doi link bugfix

PrzeChoj · PrzeChoj · commit ff0d441490c7 · 2025-03-17T21:28:16.000+01:00
diff --git a/R/gips_class.R b/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,
-#' [Journal of Statistical Software](https://doi.org/10.18637/jss.v112.i07).
+#' [Journal of Statistical Software](<doi:10.18637/jss.v112.i07>).
 #'
 #' @returns `gips()` returns an object of
 #'     a `gips` class after the safety checks.
diff --git a/README.Rmd b/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, [Journal of Statistical Software](https://doi.org/10.18637/jss.v112.i07).
+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](<doi:10.18637/jss.v112.i07>).
 
 
 # Acknowledgment
diff --git a/README.md b/README.md
@@ -267,7 +267,7 @@ 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).
+Software](doi:10.18637/jss.v112.i07).
 
 # Acknowledgment
 
diff --git a/man/gips.Rd b/man/gips.Rd
diff --git a/vignettes/Optimizers.Rmd b/vignettes/Optimizers.Rmd
@@ -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, [Journal of Statistical Software](https://doi.org/10.18637/jss.v112.i07).
+[2] "Learning permutation symmetries with gips in R" by `gips` developers Adam Chojecki, Paweł Morgen, and Bartosz Kołodziejek, [Journal of Statistical Software](<doi:10.18637/jss.v112.i07>).
 
 ```{r options_back, include = FALSE}
 options(old_options) # back to the original options
diff --git a/vignettes/Theory.Rmd b/vignettes/Theory.Rmd
@@ -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, [Journal of Statistical Software](https://doi.org/10.18637/jss.v112.i07).
+[2] "Learning permutation symmetries with gips in R" by `gips` developers Adam Chojecki, Paweł Morgen, and Bartosz Kołodziejek, [Journal of Statistical Software](<doi:10.18637/jss.v112.i07>).
diff --git a/vignettes/gips.Rmd b/vignettes/gips.Rmd
@@ -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, [Journal of Statistical Software](https://doi.org/10.18637/jss.v112.i07).
+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](<doi: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, [Journal of Statistical Software](https://doi.org/10.18637/jss.v112.i07).
+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](<doi:10.18637/jss.v112.i07>).
 
 ```{r options_back, include = FALSE}
 options(old_options) # back to the original options

Original file line number	Diff line number	Diff line change
@@ -406,4 +406,4 @@ We will consider a `g_map` better model both in terms of the AIC and the BIC.
`406`	`406`
`407`	`407`	`[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)`
`408`	`408`
`409`		-[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).
	`409`	+[2] "Learning permutation symmetries with gips in R" by `gips` developers Adam Chojecki, Paweł Morgen, and Bartosz Kołodziejek, [Journal of Statistical Software](<doi:10.18637/jss.v112.i07>).