From dd9ce549f4abd73084b695e41dbe139e8eb0fe2a Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Sat, 4 Nov 2023 22:36:00 -0500
Subject: [PATCH] ::document and use rxode2::rxReservedKeywords

---
 R/symengine.R               |   4 ++--
 data/rxReservedKeywords.rda | Bin 736 -> 733 bytes
 data/rxResidualError.rda    | Bin 1691 -> 1694 bytes
 data/rxSyntaxFunctions.rda  | Bin 2451 -> 2446 bytes
 man/reexports.Rd            |   1 -
 man/rxFun.Rd                |  21 +++++++++++++++++++++
 man/rxSolve.Rd              |  12 ++++++++----
 man/rxode2.Rd               |  14 ++++++++++++--
 8 files changed, 43 insertions(+), 9 deletions(-)

diff --git a/R/symengine.R b/R/symengine.R
index 9b33128b6..03c649e1e 100644
--- a/R/symengine.R
+++ b/R/symengine.R
@@ -3268,8 +3268,8 @@ rxSupportedFuns <- function() {
   x <- as.character(x)
   if (!exists("res", envir=envir)) {
     envir$res <- c(rxSupportedFuns(),
-                    rxReservedKeywords[, 1],
-                    strsplit(paste(rxReservedKeywords[, 3],collapse=","),"[,]+")[[1]])
+                    rxode2::rxReservedKeywords[, 1],
+                    strsplit(paste(rxode2::rxReservedKeywords[, 3],collapse=","),"[,]+")[[1]])
   }
   if (x %in% envir$funs) {
     return(paste0("_qf_", x))
diff --git a/data/rxReservedKeywords.rda b/data/rxReservedKeywords.rda
index 9e7cff144d4614822729e63d65692d7c3df83454..80fc13cd1332ee7e68cacfe73ae72df8290d41e0 100644
GIT binary patch
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diff --git a/data/rxResidualError.rda b/data/rxResidualError.rda
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diff --git a/data/rxSyntaxFunctions.rda b/data/rxSyntaxFunctions.rda
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AU;qFB

delta 2439
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F+n~!(M0x-K

diff --git a/man/reexports.Rd b/man/reexports.Rd
index 365c14ab7..f1310e9e9 100644
--- a/man/reexports.Rd
+++ b/man/reexports.Rd
@@ -82,4 +82,3 @@ below to see their documentation.
   \item{rxode2random}{\code{\link[rxode2random:dot-cbindOme]{.cbindOme}}, \code{\link[rxode2random:dot-expandPars]{.expandPars}}, \code{\link[rxode2random:dot-vecDf]{.vecDf}}, \code{\link[rxode2random]{cvPost}}, \code{\link[rxode2random]{invWR1d}}, \code{\link[rxode2random]{phi}}, \code{\link[rxode2random]{rinvchisq}}, \code{\link[rxode2random]{rLKJ1}}, \code{\link[rxode2random]{rxGetSeed}}, \code{\link[rxode2random]{rxGetSeed}}, \code{\link[rxode2random]{rxRmvn}}, \code{\link[rxode2random]{rxSeedEng}}, \code{\link[rxode2random]{rxSetSeed}}, \code{\link[rxode2random]{rxSetSeed}}, \code{\link[rxode2random]{rxSetSeed}}, \code{\link[rxode2random:rxWithSeed]{rxWithPreserveSeed}}, \code{\link[rxode2random]{rxWithSeed}}, \code{\link[rxode2random]{rxWithSeed}}}
 }}
 
