Add reference to new JSS article

Author: PrzeChoj

Diff for: DESCRIPTION

@@ -16,7 +16,10 @@ Description: Find the permutation symmetry group such that the covariance
     the covariance matrix found with 'gips' approximates the actual
     covariance with less statistical error. The methods implemented in
     this package are described in Graczyk et al. (2022)
-    <doi:10.1214/22-AOS2174>.
+    <doi:10.1214/22-AOS2174>. Documentation about 'gips' is
+    provided via its website at <https://przechoj.github.io/gips/> and
+    the paper by Chojecki, Morgen, Kołodziejek
+    (2025, <doi:10.18637/jss.v112.i07>).
 License: GPL (>= 3)
 URL: https://github.com/PrzeChoj/gips, https://przechoj.github.io/gips/
 BugReports: https://github.com/PrzeChoj/gips/issues

Diff for: R/gips_class.R

@@ -68,7 +68,7 @@
 #' For analysis of the Hyperparameters influence, see **Section 3.2.**
 #' of "Learning permutation symmetries with gips in R"
 #' by `gips` developers Adam Chojecki, Paweł Morgen, and Bartosz Kołodziejek,
-#' available on [arXiv:2307.00790](https://arxiv.org/abs/2307.00790).
+#' [Journal of Statistical Software](https://doi.org/10.18637/jss.v112.i07).
 #'
 #' @returns `gips()` returns an object of
 #'     a `gips` class after the safety checks.

Diff for: README.Rmd

@@ -228,7 +228,7 @@ Note that the rank of the `S` matrix was 4, while the rank of the `S_projected`
 
 For more examples and introduction, see `vignette("gips", package="gips")` or its [pkgdown page](https://przechoj.github.io/gips/articles/gips.html).
 
-For an in-depth analysis of the package performance, capabilities, and comparison with similar packages, see the article "Learning permutation symmetries with gips in R" by `gips` developers Adam Chojecki, Paweł Morgen, and Bartosz Kołodziejek, available on [arXiv:2307.00790](https://arxiv.org/abs/2307.00790).
+For an in-depth analysis of the package performance, capabilities, and comparison with similar packages, see the article "Learning permutation symmetries with gips in R" by `gips` developers Adam Chojecki, Paweł Morgen, and Bartosz Kołodziejek, [Journal of Statistical Software](https://doi.org/10.18637/jss.v112.i07).
 
 
 # Acknowledgment

Diff for: README.md

@@ -266,8 +266,8 @@ page](https://przechoj.github.io/gips/articles/gips.html).
 For an in-depth analysis of the package performance, capabilities, and
 comparison with similar packages, see the article “Learning permutation
 symmetries with gips in R” by `gips` developers Adam Chojecki, Paweł
-Morgen, and Bartosz Kołodziejek, available on
-[arXiv:2307.00790](https://arxiv.org/abs/2307.00790).
+Morgen, and Bartosz Kołodziejek, [Journal of Statistical
+Software](https://doi.org/10.18637/jss.v112.i07).
 
 # Acknowledgment
 

Diff for: cran-comments.md

@@ -14,3 +14,8 @@ Testing with `devtools::check_rhub()` - no Errors, no Warnings, only technical N
 0 errors | 0 warnings | 0 notes
 
 R CMD check succeeded
+
+
+## Citation Information
+
+The DOI in the CITATION is for a new JSS publication that will be registered after publication on CRAN.

Diff for: inst/CITATION

@@ -0,0 +1,19 @@
+bibentry(bibtype = "Article",
+  title        = "Learning Permutation Symmetry of a {G}aussian Vector with {gips} in {R}",
+  author       = c(person(given = "Adam",
+                          family = "Chojecki",
+                          email = "[email protected]"),
+                   person(given = "Pawe{\\l}",
+                          family = "Morgen",
+                          email = "[email protected]"),
+                   person(given = "Bartosz",
+                          family = "Ko{\\l}odziejek",
+                          email = "[email protected]")),
+  journal      = "Journal of Statistical Software",
+  year         = "2025",
+  volume       = "112",
+  number       = "7",
+  pages        = "1--38",
+  doi          = "10.18637/jss.v112.i07",
+  header       = "To cite gips in publications use:"
+)

Diff for: inst/WORDLIST

@@ -52,6 +52,7 @@ frac
 ge
 iter
 iteratively
+jss
 ldots
 le
 mapsto

Diff for: man/figures/README-example_mean_known1_1-1.png

@@ -367,7 +367,7 @@ We encourage everyone to discuss on available and potential new optimizers on [I
 
