From 67fc9b94dea2bab752e17d67f1ba51a3d0f8546c Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Thu, 1 Aug 2024 17:05:53 -0500
Subject: [PATCH 1/6] adding reset methods

---
 inst/base/mrgsolve-evtools.h | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/inst/base/mrgsolve-evtools.h b/inst/base/mrgsolve-evtools.h
index 2acae78c..cc0ecf9c 100644
--- a/inst/base/mrgsolve-evtools.h
+++ b/inst/base/mrgsolve-evtools.h
@@ -49,6 +49,42 @@ void replace(databox& self, const double amt, const int cmt) {
   return;
 }
 
+mrgsolve::evdata reset() {
+  mrgsolve::evdata ev(0, 3); 
+  ev.now = true;
+  ev.check_unique = false;
+  return ev;
+}
+
+mrgsolve::evdata reset(const double amt, const int cmt, 
+                       const double rate = 0) {
+  mrgsolve::evdata ev(0, 4);
+  ev.cmt = cmt;
+  ev.amt = amt;
+  ev.rate = rate;
+  ev.now = true;
+  ev.check_unique = false;
+  return ev;
+}
+
+void reset(databox& self) {
+  evt::ev ev = reset(); 
+  self.mevector.push_back(ev);
+  return;
+}
+
+void reset(databox& self, const double amt, const int cmt, 
+           const double rate = 0) {
+  evt::ev ev(0, 4);
+  ev.cmt = cmt;
+  ev.amt = amt;
+  ev.rate = rate;
+  ev.now = true;
+  ev.check_unique = false;
+  self.mevector.push_back(ev);
+  return;
+}
+
 void retime(mrgsolve::evdata& ev, const double time) {
   ev.time = time;
   ev.now = false;

From bf2064778d9aa3c3ccd9e0d30f6ecef3424fd4f8 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Thu, 1 Aug 2024 23:03:31 -0500
Subject: [PATCH 2/6] add tests

---
 inst/maintenance/unit-cpp/test-evtools.R | 82 ++++++++++++++++++++++--
 1 file changed, 78 insertions(+), 4 deletions(-)

diff --git a/inst/maintenance/unit-cpp/test-evtools.R b/inst/maintenance/unit-cpp/test-evtools.R
index 6eb9813c..28eb660b 100644
--- a/inst/maintenance/unit-cpp/test-evtools.R
+++ b/inst/maintenance/unit-cpp/test-evtools.R
@@ -13,16 +13,19 @@ $SET end = 12, rtol = 1e-4, atol = 1e-4, delta = 0.25
 $PLUGIN evtools
 $PARAM 
 mode = 0, f1 = 1, dose = 100, irate = 50, newtime = 2
-reptime = 5
+reptime = 5, A0 = 0, B0 = 0, C0 = 0, dosetime = 0
 $CMT A B C
 $PK
 F_A = f1;
+A_0 = A0;
+B_0 = B0;
+
 $DES
 dxdt_A = -1 * A;
 dxdt_B =  1 * A - 0.1 * B;
 dxdt_C = 0;
 $TABLE
-bool givedose = TIME==0;
+bool givedose = TIME==dosetime;
 if(mode==1 && givedose) {
   evt::bolus(self, dose, 1);
 }
@@ -58,12 +61,32 @@ if(mode==8 && givedose) {
   evt::retime(rep, reptime);
   self.push(rep);
 }
+if(mode==9 && givedose) {
+  evt::reset(self);
+}
+if(mode==10 && givedose) {
+  evt::ev res = evt::reset();
+  res.time = 15;
+  self.push(res);
+}
+if(mode==11 && givedose) {
+  evt::reset(self, 100, 3);
+}
+if(mode==12 && givedose) {
+  evt::reset(self, 100, 1, 20);
+}
+if(mode==13 && givedose) {
+  evt::ev res = evt::reset(100, 3);
+  self.push(res);
+}
+if(mode==14 && givedose) {
+  evt::ev res = evt::reset(100, 1, 20);
+  self.push(res);
+}
 '
 
 mod <- mcode("test-evtools-model-1", code)
 