-\value{ Inherited from parent routine }
diff --git a/man/rxFun.Rd b/man/rxFun.Rd
index 77c8e3c6f..2228d3a55 100644
--- a/man/rxFun.Rd
+++ b/man/rxFun.Rd
@@ -113,5 +113,26 @@ rxSolve(f, e)
 rxRmFun("gg")
 rm(gg)
 rm(f)
+
+
+# You can also automatically convert a R function to R code (and
+# calculate first derivatives)
+
+fun <- function(a, b, c) {
+  a^2+b*a+c
+}
+
+rxFun(fun)
+
+# You can see the R code if you want with rxC
+
+message(rxC("fun"))
+
+# you can also remove both the function and the
+# derivatives with rxRmFun("fun")
+
+rxRmFun("fun")
+
+
 }
 }
diff --git a/man/rxSolve.Rd b/man/rxSolve.Rd
index f90f627a3..4bd3d557a 100644
--- a/man/rxSolve.Rd
+++ b/man/rxSolve.Rd
@@ -155,7 +155,8 @@ rxSolve(
   inits = NULL,
   ...,
   theta = NULL,
-  eta = NULL
+  eta = NULL,
+  envir = parent.frame()
 )
 
 \method{rxSolve}{rxode2tos}(
@@ -165,7 +166,8 @@ rxSolve(
   inits = NULL,
   ...,
   theta = NULL,
-  eta = NULL
+  eta = NULL,
+  envir = parent.frame()
 )
 
 \method{rxSolve}{nlmixr2FitData}(
@@ -175,7 +177,8 @@ rxSolve(
   inits = NULL,
   ...,
   theta = NULL,
-  eta = NULL
+  eta = NULL,
+  envir = parent.frame()
 )
 
 \method{rxSolve}{nlmixr2FitCore}(
@@ -185,7 +188,8 @@ rxSolve(
   inits = NULL,
   ...,
   theta = NULL,
-  eta = NULL
+  eta = NULL,
+  envir = parent.frame()
 )
 
 \method{rxSolve}{default}(
diff --git a/man/rxode2.Rd b/man/rxode2.Rd
index 1a7a3c176..dc6d9aeb7 100644
--- a/man/rxode2.Rd
+++ b/man/rxode2.Rd
@@ -232,6 +232,9 @@ mod <- rxode2(\{
   d/dt(centr) <- F*KA*depot - CL*C2 - Q*C2 + Q*C3;
 \})
 }\if{html}{\out{</div>}}
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{## using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+}\if{html}{\out{</div>}}
 \itemize{
 \item Inside a \code{rxode2("")} string statement:
 }\if{html}{\out{
@@ -247,6 +250,9 @@ mod <- rxode2(\{
   d/dt(centr) <- F*KA*depot - CL*C2 - Q*C2 + Q*C3;
 ")
 }\if{html}{\out{</div>}}
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{## using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+}\if{html}{\out{</div>}}
 \itemize{
 \item In a file name to be loaded by rxode2:
 }\if{html}{\out{
@@ -325,7 +331,9 @@ compilation model.
 \if{html}{\out{<div class="sourceCode r">}}\preformatted{mod$simulationModel
 }\if{html}{\out{</div>}}
 
-\if{html}{\out{<div class="sourceCode">}}\preformatted{## rxode2 2.0.14.9000 model named rx_8223e497c83db9e334c52254bd575c98 model (ready). 
+\if{html}{\out{<div class="sourceCode">}}\preformatted{## using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+
+## rxode2 2.0.14.9000 model named rx_4d7e23c27b311c0b8fa7436caae3124f model (ready). 
 ## x$state: depot, center
 ## x$stateExtra: cp
 ## x$params: tka, tcl, tv, add.sd, eta.ka, eta.cl, eta.v, rxerr.cp
@@ -336,7 +344,9 @@ compilation model.
 mod$simulationIniModel
 }\if{html}{\out{</div>}}
 
-\if{html}{\out{<div class="sourceCode">}}\preformatted{## rxode2 2.0.14.9000 model named rx_182c47efea379394bbab84d957305170 model (ready). 
+\if{html}{\out{<div class="sourceCode">}}\preformatted{## using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
+
+## rxode2 2.0.14.9000 model named rx_175d15ed553ae1eccaf047d565b24f55 model (ready). 
 ## x$state: depot, center
 ## x$stateExtra: cp
 ## x$params: tka, tcl, tv, add.sd, eta.ka, eta.cl, eta.v, rxerr.cp