more URL fixes

Author: bgoodri

R/bayes_R2.R

@@ -15,9 +15,8 @@
 #' @references
 #' Andrew Gelman, Ben Goodrich, Jonah Gabry, and Aki Vehtari (2018). R-squared
 #' for Bayesian regression models. \emph{The American Statistician}, to appear.
-#' DOI: 10.1080/00031305.2018.1549100.
-#' (\href{https://doi.org/10.1080/00031305.2018.1549100}{Journal},
-#' \href{http://www.stat.columbia.edu/~gelman/research/published/bayes_R2_v3.pdf}{Preprint},
+#' \doi{10.1080/00031305.2018.1549100}
+#' (\href{http://www.stat.columbia.edu/~gelman/research/published/bayes_R2_v3.pdf}{Preprint},
 #' \href{https://avehtari.github.io/bayes_R2/bayes_R2.html}{Notebook})
 #' 
 #' @examples

man-roxygen/reference-loo.R

@@ -3,9 +3,8 @@
 #'   Bayesian model evaluation using leave-one-out cross-validation and WAIC.
 #'   \emph{Statistics and Computing}. 27(5), 1413--1432.
 #'   doi:10.1007/s11222-016-9696-4. arXiv preprint:
-#'   \url{https://arxiv.org/abs/1507.04544/}
+#'   \url{https://arxiv.org/abs/1507.04544}
 #'
 #'   Yao, Y., Vehtari, A., Simpson, D., and Gelman, A. (2018) Using
 #'   stacking to average Bayesian predictive distributions. \emph{Bayesian
-#'   Analysis}, advance publication,  doi:10.1214/17-BA1091.
-#'   (\href{https://projecteuclid.org/euclid.ba/1516093227}{online}).
+#'   Analysis}, advance publication,  \doi{10.1214/17-BA1091}.

vignettes/pooling.Rmd

@@ -1468,7 +1468,7 @@ variable itself?  Why might this be important in inference?
 
 * Stan Development Team (2015) *Stan Modeling Language User's Guide
   and Reference Manual*.  [ [web page]
-  ](https://mc-stan.org/documentation/)
+  ](https://mc-stan.org/documentation)
 
 * Tarone, R. E. (1982) The use of historical control information in
   testing for a trend in proportions. *Biometrics* **38**(1):215--220.
@@ -1509,7 +1509,7 @@ the Stan example models repository in R format.
 Carpenter (2009) updates Efron and Morris's (1975) data set for the
 entire set of players for the entire 2006 American League season of
 Major League Baseball.  The data was originally downloaded from the
-[baseball1.com](http://www.baseball1.com/).
+[baseball1.com](https://www.seanlahman.com/).
 
 * To load: `data(bball2006, package = "rstanarm")`
 * Data Source: [https://lingpipe-blog.com/2009/09/23/bayesian-estimators-for-the-beta-binomial-model-of-batting-ability](https://lingpipe-blog.com/2009/09/23/bayesian-estimators-for-the-beta-binomial-model-of-batting-ability/)

vignettes/rstanarm.Rmd

@@ -386,7 +386,7 @@ any(summary(good_rhat)[, "Rhat"] > 1.1)
 ```
 
 Details on the computation of Rhat and some of its limitations can be found in
-[Stan Modeling Language User's Guide and Reference Manual](https://mc-stan.org/users/documentation/).
+[Stan Modeling Language User's Guide and Reference Manual](https://mc-stan.org/users/documentation).
 
 ### Divergent transitions