From 86ffe384f3a954d86cbd02f2603305591b5c7332 Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Tue, 5 Dec 2023 12:47:04 -0600
Subject: [PATCH 1/6] .iniGetAppendArg to start aligning ini() and model()

---
 NAMESPACE                        |   1 +
 R/piping-ini.R                   |  51 +++++++++++++++++++++++++++++--
 data/rxReservedKeywords.rda      | Bin 735 -> 733 bytes
 data/rxResidualError.rda         | Bin 1694 -> 1694 bytes
 data/rxSyntaxFunctions.rda       | Bin 2439 -> 2446 bytes
 man/dot-iniGetAppendArg.Rd       |  26 ++++++++++++++++
 man/rxode2.Rd                    |  14 +++++++--
 tests/testthat/test-piping-ini.R |  13 +++++++-
 8 files changed, 100 insertions(+), 5 deletions(-)
 create mode 100644 man/dot-iniGetAppendArg.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 639ef73f2..a3797a01b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -197,6 +197,7 @@ export(.copyUi)
 export(.expandPars)
 export(.getLastIdLvl)
 export(.handleSingleErrTypeNormOrTFoceiBase)
+export(.iniGetAppendArg)
 export(.iniHandleFixOrUnfix)
 export(.iniHandleLine)
 export(.malert)
diff --git a/R/piping-ini.R b/R/piping-ini.R
index b923908b8..283576ade 100644
--- a/R/piping-ini.R
+++ b/R/piping-ini.R
@@ -369,7 +369,8 @@
     checkmate::assert_choice(append, choices = ini$name)
     appendClean <- which(ini$name == append)
   } else {
-    stop("'append' must be NULL, logical, numeric, or character", call. = FALSE)
+    stop("'append' must be NULL, logical, numeric, or character/expression of variable in model",
+         call. = FALSE)
   }
 
   lhs <- as.character(expr[[2]])
@@ -667,16 +668,59 @@
   }
   expr
 }
+#' This gets the append arg for the ini({}) piping
+#'
+#' @param f this is the `try(force(append))` argument,
+#' @param s this is the `as.character(substitute(append))` argument
+#' @return corrected ini piping argument
+#'
+#' This is exported for creating new ini methods that have the same
+#' requirements for piping
+#'
+#' @export
+#' @author Matthew L. Fidler
+#' @keywords internal
+.iniGetAppendArg <- function(f, s) {
+  if (inherits(f, "try-error") &&
+        checkmate::testCharacter(s, len=1, any.missing=FALSE,
+                                 pattern="^[.]*[a-zA-Z]+[a-zA-Z0-9._]*$",
+                                 min.chars = 1)) {
+    return(s)
+  }
+  if (is.null(f)) {
+    return(NULL)
+  } else if (checkmate::testCharacter(f, len=1, any.missing=FALSE,
+                               pattern="^[.]*[a-zA-Z]+[a-zA-Z0-9._]*$",
+                               min.chars = 1)) {
+    return(f)
+  } else if (is.infinite(f)) {
+    return(f)
+  } else if (checkmate::testIntegerish(f, len=1, any.missing=FALSE)) {
+    if (f < 0) {
+      stop("'append' cannot be a negative integer", call.=FALSE)
+    }
+    return(f)
+  } else if (checkmate::testLogical(f, len=1)) {
+    # NA for model piping prepends
+    if (is.na(f)) return(FALSE)
+    return(f)
+  }
+  stop("'append' must be NULL, logical, numeric, or character/expression of variable in model",
+       call.=FALSE)
+}
 
