From fcadc42b860e00f5b949a65c05d88f93c797d42c Mon Sep 17 00:00:00 2001
From: Bill Denney <wdenney@humanpredictions.com>
Date: Thu, 24 Oct 2024 12:40:43 -0400
Subject: [PATCH] Categorize all functions for pkgdown

---
 R/assert.R                     |  1 +
 R/linMod.R                     |  3 +--
 R/rudfui.R                     |  7 ++++++-
 _pkgdown.yml                   | 13 +++++++++++++
 man/assertCompartmentExists.Rd |  1 +
 man/assertCompartmentName.Rd   |  1 +
 man/assertCompartmentNew.Rd    |  1 +
 man/assertRxUi.Rd              |  1 +
 man/assertVariableExists.Rd    |  1 +
 man/assertVariableNew.Rd       |  1 +
 man/linMod.Rd                  | 10 ++++++++++
 man/rxUdfUiData.Rd             | 10 ++++++++++
 man/rxUdfUiEst.Rd              | 10 ++++++++++
 man/rxUdfUiIniLhs.Rd           | 10 ++++++++++
 man/rxUdfUiMv.Rd               | 10 ++++++++++
 man/rxUdfUiNum.Rd              | 11 ++++++++++-
 man/rxUdfUiParsing.Rd          | 10 ++++++++++
 man/testIniDf.Rd               | 11 +++++++++++
 man/testRxUnbounded.Rd         |  3 ++-
 19 files changed, 110 insertions(+), 5 deletions(-)

