From 25f42c7783f745dbf7047444fb376272f07523d3 Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Wed, 14 Aug 2024 16:03:37 -0500
Subject: [PATCH 1/3] Use lotri nearPD

---
 R/nearpd.R     |  5 -----
 src/cvPost.cpp |  6 ++++--
 src/nearPD.cpp | 14 ++++++++------
 3 files changed, 12 insertions(+), 13 deletions(-)
 delete mode 100644 R/nearpd.R

diff --git a/R/nearpd.R b/R/nearpd.R
deleted file mode 100644
index 1b2eb5c4e..000000000
--- a/R/nearpd.R
+++ /dev/null
@@ -1,5 +0,0 @@
-.nearPD <- function(mat) {
-  .ret <- try(Matrix::nearPD(mat), silent=TRUE)
-  if (inherits(.ret, "try-error")) return(NULL)
-  as.matrix(.ret$mat)
-}
diff --git a/src/cvPost.cpp b/src/cvPost.cpp
index 745f7a2b5..b48f6cac2 100644
--- a/src/cvPost.cpp
+++ b/src/cvPost.cpp
@@ -12,10 +12,12 @@
 #include "../inst/include/rxode2_as.h"
 #include <lotri.h>
 
+extern "C" {
+  iniLotri;
+}
+
 extern "C" SEXP chin(SEXP a, SEXP b);
 
-// place links here
-iniLotri;
 
 List etTrans(List inData, const RObject &mv, bool addCmt,
              bool dropUnits, bool allTimeVar,
diff --git a/src/nearPD.cpp b/src/nearPD.cpp
index d1245e6d2..515006197 100644
--- a/src/nearPD.cpp
+++ b/src/nearPD.cpp
@@ -5,6 +5,8 @@
 #define STRICT_R_HEADER
 #include <RcppArmadillo.h>
 #include "nearPD.h"
+#define lotriArma
+#include <lotri.h>
 
 using namespace arma;
 using namespace Rcpp;
@@ -12,14 +14,14 @@ using namespace Rcpp;
 Function getRxFn(std::string name);
 
 bool rxNearPD(arma::mat &ret, const arma::mat in) {
-  Function mnearpd = getRxFn(".nearPD");
-  RObject retRO = mnearpd(in);
-  if (Rf_isMatrix(retRO)) {
-    ret = as<arma::mat>(retRO);
+  ret = mat(in.n_rows, in.n_cols);
+  if (lotriNearPDarma(ret,  in)) {
     return true;
+  } else {
+    ret = in;
+    return false;
   }
-  ret = in;
-  return false;
+  return false;  // nocov
 }
 
 unsigned int rxNearPdChol(Rcpp::NumericMatrix &ret, Rcpp::NumericMatrix x, bool isChol) {

From f92a906085066d4cf5e997d78cb77c2c9840fc13 Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Thu, 15 Aug 2024 14:38:14 -0500
Subject: [PATCH 2/3] Fix for using lotri's nearPD

---
 src/nearPD.cpp | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/nearPD.cpp b/src/nearPD.cpp
index 515006197..67b881613 100644
--- a/src/nearPD.cpp
+++ b/src/nearPD.cpp
@@ -5,16 +5,14 @@
 #define STRICT_R_HEADER
 #include <RcppArmadillo.h>
 #include "nearPD.h"
-#define lotriArma
 #include <lotri.h>
 
+lotriNearPDarmaSetup
+
 using namespace arma;
 using namespace Rcpp;
 
-Function getRxFn(std::string name);
-
 bool rxNearPD(arma::mat &ret, const arma::mat in) {
-  ret = mat(in.n_rows, in.n_cols);
   if (lotriNearPDarma(ret,  in)) {
     return true;
   } else {
@@ -27,7 +25,6 @@ bool rxNearPD(arma::mat &ret, const arma::mat in) {
 unsigned int rxNearPdChol(Rcpp::NumericMatrix &ret, Rcpp::NumericMatrix x, bool isChol) {
   arma::mat tmpM = as<arma::mat>(x);
   arma::mat reta;
-
   if (!x.hasAttribute("dimnames")) {
     return rxNearPdChol_not_named;
   } else if (isChol) {

From 82db8ad76ffa88ff54c5251207443f004089858d Mon Sep 17 00:00:00 2001
From: "Matthew L. Fidler" <matthew.fidler@gmail.com>
Date: Thu, 15 Aug 2024 15:21:55 -0500
Subject: [PATCH 3/3] Remove reference to .nearPD

---
 tests/testthat/test-nearpd.R | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/tests/testthat/test-nearpd.R b/tests/testthat/test-nearpd.R
index a5e34fbda..4daea824c 100644
--- a/tests/testthat/test-nearpd.R
+++ b/tests/testthat/test-nearpd.R
@@ -60,7 +60,3 @@ rxTest({
                  NA)
   })
 })
-
-test_that(".nearPD expected null for matrix that cannot become positive definite", {
-  expect_null(.nearPD(matrix(Inf)))
-})