Update email and paper details

Author: kkbrum

.Rbuildignore

@@ -7,3 +7,4 @@
 ^README\.Rmd$
 ^codecov\.yml$
 ^CRAN-SUBMISSION$
+^revdep$

DESCRIPTION

@@ -1,17 +1,17 @@
 Package: optrefine
 Title: Optimally Refine Strata
-Version: 1.0.1
+Version: 1.1.1
 Authors@R: 
-    person("Katherine", "Brumberg", , "kbrum@wharton.upenn.edu", role = c("aut", "cre"),
+    person("Katherine", "Brumberg", , "kbrum@umich.edu", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-5193-6250"))
-Description: Splits initial strata into refined strata that optimize covariate balance. For more information, please email the author for a copy of the accompanying manuscript. To solve the linear program, the 'Gurobi' commercial optimization software is recommended, but not required. The 'gurobi' R package can be installed following the instructions at <https://www.gurobi.com/documentation/9.1/refman/ins_the_r_package.html>.
-URL: https://github.com/kkbrum/optrefine, https://kkbrum.github.io/optrefine/, https://www.gurobi.com/documentation/9.1/refman/ins_the_r_package.html
+Description: Splits initial strata into refined strata that optimize covariate balance. For more information, please see Brumberg, Small, and Rosenbaum (2024) <doi:10.1093/biomtc/ujae061>. To solve the linear program, the 'Gurobi' commercial optimization software is recommended, but not required. The 'gurobi' R package can be installed following the instructions at <https://docs.gurobi.com/projects/optimizer/en/current/reference/r/setup.html> after claiming your free academic license at <https://www.gurobi.com/academia/academic-program-and-licenses/>.
+URL: https://github.com/kkbrum/optrefine, https://kkbrum.github.io/optrefine/
 BugReports: https://github.com/kkbrum/optrefine/issues
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Depends: 
     R (>= 2.10),
     MASS,

NEWS.md

@@ -1,4 +1,8 @@
-# optrefine 1.0.0
+# optrefine 1.1.1
+
+* Updated author email and citations.
+
+# optrefine 1.1.0
 
 * Added a couple more possible elements to the `options` argument to the `refine` function. These are `minsplit` for the minimum number of treated or control units to allow in a split stratum and `threads` for the number of threads to use in the optimization.
 * Changed the value of `details$valueLP` to `NA` if the integer program was solved instead of giving the same value as `details$valueIP`.

cran-comments.md

@@ -1,11 +1,10 @@
-## Minor release
-This is a minor release. In this version I have:
-* Added a couple more possible elements to the `options` argument to the `refine` function. These are `minsplit` for the minimum number of treated or control units to allow in a split stratum and `threads` for the number of threads to use in the optimization.
+## Patch
+This is a patch to update my email address and paper details. Nothing else has changed.
 
 I am unable to fix the NOTE about 'gurobi' not being available for checking since it is a commercial software and the R package must be downloaded from their website. However, it is only suggested and the package works without it. Installation instructions for the R package 'gurobi' are in the description of the package.
 
 ## Test environments
-- local macOS install, R 4.2.2
+- local macOS install, R 4.5.2
 - macOS builder
 - win-builder (devel and release)
 - github actions:
@@ -21,7 +20,7 @@ There were no ERRORs or WARNINGs.
 There were 2 NOTEs:
 
  * checking CRAN incoming feasibility ... NOTE
-Maintainer: 'Katherine Brumberg <kbrum@wharton.upenn.edu>'
+Maintainer: 'Katherine Brumberg <kbrum@umich.edu>'
 
 Suggests or Enhances not in mainstream repositories:
   gurobi

inst/CITATION

@@ -0,0 +1,40 @@
+citHeader("To cite optrefine in publications use:")
+
+citEntry(entry = "Manual",
+         title = "optrefine: Optimally Refine Strata",
+         author = personList(
+           person("Katherine", "Brumberg", 
+                  email = "kbrum@umich.edu",
+                  role = c("aut", "cre"),
+                  comment = c(ORCID = "0000-0002-5193-6250"))
+         ),
+         year = "2024",
+         note = paste("R package version", packageVersion("optrefine")),
+         url = "https://github.com/kkbrum/optrefine",
+         textVersion = paste("Brumberg K (2024).",
+                            "optrefine: Optimally Refine Strata.",
+                            "R package version", packageVersion("optrefine"),
+                            "https://github.com/kkbrum/optrefine"))
+
+citHeader("To cite the accompanying paper, please use:")
+
+citEntry(entry = "Article",
+         title = "Optimal refinement of strata to balance covariates",
+         author = personList(
+           person("Katherine", "Brumberg", role = "aut",
+                  comment = c(ORCID = "0000-0002-5193-6250")),
+           person("Dylan S", "Small", role = "aut"),
+           person("Paul R", "Rosenbaum", role = "aut")
+         ),
+         journal = "Biometrics",
+         year = "2024",
+         volume = "80",
+         number = "3",
+         pages = "ujae061",
+         doi = "10.1093/biomtc/ujae061",
+         url = "https://academic.oup.com/biometrics/article/80/3/ujae061/7712595",
+         textVersion = paste("Brumberg K, Small DS, Rosenbaum PR (2024).",
+                            "Optimal refinement of strata to balance covariates.",
+                            "Biometrics, 80(3), ujae061.",
+                            "doi:10.1093/biomtc/ujae061"))
+

tests/testthat/test-refine.R

@@ -93,7 +93,7 @@ test_that("IP combo obj value calculated correctly", {
   n_st_used <- sum(table(ref$refined_strata) != 0)
   smds <- calc_smds(z = ref$z, X = ref$X, refined_strata = ref$refined_strata, abs = TRUE)
   obj <- (sum(smds$refined, na.rm = TRUE) +
-            wMax * sum(sapply(1:4, function(x) {max(smds$refined[(2*x-1):(2*x), ], na.rm = TRUE)}))) /
+            wMax * sum(sapply(1:nstrata, function(x) {max(smds$refined[(2*x-1):(2*x), ], na.rm = TRUE)}))) /
     ((ncov+1)*n_st_used + nstrata * wMax)
   expect_equal(ref$details$valueIP, obj)
 })