-mrgsim(mod, param = list(mode = 1, f1 = 1)) 
-
 test_that("evtools - bolus now", {
   
   out <- mrgsim(mod, param = list(mode = 1))
@@ -138,3 +161,54 @@ test_that("evtools - replace", {
   after <- filter(c, time >= 8) # note: >= 8
   expect_true(all(after$C==10))
 })
+
+test_that("evtools - reset", {
+  mod <- param(mod, dosetime = 5, B0 = 50, mode = 9)
+  out <- mrgsim(mod)
+  expect_true(all(out$A==0))
+  expect_true(all(out$C==0))
+  x <- filter(out, time %in% c(0,5))
+  expect_true(all(x$B==50))
+  x <- filter(out, time==4)
+  expect_equal(x$B, 50*exp(-0.1*4), tolerance = 1e-2)
+  mod <- param(mod, mode = 10)
+  out2 <- mrgsim(mod)
+  expect_equal(out@data, out2@data)
+})
+
+test_that("evtools - reset with bolus", {
+  mod <- param(mod, dosetime = 5, B0 = 50, mode = 11)
+  out <- mrgsim(mod)
+  x <- filter(out, time==5)
+  expect_equal(x$A, 0)
+  expect_equal(x$B, 50)
+  expect_equal(x$C, 100)
+  x <- filter(out, time==4.75)
+  expect_equal(x$C, 0)
+  x <- filter(out, time > 5)
+  expect_true(all(x$C==100))
+})
+
+
+test_that("evtools - reset with infusion", {
+  mod <- param(mod, dosetime = 5, B0 = 50, mode = 12)
+  out <- mrgsim(mod, rtol = 1e-12)
+  x <- filter(out, time %in% c(0,5))
+  expect_true(all(x$B==50))
+  expect_true(all(x$A==0))
+  x <- filter(out, time == 4.75)
+  expect_equal(x$A, 0)
+  expect_equal(x$B, 50*exp(-0.1*4.75), tolerance = 1e-2)
+  # Maximum A is at the end of the infusion
+  x <- filter(out, A==max(A))
+  expect_equal(x$time, 10)
+  
+  # Identical results
+  out1 <- mrgsim(mod, param = list(mode = 11))
+  out2 <- mrgsim(mod, param = list(mode = 12))
+  out3 <- mrgsim(mod, param = list(mode = 13))
+  out4 <- mrgsim(mod, param = list(mode = 14))
+  
+  expect_identical(out1@data, out3@data)
+  expect_identical(out2@data, out4@data)
+})

From efac0a6073f320ab12c6e5e911c4c9a73d87b690 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Fri, 2 Aug 2024 07:04:51 -0500
Subject: [PATCH 3/6] refactor / comment tests; explicit namespace references

---
 inst/base/mrgsolve-evtools.h             | 16 +++-----
 inst/maintenance/unit-cpp/test-evtools.R | 49 ++++++++++++++----------
 2 files changed, 35 insertions(+), 30 deletions(-)

diff --git a/inst/base/mrgsolve-evtools.h b/inst/base/mrgsolve-evtools.h
index cc0ecf9c..98272135 100644
--- a/inst/base/mrgsolve-evtools.h
+++ b/inst/base/mrgsolve-evtools.h
@@ -13,7 +13,7 @@ mrgsolve::evdata bolus(const double amt, const int cmt) {
 }
 
 void bolus(databox& self, const double amt, const int cmt) {
-  mrgsolve::evdata ev = bolus(amt, cmt);
+  mrgsolve::evdata ev = evt::bolus(amt, cmt);
   self.mevector.push_back(ev);
   return;
 }
@@ -29,7 +29,7 @@ mrgsolve::evdata infuse(const double amt, const int cmt, const double rate) {
 }
 
 void infuse(databox& self, const double amt, const int cmt, const double rate) {
-  mrgsolve::evdata ev = infuse(amt, cmt, rate);
+  mrgsolve::evdata ev = evt::infuse(amt, cmt, rate);
   self.mevector.push_back(ev);
   return;
 }
@@ -44,7 +44,7 @@ mrgsolve::evdata replace(const double amt, const int cmt) {
 }
 
 void replace(databox& self, const double amt, const int cmt) {
-  mrgsolve::evdata ev = replace(amt, cmt);
+  mrgsolve::evdata ev = evt::replace(amt, cmt);
   self.mevector.push_back(ev);
   return;
 }
@@ -58,29 +58,25 @@ mrgsolve::evdata reset() {
 
 mrgsolve::evdata reset(const double amt, const int cmt, 
                        const double rate = 0) {
-  mrgsolve::evdata ev(0, 4);
+  mrgsolve::evdata ev = evt::reset();
   ev.cmt = cmt;
   ev.amt = amt;
   ev.rate = rate;
-  ev.now = true;
-  ev.check_unique = false;
   return ev;
 }
 
 void reset(databox& self) {
-  evt::ev ev = reset(); 
+  mrgsolve::evdata ev = evt::reset(); 
   self.mevector.push_back(ev);
   return;
 }
 