 #' @export
 #' @rdname ini
 ini.rxUi <- function(x, ..., envir=parent.frame(), append = NULL) {
+  .s  <- as.character(substitute(append))
+  .f <- try(force(append), silent=TRUE)
+  append <- .iniGetAppendArg(.f, .s)
   .ret <- rxUiDecompress(.copyUi(x)) # copy so (as expected) old UI isn't affected by the call
   .iniDf <- .ret$iniDf
   .iniLines <- .quoteCallInfoLines(match.call(expand.dots = TRUE)[-(1:2)], envir=envir, iniDf= .iniDf)
   if (length(.iniLines) == 0L) return(.ret$iniFun)
   lapply(.iniLines, function(line) {
-    .iniHandleLine(expr = line, rxui = .ret, envir = envir, append = append)
+    .iniHandleLine(expr = line, rxui = .ret, envir = envir, append=append)
   })
   if (inherits(x, "rxUi")) {
     .x <- rxUiDecompress(x)
@@ -695,6 +739,9 @@ ini.rxUi <- function(x, ..., envir=parent.frame(), append = NULL) {
 #' @rdname ini
 #' @export
 ini.default <- function(x, ..., envir=parent.frame(), append = NULL) {
+  .s  <- as.character(substitute(append))
+  .f <- try(force(append), silent=TRUE)
+  append <- .iniGetAppendArg(.f, .s)
   .ret <- try(as.rxUi(x), silent = TRUE)
   if (inherits(.ret, "try-error")) {
     stop("cannot figure out what to do with the ini({}) function", call.=FALSE)
diff --git a/data/rxReservedKeywords.rda b/data/rxReservedKeywords.rda
index 310c21c71569c2828be7b511ca538d5f198f14e8..80fc13cd1332ee7e68cacfe73ae72df8290d41e0 100644
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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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diff --git a/man/dot-iniGetAppendArg.Rd b/man/dot-iniGetAppendArg.Rd
new file mode 100644
index 000000000..14d2fd49c
--- /dev/null
+++ b/man/dot-iniGetAppendArg.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/piping-ini.R
+\name{.iniGetAppendArg}
+\alias{.iniGetAppendArg}
+\title{This gets the append arg for the ini({}) piping}
+\usage{
+.iniGetAppendArg(f, s)
+}
+\arguments{
+\item{f}{this is the \code{try(force(append))} argument,}
+
+\item{s}{this is the \code{as.character(substitute(append))} argument}
+}
+\value{
+corrected ini piping argument
+
+This is exported for creating new ini methods that have the same
+requirements for piping
+}
+\description{
+This gets the append arg for the ini({}) piping
+}
+\author{
+Matthew L. Fidler
+}
+\keyword{internal}
diff --git a/man/rxode2.Rd b/man/rxode2.Rd
index 415c922b4..9de61ca9a 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_9140ece6c151a5d4341598adc0f7f3b6 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_85848c9248e14e8cbf9a9b4a606b2010 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_3696701c79e711bcf4b2c8ac921b3f65 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_40b4a6f44b577c0e14f674ccc10f618e model (ready). 
 ## x$state: depot, center
 ## x$stateExtra: cp
 ## x$params: tka, tcl, tv, add.sd, eta.ka, eta.cl, eta.v, rxerr.cp
diff --git a/tests/testthat/test-piping-ini.R b/tests/testthat/test-piping-ini.R
index b7f655d0a..a600133ea 100644
--- a/tests/testthat/test-piping-ini.R
+++ b/tests/testthat/test-piping-ini.R
@@ -145,6 +145,7 @@ test_that(".iniSimplifyAssignArrow", {
 })
 
 test_that("piping with ini can update reorder parameters (rxode2/issues#352)", {
+
   mod <- function() {
     ini({
       a <- 1
@@ -157,7 +158,9 @@ test_that("piping with ini can update reorder parameters (rxode2/issues#352)", {
       b ~ add(addSd)
     })
   }
+
   ui <- rxode2(mod)
+
   # No modification
   expect_equal(ui$iniDf$name, c("a", "b", "c", "addSd"))
   # b to the top by number
@@ -170,6 +173,9 @@ test_that("piping with ini can update reorder parameters (rxode2/issues#352)", {
   expect_equal(suppressMessages(ini(ui, b <- 1, append = TRUE))$iniDf$name, c("a", "c", "addSd", "b"))
   # b to the bottom by name
   expect_equal(suppressMessages(ini(ui, b <- 1, append = "addSd"))$iniDf$name, c("a", "c", "addSd", "b"))
+
+  expect_equal(suppressMessages(ini(ui, b <- 1, append = addSd))$iniDf$name, c("a", "c", "addSd", "b"))
+
   # b after c
   expect_equal(suppressMessages(ini(ui, b <- 1, append = "c"))$iniDf$name, c("a", "c", "b", "addSd"))
   # a and b after c; counter-intuitive: the order of a and b are reversed
@@ -180,11 +186,16 @@ test_that("piping with ini can update reorder parameters (rxode2/issues#352)", {
     regexp = "parameter 'b' set to be moved after itself, no change in order made"
   )
 
