diff --git a/R/adjust_weights.R b/R/adjust_weights.R index 1041318..ca64bfe 100644 --- a/R/adjust_weights.R +++ b/R/adjust_weights.R @@ -53,8 +53,8 @@ #' dimensions as `matrix_weights`, whose hypothesis weights have been #' adjusted according to Simes tests. #' * `graphicalMCP:::c_value_function()` returns the difference between -#' \eqn{\alpha} and the Type I error of the parametric test with the $c$ value -#' of `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 `x`, adjusted for the correlation between test statistics using #' parametric tests based on equation (6) of Xi et al. (2017). #' * `graphicalMCP:::solve_c_parametric()` returns the c value adjusted for the #' correlation between test statistics using parametric tests based on diff --git a/R/graph_generate_weights.R b/R/graph_generate_weights.R index 88d01ea..a0472f3 100644 --- a/R/graph_generate_weights.R +++ b/R/graph_generate_weights.R @@ -10,19 +10,19 @@ #' #' 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). #' #' @inheritParams graph_update #' #' @return 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. @@ -30,7 +30,7 @@ #' @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 #' `vignette("generate-closure")` for more information about generating #' intersection hypotheses and comparisons of different approaches to calculate diff --git a/R/graph_test_closure.R b/R/graph_test_closure.R index 0c48be9..77901b5 100644 --- a/R/graph_test_closure.R +++ b/R/graph_test_closure.R @@ -10,7 +10,7 @@ #' 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/R/plot.initial_graph.R b/R/plot.initial_graph.R index cec7633..65d2540 100644 --- a/R/plot.initial_graph.R +++ b/R/plot.initial_graph.R @@ -8,7 +8,7 @@ #' of commonly used multiple comparison procedure using graphs. #' #' @param x An object of class `initial_graph` to plot. -#' @param ... Other arguments passed on to [igraph::plot.igraph()]. +#' @param ... Other arguments passed on to `igraph::plot.igraph()`. #' @param v_palette A character vector of length two specifying the colors for #' retained and deleted hypotheses. More extensive color customization must be #' done with `vertex.color`. diff --git a/_pkgdown.yml b/_pkgdown.yml index 7a1e671..cd7fbb8 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -5,7 +5,7 @@ template: reference: - title: Creating an initial graph -- desc: Functions for creating a multiple comparison procedure graph +- desc: Functions for creating a graphical multiple comparison procedure - contents: - graph_create - print.initial_graph @@ -14,29 +14,29 @@ reference: - as_graphMCP - as_igraph - title: Updating a graph -- desc: Functions for removing hypotheses from a graph +- desc: Functions for updating a graphical multiple comparison procedure after deleting hypotheses - contents: - graph_update - print.updated_graph - plot.updated_graph -- title: Calculating sub-graph weights -- desc: Functions for generating the weights of the closure +- title: Calculating hypothesis weights in a closure +- desc: Function for generating the weighting strategy - contents: - graph_generate_weights -- title: Test a graph -- desc: Functions for running Bonferroni, parametric, and Simes tests +- title: Testing a graphical multiple comparison procedure +- desc: Functions for performing a graphical multiple comparison procedure - contents: - graph_test_closure - graph_test_shortcut - print.graph_report - graph_rejection_orderings -- title: Run a power simulation -- desc: Functions for running power simulations +- title: Power simulation +- desc: Functions for performing power simulations - contents: - graph_calculate_power - print.power_report - title: Example graphs -- desc: Functions for creating example graphs from a variety of papers +- desc: Functions for creating example graphical multiple comparison procedures - contents: - bonferroni - bonferroni_holm