From 8a2c71224034bcce23c923d648c7c937bd0b6613 Mon Sep 17 00:00:00 2001
From: Bob Kubinec <bobkubinec@gmail.com>
Date: Thu, 2 Jan 2025 15:13:05 -0500
Subject: [PATCH] fix some bugs

---
 R/Helpers.R                        |  2 +-
 R/Plot.R                           |  4 ++--
 man/id_estimate.Rd                 |  5 +----
 vignettes/Package_Introduction.qmd |  7 +++++--
 vignettes/Time_Series.qmd          | 10 ++++++----
 5 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/R/Helpers.R b/R/Helpers.R
index fafa3c0..1ffb964 100755
--- a/R/Helpers.R
+++ b/R/Helpers.R
@@ -1358,7 +1358,7 @@ process_init_pathfinder <- function(init, num_procs, model_variables = NULL,
 .check_quoted <- function(quoted=NULL,default_val) {
   if(is.null(quoted)) {
     quoted <- default_val
-  } else if(class(quoted)=='character') {
+  } else if(inherits(quoted,'character')) {
     quoted <- as.name(quoted)
     quoted <- enquo(quoted)
   } else {
diff --git a/R/Plot.R b/R/Plot.R
index ee2d52d..7aca2f4 100755
--- a/R/Plot.R
+++ b/R/Plot.R
@@ -124,7 +124,7 @@ id_plot_legis <- function(object,return_data=FALSE,
   }
   
   
-  if(class(object)=='idealstan') {
+  if(inherits(object,'idealstan')) {
     person_params <- .prepare_legis_data(object,
                                          high_limit=high_limit,
                                          low_limit=low_limit,include=include,
@@ -635,7 +635,7 @@ id_plot_legis_dyn <- function(object,return_data=FALSE,
 
     }
   
-  if(class(object)=='idealstan') {
+  if(inherits(object,'idealstan')) {
     person_params <- .prepare_legis_data(object,
                                          high_limit=high_limit,
                                          low_limit=low_limit,
diff --git a/man/id_estimate.Rd b/man/id_estimate.Rd
index 26bcba8..0faa7c2 100755
--- a/man/id_estimate.Rd
+++ b/man/id_estimate.Rd
@@ -86,10 +86,7 @@ See below.}
 
 \item{inflate_zero}{If the outcome is distributed as Poisson (count/unbounded integer), 
 setting this to 
-\code{TRUE} will fit a traditional zero-inflated model. 
-To use correctly, the value for 
-zero must be passed as the \code{miss_val} option to \code{\link{id_make}} before
-running a model so that zeroes are coded as missing data.}
+\code{TRUE} will fit a traditional zero-inflated model.}
 
 \item{vary_ideal_pts}{Default \code{'none'}. If \code{'random_walk'}, \code{'AR1'}, 
 \code{'GP'}, or \code{'splines'}, a 
diff --git a/vignettes/Package_Introduction.qmd b/vignettes/Package_Introduction.qmd
index 5d5e3cd..4714bd8 100755
--- a/vignettes/Package_Introduction.qmd
+++ b/vignettes/Package_Introduction.qmd
@@ -3,6 +3,7 @@ title: "Introduction to Idealstan"
 author: "Robert Kubinec"
 date: last-modified
 format: html
+cache: false
 vignette: >
   %\VignetteIndexEntry{Time-Varying Ideal Points}
   %\VignetteEngine{R.rsp::asis}
@@ -11,12 +12,14 @@ vignette: >
 
 ```{r setup, include=FALSE}
 knitr::opts_chunk$set(echo = TRUE,warning=FALSE,fig.align = 'center',fig.width=6, fig.height=5)
-options(cmdstanr_warn_inits = FALSE)
+
 library(idealstan)
 library(dplyr)
 library(ggplot2)
 library(tidyr)
 library(tinytable)
+
+options(cmdstanr_warn_inits = FALSE)
 ```
 
 *Note: To report bugs with the package, please file an issue on the [Github page](https://github.com/saudiwin/idealstan/issues).*
@@ -36,7 +39,7 @@ The approach to handling missing data in this package is to model cases where mi
 The package includes the following models:
 
 | Model ID | Model Type | Response Type | Missing Data Adjustment |
-|-----------------|---------------------|-----------------|-----------------|
+|----|----|----|----|
 | 1 | IRT 2-PL | Binary | No |
 | 2 | IRT 2-PL | Binary | Yes |
 | 3 | IRT rating scale | Ordinal | No |
diff --git a/vignettes/Time_Series.qmd b/vignettes/Time_Series.qmd
index d0eea4c..0b6b0a5 100755
--- a/vignettes/Time_Series.qmd
+++ b/vignettes/Time_Series.qmd
@@ -12,10 +12,12 @@ vignette: >
 
 ```{r setup, include=FALSE}
 knitr::opts_chunk$set(echo = TRUE,message = FALSE,warning=FALSE,fig.align = 'center',fig.width=6, fig.height=5)
-require(idealstan)
-require(dplyr)
-require(ggplot2)
-require(lubridate)
+library(idealstan)
+library(dplyr)
+library(ggplot2)
+library(lubridate)
+
+options(cmdstanr_warn_inits = FALSE)
 ```
 
 *Note: To report bugs with the package, please file an issue on the [Github page](https://github.com/saudiwin/idealstan/issues).*