 [1] Piotr Graczyk, Hideyuki Ishi, Bartosz Kołodziejek, Hélène Massam. "Model selection in the space of Gaussian models invariant by symmetry." The Annals of Statistics, 50(3) 1747-1774 June 2022. [arXiv link](https://arxiv.org/abs/2004.03503); [DOI: 10.1214/22-AOS2174](https://doi.org/10.1214/22-AOS2174)
 
-[2] "Learning permutation symmetries with gips in R" by `gips` developers Adam Chojecki, Paweł Morgen, and Bartosz Kołodziejek, available on [arXiv:2307.00790](https://arxiv.org/abs/2307.00790).
+[2] "Learning permutation symmetries with gips in R" by `gips` developers Adam Chojecki, Paweł Morgen, and Bartosz Kołodziejek, [Journal of Statistical Software](https://doi.org/10.18637/jss.v112.i07).
 
 ```{r options_back, include = FALSE}
 options(old_options) # back to the original options

Diff for: man/figures/README-example_mean_known3_1-1.png

@@ -406,4 +406,4 @@ We will consider a `g_map` better model both in terms of the AIC and the BIC.
 
 [1] Piotr Graczyk, Hideyuki Ishi, Bartosz Kołodziejek, Hélène Massam. "Model selection in the space of Gaussian models invariant by symmetry." The Annals of Statistics, 50(3) 1747-1774 June 2022. [arXiv link](https://arxiv.org/abs/2004.03503); [DOI: 10.1214/22-AOS2174](https://doi.org/10.1214/22-AOS2174)
 
-[2] "Learning permutation symmetries with gips in R" by `gips` developers Adam Chojecki, Paweł Morgen, and Bartosz Kołodziejek, available on [arXiv:2307.00790](https://arxiv.org/abs/2307.00790).
+[2] "Learning permutation symmetries with gips in R" by `gips` developers Adam Chojecki, Paweł Morgen, and Bartosz Kołodziejek, [Journal of Statistical Software](https://doi.org/10.18637/jss.v112.i07).

Diff for: man/figures/README-example_mean_known6-1.png

@@ -58,7 +58,7 @@ We propose creating a set of constraints on the covariance matrix to use the max
 
 This package provides a way to find a *reasonable* permutation to be used as a constraint in covariance matrix estimation. In this case, *reasonable* means maximizing the Bayesian posterior distribution when using a Wishart-like distribution on symmetric, positive definite matrices as a prior. The idea, exact formulas, and algorithm sketch are explored in another vignette that can be accessed by `vignette("Theory", package="gips")` or on its [pkgdown page](https://przechoj.github.io/gips/articles/Theory.html).
 
-For an in-depth analysis of the package performance, capabilities, and comparison with other packages, see the article "Learning permutation symmetries with gips in R" by `gips`' developers Adam Chojecki, Paweł Morgen, and Bartosz Kołodziejek, available on [arXiv:2307.00790](https://arxiv.org/abs/2307.00790).
+For an in-depth analysis of the package performance, capabilities, and comparison with other packages, see the article "Learning permutation symmetries with gips in R" by `gips`' developers Adam Chojecki, Paweł Morgen, and Bartosz Kołodziejek, [Journal of Statistical Software](https://doi.org/10.18637/jss.v112.i07).
 
 
 # Practical example
@@ -239,7 +239,7 @@ Now, the estimated covariance matrix is of full rank (5).
 
 1. To learn more about the available optimizers in `find_MAP()` and how to use those, see `vignette("Optimizers", package="gips")` or its [pkgdown page](https://przechoj.github.io/gips/articles/Optimizers.html).
 2. To learn more about the math and theory behind the `gips` package, see `vignette("Theory", package="gips")` or its [pkgdown page](https://przechoj.github.io/gips/articles/Theory.html).
-3. For an in-depth analysis of the package performance, capabilities, and comparison with other packages, see the article "Learning permutation symmetries with gips in R" by `gips` developers Adam Chojecki, Paweł Morgen, and Bartosz Kołodziejek, available on [arXiv:2307.00790](https://arxiv.org/abs/2307.00790).
+3. For an in-depth analysis of the package performance, capabilities, and comparison with other packages, see the article "Learning permutation symmetries with gips in R" by `gips` developers Adam Chojecki, Paweł Morgen, and Bartosz Kołodziejek, [Journal of Statistical Software](https://doi.org/10.18637/jss.v112.i07).
 
 ```{r options_back, include = FALSE}
 options(old_options) # back to the original options