From c9ababb2098e505dc18f4e504bed6b869185968e Mon Sep 17 00:00:00 2001
From: Josh Sumner <51797700+joshqsumner@users.noreply.github.com>
Date: Wed, 17 Sep 2025 09:31:39 -0500
Subject: [PATCH 1/3] docs clarity

---
 R/conjugate.R    | 2 +-
 man/conjugate.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/conjugate.R b/R/conjugate.R
index 28885b48..ac45eff4 100644
--- a/R/conjugate.R
+++ b/R/conjugate.R
@@ -84,7 +84,7 @@
 #'     where shape and scale are the respective parameters of the gamma distributed rate
 #'     (inverse of scale) parameter of gamma distributed data.}
 #'    \item{\strong{"poisson" and "exponential": } \code{priors = list(a = 0.5,b = 0.5)},
-#'     where a and b are shape parameters of the gamma distribution.}
+#'     where a and b are shape and rate parameters of the gamma distribution.}
 #'    \item{\strong{"negbin": } \code{priors = list(r = 10, a = 0.5, b = 0.5)},
 #'     where r is the r parameter of the negative binomial distribution
 #'     (representing the number of successes required)
diff --git a/man/conjugate.Rd b/man/conjugate.Rd
index b1ded573..152fc8ab 100644
--- a/man/conjugate.Rd
+++ b/man/conjugate.Rd
@@ -130,7 +130,7 @@ Prior distributions default to be weakly informative and in some cases you may w
     where shape and scale are the respective parameters of the gamma distributed rate
     (inverse of scale) parameter of gamma distributed data.}
    \item{\strong{"poisson" and "exponential": } \code{priors = list(a = 0.5,b = 0.5)},
-    where a and b are shape parameters of the gamma distribution.}
+    where a and b are shape and rate parameters of the gamma distribution.}
    \item{\strong{"negbin": } \code{priors = list(r = 10, a = 0.5, b = 0.5)},
     where r is the r parameter of the negative binomial distribution
     (representing the number of successes required)

From 60733deca2699af7a4a4d4fc53f6b4dc844fc1e7 Mon Sep 17 00:00:00 2001
From: Josh Sumner <51797700+joshqsumner@users.noreply.github.com>
Date: Wed, 17 Sep 2025 09:31:46 -0500
Subject: [PATCH 2/3] package level doc

---
 R/pcvr-package.R    | 25 +++++++++++++++++++++++++
 man/pcvr-package.Rd | 41 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 66 insertions(+)
 create mode 100644 R/pcvr-package.R
 create mode 100644 man/pcvr-package.Rd

diff --git a/R/pcvr-package.R b/R/pcvr-package.R
new file mode 100644
index 00000000..a87d0793
--- /dev/null
+++ b/R/pcvr-package.R
@@ -0,0 +1,25 @@
+#' Plant Phenotyping and Bayesian Statistics
+#'
+#' @name pcvr-package
+#' @aliases pcvr
+#'
+#' @description
+#' \if{html}{
+#'    \figure{pcvr_logo.png}{options: width="100" alt="logo" style="float: right"}
+#' }
+#'
+#' The \pkg{pcvr} package is meant to interface with any datatypes returned from \pkg{PlantCV}
+#' including single and multi value trait phenotypes as well as common metadata for plant science
+#' experiments as well as lower the barrier to entry for select Bayesian statistics and longitudinal
+#' models of particular use in plant science.
+#'
+#'
+#' @seealso
+#' Useful links:
+#' \itemize{
+#' \item \url{https://plantcv.org}
+#' \item Report bugs at \url{https://github.com/danforthcenter/pcvr}
+#' }
+#' \code{\link{growthSS}}
+#' \code{\link{conjugate}}
+"_PACKAGE"
diff --git a/man/pcvr-package.Rd b/man/pcvr-package.Rd
new file mode 100644
index 00000000..5efb5e3a
--- /dev/null
+++ b/man/pcvr-package.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/pcvr-package.R
+\docType{package}
+\name{pcvr-package}
+\alias{pcvr-package}
+\alias{pcvr}
+\title{Plant Phenotyping and Bayesian Statistics}
+\description{
+\if{html}{
+   \figure{pcvr_logo.png}{options: width="100" alt="logo" style="float: right"}
+}
+
+The \pkg{pcvr} package is meant to interface with any datatypes returned from \pkg{PlantCV}
+including single and multi value trait phenotypes as well as common metadata for plant science
+experiments as well as lower the barrier to entry for select Bayesian statistics and longitudinal
+models of particular use in plant science.
+}
+\seealso{
+Useful links:
+\itemize{
+\item \url{https://plantcv.org}
+\item Report bugs at \url{https://github.com/danforthcenter/pcvr}
+}
+\code{\link{growthSS}}
+\code{\link{conjugate}}
+}
+\author{
+\strong{Maintainer}: Josh Sumner \email{jsumner@danforthcenter.org} (\href{https://orcid.org/0000-0002-3399-9063}{ORCID})
+
+Authors:
+\itemize{
+  \item Jeffrey Berry (\href{https://orcid.org/0000-0002-8064-9787}{ORCID})
+}
+
+Other contributors:
+\itemize{
+  \item Noah Fahlgren (\href{https://orcid.org/0000-0002-5597-4537}{ORCID}) [reviewer]
+  \item Donald Danforth Plant Science Center [copyright holder]
+}
+
+}

From 92158ebfccb6bc020a0c050d1ed4b104ddb6bd98 Mon Sep 17 00:00:00 2001
From: Josh Sumner <51797700+joshqsumner@users.noreply.github.com>
Date: Wed, 17 Sep 2025 09:34:46 -0500
Subject: [PATCH 3/3] adding package to internal part of website since it is
 similar to readme

---
 _pkgdown.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index a21f261f..e87aa28a 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -174,3 +174,4 @@ reference:
       - summary.conjugate
       - plot.conjugate
       - conjugate-class
+      - pcvr-package