diff --git a/R/assert.R b/R/assert.R
index 8a51820d0..fef90bb5b 100644
--- a/R/assert.R
+++ b/R/assert.R
@@ -625,6 +625,7 @@ warnRxBounded <- function(ui, extra="", .var.name=.vname(ui)) {
 #' @return boolean, indicating if the object is a valid initialization data frame
 #' @export
 #' @author Matthew L. Fidler
+#' @family Assertions
 #' @examples
 #' testIniDf(TRUE)
 testIniDf <- function(iniDf) {
diff --git a/R/linMod.R b/R/linMod.R
index d1266dc3d..9a62977dd 100644
--- a/R/linMod.R
+++ b/R/linMod.R
@@ -95,9 +95,8 @@ rxUdfUi.default <- function(fun) {
 #'   `rxUdfUi()` for details.
 #'
 #' @export
-#'
+#' @family User functions
 #' @author Matthew L. Fidler
-#'
 #' @examples
 #'
 #' linMod(x, 3)
diff --git a/R/rudfui.R b/R/rudfui.R
index 83df37f21..52b576a56 100644
--- a/R/rudfui.R
+++ b/R/rudfui.R
@@ -30,12 +30,12 @@ rxUdfUiReset()
 #' UI functions
 #'
 #' @return integer greater than 1L
+#' @family User functions
 #' @export
 #' @author Matthew L. Fidler
 #' @examples
 #'
 #' rxUdfUiNum()
-#'
 rxUdfUiNum <- function() {
   if (checkmate::testIntegerish(.udfUiEnv$num, lower=1L, len=1L, any.missing=FALSE))  {
     as.integer(.udfUiEnv$num)
@@ -64,6 +64,7 @@ rxUdfUiIniDf <- function() {
 #' Return the lhs parsed language expression
 #'
 #' @return lhs language expression or NULL
+#' @family User functions
 #' @export
 #' @author Matthew L. Fidler
 #' @examples
@@ -87,6 +88,7 @@ rxUdfUiIniLhs <- function() {
 #'
 #' @return value of the `modelVariables` being processed or `NULL`.
 #'
+#' @family User functions
 #' @export
 #' @author Matthew L. Fidler
 #' @examples
@@ -113,6 +115,7 @@ rxUdfUiMv <- function(value) {
 #' @return value of the `data.frame` being processed or `NULL`.
 #'
 #' @export
+#' @family User functions
 #' @author Matthew L. Fidler
 #' @examples
 #'
@@ -135,6 +138,7 @@ rxUdfUiData <- function(value) {
 #' @param value when specified, this assigns the character value of
 #'   the estimation method or NULL if there is nothing being estimated
 #' @return value of the estimation method being processed or NULL
+#' @family User functions
 #' @export
 #' @author Matthew L. Fidler
 #' @examples
@@ -156,6 +160,7 @@ rxUdfUiEst <- function(value) {
 #' Returns if the current ui function is being parsed
 #'
 #' @return logical if the current ui function is being parsed
+#' @family User functions
 #' @export
 #' @author Matthew L. Fidler
 #' @examples
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 838f424c9..a4b51a1d3 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -55,6 +55,7 @@ reference:
   - rxUiCompress
   - rxUiDecompress
   - rxode2<-
+  - testIniDf
   - testRxLinCmt
   - testRxUnbounded
   - update.rxUi
@@ -160,6 +161,18 @@ reference:
   - rxSymInvChol
   - swapMatListWithCube
   - uppergamma
+- title: User functions
+  contents:
+  - linMod
+  - rxIntToBase
+  - rxIntToLetter
+  - rxUdfUiData
+  - rxUdfUiEst
+  - rxUdfUiIniDf
+  - rxUdfUiIniLhs
+  - rxUdfUiMv
+  - rxUdfUiNum
+  - rxUdfUiParsing
 - title: Internal Functions
   contents:
   - .cbindOme
diff --git a/man/assertCompartmentExists.Rd b/man/assertCompartmentExists.Rd
index 2b570facb..3784cf354 100644
--- a/man/assertCompartmentExists.Rd
+++ b/man/assertCompartmentExists.Rd
@@ -33,6 +33,7 @@ Other Assertions:
 \code{\link{assertRxUi}()},
 \code{\link{assertVariableExists}()},
 \code{\link{assertVariableNew}()},
+\code{\link{testIniDf}()},
 \code{\link{testRxUnbounded}()}
 }
 \author{
diff --git a/man/assertCompartmentName.Rd b/man/assertCompartmentName.Rd
index d6e121f73..1ab647ffd 100644
--- a/man/assertCompartmentName.Rd
+++ b/man/assertCompartmentName.Rd
@@ -49,6 +49,7 @@ Other Assertions:
 \code{\link{assertRxUi}()},
 \code{\link{assertVariableExists}()},
 \code{\link{assertVariableNew}()},
+\code{\link{testIniDf}()},
 \code{\link{testRxUnbounded}()}
 }
 \author{
diff --git a/man/assertCompartmentNew.Rd b/man/assertCompartmentNew.Rd
index e62fa9703..47ceb0281 100644
--- a/man/assertCompartmentNew.Rd
+++ b/man/assertCompartmentNew.Rd
@@ -24,6 +24,7 @@ Other Assertions:
 \code{\link{assertRxUi}()},
 \code{\link{assertVariableExists}()},
 \code{\link{assertVariableNew}()},
+\code{\link{testIniDf}()},
 \code{\link{testRxUnbounded}()}
 }
 \author{
diff --git a/man/assertRxUi.Rd b/man/assertRxUi.Rd
index ee4d4e725..4dfdbdc86 100644
--- a/man/assertRxUi.Rd
+++ b/man/assertRxUi.Rd
@@ -103,6 +103,7 @@ Other Assertions:
 \code{\link{assertCompartmentNew}()},
 \code{\link{assertVariableExists}()},
 \code{\link{assertVariableNew}()},
+\code{\link{testIniDf}()},
 \code{\link{testRxUnbounded}()}
 }
 \author{
diff --git a/man/assertVariableExists.Rd b/man/assertVariableExists.Rd
index 2f657e098..7cad9157b 100644
--- a/man/assertVariableExists.Rd
+++ b/man/assertVariableExists.Rd
@@ -35,6 +35,7 @@ Other Assertions:
 \code{\link{assertCompartmentNew}()},
 \code{\link{assertRxUi}()},
 \code{\link{assertVariableNew}()},
+\code{\link{testIniDf}()},
 \code{\link{testRxUnbounded}()}
 }
 \author{
diff --git a/man/assertVariableNew.Rd b/man/assertVariableNew.Rd
index b596b60e5..d11298b97 100644
--- a/man/assertVariableNew.Rd
+++ b/man/assertVariableNew.Rd
@@ -24,6 +24,7 @@ Other Assertions:
 \code{\link{assertCompartmentNew}()},
 \code{\link{assertRxUi}()},
 \code{\link{assertVariableExists}()},
+\code{\link{testIniDf}()},
 \code{\link{testRxUnbounded}()}
 }
 \author{
diff --git a/man/linMod.Rd b/man/linMod.Rd
index e3242238f..1b72580dd 100644
--- a/man/linMod.Rd
+++ b/man/linMod.Rd
@@ -102,6 +102,16 @@ Linear model to replace in rxode2 ui model
 
