From 393e3c942b9562865a43a644578b853f61d6f224 Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Mon, 27 May 2024 23:35:03 -0500
Subject: [PATCH] Add dplyr for equations too

---
 R/covEq.R      | 5 +++--
 R/dataCov.R    | 7 +++++++
 R/dataImport.R | 1 -
 3 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/R/covEq.R b/R/covEq.R
index 1caa8c8..b7eec84 100644
--- a/R/covEq.R
+++ b/R/covEq.R
@@ -9,8 +9,9 @@
   .monolix2rx$odeType <- "nonStiff"
   .Call(`_monolix2rx_trans_equation`, text, "<MODEL> [COVARIATE] EQUATION:")
   .ret <- list(monolix=text,
-               rx=c(.monolix2rx$equationLine,
-                    .monolix2rx$pk$equation$endLines),
+               dplyr=gsub("<-", "=",
+                          c(.monolix2rx$equationLine,
+                            .monolix2rx$pk$equation$endLines), fixed=TRUE),
                odeType=.monolix2rx$odeType)
   class(.ret) <- "monolix2rxCovEq"
   .ret
diff --git a/R/dataCov.R b/R/dataCov.R
index 1139dac..ab3a05d 100644
--- a/R/dataCov.R
+++ b/R/dataCov.R
@@ -46,6 +46,13 @@ mlxtranGetMutate <- function(mlxtran) {
                         }, character(1),
                         USE.NAMES=FALSE))
   }
+  .cov <- mlxtran$MODEL$COVARIATE$EQUATION
+  if (!is.null(.cov)) {
+    .mutate <- c(.mutate,
+                 paste0("dplyr::mutate(",
+                        paste(.cov$dplyr, collapse=",\n\t\t"),
+                       ")"))
+  }
   if (length(.mutate) == 0) return(NULL)
   # Add equations
   paste(.mutate, collapse=" |> \n\t")
diff --git a/R/dataImport.R b/R/dataImport.R
index 4d84c3b..410eecf 100644
--- a/R/dataImport.R
+++ b/R/dataImport.R
@@ -22,7 +22,6 @@
       }
     }
   }
-  browser()
   .mutate <- mlxtranGetMutate(mlxtran)
   if (!is.null(.mutate)) {
     .minfo("modifying input data to match monolix transformations")