update page numbers for statistica sinica paper

dcgerard · Jul 6, 2021 · f7a8f4e · f7a8f4e
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diff --git a/R/ruv2.R b/R/ruv2.R
@@ -94,7 +94,7 @@
 #' \itemize{
 #'   \item{Buja, A. and Eyuboglu, N., 1992. "Remarks on parallel analysis." \emph{Multivariate behavioral research}, 27(4), pp.509-540. \doi{10.1207/s15327906mbr2704_2}}
 #'   \item{Gagnon-Bartsch, J., Laurent Jacob, and Terence P. Speed, 2013. "Removing unwanted variation from high dimensional data with negative controls." Berkeley: Department of Statistics. University of California. \url{https://statistics.berkeley.edu/tech-reports/820}}
-#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1-22. \doi{10.5705/ss.202018.0345}}
+#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1145-1166. \doi{10.5705/ss.202018.0345}}
 #' }
 vruv2 <- function(Y, X, ctl, k = NULL, cov_of_interest = ncol(X),
                   likelihood = c("t", "normal"), limmashrink = TRUE,
@@ -307,7 +307,7 @@ vruv2 <- function(Y, X, ctl, k = NULL, cov_of_interest = ncol(X),
 #' \itemize{
 #'   \item{Buja, A. and Eyuboglu, N., 1992. "Remarks on parallel analysis." \emph{Multivariate behavioral research}, 27(4), pp.509-540. \doi{10.1207/s15327906mbr2704_2}}
 #'   \item{Gagnon-Bartsch, J., Laurent Jacob, and Terence P. Speed, 2013. "Removing unwanted variation from high dimensional data with negative controls." Berkeley: Department of Statistics. University of California. \url{https://statistics.berkeley.edu/tech-reports/820}}
-#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1-22. \doi{10.5705/ss.202018.0345}}
+#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1145-1166. \doi{10.5705/ss.202018.0345}}
 #' }
 #'
 vruv2_old <- function(Y, X, ctl, k = NULL,

diff --git a/R/ruv3.R b/R/ruv3.R
@@ -94,7 +94,7 @@
 #'
 #' @references
 #' \itemize{
-#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1-22. \doi{10.5705/ss.202018.0345}}
+#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1145-1166. \doi{10.5705/ss.202018.0345}}
 #' }
 #'
 #' @examples

diff --git a/R/ruv4.R b/R/ruv4.R
@@ -163,7 +163,7 @@
 #'   \item{Buja, A. and Eyuboglu, N., 1992. "Remarks on parallel analysis." \emph{Multivariate behavioral research}, 27(4), pp.509-540. \doi{10.1207/s15327906mbr2704_2}}
 #'   \item{Efron, B., 2004. "Large-scale simultaneous hypothesis testing: the choice of a null hypothesis." \emph{Journal of the American Statistical Association}, 99(465), pp.96-104. \doi{10.1198/016214504000000089}}
 #'   \item{Gagnon-Bartsch, J., Laurent Jacob, and Terence P. Speed, 2013. "Removing unwanted variation from high dimensional data with negative controls." Berkeley: Department of Statistics. University of California. \url{https://statistics.berkeley.edu/tech-reports/820}}
-#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1-22. \doi{10.5705/ss.202018.0345}}
+#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1145-1166. \doi{10.5705/ss.202018.0345}}
 #'   \item{Wang, Jingshu, Qingyuan Zhao, Trevor Hastie, and Art B. Owen. 2017. "Confounder adjustment in multiple hypothesis testing." \emph{The Annals of Statistics} 45, no. 5: 1863-1894. \doi{10.1214/16-AOS1511}}
 #' }
 #'

diff --git a/R/ruvb.R b/R/ruvb.R
@@ -124,7 +124,7 @@
 #'
 #' @references
 #' \itemize{
-#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1-22. \doi{10.5705/ss.202018.0345}}
+#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1145-1166. \doi{10.5705/ss.202018.0345}}
 #' }
 #'
 #' @examples
@@ -376,7 +376,7 @@ prior_fun_wrapper <- function(beta_mat, prior_fun, prior_args = list()) {
 #'
 #' @references
 #' \itemize{
-#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1-22. \doi{10.5705/ss.202018.0345}}
+#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1145-1166. \doi{10.5705/ss.202018.0345}}
 #' }
 #'
 #' @export
@@ -728,7 +728,7 @@ bsvd <- function(Y21, Y31, Y32, k, nsamp = 10000,
 #' @references
 #' @references
 #' \itemize{
-#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1-22. \doi{10.5705/ss.202018.0345}}
+#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1145-1166. \doi{10.5705/ss.202018.0345}}
 #' }
 #'
 bfa_gs_linked <- function(Y21, Y31, Y32, k, nsamp = 10000,
@@ -957,7 +957,7 @@ bfa_gs_linked_gibbs_r <- function(Linit, Finit, xi_init, phi_init,
 #' @references
 #' @references
 #' \itemize{
-#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1-22. \doi{10.5705/ss.202018.0345}}
+#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1145-1166. \doi{10.5705/ss.202018.0345}}
 #' }
 #'
 bfl <- function(Y21, Y31, Y32, k, nsamp = 10000,
@@ -1201,7 +1201,7 @@ bfa_wrapper <- function(Y21, Y31, Y32, k, nsamp = 10000, burnin = round(nsamp /
 #' @references
 #' @references
 #' \itemize{
-#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1-22. \doi{10.5705/ss.202018.0345}}
+#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1145-1166. \doi{10.5705/ss.202018.0345}}
 #'   \item{Ghosh, J. and Dunson, D.B., 2009. "Default prior distributions and efficient posterior computation in Bayesian factor analysis." \emph{Journal of Computational and Graphical Statistics}, 18(2), pp.306-320. \doi{10.1198/jcgs.2009.07145}}
 #' }
 #'