+  expect_error(
+    ini(ui, b <- 1, append = d/dt(fun)),
+  "append")
+
   # Invalid parameter is correctly caught
   expect_error(
     ini(ui, b <- 1, append = "foo"),
     "append"
   )
+
 })
 
 test_that(".iniAddCovarianceBetweenTwoEtaValues", {
@@ -277,7 +288,7 @@ test_that(".iniHandleAppend", {
   }
   expect_error(
     ini(mod, a <- 1, append=factor("A")),
-    regexp = "'append' must be NULL, logical, numeric, or character"
+    regexp = "'append' must be NULL, logical, numeric, or character/expression of variable in model"
   )
   expect_error(
     ini(mod, q <- 1, append=0),

From e18bec776a59534b4516c326da44b27b36aa9e12 Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Tue, 5 Dec 2023 14:02:08 -0600
Subject: [PATCH 2/6] align argument types with ini(append)

---
 R/piping-ini.R                   |  4 ++--
 R/piping-model.R                 | 25 +++++++++++++++++++++----
 R/piping.R                       |  2 +-
 man/dot-modelHandleModelLines.Rd |  2 +-
 man/model.Rd                     |  8 ++++----
 man/reexports.Rd                 |  1 -
 man/rxode2.Rd                    | 14 ++------------
 tests/testthat/test-piping-ini.R |  1 +
 8 files changed, 32 insertions(+), 25 deletions(-)

diff --git a/R/piping-ini.R b/R/piping-ini.R
index 283576ade..f636d3add 100644
--- a/R/piping-ini.R
+++ b/R/piping-ini.R
@@ -690,8 +690,8 @@
   if (is.null(f)) {
     return(NULL)
   } else if (checkmate::testCharacter(f, len=1, any.missing=FALSE,
-                               pattern="^[.]*[a-zA-Z]+[a-zA-Z0-9._]*$",
-                               min.chars = 1)) {
+                                      pattern="^[.]*[a-zA-Z]+[a-zA-Z0-9._]*$",
+                                      min.chars = 1)) {
     return(f)
   } else if (is.infinite(f)) {
     return(f)
diff --git a/R/piping-model.R b/R/piping-model.R
index df4f62812..b62c8ea5a 100644
--- a/R/piping-model.R
+++ b/R/piping-model.R
@@ -1,6 +1,6 @@
 #' @export
 #' @rdname model
-model.function <- function(x, ..., append=FALSE, auto=getOption("rxode2.autoVarPiping", TRUE),
+model.function <- function(x, ..., append=NULL, auto=getOption("rxode2.autoVarPiping", TRUE),
                            cov=NULL, envir=parent.frame()) {
   .modelLines <- .quoteCallInfoLines(match.call(expand.dots = TRUE)[-(1:2)], envir=envir)
   .ret <- rxUiDecompress(rxode2(x))
@@ -11,7 +11,7 @@ model.function <- function(x, ..., append=FALSE, auto=getOption("rxode2.autoVarP
 
 #' @export
 #' @rdname model
-model.rxUi <- function(x, ..., append=FALSE, auto=getOption("rxode2.autoVarPiping", TRUE),
+model.rxUi <- function(x, ..., append=NULL, auto=getOption("rxode2.autoVarPiping", TRUE),
                        cov=NULL, envir=parent.frame()) {
   .modelLines <- .quoteCallInfoLines(match.call(expand.dots = TRUE)[-(1:2)], envir=envir)
   .ret <- rxUiDecompress(.copyUi(x)) # copy so (as expected) old UI isn't affected by the call
@@ -32,7 +32,7 @@ model.rxUi <- function(x, ..., append=FALSE, auto=getOption("rxode2.autoVarPipin
 
