | ||
| pull_request: | ||
| branches: [main, master] | ||
|
|
||
| name: R-CMD-check | ||
|
|
||
| jobs: | ||
| R-CMD-check: | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| R_KEEP_PKG_SOURCE: yes | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
|
|
||
| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
|
|
||
| - uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: any::rcmdcheck | ||
| needs: check | ||
|
|
||
| - uses: r-lib/actions/check-r-package@v2 |
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| # nat.templatebrains | ||
| <!-- badges: start --> | ||
| [](https://natverse.org) | ||
| [](https://natverse.org/nat.templatebrains/reference/) | ||
| [](https://CRAN.R-project.org/package=nat.templatebrains) | ||
| [](https://github.com/natverse/nat.templatebrains/releases/latest) | ||
| [](https://app.travis-ci.com/natverse/nat.templatebrains) | ||
| [](https://coveralls.io/github/natverse/nat.templatebrains) | ||
| [](https://lifecycle.r-lib.org/articles/stages.html#stable) | ||
| [](https://www.r-pkg.org/pkg/nat.templatebrains) | ||
| <!-- badges: end --> | ||
|
|
||
| ## Quick Start | ||
|
|
||
| For the impatient ... | ||
|
|
||
| ```r | ||
| # install | ||
| install.packages("nat.templatebrains") | ||
|
|
||
| # use | ||
| library(nat.templatebrains) | ||
|
|
||
| # basic examples for templatebrain class | ||
| example("as.templatebrain") | ||
| example("templatebrain-meths") | ||
|
|
||
| # run examples for mirroring | ||
| example("mirror_brain") | ||
| # ... and bridging | ||
| # NB you need to install nat.flybrains package to run some examples which are | ||
| # not run by default | ||
| example("xform_brain") | ||
|
|
||
| # get overview help for package | ||
| ?nat.templatebrains | ||
| # help for main functions | ||
| ?mirror_brain | ||
| ?xform_brain | ||
| # if you want to construct your own templatebrains | ||
| ?templatebrain | ||
|
|
||
| # run tests | ||
| library(testthat) | ||
| test_package("nat.templatebrains") | ||
| ``` | ||
|
|
||
| **nat.templatebrains** provides additional functions for use with the [NeuroAnatomy Toolbox](https://natverse.org/nat/) (nat). In particular, it defines the notion of a template brain, as used in image registration of 3D data, along with bridging registrations between template brains (see https://github.com/jefferislab/BridgingRegistrations) and mirroring registrations from one brain hemisphere to the other. | ||
|
|
||
| This is a generic package, usable with data from any species. For _Drosophila_ specific functions and data, see our [nat.flybrains](https://github.com/natverse/nat.flybrains) package. Installing/loading **nat.flybrains** will automatically | ||
| install/load **nat.templatebrains**. | ||
|
|
||
| ## Installation | ||
| This package has now been released to CRAN (since v0.4.1), but since there are | ||
| regular updates between CRAN releases we generally recommend that you install | ||
| the development version from GitHub. | ||
|
|
||
| ### CRAN release | ||
| ```r | ||
| install.packages("nat.templatebrains") | ||
| ``` | ||
|
|
||
| ### Development version | ||
| If you want to install the development version of nat.templatebrains, you can do | ||
| this using devtools. You will probably also wish to install the development | ||
| version of the nat package if you do this. | ||
|
|
||
| ```r | ||
| if (!require("remotes")) install.packages("remotes") | ||
| remotes::install_github("natverse/nat") | ||
| remotes::install_github("natverse/nat.templatebrains") | ||
| ``` | ||
|
|
||
| Note: Windows users may need [Rtools](https://www.murdoch-sutherland.com/Rtools/) as | ||
| well as [remotes](https://CRAN.R-project.org/package=remotes) to install this way. | ||
| # nat.templatebrains | ||
| <!-- badges: start --> | ||
| [](https://natverse.org) | ||
| [](https://natverse.org/nat.templatebrains/reference/) | ||
| [](https://CRAN.R-project.org/package=nat.templatebrains) | ||
| [](https://github.com/natverse/nat.templatebrains/releases/latest) | ||
| [](https://github.com/natverse/nat.templatebrains/actions/workflows/R-CMD-check.yaml) | ||
| [](https://coveralls.io/github/natverse/nat.templatebrains) | ||
| [](https://lifecycle.r-lib.org/articles/stages.html#stable) | ||
| [](https://www.r-pkg.org/pkg/nat.templatebrains) | ||
| <!-- badges: end --> | ||
|
|
||
| ## Quick Start | ||
|
|
||
| For the impatient ... | ||
|
|
||
| ```r | ||
| # install | ||
| install.packages("nat.templatebrains") | ||
|
|
||
| # use | ||
| library(nat.templatebrains) | ||
|
|
||
| # basic examples for templatebrain class | ||
| example("as.templatebrain") | ||
| example("templatebrain-meths") | ||
|
|
||
| # run examples for mirroring | ||
| example("mirror_brain") | ||
| # ... and bridging | ||
| # NB you need to install nat.flybrains package to run some examples which are | ||
| # not run by default | ||
| example("xform_brain") | ||
|
|
||
| # get overview help for package | ||
| ?nat.templatebrains | ||
| # help for main functions | ||
| ?mirror_brain | ||
| ?xform_brain | ||
| # if you want to construct your own templatebrains | ||
| ?templatebrain | ||
|
|
||
| # run tests | ||
| library(testthat) | ||
| test_package("nat.templatebrains") | ||
| ``` | ||
|
|
||
| **nat.templatebrains** provides additional functions for use with the [NeuroAnatomy Toolbox](https://natverse.org/nat/) (nat). In particular, it defines the notion of a template brain, as used in image registration of 3D data, along with bridging registrations between template brains (see https://github.com/jefferislab/BridgingRegistrations) and mirroring registrations from one brain hemisphere to the other. | ||
|
|
||
| This is a generic package, usable with data from any species. For _Drosophila_ specific functions and data, see our [nat.flybrains](https://github.com/natverse/nat.flybrains) package. Installing/loading **nat.flybrains** will automatically | ||
| install/load **nat.templatebrains**. | ||
|
|
||
| ## Installation | ||
| This package has now been released to CRAN (since v0.4.1), but since there are | ||
| regular updates between CRAN releases we generally recommend that you install | ||
| the development version from GitHub. | ||
|
|
||
| ### CRAN release | ||
| ```r | ||
| install.packages("nat.templatebrains") | ||
| ``` | ||
|
|
||
| ### Development version | ||
| If you want to install the development version of nat.templatebrains, you can do | ||
| this using devtools. You will probably also wish to install the development | ||
| version of the nat package if you do this. | ||
|
|
||
| ```r | ||
| if (!require("remotes")) install.packages("remotes") | ||
| remotes::install_github("natverse/nat") | ||
| remotes::install_github("natverse/nat.templatebrains") | ||
| ``` | ||
|
|
||
| Note: Windows users may need [Rtools](https://www.murdoch-sutherland.com/Rtools/) as | ||
| well as [remotes](https://CRAN.R-project.org/package=remotes) to install this way. |