From fd0e063fdfaadeb11ccc61a2540ef63a9b29eb4a Mon Sep 17 00:00:00 2001
From: erik-ringen <ringen.erik@gmail.com>
Date: Wed, 7 Aug 2024 15:33:21 -0400
Subject: [PATCH] Make extract_samples a method of coevfit

---
 DESCRIPTION                                   |  2 +-
 NAMESPACE                                     |  3 +-
 R/coev_extract_samples.R                      | 32 -------------------
 R/extract_samples.R                           | 19 +++++++++++
 ..._extract_samples.Rd => extract_samples.Rd} |  8 ++---
 5 files changed, 26 insertions(+), 38 deletions(-)
 delete mode 100644 R/coev_extract_samples.R
 create mode 100644 R/extract_samples.R
 rename man/{coev_extract_samples.Rd => extract_samples.Rd} (68%)

diff --git a/DESCRIPTION b/DESCRIPTION
index 2826b22..4671869 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -16,7 +16,7 @@ URL: https://github.com/ScottClaessens/coevolve
 BugReports: https://github.com/ScottClaessens/coevolve/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests: 
     knitr,
     rmarkdown,
diff --git a/NAMESPACE b/NAMESPACE
index 94c0eb3..06f3597 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,11 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(extract_samples,coevfit)
 S3method(print,coevfit)
 S3method(print,coevsummary)
 S3method(summary,coevfit)
 export(coev_calculate_delta_theta)
 export(coev_calculate_theta)
-export(coev_extract_samples)
 export(coev_fit)
 export(coev_make_stancode)
 export(coev_make_standata)
@@ -14,4 +14,5 @@ export(coev_plot_flowfield)
 export(coev_plot_predictive_check)
 export(coev_plot_selection_gradient)
 export(coev_simulate_coevolution)
+export(extract_samples)
 importFrom(rlang,.data)
diff --git a/R/coev_extract_samples.R b/R/coev_extract_samples.R
deleted file mode 100644
index 281e6df..0000000
--- a/R/coev_extract_samples.R
+++ /dev/null
@@ -1,32 +0,0 @@
-#' Extract samples (draws) from a fitted \code{coevfit} object
-#'
-#' @param object An object of class \code{coevfit}
-#'
-#' @return Samples in 'rethinking' style list format
-#' @export
-#' 
-coev_extract_samples <- function(object) {
-  # stop if object is not of class coevfit
-  if (!methods::is(object, "coevfit")) {
-    stop2(
-      paste0(
-        "Argument 'object' must be a fitted coevolutionary model ",
-        "of class coevfit."
-        )
-      )
-  }
-  # stop if rethinking package not installed
-  if (!requireNamespace("rethinking", quietly = TRUE)) {
-    stop2(
-      paste0(
-        "'rethinking' package must be installed to use this function. See https://github.com/rmcelreath/rethinking"
-        )
-      )
-  }
-    vars <- object$fit$metadata()$stan_variables
-    draws <- posterior::as_draws_rvars(object$fit$draws())
-    
-    return(lapply(vars, \(var_name){  
-      posterior::draws_of(draws[[var_name]], with_chains = FALSE)
-    }) |> setNames(vars))
-}
diff --git a/R/extract_samples.R b/R/extract_samples.R
new file mode 100644
index 0000000..570a92e
--- /dev/null
+++ b/R/extract_samples.R
@@ -0,0 +1,19 @@
+#' Extract samples (draws) from a fitted \code{coevfit} object
+#'
+#' @param object An object of class \code{coevfit}
+#'
+#' @return Samples in 'rethinking' style list format
+#' @export
+extract_samples <- function(object) {
+    UseMethod("extract_samples")
+}
+
+#' @export
+extract_samples.coevfit <- function(object) {
+  vars <- object$fit$metadata()$stan_variables
+  draws <- posterior::as_draws_rvars(object$fit$draws())
+  
+  return(lapply(vars, \(var_name){  
+    posterior::draws_of(draws[[var_name]], with_chains = FALSE)
+  }) |> setNames(vars))
+}
\ No newline at end of file
diff --git a/man/coev_extract_samples.Rd b/man/extract_samples.Rd
similarity index 68%
rename from man/coev_extract_samples.Rd
rename to man/extract_samples.Rd
index 3ff2d31..166905f 100644
--- a/man/coev_extract_samples.Rd
+++ b/man/extract_samples.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/coev_extract_samples.R
-\name{coev_extract_samples}
-\alias{coev_extract_samples}
+% Please edit documentation in R/extract_samples.R
+\name{extract_samples}
+\alias{extract_samples}
 \title{Extract samples (draws) from a fitted \code{coevfit} object}
 \usage{
-coev_extract_samples(object)
+extract_samples(object)
 }
 \arguments{
 \item{object}{An object of class \code{coevfit}}