 linMod(x, 3)
 }
+\seealso{
+Other User functions: 
+\code{\link{rxUdfUiData}()},
+\code{\link{rxUdfUiEst}()},
+\code{\link{rxUdfUiIniLhs}()},
+\code{\link{rxUdfUiMv}()},
+\code{\link{rxUdfUiNum}()},
+\code{\link{rxUdfUiParsing}()}
+}
 \author{
 Matthew L. Fidler
 }
+\concept{User functions}
diff --git a/man/rxUdfUiData.Rd b/man/rxUdfUiData.Rd
index c43dd2cc2..284d5369f 100644
--- a/man/rxUdfUiData.Rd
+++ b/man/rxUdfUiData.Rd
@@ -19,7 +19,17 @@ Return the data.frame that is being processed or setup data.frame for processing
 
 rxUdfUiData()
 
+}
+\seealso{
+Other User functions: 
+\code{\link{linMod}()},
+\code{\link{rxUdfUiEst}()},
+\code{\link{rxUdfUiIniLhs}()},
+\code{\link{rxUdfUiMv}()},
+\code{\link{rxUdfUiNum}()},
+\code{\link{rxUdfUiParsing}()}
 }
 \author{
 Matthew L. Fidler
 }
+\concept{User functions}
diff --git a/man/rxUdfUiEst.Rd b/man/rxUdfUiEst.Rd
index c06b705cc..fbcde6a43 100644
--- a/man/rxUdfUiEst.Rd
+++ b/man/rxUdfUiEst.Rd
@@ -20,7 +20,17 @@ Return the current estimation method for the UI processing
 
 rxUdfUiEst()
 
+}
+\seealso{
+Other User functions: 
+\code{\link{linMod}()},
+\code{\link{rxUdfUiData}()},
+\code{\link{rxUdfUiIniLhs}()},
+\code{\link{rxUdfUiMv}()},
+\code{\link{rxUdfUiNum}()},
+\code{\link{rxUdfUiParsing}()}
 }
 \author{
 Matthew L. Fidler
 }
+\concept{User functions}
diff --git a/man/rxUdfUiIniLhs.Rd b/man/rxUdfUiIniLhs.Rd
index 2c45a4d41..1b65b69f5 100644
--- a/man/rxUdfUiIniLhs.Rd
+++ b/man/rxUdfUiIniLhs.Rd
@@ -16,7 +16,17 @@ Return the lhs parsed language expression
 
 rxUdfUiIniLhs()
 
