Merge pull request #14 from bips-hb/JSS_publication

JSS Publication

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: innsight
 Title: Get the Insights of Your Neural Network
-Version: 0.3.0
+Version: 0.3.1
 Authors@R: c(
     person("Niklas", "Koenen", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4623-8271")),
@@ -18,6 +18,8 @@ Description: Interpretation methods for analyzing the behavior and individual
     and gradient-based methods like 'SmoothGrad' described by Smilkov et
     al. (2017) <arXiv:1706.03825>, 'Gradient x Input' described by
     Baehrens et al. (2009) <arXiv:0912.1128> or 'Vanilla Gradient'.
+    Details can be found in the accompanying scientific paper: Koenen & Wright 
+    (2024, Journal of Statistical Software, <doi:10.18637/jss.v111.i08>).
 License: MIT + file LICENSE
 URL: https://bips-hb.github.io/innsight/,
     https://github.com/bips-hb/innsight/

NEWS.md

@@ -1,3 +1,8 @@
+# innsight 0.3.1
+
+* Added citation information for the accompanying scientific publication in the
+documentation and the package metadata.
+
 # innsight 0.3.0
 
 This is a minor release but does contain a range of substantial new features 

R/innsight.R

@@ -41,6 +41,17 @@
 #' It is also possible to pass an arbitrary net in form of a named list
 #' (see details in [`Converter`]).
 #'
+#' The scientific background and implementation details of `innsight` are
+#' described in the paper "Interpreting Deep Neural Networks with the Package
+#' innsight" by Koenen & Wright (2024), published in the
+#' *Journal of Statistical Software*. For a detailed explanation of the
+#' methods and use cases, please refer to the publication
+#' (doi: [10.18637/jss.v111.i08](https://doi.org/10.18637/jss.v111.i08)).
+#'
+#' @references
+#' Koenen, N., & Wright, M. N. (2024). Interpreting Deep Neural Networks with
+#' the Package innsight. Journal of Statistical Software, 111(8), 1-52. doi:
+#' [10.18637/jss.v111.i08](https://doi.org/10.18637/jss.v111.i08)
 #'
 "_PACKAGE"
 

README.Rmd

@@ -178,6 +178,24 @@ have great ideas for extending this package. Currently, we are working on the fo
 - [ ]  More examples and documentation (contact me if you have a non-trivial
 application for me)
 
+## Citation
+
+If you use this package in your research, please cite it as follows:
+
+```{}
+@Article{,
+    title = {Interpreting Deep Neural Networks with the Package {innsight}},
+    author = {Niklas Koenen and Marvin N. Wright},
+    journal = {Journal of Statistical Software},
+    year = {2024},
+    volume = {111},
+    number = {8},
+    pages = {1--52},
+    doi = {10.18637/jss.v111.i08},
+}
+```
+
+
 ## Funding
 This work is funded by the German Research Foundation (DFG) in the context
 of the Emmy Noether Grant 437611051.

README.md

@@ -180,6 +180,21 @@ this package. Currently, we are working on the following:
 - [ ] More examples and documentation (contact me if you have a
   non-trivial application for me)
 
+## Citation
+
+If you use this package in your research, please cite it as follows:
+
+    @Article{,
+        title = {Interpreting Deep Neural Networks with the Package {innsight}},
+        author = {Niklas Koenen and Marvin N. Wright},
+        journal = {Journal of Statistical Software},
+        year = {2024},
+        volume = {111},
+        number = {8},
+        pages = {1--52},
+        doi = {10.18637/jss.v111.i08},
+    }
+
 ## Funding
 
 This work is funded by the German Research Foundation (DFG) in the

cran-comments.md

@@ -1,4 +1,7 @@
-## --- `innsight` 0.3.0 ------------------------------------------------------
+## --- `innsight` 0.3.1 --------------------------------------------------------
+
+* The DOI in the CITATION is for a new JSS publication that will be registered 
+after publication on CRAN.
 
 ### Test environments with LibTorch
 * GitHub Actions (ubuntu-22.04): 4.1, 4.2, release, devel

inst/CITATION

@@ -0,0 +1,17 @@
+bibentry(bibtype = "Article",
+  title        = "Interpreting Deep Neural Networks with the Package {innsight}",
+  author       = c(person(given = "Niklas",
+                          family = "Koenen",
+                          email = "[email protected]"),
+                   person(given = c("Marvin", "N."),
+                          family = "Wright",
+                          email = "[email protected]")),
+  journal      = "Journal of Statistical Software",
+  year         = "2024",
+  volume       = "111",
+  number       = "8",
+  pages        = "1--52",
+  doi          = "10.18637/jss.v111.i08",
+  header       = "To cite innsight in publications use:"
+)
+