From b81b5a4d4218b705a4e0e57203d9cdf59f004b22 Mon Sep 17 00:00:00 2001
From: mihaiconstantin <mihai@mihaiconstantin.com>
Date: Wed, 28 Sep 2022 16:52:27 +0200
Subject: [PATCH] Docs: update package docs with Ising model information

---
 man-roxygen/generate_model.R |  2 +-
 man-roxygen/powerly.R        | 11 ++++++++++-
 man/generate_model.Rd        |  2 +-
 man/powerly.Rd               | 15 ++++++++++++++-
 4 files changed, 26 insertions(+), 4 deletions(-)

diff --git a/man-roxygen/generate_model.R b/man-roxygen/generate_model.R
index 9546af0..0523b11 100644
--- a/man-roxygen/generate_model.R
+++ b/man-roxygen/generate_model.R
@@ -7,7 +7,7 @@
 #' [powerly::powerly()].
 #'
 #' @param type Character string representing the type of true model. Possible
-#' values are `"ggm"` (the default).
+#' values are `"ggm"` (the default) or `"ising"`.
 #'
 #' @param ... Required arguments used for the generation of the true model. See
 #' the **True Models** section of [powerly::powerly()] for the arguments
diff --git a/man-roxygen/powerly.R b/man-roxygen/powerly.R
index a12ce75..460ca27 100644
--- a/man-roxygen/powerly.R
+++ b/man-roxygen/powerly.R
@@ -20,7 +20,7 @@
 #' candidate range.
 #'
 #' @param model A character string representing the type of true model to find a
-#' sample size for. Possible values are `"ggm"` (the default).
+#' sample size for. Possible values are `"ggm"` (the default) or `"ising"`.
 #'
 #' @param ... Required arguments used for the generation of the true model. See
 #' the **True Models** section for the arguments required for each true model.
@@ -142,6 +142,15 @@
 #'     - Yin, J., and Li, H. (2011). A sparse conditional gaussian graphical model for analysis of genetical genomics data. *The annals of applied statistics*, 5(4), 2630.
 #' - supported performance measures: `sen`, `spe`, `mcc`, `rho`
 #'
+#' **Ising Model**
+#' - type: cross-sectional
+#' - symbol: `ising`
+#' - `...` arguments for generating true models:
+#'   - `nodes`: A single positive integer representing the number of nodes in the network (e.g., `10`).
+#'   - `density`: A single numerical value indicating the density of the network (e.g., `0.4`).
+#'   - `positive`: A single numerical value representing the proportion of positive edges in the network (e.g., `0.9` for 90% positive edges).
+#' - supported performance measures: `sen`, `spe`, `mcc`, `rho`
+#'
 #' @section Performance Measures:
 #'
 #' | **Performance Measure**  | **Symbol** | **Lower**   | **Upper**  |
diff --git a/man/generate_model.Rd b/man/generate_model.Rd
index db047ad..08614f5 100644
--- a/man/generate_model.Rd
+++ b/man/generate_model.Rd
@@ -8,7 +8,7 @@ generate_model(type, ...)
 }
 \arguments{
 \item{type}{Character string representing the type of true model. Possible
-values are \code{"ggm"} (the default).}
+values are \code{"ggm"} (the default) or \code{"ising"}.}
 
 \item{...}{Required arguments used for the generation of the true model. See
 the \strong{True Models} section of \code{\link[=powerly]{powerly()}} for the arguments
diff --git a/man/powerly.Rd b/man/powerly.Rd
index 536b4e0..c6a8a8e 100644
--- a/man/powerly.Rd
+++ b/man/powerly.Rd
@@ -46,7 +46,7 @@ Monte Carlo replications to perform for each sample size selected from the
 candidate range.}
 
 \item{model}{A character string representing the type of true model to find a
-sample size for. Possible values are \code{"ggm"} (the default).}
+sample size for. Possible values are \code{"ggm"} (the default) or \code{"ising"}.}
 
 \item{...}{Required arguments used for the generation of the true model. See
 the \strong{True Models} section for the arguments required for each true model.}
@@ -205,6 +205,19 @@ search shrinks below a specified value.
 }
 \item supported performance measures: \code{sen}, \code{spe}, \code{mcc}, \code{rho}
 }
+
+\strong{Ising Model}
+\itemize{
+\item type: cross-sectional
+\item symbol: \code{ising}
+\item \code{...} arguments for generating true models:
+\itemize{
+\item \code{nodes}: A single positive integer representing the number of nodes in the network (e.g., \code{10}).
+\item \code{density}: A single numerical value indicating the density of the network (e.g., \code{0.4}).
+\item \code{positive}: A single numerical value representing the proportion of positive edges in the network (e.g., \code{0.9} for 90\% positive edges).
+}
+\item supported performance measures: \code{sen}, \code{spe}, \code{mcc}, \code{rho}
+}
 }
 
 \section{Performance Measures}{