From c73a698a65579069dec824705bbf8726d29f9b36 Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Fri, 8 Dec 2023 10:31:27 -0600
Subject: [PATCH] Add tests and fixes for rxRename (w/sigma and thetaMat)

---
 R/ui-rename.R                   |   5 +-
 tests/testthat/test-ui-rename.R | 105 ++++++++++++++++++++++++++++++++
 2 files changed, 108 insertions(+), 2 deletions(-)

diff --git a/R/ui-rename.R b/R/ui-rename.R
index 3ead05823..b376d144e 100644
--- a/R/ui-rename.R
+++ b/R/ui-rename.R
@@ -146,6 +146,7 @@
 #' @noRd
 #' @author Matthew L. Fidler
 .rxRenameAll <- function(rxui, lst) {
+  rxui <- rxUiDecompress(rxui)
   .iniDf <- rxui$iniDf
   .iniDf$name <- vapply(seq_along(.iniDf$name),
                         function(i) {
@@ -174,10 +175,10 @@
   if (exists("meta", rxui)) {
     .meta <- get("meta", rxui)
     if (exists("sigma", .meta)) {
-      assign("sigma", .rxRenameAllMat(get("sigma", envir=rxui), lst), envir=.meta)
+      assign("sigma", .rxRenameAllMat(get("sigma", envir=.meta), lst), envir=.meta)
     }
     if (exists("thetaMat", .meta)) {
-      assign("thetaMat", .rxRenameAllMat(get("thetaMat", envir=rxui), lst), envir=.meta)
+      assign("thetaMat", .rxRenameAllMat(get("thetaMat", envir=.meta), lst), envir=.meta)
     }
   }
   rxui$lstExpr <- lapply(seq_along(rxui$lstExpr),
diff --git a/tests/testthat/test-ui-rename.R b/tests/testthat/test-ui-rename.R
index ad1b4e644..d405f161a 100644
--- a/tests/testthat/test-ui-rename.R
+++ b/tests/testthat/test-ui-rename.R
@@ -149,7 +149,112 @@ rxTest({
     expect_equal(tmp$lstExpr[[7]], quote(dur(dcmt) <- 1))
     expect_equal(tmp$lstExpr[[8]], quote(alag(dcmt) <- 1))
 
+  })
+
+  test_that("rename with sigma and thetaMat", {
+
+    f <- function() {
+      description <- "BOLUS_2CPT_CLV1QV2 SINGLE DOSE FOCEI (120 Ind/2280 Obs) runODE032"
+      dfObs <- 2280
+      dfSub <- 120
+      sigma <- lotri({
+        eps1 ~ 1
+      })
+      thetaMat <- lotri({
+        theta1 + theta2 + theta3 + theta4 + RSV + eps1 + eta1 +
+          omega.2.1 + eta2 + omega.3.1 + omega.3.2 + eta3 +
+          omega.4.1 + omega.4.2 + omega.4.3 + eta4 ~
+            c(0.000887681,
+              -0.00010551, 0.000871409, 0.000184416, -0.000106195,
+              0.00299336, -0.000120234, -5.06663e-05, 0.000165252,
+              0.00121347, 5.2783e-08, -1.56562e-05, 5.99331e-06,
+              -2.53991e-05, 9.94218e-06, 0, 0, 0, 0, 0, 0, -4.71273e-05,
+              4.69667e-05, -3.64271e-05, 2.54796e-05, -8.16885e-06,
+              0, 0.000169296, 0, 0, 0, 0, 0, 0, 0, 0, -7.37156e-05,
+              2.56634e-05, -8.08349e-05, 1.37e-05, -4.36564e-06,
+              0, 8.75181e-06, 0, 0.00015125, 0, 0, 0, 0, 0, 0,
+              0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6.63383e-05,
+              -8.19002e-05, 0.000548985, 0.000168356, 1.59122e-06,
+              0, 3.48714e-05, 0, 4.31593e-07, 0, 0, 0.000959029,
+              0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+              0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+              0, 0, 0, 0, 0, 0, 0, 0, -9.49661e-06, 0.000110108,
+              -0.000306537, -9.12897e-05, 3.1877e-06, 0, 1.36628e-05,
+              0, -1.95096e-05, 0, 0, -0.00012977, 0, 0, 0, 0.00051019)
+      })
+      ini({
+        theta1 <- 1.37034036528946
+        label("log Cl")
+        theta2 <- 4.19814911033061
+        label("log Vc")
+        theta3 <- 1.38003493562413
+        label("log Q")
+        theta4 <- 3.87657341967489
+        label("log Vp")
+        RSV <- c(0, 0.196446108190896, 1)
+        label("RSV")
+        eta1 ~ 0.101251418415006
+        eta2 ~ 0.0993872449483344
+        eta3 ~ 0.101302674763154
+        eta4 ~ 0.0730497519364148
+      })
+      model({
+        cmt(CENTRAL)
+        cmt(PERI)
+        cl <- exp(theta1 + eta1)
+        v <- exp(theta2 + eta2)
+        q <- exp(theta3 + eta3)
+        v2 <- exp(theta4 + eta4)
+        v1 <- v
+        scale1 <- v
+        k21 <- q/v2
+        k12 <- q/v
+        d/dt(CENTRAL) <- k21 * PERI - k12 * CENTRAL - cl * CENTRAL/v1
+        d/dt(PERI) <- -k21 * PERI + k12 * CENTRAL
+        f <- CENTRAL/scale1
+        ipred <- f
+        rescv <- RSV
+        w <- ipred * rescv
+        ires <- DV - ipred
+        iwres <- ires/w
+        y <- ipred + w * eps1
+      })
+    }
+
+    f <- f()
 
+    f2 <- rxRename(f, eta.cl=eta1, eta.v=eta2, eta.q=eta3, eta.v2=eta4, eps=eps1)
+
+    expect_equal(sort(intersect(dimnames(f2$omega)[[1]],
+                                c("eta.cl", "eta.v", "eta.q", "eta.v2"))),
+                 c("eta.cl", "eta.q", "eta.v", "eta.v2"))
+
+    expect_equal(sort(intersect(dimnames(f2$thetaMat)[[1]],
+                                c("eta.cl", "eta.v", "eta.q", "eta.v2", "eps"))),
+                 c("eps", "eta.cl", "eta.q", "eta.v", "eta.v2"))
+
+    expect_equal(dimnames(f2$sigma)[[1]], "eps")
+
+    f <- rxUiDecompress(f)
+    f$sigma <- f$meta$sigma
+    f$thetaMat <- f$meta$thetaMat
+    rm("sigma", envir=f$meta)
+    rm("thetaMat", envir=f$meta)
+    f <- rxUiCompress(f)
+
+    f3 <- rxRename(f, eta.cl=eta1, eta.v=eta2, eta.q=eta3, eta.v2=eta4, eps=eps1)
+
+    expect_equal(sort(intersect(dimnames(f3$omega)[[1]],
+                                c("eta.cl", "eta.v", "eta.q", "eta.v2"))),
+                 c("eta.cl", "eta.q", "eta.v", "eta.v2"))
+
+    expect_equal(sort(intersect(dimnames(f3$thetaMat)[[1]],
+                                c("eta.cl", "eta.v", "eta.q", "eta.v2", "eps"))),
+                 c("eps", "eta.cl", "eta.q", "eta.v", "eta.v2"))
+
+    expect_equal(dimnames(f3$sigma)[[1]], "eps")
 
   })
+
+
 })