fix urls

R/dynamite.R

@@ -137,12 +137,12 @@
 #' @references
 #' Santtu Tikka and Jouni Helske (2024). \pkg{dynamite}: An \R Package for
 #' Dynamic Multivariate Panel Models. arXiv preprint,
-#' <https://arxiv.org/abs/2302.01607>.
+#' <doi:10.48550/arXiv.2302.01607>.
 #'
 #' Jouni Helske and Santtu Tikka (2022). Estimating Causal Effects
 #' from Panel Data with Dynamic Multivariate Panel Models.
 #' *Advances in Life Course Research*, 60, 100617.
-#' <https://doi.org/10.1016/j.alcr.2024.100617>.
+#' <doi:10.1016/j.alcr.2024.100617>.
 #' @examples
 #' data.table::setDTthreads(1) # For CRAN
 #' \donttest{

README.Rmd

@@ -47,7 +47,7 @@ The `dynamite` package is developed with the support of the Research Council of
 
 ## Installation
 
-You can install the most recent stable version of `dynamite` from [CRAN](https://cran.r-project.org/package=dynamite) or the development version from [R-universe](https://r-universe.dev/search/) by running one the following lines:
+You can install the most recent stable version of `dynamite` from [CRAN](https://cran.r-project.org/package=dynamite) or the development version from [R-universe](https://r-universe.dev/search) by running one the following lines:
 
 ```{r, eval = FALSE}
 install.packages("dynamite")

README.md

@@ -66,7 +66,7 @@ on DMPMs and the `dynamite` package, see the related papers:
 
 You can install the most recent stable version of `dynamite` from
 [CRAN](https://cran.r-project.org/package=dynamite) or the development
-version from [R-universe](https://r-universe.dev/search/) by running one
+version from [R-universe](https://r-universe.dev/search) by running one
 the following lines:
 
 ``` r
@@ -115,8 +115,8 @@ print(gaussian_example_fit)
 #> 
 #> Elapsed time (seconds):
 #>         warmup sample
-#> chain:1 10.157  6.377
-#> chain:2 10.431  5.864
+#> chain:1  7.851  5.239
+#> chain:2  8.104  4.531
 #> 
 #> Summary statistics of the time- and group-invariant parameters:
 #> # A tibble: 6 × 10

vignettes/dynamite.bib

@@ -647,7 +647,7 @@ @article{hoffman2014
   number = {47},
   pages = {1593--1623},
   year = {2014},
-  url = {http://jmlr.org/papers/v15/hoffman14a.html}
+  url = {https://jmlr.org/papers/v15/hoffman14a.html}
 }
 
 @Article{Papastamoulis2016,
@@ -713,7 +713,7 @@ @incollection{Neal2011
   title = {{MCMC} Using {Hamiltonian} Dynamics},
   booktitle={Handbook of Markov Chain Monte Carlo},
   ISBN={9780429138508},
-  url={http://dx.doi.org/10.1201/b10905},
+  url={https://dx.doi.org/10.1201/b10905},
   DOI={10.1201/b10905},
   publisher={Chapman and Hall/CRC},
   editor={Brooks, Steve and Gelman, Andrew and Jones, Galin and Meng, Xiao-Li},