diff --git a/R/ruvimpute.R b/R/ruvimpute.R
@@ -42,7 +42,7 @@
 #'
 #' @references
 #' \itemize{
-#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1-22. \doi{10.5705/ss.202018.0345}}
+#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1145-1166. \doi{10.5705/ss.202018.0345}}
 #' }
 #'
 #' @export
@@ -146,7 +146,7 @@ ruvimpute <- function(Y, X, ctl, k = NULL, impute_func = em_miss,
 #'
 #' @references
 #' \itemize{
-#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1-22. \doi{10.5705/ss.202018.0345}}
+#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1145-1166. \doi{10.5705/ss.202018.0345}}
 #' }
 #' @seealso \code{\link{ruvimpute}}, \code{\link{em_miss}}.
 ruvem <- function(Y, X, ctl, k = NULL, impute_args = list(),
@@ -484,7 +484,7 @@ hard_impute <- function(Y21, Y31, Y32, k, tol = 10 ^ -5, maxit = 1000,
 #'
 #' @references
 #' \itemize{
-#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1-22. \doi{10.5705/ss.202018.0345}}
+#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1145-1166. \doi{10.5705/ss.202018.0345}}
 #' }
 #'
 #' @author David Gerard

diff --git a/R/vicar.R b/R/vicar.R
@@ -38,7 +38,7 @@
 #' @references
 #' \itemize{
 #'   \item{Gerard, D., and Stephens, M. 2020. "Empirical Bayes shrinkage and false discovery rate estimation, allowing for unwanted variation", \emph{Biostatistics}, 21(1), 15-32 \doi{10.1093/biostatistics/kxy029}}
-#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1-22. \doi{10.5705/ss.202018.0345}}
+#'   \item{Gerard, David, and Matthew Stephens. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls." \emph{Statistica Sinica}, 31(3), 1145-1166. \doi{10.5705/ss.202018.0345}}
 #' }
 #'
 #' @useDynLib vicar

diff --git a/README.Rmd b/README.Rmd
@@ -72,7 +72,7 @@ Check out [NEWS.md](NEWS.md) to see what's new with each version.
 
 If you use any of the control-gene based methods, please cite:
 
-> Gerard, D., & Stephens, M. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls". *Statistica Sinica*, 31(3), 1-22 <[doi:10.5705/ss.202018.0345](https://doi.org/10.5705/ss.202018.0345)>.
+> Gerard, D., & Stephens, M. 2021. "Unifying and Generalizing Methods for Removing Unwanted Variation Based on Negative Controls". *Statistica Sinica*, 31(3), 1145-1166 <[doi:10.5705/ss.202018.0345](https://doi.org/10.5705/ss.202018.0345)>.
 
 Or, using BibTex:
 ``` tex
@@ -83,7 +83,7 @@ Or, using BibTex:
   doi={10.5705/ss.202018.0345},
   volume={31},
   number={3},
-  pages={1--22},
+  pages={1145--1166},
   year={2021}
 }
 ```

diff --git a/README.md b/README.md
@@ -75,7 +75,7 @@ If you use any of the control-gene based methods, please cite:
 
 > Gerard, D., & Stephens, M. 2021. “Unifying and Generalizing Methods
 > for Removing Unwanted Variation Based on Negative Controls.”
-> *Statistica Sinica*, 31(3), 1-22
+> *Statistica Sinica*, 31(3), 1145-1166
 > &lt;[doi:10.5705/ss.202018.0345](https://doi.org/10.5705/ss.202018.0345)&gt;.
 
 Or, using BibTex:
@@ -88,7 +88,7 @@ Or, using BibTex:
   doi={10.5705/ss.202018.0345},
   volume={31},
   number={3},
-  pages={1--22},
+  pages={1145--1166},
   year={2021}
 }
 ```
@@ -224,8 +224,8 @@ estimation, allowing for unwanted variation</span>.” *Biostatistics* 21
 <div id="ref-gerard2021unifying" class="csl-entry">
 
 ———. 2021. “Unifying and Generalizing Methods for Removing Unwanted
-Variation Based on Negative Controls.” *Statistica Sinica* 31 (3): 1–22.
-<https://doi.org/10.5705/ss.202018.0345>.
+Variation Based on Negative Controls.” *Statistica Sinica* 31 (3):
+1145–66. <https://doi.org/10.5705/ss.202018.0345>.
 
 </div>
 

diff --git a/docs/articles/customFA.html b/docs/articles/customFA.html
diff --git a/docs/articles/customFA_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/customFA_files/figure-html/unnamed-chunk-4-1.png
diff --git a/docs/articles/customFA_files/figure-html/unnamed-chunk-7-1.png b/docs/articles/customFA_files/figure-html/unnamed-chunk-7-1.png
diff --git a/docs/articles/customFA_files/header-attrs-2.9/header-attrs.js b/docs/articles/customFA_files/header-attrs-2.9/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});
diff --git a/docs/articles/custom_prior.html b/docs/articles/custom_prior.html
diff --git a/docs/articles/custom_prior_files/header-attrs-2.9/header-attrs.js b/docs/articles/custom_prior_files/header-attrs-2.9/header-attrs.js
@@ -0,0 +1,12 @@
+// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
+// be compatible with the behavior of Pandoc < 2.8).
+document.addEventListener('DOMContentLoaded', function(e) {
+  var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
+  var i, h, a;
+  for (i = 0; i < hs.length; i++) {
+    h = hs[i];
+    if (!/^h[1-6]$/i.test(h.tagName)) continue;  // it should be a header h1-h6
+    a = h.attributes;
+    while (a.length > 0) h.removeAttribute(a[0].name);
+  }
+});