diff --git a/DESCRIPTION b/DESCRIPTION index 96ba6c1..e5d424e 100644 --- a/DESCRIPTION +++ b/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 diff --git a/R/graph_calculate_power.R b/R/graph_calculate_power.R index ea85b3e..4c192e5 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/README.Rmd b/README.Rmd index 68fb188..6b326b0 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 b199334..91d3869 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 0b3b1b0..5c4258d 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", @@ -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": [ @@ -48,7 +48,7 @@ "@type": "Person", "givenName": "Dong", "familyName": "Xi", - "email": "dong.xi@gilead.com" + "email": "dong.xi1@gilead.com" } ], "softwareSuggestions": [ diff --git a/man/graph_calculate_power.Rd b/man/graph_calculate_power.Rd index 42f8588..0a1cf4e 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 186651a..13c59a0 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{ @@ -28,8 +28,7 @@ Authors: Other contributors: \itemize{ - \item Gilead Biostatistics [copyright holder, funder] - \item Atorus Research LLC [copyright holder] + \item Gilead Sciences, Inc. [copyright holder, funder] } } diff --git a/vignettes/closed-testing.Rmd b/vignettes/closed-testing.Rmd index 8e25693..0231fea 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),