From 7db6f8ee78b43c1faee250ea532f12a1751a7f90 Mon Sep 17 00:00:00 2001 From: EeethB Date: Thu, 21 Dec 2023 09:19:57 -0600 Subject: [PATCH 1/5] Update to prep for release --- DESCRIPTION | 2 +- R/graph_calculate_power.R | 5 ++--- codemeta.json | 4 ++-- 3 files changed, 5 insertions(+), 6 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 96ba6c12..040e9d2a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,7 +3,7 @@ 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") diff --git a/R/graph_calculate_power.R b/R/graph_calculate_power.R index ea85b3ef..4c192e5e 100644 --- a/R/graph_calculate_power.R +++ b/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] diff --git a/codemeta.json b/codemeta.json index 0b3b1b03..5c5d01be 100644 --- a/codemeta.json +++ b/codemeta.json @@ -18,7 +18,7 @@ "@type": "Person", "givenName": "Dong", "familyName": "Xi", - "email": "dong.xi@gilead.com" + "email": "dong.xi1@gilead.com" }, { "@type": "Person", @@ -48,7 +48,7 @@ "@type": "Person", "givenName": "Dong", "familyName": "Xi", - "email": "dong.xi@gilead.com" + "email": "dong.xi1@gilead.com" } ], "softwareSuggestions": [ From 32fb9c2456b649d42a5e0edd0e8a57a9e82da606 Mon Sep 17 00:00:00 2001 From: EeethB Date: Tue, 26 Dec 2023 13:52:17 -0600 Subject: [PATCH 2/5] Make a variety of secretarial changes --- DESCRIPTION | 4 +++- README.Rmd | 6 ------ README.md | 22 ---------------------- codemeta.json | 4 ++-- man/graph_calculate_power.Rd | 5 ++--- man/graphicalMCP-package.Rd | 4 ++-- 6 files changed, 9 insertions(+), 36 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 040e9d2a..0874b773 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,7 +5,7 @@ Version: 0.1.0 Authors@R: c( 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("Gilead Sciences, Inc.", role = c("cph", "fnd")), person("Atorus Research LLC", role = "cph") ) Description: A multiple comparison procedure (or multiple test procedure) @@ -20,6 +20,8 @@ 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 (>= 3.5.0) Imports: matrixStats, mvtnorm diff --git a/README.Rmd b/README.Rmd index 68fb1887..6b326b0a 100644 --- a/README.Rmd +++ b/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: diff --git a/README.md b/README.md index b1993343..91d38691 100644 --- a/README.md +++ b/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 diff --git a/codemeta.json b/codemeta.json index 5c5d01be..5c4258dc 100644 --- a/codemeta.json +++ b/codemeta.json @@ -30,7 +30,7 @@ "copyrightHolder": [ { "@type": "Organization", - "name": "Gilead Biostatistics" + "name": "Gilead Sciences, Inc." }, { "@type": "Organization", @@ -40,7 +40,7 @@ "funder": [ { "@type": "Organization", - "name": "Gilead Biostatistics" + "name": "Gilead Sciences, Inc." } ], "maintainer": [ diff --git a/man/graph_calculate_power.Rd b/man/graph_calculate_power.Rd index 42f85881..0a1cf4e4 100644 --- a/man/graph_calculate_power.Rd +++ b/man/graph_calculate_power.Rd @@ -101,8 +101,7 @@ par_gate <- simple_successive_1() # 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 @@ -112,7 +111,7 @@ graph_calculate_power( 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] diff --git a/man/graphicalMCP-package.Rd b/man/graphicalMCP-package.Rd index 186651a8..72595005 100644 --- a/man/graphicalMCP-package.Rd +++ b/man/graphicalMCP-package.Rd @@ -19,7 +19,7 @@ Useful links: } \author{ -\strong{Maintainer}: Dong Xi \email{dong.xi@gilead.com} +\strong{Maintainer}: Dong Xi \email{dong.xi1@gilead.com} Authors: \itemize{ @@ -28,7 +28,7 @@ Authors: Other contributors: \itemize{ - \item Gilead Biostatistics [copyright holder, funder] + \item Gilead Sciences, Inc. [copyright holder, funder] \item Atorus Research LLC [copyright holder] } From 3e91b2405e799f477ab393a5c02b377d329a65be Mon Sep 17 00:00:00 2001 From: EeethB Date: Tue, 26 Dec 2023 22:12:49 +0000 Subject: [PATCH 3/5] Update R dependency --- DESCRIPTION | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0874b773..f3a4f8e3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,8 +5,7 @@ Version: 0.1.0 Authors@R: c( person("Dong", "Xi", , "dong.xi1@gilead.com", role = c("aut", "cre")), person("Ethan", "Brockmann", , "ethan.brockmann@atorusresearch.com", role = "aut"), - person("Gilead Sciences, Inc.", 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 @@ -21,7 +20,7 @@ License: Apache License (>= 2) URL: https://urban-sniffle-p11zlpj.pages.github.io/ BugReports: https://github.com/Gilead-BioStats/graphicalMCP/issues Depends: - R (>= 3.5.0) + R (>= 4.1.0) Imports: matrixStats, mvtnorm From 411d30af86a72ba132725fe74c69f9721d08e3f0 Mon Sep 17 00:00:00 2001 From: EeethB Date: Fri, 12 Jan 2024 08:17:25 -0600 Subject: [PATCH 4/5] Fix incorrect plot --- vignettes/closed-testing.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/closed-testing.Rmd b/vignettes/closed-testing.Rmd index 8e25693a..0231fea9 100644 --- a/vignettes/closed-testing.Rmd +++ b/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), From 0ab525fc78af95cfe5565efc9efb1c4171d3d634 Mon Sep 17 00:00:00 2001 From: EeethB Date: Fri, 12 Jan 2024 14:36:29 +0000 Subject: [PATCH 5/5] Update documentation --- DESCRIPTION | 2 +- man/graphicalMCP-package.Rd | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f3a4f8e3..e5d424e3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -50,4 +50,4 @@ Config/testthat/edition: 3 Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.0 diff --git a/man/graphicalMCP-package.Rd b/man/graphicalMCP-package.Rd index 72595005..13c59a00 100644 --- a/man/graphicalMCP-package.Rd +++ b/man/graphicalMCP-package.Rd @@ -29,7 +29,6 @@ Authors: Other contributors: \itemize{ \item Gilead Sciences, Inc. [copyright holder, funder] - \item Atorus Research LLC [copyright holder] } }