 #' @export
 #' @rdname model
-model.rxode2 <- function(x, ..., append=FALSE, auto=getOption("rxode2.autoVarPiping", TRUE),
+model.rxode2 <- function(x, ..., append=NULL, auto=getOption("rxode2.autoVarPiping", TRUE),
                          cov=NULL, envir=parent.frame()) {
   .modelLines <- .quoteCallInfoLines(match.call(expand.dots = TRUE)[-(1:2)], envir=envir)
   x <- as.function(x)
@@ -56,7 +56,7 @@ model.rxModelVars <- model.rxode2
 #' @return New UI
 #' @author Matthew L. Fidler
 #' @export
-.modelHandleModelLines <- function(modelLines, rxui, modifyIni=FALSE, append=FALSE,
+.modelHandleModelLines <- function(modelLines, rxui, modifyIni=FALSE, append=NULL,
                                    auto=getOption("rxode2.autoVarPiping", TRUE),
                                    cov=NULL, envir) {
   checkmate::assertLogical(modifyIni, any.missing=FALSE, len=1)
@@ -68,6 +68,23 @@ model.rxModelVars <- model.rxode2
   rxui <- rxUiDecompress(rxui)
   if (!is.null(.nsEnv$.quoteCallInfoLinesAppend)) {
     .ll <- length(rxui$lstExpr)
+    if (identical(.nsEnv$.quoteCallInfoLinesAppend, quote(Inf))) {
+      .nsEnv$.quoteCallInfoLinesAppend <- TRUE
+    } else if (identical(.nsEnv$.quoteCallInfoLinesAppend, quote(-Inf))) {
+      .nsEnv$.quoteCallInfoLinesAppend <- NA
+    } else if (identical(.nsEnv$.quoteCallInfoLinesAppend, quote(FALSE))) {
+      .nsEnv$.quoteCallInfoLinesAppend <- NA
+    } else if (identical(.nsEnv$.quoteCallInfoLinesAppend, quote(0))) {
+      .nsEnv$.quoteCallInfoLinesAppend <- NA
+    } else if (checkmate::testIntegerish(.nsEnv$.quoteCallInfoLinesAppend, lower=.ll)) {
+      .nsEnv$.quoteCallInfoLinesAppend <- TRUE
+    } else if (checkmate::testIntegerish(.nsEnv$.quoteCallInfoLinesAppend, lower=0, upper=.ll)) {
+      .nsEnv$.quoteCallInfoLinesAppend <- .getLhs(rxui$lstExpr[[.nsEnv$.quoteCallInfoLinesAppend]])
+    } else if (checkmate::testCharacter(.nsEnv$.quoteCallInfoLinesAppend, len=1, any.missing=FALSE,
+                                        pattern="^[.]*[a-zA-Z]+[a-zA-Z0-9._]*$",
+                                        min.chars = 1)) {
+      .nsEnv$.quoteCallInfoLinesAppend <- str2lang(.nsEnv$.quoteCallInfoLinesAppend)
+    }
     .w <- which(vapply(seq_len(.ll),
                        function(i) {
                          .lhs <- .getLhs(rxui$lstExpr[[i]])
diff --git a/R/piping.R b/R/piping.R
index 93da808b6..b75984aeb 100644
--- a/R/piping.R
+++ b/R/piping.R
@@ -1,4 +1,4 @@
-#'  This copies the rxode2 UI object so it can be modified
+#' This copies the rxode2 UI object so it can be modified
 #'
 #' @param ui Original UI object
 #' @return Copied UI object
diff --git a/man/dot-modelHandleModelLines.Rd b/man/dot-modelHandleModelLines.Rd
index e9cb9b76b..a60da6ef4 100644
--- a/man/dot-modelHandleModelLines.Rd
