From 7e142648cf1d4658a622a1747890cddfb30eec87 Mon Sep 17 00:00:00 2001 From: EeethB Date: Fri, 7 Jun 2024 12:54:00 -0500 Subject: [PATCH 1/2] Correct typo --- man/adjust_weights.Rd | 4 ++-- man/graph_generate_weights.Rd | 20 ++++++++++---------- man/graph_test_closure.Rd | 2 +- man/plot.initial_graph.Rd | 2 +- vignettes/generate-closure.Rmd | 2 +- 5 files changed, 15 insertions(+), 15 deletions(-) diff --git a/man/adjust_weights.Rd b/man/adjust_weights.Rd index 160a2f3..d5461aa 100644 --- a/man/adjust_weights.Rd +++ b/man/adjust_weights.Rd @@ -94,8 +94,8 @@ adjusted according to parametric tests. dimensions as \code{matrix_weights}, whose hypothesis weights have been adjusted according to Simes tests. \item \code{graphicalMCP:::c_value_function()} returns the difference between -\eqn{\alpha} and the Type I error of the parametric test with the $c$ value -of \code{x}, adjusted for the correlation between test statistics using +\eqn{\alpha} and the Type I error of the parametric test with the \eqn{c} +value of \code{x}, adjusted for the correlation between test statistics using parametric tests based on equation (6) of Xi et al. (2017). \item \code{graphicalMCP:::solve_c_parametric()} returns the c value adjusted for the correlation between test statistics using parametric tests based on diff --git a/man/graph_generate_weights.Rd b/man/graph_generate_weights.Rd index 2b3e226..67ddb2e 100644 --- a/man/graph_generate_weights.Rd +++ b/man/graph_generate_weights.Rd @@ -12,9 +12,9 @@ graph_generate_weights(graph) } \value{ A numeric matrix of all intersection hypotheses and their hypothesis -weights. For a graphical multiple comparison procedure with $m$ hypotheses, -the number of rows is $2^{m}-1$, each of which corresponds to an intersection -hypothesis. The number of columns is \eqn{2\cdot m}$. The first $m$ columns +weights. For a graphical multiple comparison procedure with \eqn{m} hypotheses, +the number of rows is \eqn{2^{m}-1}, each of which corresponds to an intersection +hypothesis. The number of columns is \eqn{2\cdot m}. The first \eqn{m} columns indicate which individual hypotheses are included in a given intersection hypothesis and the second half of columns provide hypothesis weights for each individual hypothesis for a given intersection hypothesis. @@ -28,18 +28,18 @@ hypotheses involved are true simultaneously. The closure based on a graph consists of all updated graphs (corresponding to intersection hypotheses) after all combinations of hypotheses are deleted. -For a graphical multiple comparison procedure with $m$ hypotheses, there are -$2^{m}-1$ updated graphs (intersection hypotheses), including the initial -graph (the overall intersection hypothesis). The weighting strategy of this -graph consists of hypothesis weights from all $2^{m}-1$ updated graphs -(intersection hypotheses). The algorithm to derive the weighting strategy is -based on Algorithm 1 in Bretz et al. (2011). +For a graphical multiple comparison procedure with \eqn{m} hypotheses, there +are \eqn{2^{m}-1} updated graphs (intersection hypotheses), including the +initial graph (the overall intersection hypothesis). The weighting strategy +of this graph consists of hypothesis weights from all \eqn{2^{m}-1} updated +graphs (intersection hypotheses). The algorithm to derive the weighting +strategy is based on Algorithm 1 in Bretz et al. (2011). } \section{Performance}{ Generation of intersection hypotheses is closely related to the power set of a given set of indices. As the number of hypotheses increases, the memory -and time usage can grow quickly (e.g., at a rate of $O(2^n)$). There are also +and time usage can grow quickly (e.g., at a rate of \eqn{O(2^n)}). There are also multiple ways to implement Algorithm 1 in Bretz et al. (2011). See \code{vignette("generate-closure")} for more information about generating intersection hypotheses and comparisons of different approaches to calculate diff --git a/man/graph_test_closure.Rd b/man/graph_test_closure.Rd index 5baf581..d8ea02e 100644 --- a/man/graph_test_closure.Rd +++ b/man/graph_test_closure.Rd @@ -90,7 +90,7 @@ represents the parameter space where individual null hypotheses involved are true simultaneously. For a graphical multiple comparison procedure with $m$ hypotheses, there are -$2^{m}-1$ intersection hypotheses. For each intersection hypothesis, a test +\eqn{2^m-1} intersection hypotheses. For each intersection hypothesis, a test type could be chosen to determine how to reject the intersection hypothesis. Current choices of test types include Bonferroni, Simes and parametric. This implementation offers a more general framework covering Bretz et al. (2011), diff --git a/man/plot.initial_graph.Rd b/man/plot.initial_graph.Rd index 0ca6b42..fc32c7c 100644 --- a/man/plot.initial_graph.Rd +++ b/man/plot.initial_graph.Rd @@ -21,7 +21,7 @@ \arguments{ \item{x}{An object of class \code{initial_graph} to plot.} -\item{...}{Other arguments passed on to \code{\link[igraph:plot.igraph]{igraph::plot.igraph()}}.} +\item{...}{Other arguments passed on to \code{igraph::plot.igraph()}.} \item{v_palette}{A character vector of length two specifying the colors for retained and deleted hypotheses. More extensive color customization must be diff --git a/vignettes/generate-closure.Rmd b/vignettes/generate-closure.Rmd index e6625e9..4312245 100644 --- a/vignettes/generate-closure.Rmd +++ b/vignettes/generate-closure.Rmd @@ -123,7 +123,7 @@ The conventional approach for power simulations is to repeat the following proce + Remove the rejected hypothesis and update the graph + Repeat until no more hypotheses can be rejected -Note that the same step to update the graph may repeat in many replications, whichmay be repetitive. For $m$ hypotheses, there are at most $2^m-1$ graphs depending on which hypotheses are rejected. These graphs correspond to the closure and the weighting strategy. Thus an idea to avoid redundant updating of graphs is to utilize the weighting strategy. +Note that the same step to update the graph may repeat in many replications, which may be repetitive. For $m$ hypotheses, there are at most $2^m-1$ graphs depending on which hypotheses are rejected. These graphs correspond to the closure and the weighting strategy. Thus an idea to avoid redundant updating of graphs is to utilize the weighting strategy. ## Power simulations using parent-child relationships From 28124fae7a7361bc4bcbee6c05a1f45d9212cbfe Mon Sep 17 00:00:00 2001 From: EeethB Date: Fri, 7 Jun 2024 13:43:23 -0500 Subject: [PATCH 2/2] Update news and cran comments --- NEWS.md | 6 ++++++ cran-comments.md | 5 +++++ 2 files changed, 11 insertions(+) create mode 100644 cran-comments.md diff --git a/NEWS.md b/NEWS.md index 0019091..a3ffb14 100644 --- a/NEWS.md +++ b/NEWS.md @@ -11,3 +11,9 @@ * Updated function documentation * Updated references + +# graphicalMCP 0.2.0 + +* Corrected typos +* First CRAN release + diff --git a/cran-comments.md b/cran-comments.md new file mode 100644 index 0000000..c31fff6 --- /dev/null +++ b/cran-comments.md @@ -0,0 +1,5 @@ +## R CMD check results + +0 errors | 0 warnings | 0 notes + +* This is a new release.