+}
+\seealso{
+Other User functions: 
+\code{\link{linMod}()},
+\code{\link{rxUdfUiData}()},
+\code{\link{rxUdfUiEst}()},
+\code{\link{rxUdfUiMv}()},
+\code{\link{rxUdfUiNum}()},
+\code{\link{rxUdfUiParsing}()}
 }
 \author{
 Matthew L. Fidler
 }
+\concept{User functions}
diff --git a/man/rxUdfUiMv.Rd b/man/rxUdfUiMv.Rd
index d6c9989c1..588f79148 100644
--- a/man/rxUdfUiMv.Rd
+++ b/man/rxUdfUiMv.Rd
@@ -22,7 +22,17 @@ variables for processing
 
 rxUdfUiMv()
 
+}
+\seealso{
+Other User functions: 
+\code{\link{linMod}()},
+\code{\link{rxUdfUiData}()},
+\code{\link{rxUdfUiEst}()},
+\code{\link{rxUdfUiIniLhs}()},
+\code{\link{rxUdfUiNum}()},
+\code{\link{rxUdfUiParsing}()}
 }
 \author{
 Matthew L. Fidler
 }
+\concept{User functions}
diff --git a/man/rxUdfUiNum.Rd b/man/rxUdfUiNum.Rd
index ad161016a..07a5f5e48 100644
--- a/man/rxUdfUiNum.Rd
+++ b/man/rxUdfUiNum.Rd
@@ -17,8 +17,17 @@ UI functions
 \examples{
 
 rxUdfUiNum()
-
+}
+\seealso{
+Other User functions: 
+\code{\link{linMod}()},
+\code{\link{rxUdfUiData}()},
+\code{\link{rxUdfUiEst}()},
+\code{\link{rxUdfUiIniLhs}()},
+\code{\link{rxUdfUiMv}()},
+\code{\link{rxUdfUiParsing}()}
 }
 \author{
 Matthew L. Fidler
 }
+\concept{User functions}
diff --git a/man/rxUdfUiParsing.Rd b/man/rxUdfUiParsing.Rd
index 53ecb6949..eab3e5877 100644
--- a/man/rxUdfUiParsing.Rd
+++ b/man/rxUdfUiParsing.Rd
@@ -15,6 +15,16 @@ Returns if the current ui function is being parsed
 \examples{
 rxUdfUiParsing()
 }
+\seealso{
+Other User functions: 
+\code{\link{linMod}()},
+\code{\link{rxUdfUiData}()},
+\code{\link{rxUdfUiEst}()},
+\code{\link{rxUdfUiIniLhs}()},
+\code{\link{rxUdfUiMv}()},
+\code{\link{rxUdfUiNum}()}
+}
 \author{
 Matthew L. Fidler
 }
+\concept{User functions}
diff --git a/man/testIniDf.Rd b/man/testIniDf.Rd
index aa0713a4b..a82d79451 100644
--- a/man/testIniDf.Rd
+++ b/man/testIniDf.Rd
@@ -36,6 +36,17 @@ This function tests if this object is a iniDf as needed by the UI
 \examples{
 testIniDf(TRUE)
 }
+\seealso{
+Other Assertions: 
+\code{\link{assertCompartmentExists}()},
+\code{\link{assertCompartmentName}()},
+\code{\link{assertCompartmentNew}()},
+\code{\link{assertRxUi}()},
+\code{\link{assertVariableExists}()},
+\code{\link{assertVariableNew}()},
+\code{\link{testRxUnbounded}()}
+}
 \author{
 Matthew L. Fidler
 }
+\concept{Assertions}
diff --git a/man/testRxUnbounded.Rd b/man/testRxUnbounded.Rd
index bf914828f..21b013508 100644
--- a/man/testRxUnbounded.Rd
+++ b/man/testRxUnbounded.Rd
@@ -65,7 +65,8 @@ Other Assertions:
 \code{\link{assertCompartmentNew}()},
 \code{\link{assertRxUi}()},
 \code{\link{assertVariableExists}()},
-\code{\link{assertVariableNew}()}
+\code{\link{assertVariableNew}()},
+\code{\link{testIniDf}()}
 }
 \author{
 Matthew L. Fidler