+++ b/man/dot-modelHandleModelLines.Rd
@@ -8,7 +8,7 @@
   modelLines,
   rxui,
   modifyIni = FALSE,
-  append = FALSE,
+  append = NULL,
   auto = getOption("rxode2.autoVarPiping", TRUE),
   cov = NULL,
   envir
diff --git a/man/model.Rd b/man/model.Rd
index 02f0ca563..bc081d0a9 100644
--- a/man/model.Rd
+++ b/man/model.Rd
@@ -12,7 +12,7 @@
 \method{model}{`function`}(
   x,
   ...,
-  append = FALSE,
+  append = NULL,
   auto = getOption("rxode2.autoVarPiping", TRUE),
   cov = NULL,
   envir = parent.frame()
@@ -21,7 +21,7 @@
 \method{model}{rxUi}(
   x,
   ...,
-  append = FALSE,
+  append = NULL,
   auto = getOption("rxode2.autoVarPiping", TRUE),
   cov = NULL,
   envir = parent.frame()
@@ -30,7 +30,7 @@
 \method{model}{rxode2}(
   x,
   ...,
-  append = FALSE,
+  append = NULL,
   auto = getOption("rxode2.autoVarPiping", TRUE),
   cov = NULL,
   envir = parent.frame()
@@ -39,7 +39,7 @@
 \method{model}{rxModelVars}(
   x,
   ...,
-  append = FALSE,
+  append = NULL,
   auto = getOption("rxode2.autoVarPiping", TRUE),
   cov = NULL,
   envir = parent.frame()
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/rxode2.Rd b/man/rxode2.Rd
index 9de61ca9a..43b14e371 100644
--- a/man/rxode2.Rd
+++ b/man/rxode2.Rd
@@ -232,9 +232,6 @@ 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{
@@ -250,9 +247,6 @@ 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{
@@ -331,9 +325,7 @@ compilation model.
 \if{html}{\out{<div class="sourceCode r">}}\preformatted{mod$simulationModel
 }\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’
-
-## rxode2 2.0.14.9000 model named rx_85848c9248e14e8cbf9a9b4a606b2010 model (ready). 
+\if{html}{\out{<div class="sourceCode">}}\preformatted{## rxode2 2.0.14.9000 model named rx_85848c9248e14e8cbf9a9b4a606b2010 model (ready). 
 ## x$state: depot, center
 ## x$stateExtra: cp
 ## x$params: tka, tcl, tv, add.sd, eta.ka, eta.cl, eta.v, rxerr.cp
@@ -344,9 +336,7 @@ compilation model.
 mod$simulationIniModel
 }\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’
-
-## rxode2 2.0.14.9000 model named rx_40b4a6f44b577c0e14f674ccc10f618e model (ready). 
+\if{html}{\out{<div class="sourceCode">}}\preformatted{## rxode2 2.0.14.9000 model named rx_40b4a6f44b577c0e14f674ccc10f618e model (ready). 
 ## x$state: depot, center
 ## x$stateExtra: cp
 ## x$params: tka, tcl, tv, add.sd, eta.ka, eta.cl, eta.v, rxerr.cp
diff --git a/tests/testthat/test-piping-ini.R b/tests/testthat/test-piping-ini.R
index a600133ea..a0b63fedf 100644
--- a/tests/testthat/test-piping-ini.R
+++ b/tests/testthat/test-piping-ini.R
@@ -286,6 +286,7 @@ test_that(".iniHandleAppend", {
       b ~ add(addSd)
     })
   }
+
   expect_error(
     ini(mod, a <- 1, append=factor("A")),
     regexp = "'append' must be NULL, logical, numeric, or character/expression of variable in model"

From 7eb86db122c7005ebbd7c370af7afa7cad34f95a Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Tue, 5 Dec 2023 14:45:04 -0600
Subject: [PATCH 3/6] Add some tests and fixes for appending models

---
 R/piping-model.R                | 12 ++++----
 tests/testthat/test-ui-piping.R | 51 +++++++++++++++++++++++++++++++++
 2 files changed, 58 insertions(+), 5 deletions(-)

diff --git a/R/piping-model.R b/R/piping-model.R
index b62c8ea5a..ba41337ea 100644
--- a/R/piping-model.R
+++ b/R/piping-model.R
@@ -72,8 +72,6 @@ model.rxModelVars <- model.rxode2
       .nsEnv$.quoteCallInfoLinesAppend <- TRUE
     } else if (identical(.nsEnv$.quoteCallInfoLinesAppend, quote(-Inf))) {
       .nsEnv$.quoteCallInfoLinesAppend <- NA
-    } else if (identical(.nsEnv$.quoteCallInfoLinesAppend, quote(FALSE))) {
-      .nsEnv$.quoteCallInfoLinesAppend <- NA
     } else if (identical(.nsEnv$.quoteCallInfoLinesAppend, quote(0))) {
       .nsEnv$.quoteCallInfoLinesAppend <- NA
     } else if (checkmate::testIntegerish(.nsEnv$.quoteCallInfoLinesAppend, lower=.ll)) {
@@ -81,9 +79,13 @@ model.rxModelVars <- model.rxode2
     } else if (checkmate::testIntegerish(.nsEnv$.quoteCallInfoLinesAppend, lower=0, upper=.ll)) {
       .nsEnv$.quoteCallInfoLinesAppend <- .getLhs(rxui$lstExpr[[.nsEnv$.quoteCallInfoLinesAppend]])
     } else if (checkmate::testCharacter(.nsEnv$.quoteCallInfoLinesAppend, len=1, any.missing=FALSE,
-                                        pattern="^[.]*[a-zA-Z]+[a-zA-Z0-9._]*$",
                                         min.chars = 1)) {
-      .nsEnv$.quoteCallInfoLinesAppend <- str2lang(.nsEnv$.quoteCallInfoLinesAppend)
+      .tmp <- try(str2lang(.nsEnv$.quoteCallInfoLinesAppend), silent=TRUE)
+      if (inherits(.tmp, "try-error")) {
+        stop("'append' must refer to a model line when a character",
+             call. = FALSE)
+      }
+      .nsEnv$.quoteCallInfoLinesAppend <- .tmp
     }
     .w <- which(vapply(seq_len(.ll),
                        function(i) {
@@ -129,7 +131,7 @@ model.rxModelVars <- model.rxode2
              envir=rxui)
     }
     .doAppend <- TRUE
-  } else if (is.logical(append) && length(append) == 1L && is.na(append)) {
+  } else if (is.logical(append) && length(append) == 1L && (is.na(append) || !append)) {
     assign("lstExpr", c(modelLines, rxui$lstExpr), envir=rxui)
     .doAppend <- TRUE
   } else if (isTRUE(append)) {
diff --git a/tests/testthat/test-ui-piping.R b/tests/testthat/test-ui-piping.R
index 2aac8fe55..24027b836 100644
--- a/tests/testthat/test-ui-piping.R
+++ b/tests/testthat/test-ui-piping.R
@@ -2037,6 +2037,17 @@ test_that("piping append", {
 
   expect_equal(mod5$theta, c(tka = 0.45, tcl = 1, tv = 3.45, add.sd = 0.7))
 
+  mod5 <- mod |>
+    model({
+      PD <- 1-emax*cp/(ec50+cp)
+      ##
+      effect(0) <- e0
+      kin <- e0*kout
+      d/dt(effect) <- kin*PD -kout*effect
+    }, append="d/dt(center)")
+
+  expect_equal(mod5$theta, c(tka = 0.45, tcl = 1, tv = 3.45, add.sd = 0.7))
+
   mod6 <- mod5 |>
     model({
       emax <- exp(temax)
@@ -2057,6 +2068,46 @@ test_that("piping append", {
       eta.e0 ~ 1
     }))
 
+  mod6 <- mod5 |>
+    model({
+      emax <- exp(temax)
+      e0 <- exp(te0 + eta.e0)
+      ec50 <- exp(tec50)
+      kin <- exp(tkin)
+      kout <- exp(tkout)
+    }, append=FALSE)
+
+  expect_equal(
+    mod6$omega,
+    lotri({
+      eta.cl ~ 0.3
+      eta.v ~ 0.1
+      eta.e0 ~ 1
+    }))
+
+  expect_equal(mod6$theta,
+               c(tka = 0.45, tcl = 1, tv = 3.45, add.sd = 0.7, temax = 1, te0 = 1, tec50 = 1, tkin = 1, tkout = 1))
+
+  mod6 <- mod5 |>
+    model({
+      emax <- exp(temax)
+      e0 <- exp(te0 + eta.e0)
+      ec50 <- exp(tec50)
+      kin <- exp(tkin)
+      kout <- exp(tkout)
+    }, append=0)
+
+  expect_equal(
+    mod6$omega,
+    lotri({
+      eta.cl ~ 0.3
+      eta.v ~ 0.1
+      eta.e0 ~ 1
+    }))
+
+  expect_equal(mod6$theta,
+               c(tka = 0.45, tcl = 1, tv = 3.45, add.sd = 0.7, temax = 1, te0 = 1, tec50 = 1, tkin = 1, tkout = 1))
+
   # make sure auto model piping turns off
 
   withr::with_options(list(rxode2.autoVarPiping=FALSE),

From 6083cb2ff6f0ef154c3d60a1306a95f0a23f1e38 Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Tue, 5 Dec 2023 14:56:02 -0600
Subject: [PATCH 4/6] Align/test behavior of append in `ini()` and `model()`
 piping

---
 R/piping-model.R                | 21 ++++++++++++++-------
 tests/testthat/test-ui-piping.R | 12 ++++++++++++
 2 files changed, 26 insertions(+), 7 deletions(-)

diff --git a/R/piping-model.R b/R/piping-model.R
index ba41337ea..c6633755f 100644
--- a/R/piping-model.R
+++ b/R/piping-model.R
@@ -66,23 +66,30 @@ model.rxModelVars <- model.rxode2
   .varSelect$cov <- cov
   .doAppend <- FALSE
   rxui <- rxUiDecompress(rxui)
+  .ll <- length(rxui$lstExpr)
   if (!is.null(.nsEnv$.quoteCallInfoLinesAppend)) {
-    .ll <- length(rxui$lstExpr)
     if (identical(.nsEnv$.quoteCallInfoLinesAppend, quote(Inf))) {
-      .nsEnv$.quoteCallInfoLinesAppend <- TRUE
+      .nsEnv$.quoteCallInfoLinesAppend <- NULL
+      append <- TRUE
     } else if (identical(.nsEnv$.quoteCallInfoLinesAppend, quote(-Inf))) {
-      .nsEnv$.quoteCallInfoLinesAppend <- NA
+      .nsEnv$.quoteCallInfoLinesAppend <- NULL
+      append <- NA
     } else if (identical(.nsEnv$.quoteCallInfoLinesAppend, quote(0))) {
-      .nsEnv$.quoteCallInfoLinesAppend <- NA
+      .nsEnv$.quoteCallInfoLinesAppend <- NULL
+      append <- NA
     } else if (checkmate::testIntegerish(.nsEnv$.quoteCallInfoLinesAppend, lower=.ll)) {
-      .nsEnv$.quoteCallInfoLinesAppend <- TRUE
-    } else if (checkmate::testIntegerish(.nsEnv$.quoteCallInfoLinesAppend, lower=0, upper=.ll)) {
+      .nsEnv$.quoteCallInfoLinesAppend <- NULL
+      append <- TRUE
+    }
+  }
+  if (!is.null(.nsEnv$.quoteCallInfoLinesAppend)) {
+    if (checkmate::testIntegerish(.nsEnv$.quoteCallInfoLinesAppend, lower=0, upper=.ll)) {
       .nsEnv$.quoteCallInfoLinesAppend <- .getLhs(rxui$lstExpr[[.nsEnv$.quoteCallInfoLinesAppend]])
     } else if (checkmate::testCharacter(.nsEnv$.quoteCallInfoLinesAppend, len=1, any.missing=FALSE,
                                         min.chars = 1)) {
       .tmp <- try(str2lang(.nsEnv$.quoteCallInfoLinesAppend), silent=TRUE)
       if (inherits(.tmp, "try-error")) {
-        stop("'append' must refer to a model line when a character",
+        stop("'append' must refer to a LHS model line when a character",
              call. = FALSE)
       }
       .nsEnv$.quoteCallInfoLinesAppend <- .tmp
diff --git a/tests/testthat/test-ui-piping.R b/tests/testthat/test-ui-piping.R
index 24027b836..0103e6420 100644
--- a/tests/testthat/test-ui-piping.R
+++ b/tests/testthat/test-ui-piping.R
@@ -1428,6 +1428,18 @@ rxTest({
     expect_true("cp1" %in% f2$mv0$lhs)
     expect_equal(f2$lstExpr[[length(f2$lstExpr)]], quote(cp1 <- cp))
 
+    f <- rxode2(ocmt)
+    f2 <- f %>% model(cp1 <- cp, append=Inf)
+
+    expect_true("cp1" %in% f2$mv0$lhs)
+    expect_equal(f2$lstExpr[[length(f2$lstExpr)]], quote(cp1 <- cp))
+
+    f <- rxode2(ocmt)
+    f2 <- f %>% model(cp1 <- cp, append=100)
+
+    expect_true("cp1" %in% f2$mv0$lhs)
+    expect_equal(f2$lstExpr[[length(f2$lstExpr)]], quote(cp1 <- cp))
+
     f2 <- f %>% model(f2 <- 3 * 2, append=NA)
     expect_true("f2" %in% f2$mv0$lhs)
     expect_equal(f2$lstExpr[[1]], quote(f2 <- 3 * 2))

From 7898ae92bcd78b5b2f7c2a3384287e8e546fed9a Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Tue, 5 Dec 2023 15:07:26 -0600
Subject: [PATCH 5/6] Add news about alignment

---
 NEWS.md | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index f1e0fcde2..2b6947a23 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -150,6 +150,20 @@ mu-referencing style to run the optimization.
   be kept carrying more information with it (for example ordered
   factors, data frame columns with unit information, etc)
 
+- Piping arguments `append` for `ini()` and `model()` have been
+  aligned to perform similarly.  Therefore `ini(append=)` now can take
+  expressions instead of simply strings and `model(append=)` can also
+  take strings.  Also model piping now can specify the integer line
+  number to be modified just like the `ini()` could.  Also
+  `model(append=FALSE)` has been changed to `model(append=NULL)`.
+  While the behavior is the same when you don't specify the argument,
+  the behavior has changed to align with `ini()` when piping.  Hence
+  `model(append=TRUE)` will append and `model(append=FALSE)` will now
+  pre-pend to the model.  `model(append=NULL)` will modify lines like
+  the behavior of `ini(append=NULL)`.  The default of `model(line)`
+  modifying a line in-place still applies.  While this is a breaking
+  change, most code will perform the same.
+
 ## Internal new features
 
 - Add `as.model()` for list expressions, which implies `model(ui) <-

From 8ce15c478e6f5548567686cba7ae07554dcb63c8 Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Tue, 5 Dec 2023 15:40:28 -0600
Subject: [PATCH 6/6] Add call.=FALSE

---
 R/piping-ini.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/piping-ini.R b/R/piping-ini.R
index f636d3add..ffa89fe51 100644
--- a/R/piping-ini.R
+++ b/R/piping-ini.R
@@ -331,7 +331,8 @@
   if (length(.w) != 1) {
     stop("cannot find parameter '", lhs, "'", call.=FALSE)
   } else if (!is.character(newLabel) || !(length(newLabel) == 1)) {
-    stop("the new label for '", lhs, "' must be a character string")
+    stop("the new label for '", lhs, "' must be a character string",
+         call.=FALSE)
   }
   ini$label[.w] <- newLabel
   assign("iniDf", ini, envir=rxui)