From cd2e9430058c55e4b98321568b23948c7c0784d1 Mon Sep 17 00:00:00 2001
From: Jouni Helske <jouni.helske@utu.fi>
Date: Thu, 21 Nov 2024 11:36:29 +0200
Subject: [PATCH] update docs

---
 NAMESPACE                               |  2 +-
 R/plot.ame.R                            |  6 +++---
 man/{plot.ame.Rd => plot.ame_params.Rd} | 12 ++++++------
 3 files changed, 10 insertions(+), 10 deletions(-)
 rename man/{plot.ame.Rd => plot.ame_params.Rd} (62%)

diff --git a/NAMESPACE b/NAMESPACE
index 6f16305..7d81419 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -48,7 +48,7 @@ S3method(nobs,hmm)
 S3method(nobs,mhmm)
 S3method(nobs,mnhmm)
 S3method(nobs,nhmm)
-S3method(plot,ame)
+S3method(plot,ame_params)
 S3method(plot,hmm)
 S3method(plot,mhmm)
 S3method(plot,ssp)
diff --git a/R/plot.ame.R b/R/plot.ame.R
index 1ed3ad6..669744d 100644
--- a/R/plot.ame.R
+++ b/R/plot.ame.R
@@ -1,6 +1,6 @@
-#' Visualize Average Marginal Effects
+#' Visualize Average Marginal Effects on NHMM parameters
 #' 
-#' @param x Output from [ame_param() or ame_prob()].
+#' @param x Output from [ame_param()].
 #' @param type Type of plot to create. One of `"initial"`, `"transition"`,
 #'  `"emission"`, or `"cluster"`.
 #' @param probs A numeric vector of length 2 with the lower and upper limits for 
@@ -8,7 +8,7 @@
 #' found in the input object `x`, an error is thrown.
 #' @param ... Ignored.
 #' @export
-plot.ame <- function(x, type, probs = c(0.025, 0.975), ...) {
+plot.ame_params <- function(x, type, probs = c(0.025, 0.975), ...) {
   
   type <- match.arg(type, c("initial", "transition", "emission", "cluster"))
   
diff --git a/man/plot.ame.Rd b/man/plot.ame_params.Rd
similarity index 62%
rename from man/plot.ame.Rd
rename to man/plot.ame_params.Rd
index a4eec8d..deeddc5 100644
--- a/man/plot.ame.Rd
+++ b/man/plot.ame_params.Rd
@@ -1,13 +1,13 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/plot.ame.R
-\name{plot.ame}
-\alias{plot.ame}
-\title{Visualize Average Marginal Effects}
+\name{plot.ame_params}
+\alias{plot.ame_params}
+\title{Visualize Average Marginal Effects on NHMM parameters}
 \usage{
-\method{plot}{ame}(x, type, probs = c(0.025, 0.975), ...)
+\method{plot}{ame_params}(x, type, probs = c(0.025, 0.975), ...)
 }
 \arguments{
-\item{x}{Output from \code{\link[=ame_param() or ame_prob]{ame_param() or ame_prob()}}.}
+\item{x}{Output from \code{\link[=ame_param]{ame_param()}}.}
 
 \item{type}{Type of plot to create. One of \code{"initial"}, \code{"transition"},
 \code{"emission"}, or \code{"cluster"}.}
@@ -19,5 +19,5 @@ found in the input object \code{x}, an error is thrown.}
 \item{...}{Ignored.}
 }
 \description{
-Visualize Average Marginal Effects
+Visualize Average Marginal Effects on NHMM parameters
 }