Prep for release

DESCRIPTION

@@ -3,10 +3,9 @@ Package: graphicalMCP
 Title: Graphical Approach for Multiple Comparison Procedures
 Version: 0.1.0
 Authors@R: c(
-    person("Dong", "Xi", , "dong.xi@gilead.com", role = c("aut", "cre")),
+    person("Dong", "Xi", , "dong.xi1@gilead.com", role = c("aut", "cre")),
     person("Ethan", "Brockmann", , "ethan.brockmann@atorusresearch.com", role = "aut"),
-    person("Gilead Biostatistics", role = c("cph", "fnd")),
-    person("Atorus Research LLC", role = "cph")
+    person("Gilead Sciences, Inc.", role = c("cph", "fnd"))
   )
 Description: A multiple comparison procedure (or multiple test procedure)
     is a a statistical analysis method for determining efficacy of
@@ -20,6 +19,8 @@ Description: A multiple comparison procedure (or multiple test procedure)
 License: Apache License (>= 2)
 URL: https://urban-sniffle-p11zlpj.pages.github.io/
 BugReports: https://github.com/Gilead-BioStats/graphicalMCP/issues
+Depends:
+    R (>= 4.1.0)
 Imports: 
     matrixStats,
     mvtnorm
@@ -49,4 +50,4 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0

R/graph_calculate_power.R

@@ -70,8 +70,7 @@
 #' # The default is to test all hypotheses with: Bonferroni testing at alpha
 #' # level .025, 0 mean under the alternative, and 0 correlation between
 #' # hypotheses under the alternative
-#' # The default of 100 simulations will usually need to be increased
-#' graph_calculate_power(par_gate, sim_n = 1e5)
+#' graph_calculate_power(par_gate, sim_n = 1e4)
 #'
 #' # But any test group/type combination that works for [graph_test_closure()]
 #' # can be used
@@ -81,7 +80,7 @@
 #'   test_groups = list(1:2, 3:4),
 #'   test_types = c("s", "p"),
 #'   test_corr = list(NA, diag(2)),
-#'   sim_n = 1e5,
+#'   sim_n = 1e4,
 #'   sim_success = list(
 #'     function(.) .[1] || .[2],
 #'     function(.) .[1] && .[2]

README.Rmd

@@ -54,12 +54,6 @@ pak::pak("Gilead-BioStats/graphicalMCP@dev")
 
 Built upon these packages, we hope to implement graphical MCPs in a more general framework, with fewer dependencies and simpler S3 classes, and without losing computational efficiency.
 
-# Citation
-
-```{r citation, results="markup"}
-citation("graphicalMCP")
-```
-
 # Acknowledgments
 
 Along with the authors and contributors, thanks to the following people for their suggestions and inspirations on the package:

README.md

@@ -57,28 +57,6 @@ Built upon these packages, we hope to implement graphical MCPs in a more
 general framework, with fewer dependencies and simpler S3 classes, and
 without losing computational efficiency.
 
-# Citation
-
-``` r
-citation("graphicalMCP")
-#> To cite graphicalMCP in publications use:
-#> 
-#>   Xi, D.; Brockmann, E. (2023). graphicalMCP: Graph-based multiple
-#>   comparison procedures. version 0.1.0. Gilead Sciences, Inc. Foster
-#>   City, California. https://github.com/Gilead-BioStats/graphicalMCP
-#> 
-#> A BibTeX entry for LaTeX users is
-#> 
-#>   @Manual{,
-#>     title = {{graphicalMCP}: Graph-based multiple comparison procedures.},
-#>     author = {Dong Xi and Ethan Brockmann},
-#>     organization = {Gilead Sciences, Inc},
-#>     note = {version 0.1.0},
-#>     year = {2023},
-#>     url = {https://github.com/Gilead-BioStats/graphicalMCP},
-#>   }
-```
-
 # Acknowledgments
 
 Along with the authors and contributors, thanks to the following people

codemeta.json

@@ -18,7 +18,7 @@
       "@type": "Person",
       "givenName": "Dong",
       "familyName": "Xi",
-      "email": "dong.xi@gilead.com"
+      "email": "dong.xi1@gilead.com"
     },
     {
       "@type": "Person",
@@ -30,7 +30,7 @@
   "copyrightHolder": [
     {
       "@type": "Organization",
-      "name": "Gilead Biostatistics"
+      "name": "Gilead Sciences, Inc."
     },
     {
       "@type": "Organization",
@@ -40,15 +40,15 @@
   "funder": [
     {
       "@type": "Organization",
-      "name": "Gilead Biostatistics"
+      "name": "Gilead Sciences, Inc."
     }
   ],
   "maintainer": [
     {
       "@type": "Person",
       "givenName": "Dong",
       "familyName": "Xi",
-      "email": "dong.xi@gilead.com"
+      "email": "dong.xi1@gilead.com"
     }
   ],
   "softwareSuggestions": [

vignettes/closed-testing.Rmd

@@ -64,7 +64,7 @@ plot_layout <- rbind(
 )
 
 plot(
-  graph_update(g, c(2, 4)),
+  g,
   layout = plot_layout,
   eps = epsilon,
   edge_curves = c(pairs = .8),