From c7a3a6303a6873959d55ba125297f1c09ff10cf7 Mon Sep 17 00:00:00 2001
From: Bill Denney <wdenney@humanpredictions.com>
Date: Wed, 7 Aug 2024 23:31:07 -0400
Subject: [PATCH] Update documentation

---
 DESCRIPTION                      |  2 +-
 NAMESPACE                        | 10 +++++
 R/knit_printEquation.R           | 10 +++++
 man/extract_eq.nlmixr2FitCore.Rd | 75 --------------------------------
 4 files changed, 21 insertions(+), 76 deletions(-)
 delete mode 100644 man/extract_eq.nlmixr2FitCore.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 74fe1e0..2b085ad 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -59,5 +59,5 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 NeedsCompilation: yes
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 LazyData: true
diff --git a/NAMESPACE b/NAMESPACE
index 0c4c784..e54e5ea 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,16 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(bootplot,nlmixr2FitCore)
+S3method(extractEqHelper,"(")
+S3method(extractEqHelper,"function")
+S3method(extractEqHelper,"{")
+S3method(extractEqHelper,call)
+S3method(extractEqHelper,character)
+S3method(extractEqHelper,default)
+S3method(extractEqHelper,name)
+S3method(extractEqHelper,nlmixr2FitCore)
+S3method(extractEqHelper,numeric)
+S3method(extractEqHelper,rxUi)
 S3method(knit_print,nlmixr2FitCore)
 S3method(knit_print,rxUi)
 S3method(print,nlmixr2BoostrapSummary)
diff --git a/R/knit_printEquation.R b/R/knit_printEquation.R
index 696d41e..faf8c28 100644
--- a/R/knit_printEquation.R
+++ b/R/knit_printEquation.R
@@ -69,22 +69,27 @@ extractEqHelperLhsRhs <- function(x, ..., inModel, prefix = "", middle, suffix =
   paste0(prefix, lhs, middle, rhs, suffix)
 }
 
+#' @export
 extractEqHelper.nlmixr2FitCore <- function(x, ..., inModel) {
   extractEqHelper(as.function(x), ..., inModel=FALSE)
 }
 
+#' @export
 extractEqHelper.rxUi <- function(x, ..., inModel, name) {
   extractEqHelper(as.function(x), ..., inModel=FALSE)
 }
 
+#' @export
 extractEqHelper.function <- function(x, ..., inModel, name) {
   extractEqHelper(methods::functionBody(x), ..., inModel=FALSE)
 }
 
+#' @export
 "extractEqHelper.{" <- function(x, ..., inModel, name) {
   extractEqHelperSeqDrop(x, ..., inModel = inModel)
 }
 
+#' @export
 "extractEqHelper.(" <- function(x, ..., inModel, dropParen = FALSE, name) {
   stopifnot(length(x) == 2)
   if (dropParen) {
@@ -178,6 +183,7 @@ latexOpMap <-
     "!"="{\\lnot}"
   )
 
+#' @export
 extractEqHelper.call <- function(x, ..., inModel, name) {
   if (inModel) {
     if (is.name(x[[1]])) {
@@ -270,6 +276,7 @@ extractEqHelper.call <- function(x, ..., inModel, name) {
   ret
 }
 
+#' @export
 extractEqHelper.name <- function(x, ..., inModel, underscoreToSubscript = FALSE, name) {
   if (inModel) {
     ret <- as.character(x)
@@ -292,6 +299,7 @@ extractEqHelper.name <- function(x, ..., inModel, underscoreToSubscript = FALSE,
   ret
 }
 
+#' @export
 extractEqHelper.numeric <- function(x, ..., inModel, name = NULL) {
   if (inModel) {
     ret <- format(x)
@@ -329,6 +337,7 @@ escapeLatex <- function (x, newlines = FALSE, spaces = FALSE) {
   x
 }
 
+#' @export
 extractEqHelper.character <- function(x, ..., inModel, name = NULL) {
   if (inModel) {
     ret <- sprintf('\\text{"%s"}', escapeLatex(x))
@@ -394,6 +403,7 @@ extractEqHelper.if <- function(x, ..., inModel, alignment, indent = 0L, firstIf
   ret
 }
 
+#' @export
 extractEqHelper.default <- function(x, ..., inModel) {
   if (inherits(x, "<-") | inherits(x, "=")) {
     # The assignment classes go via extractEqHelper.default to fix an R CMD
diff --git a/man/extract_eq.nlmixr2FitCore.Rd b/man/extract_eq.nlmixr2FitCore.Rd
deleted file mode 100644
index 7fbce54..0000000
--- a/man/extract_eq.nlmixr2FitCore.Rd
+++ /dev/null
@@ -1,75 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/extract_eq.R
-\name{extract_eq.nlmixr2FitCore}
-\alias{extract_eq.nlmixr2FitCore}
-\alias{extract_eq.rxUi}
-\title{Extract the equations from an nlmixr2/rxode2 model to produce a 'LaTeX'
-equation.}
-\usage{
-\method{extract_eq}{nlmixr2FitCore}(
-  model,
-  intercept = "alpha",
-  greek = "beta",
-  greek_colors = NULL,
-  subscript_colors = NULL,
-  var_colors = NULL,
-  var_subscript_colors = NULL,
-  raw_tex = FALSE,
-  swap_var_names = NULL,
-  swap_subscript_names = NULL,
-  ital_vars = FALSE,
-  label = NULL,
-  index_factors = FALSE,
-  show_distribution = FALSE,
-  wrap = FALSE,
-  terms_per_line = 4,
-  operator_location = "end",
-  align_env = "aligned",
-  use_coefs = FALSE,
-  coef_digits = 2,
-  fix_signs = TRUE,
-  font_size = NULL,
-  mean_separate,
-  return_variances = FALSE,
-  se_subscripts = FALSE,
-  ...
-)
-
-\method{extract_eq}{rxUi}(
-  model,
-  intercept = "alpha",
-  greek = "beta",
-  greek_colors = NULL,
-  subscript_colors = NULL,
-  var_colors = NULL,
-  var_subscript_colors = NULL,
-  raw_tex = FALSE,
-  swap_var_names = NULL,
-  swap_subscript_names = NULL,
-  ital_vars = FALSE,
-  label = NULL,
-  index_factors = FALSE,
-  show_distribution = FALSE,
-  wrap = FALSE,
-  terms_per_line = 4,
-  operator_location = "end",
-  align_env = "aligned",
-  use_coefs = FALSE,
-  coef_digits = 2,
-  fix_signs = TRUE,
-  font_size = NULL,
-  mean_separate,
-  return_variances = FALSE,
-  se_subscripts = FALSE,
-  ...
-)
-}
-\arguments{
-\item{model}{The model to extract equations from}
-
-\item{intercept, greek, greek_colors, subscript_colors, var_colors, var_subscript_colors, raw_tex, swap_var_names, swap_subscript_names, ital_vars, label, index_factors, show_distribution, wrap, terms_per_line, operator_location, align_env, use_coefs, coef_digits, fix_signs, font_size, mean_separate, return_variances, se_subscripts}{Ignored}
-}
-\description{
-Extract the equations from an nlmixr2/rxode2 model to produce a 'LaTeX'
-equation.
-}