From b3eb09bc485bf7f3301cd4ff852520f3acb445ee Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Wed, 29 Nov 2023 20:04:12 -0600
Subject: [PATCH 1/2] Add failing test

---
 tests/testthat/test-ui-piping.R | 44 ++++++++++++++++++++++++++++++---
 1 file changed, 40 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-ui-piping.R b/tests/testthat/test-ui-piping.R
index b8c4c5547..7fc54c6e6 100644
--- a/tests/testthat/test-ui-piping.R
+++ b/tests/testthat/test-ui-piping.R
@@ -1921,12 +1921,12 @@ test_that("piping with append=lhs", {
 
 
 test_that("test ui appending of derived variables like `sim` can work", {
-  
+
   one.compartment <- function() {
     ini({
       tka <- 0.45
-      tcl <- 1 
-      tv <- 3.45 
+      tcl <- 1
+      tv <- 3.45
       eta.ka ~ 0.6
       eta.cl ~ 0.3
       eta.v ~ 0.1
@@ -1946,5 +1946,41 @@ test_that("test ui appending of derived variables like `sim` can work", {
   f <- rxode2(one.compartment)
 
   expect_error(model(f$simulationModel, sim2=sim+1, append=sim), NA)
-  
+
+})
+
+
+test_that("off-diagonal piping issue #518", {
+
+  mod <- function() {
+    ini({
+      a <- 1
+      b <- 2
+      etaa + etab ~ c(3, 0.1, 4)
+      c <- 5
+      etac ~ 6
+      d <- 7
+      f <- 9
+      etad + etaf ~ c(8, 0.2, 10)
+    })
+    model({
+      g <- (a + etaa)/(b + etab)
+      h <- (c + etac)
+      i <- (d + etad)
+      j <- f + etaf
+    })
+  }
+
+  modNew <-
+    ini(
+      rxode2(mod),
+      etab + etac + etad ~
+        c(7,
+          0.2, 8,
+          0.3, 0.4, 9),
+      etaa ~ 0
+    )
+
+  expect_error(modNew$omega, NA)
+
 })

From 361132dbdf2f3ed72f4ea310668890c97b894f7e Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Wed, 29 Nov 2023 20:04:19 -0600
Subject: [PATCH 2/2] Add piping ini fix

---
 R/piping-ini.R | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/R/piping-ini.R b/R/piping-ini.R
index 7cc279c62..4aa99fb16 100644
--- a/R/piping-ini.R
+++ b/R/piping-ini.R
@@ -474,6 +474,24 @@
   # (Maybe) update parameter order; this must be at the end so that the
   # parameter exists in case it is promoted from a covariate
   .iniHandleAppend(expr = expr, rxui = rxui, envir = envir, append = append)
+
+  # now take out ETAs that no longer exist
+  .iniDf <- get("iniDf", envir=rxui)
+  .w <- which(is.na(.iniDf$neta1) & !is.na(.iniDf$neta2))
+  .reassign <- FALSE
+  if (length(.w) > 0) {
+    .iniDf <- .iniDf[-.w, ]
+    .reassign <- TRUE
+  }
+  .iniDf <- get("iniDf", envir=rxui)
+  .w <- which(!is.na(.iniDf$neta1) & is.na(.iniDf$neta2))
+  if (length(.w) > 0) {
+    .iniDf <- .iniDf[-.w, ]
+    .reassign <- TRUE
+  }
+  if (.reassign) {
+    assign("iniDf", .iniDf, envir=rxui)
+  }
 }
 
 # TODO: while nlmixr2est is changed