From 8b8c3f7f2d4996e080a69252914e3ee92d76ca58 Mon Sep 17 00:00:00 2001
From: nkoenen <niklas.koenen@gmail.com>
Date: Tue, 26 Nov 2024 11:54:30 +0100
Subject: [PATCH] final changes for cran submission version 0.3.1

---
 .Rbuildignore           | 1 +
 DESCRIPTION             | 6 +++---
 R/innsight.R            | 4 ++--
 README.Rmd              | 3 ++-
 README.md               | 4 ++--
 cran-comments.md        | 3 ++-
 man/innsight-package.Rd | 4 ++--
 7 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index 120cb26..413d4c6 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -15,3 +15,4 @@
 ^vignettes/figure$
 ^vignettes/articles$
 ^codecov\.yml$
+^CRAN-SUBMISSION$
diff --git a/DESCRIPTION b/DESCRIPTION
index 04bfcb9..de1d4b6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -14,10 +14,10 @@ Description: Interpretation methods for analyzing the behavior and individual
     <doi:10.1016/j.ecolmodel.2004.03.013>, layer-wise relevance
     propagation ('LRP') described by Bach et al. (2015)
     <doi:10.1371/journal.pone.0130140>, deep learning important features
-    ('DeepLIFT') described by Shrikumar et al.  (2017) <arXiv:1704.02685>
+    ('DeepLIFT') described by Shrikumar et al.  (2017) <doi:10.48550/arXiv.1704.02685>
     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'.
+    al. (2017) <doi:10.48550/arXiv.1706.03825>, 'Gradient x Input' 
+    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
diff --git a/R/innsight.R b/R/innsight.R
index 80240d9..448a854 100644
--- a/R/innsight.R
+++ b/R/innsight.R
@@ -46,12 +46,12 @@
 #' 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)).
+#' (doi: \doi{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)
+#' \doi{10.18637/jss.v111.i08}
 #'
 "_PACKAGE"
 
diff --git a/README.Rmd b/README.Rmd
index 7bc8cca..6d27f1b 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -29,6 +29,7 @@ knitr::opts_chunk$set(
 * [Usage](#usage)
 * [Examples](#examples)
 * [Contributing and future work](#contributing-and-future-work)
+* [Citation](#citation)
 * [Funding](#funding)
 
 ## Introduction
@@ -82,7 +83,7 @@ for details).
 
 The package can be installed directly from CRAN and the development version
 from GitHub with the following commands (successful 
-installation of [`devtools`](https://www.r-project.org/nosvn/pandoc/devtools.html) is required)
+installation of [`devtools`](https://devtools.r-lib.org/) is required)
 
 ```{r, eval = FALSE}
 # Stable version
diff --git a/README.md b/README.md
index 3f4b827..b7c0772 100644
--- a/README.md
+++ b/README.md
@@ -21,6 +21,7 @@ coverage](https://codecov.io/gh/bips-hb/innsight/branch/master/graph/badge.svg)]
 - [Usage](#usage)
 - [Examples](#examples)
 - [Contributing and future work](#contributing-and-future-work)
+- [Citation](#citation)
 - [Funding](#funding)
 
 ## Introduction
@@ -80,8 +81,7 @@ for details).
 
 The package can be installed directly from CRAN and the development
 version from GitHub with the following commands (successful installation
-of [`devtools`](https://www.r-project.org/nosvn/pandoc/devtools.html) is
-required)
+of [`devtools`](https://devtools.r-lib.org/) is required)
 
 ``` r
 # Stable version
diff --git a/cran-comments.md b/cran-comments.md
index fee242c..09ba3ba 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -42,4 +42,5 @@ and disabled their execution on CRAN.
 
 #### R CMD check results
 
-There were no errors, warnings or notes.
+There were no errors, warnings or notes (only the already mentioned note on 
+the DOI).
diff --git a/man/innsight-package.Rd b/man/innsight-package.Rd
index 4d0ea32..aa952b7 100644
--- a/man/innsight-package.Rd
+++ b/man/innsight-package.Rd
@@ -62,12 +62,12 @@ described in the paper "Interpreting Deep Neural Networks with the Package
 innsight" by Koenen & Wright (2024), published in the
 \emph{Journal of Statistical Software}. For a detailed explanation of the
 methods and use cases, please refer to the publication
-(doi: \href{https://doi.org/10.18637/jss.v111.i08}{10.18637/jss.v111.i08}).
+(doi: \doi{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:
-\href{https://doi.org/10.18637/jss.v111.i08}{10.18637/jss.v111.i08}
+\doi{10.18637/jss.v111.i08}
 }
 \seealso{
 Useful links: