From 5f57160fb0d5679f58f2eaf3d58473e747bfc2d3 Mon Sep 17 00:00:00 2001
From: Mahendra Mariadassou <mahendra.mariadassou@gmail.com>
Date: Fri, 17 Nov 2023 11:25:19 +0100
Subject: [PATCH] Update documentation of `starting_point()` to avoid warnings
 when checking the package.

---
 R/utils.R             | 10 +++++++++-
 man/starting_point.Rd | 13 +++++++++++--
 2 files changed, 20 insertions(+), 3 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 8f2a5bd5..1e1ffdb7 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -253,8 +253,16 @@ create_parameters <- function(
        depths = depths)
 }
 
-#' Barebone function to compute starting points for B, M and S
+#' Helper function for PLNfit initialization.
+#'
+#' @description
+#' Barebone helper function to compute starting points for B, M and S when fitting a PLN. Intended for internal use only.
+#'
 #' @importFrom stats lm.fit
+#' @param Y Response matrix
+#' @param X Covariate matrix
+#' @param O Offset matrix
+#' @param w Weight vector
 starting_point <- function(Y, X, O, w) {
   # Y = responses, X = covariates, O = offsets (in log scale), w = weights
   n <- nrow(Y); p <- ncol(Y); d <- ncol(X)
diff --git a/man/starting_point.Rd b/man/starting_point.Rd
index 73d8ed53..8860323d 100644
--- a/man/starting_point.Rd
+++ b/man/starting_point.Rd
@@ -2,10 +2,19 @@
 % Please edit documentation in R/utils.R
 \name{starting_point}
 \alias{starting_point}
-\title{Barebone function to compute starting points for B, M and S}
+\title{Helper function for PLNfit initialization.}
 \usage{
 starting_point(Y, X, O, w)
 }
+\arguments{
+\item{Y}{Response matrix}
+
+\item{X}{Covariate matrix}
+
+\item{O}{Offset matrix}
+
+\item{w}{Weight vector}
+}
 \description{
-Barebone function to compute starting points for B, M and S
+Barebone helper function to compute starting points for B, M and S when fitting a PLN. Intended for internal use only.
 }