 void reset(databox& self, const double amt, const int cmt, 
            const double rate = 0) {
-  evt::ev ev(0, 4);
+  mrgsolve::evdata ev = evt::reset();
   ev.cmt = cmt;
   ev.amt = amt;
   ev.rate = rate;
-  ev.now = true;
-  ev.check_unique = false;
   self.mevector.push_back(ev);
   return;
 }
diff --git a/inst/maintenance/unit-cpp/test-evtools.R b/inst/maintenance/unit-cpp/test-evtools.R
index 28eb660b..43c84737 100644
--- a/inst/maintenance/unit-cpp/test-evtools.R
+++ b/inst/maintenance/unit-cpp/test-evtools.R
@@ -61,26 +61,26 @@ if(mode==8 && givedose) {
   evt::retime(rep, reptime);
   self.push(rep);
 }
-if(mode==9 && givedose) {
+if(mode==9 && givedose) { // reset
   evt::reset(self);
-}
-if(mode==10 && givedose) {
+} 
+if(mode==10 && givedose) { // reset, non-self
   evt::ev res = evt::reset();
   res.time = 15;
   self.push(res);
 }
-if(mode==11 && givedose) {
+if(mode==11 && givedose) { // reset with bolus
   evt::reset(self, 100, 3);
 }
-if(mode==12 && givedose) {
+if(mode==12 && givedose) { // reset with infusion
   evt::reset(self, 100, 1, 20);
 }
-if(mode==13 && givedose) {
+if(mode==13 && givedose) { // reset with bolus, non-self
   evt::ev res = evt::reset(100, 3);
   self.push(res);
 }
-if(mode==14 && givedose) {
-  evt::ev res = evt::reset(100, 1, 20);
+if(mode==14 && givedose) { // reset with infusion, non-self
+  evt::ev res = evt::reset(100, 1, 100.0/5.0);
   self.push(res);
 }
 '
@@ -167,13 +167,17 @@ test_that("evtools - reset", {
   out <- mrgsim(mod)
   expect_true(all(out$A==0))
   expect_true(all(out$C==0))
-  x <- filter(out, time %in% c(0,5))
+  # B starts at 50 and then is reset at time==5
+  x <- filter(out, time %in% c(0, 5))
   expect_true(all(x$B==50))
+  # Verify value of B just before reset
   x <- filter(out, time==4)
   expect_equal(x$B, 50*exp(-0.1*4), tolerance = 1e-2)
   mod <- param(mod, mode = 10)
-  out2 <- mrgsim(mod)
-  expect_equal(out@data, out2@data)
+  # Identical results if the self or non-self function is called
+  out1 <- mrgsim(mod, param = list(mode = 9))
+  out2 <- mrgsim(mod, param = list(mode = 10))
+  expect_equal(out1@data, out2@data)
 })
 
 test_that("evtools - reset with bolus", {
@@ -187,28 +191,33 @@ test_that("evtools - reset with bolus", {
   expect_equal(x$C, 0)
   x <- filter(out, time > 5)
   expect_true(all(x$C==100))
+  
+  # Identical results if the self method called or non-self 
+  out1 <- mrgsim(mod, param = list(mode = 11))
+  out2 <- mrgsim(mod, param = list(mode = 12))
+  
+  expect_identical(out1@data, out3@data)
 })
 
 
 test_that("evtools - reset with infusion", {
   mod <- param(mod, dosetime = 5, B0 = 50, mode = 12)
-  out <- mrgsim(mod, rtol = 1e-12)
-  x <- filter(out, time %in% c(0,5))
+  out <- mrgsim(mod, rtol = 1e-12, delta = 0.25)
+  # B should be 50 to start and the reset time
+  x <- filter(out, time %in% c(0, 5))
   expect_true(all(x$B==50))
   expect_true(all(x$A==0))
+  # Check values of A and B just before reset
   x <- filter(out, time == 4.75)
   expect_equal(x$A, 0)
   expect_equal(x$B, 50*exp(-0.1*4.75), tolerance = 1e-2)
-  # Maximum A is at the end of the infusion
+  # Check the infusion; Amax should be at the end of the 5 hr infusion
   x <- filter(out, A==max(A))
   expect_equal(x$time, 10)
   
-  # Identical results
-  out1 <- mrgsim(mod, param = list(mode = 11))
-  out2 <- mrgsim(mod, param = list(mode = 12))
-  out3 <- mrgsim(mod, param = list(mode = 13))
-  out4 <- mrgsim(mod, param = list(mode = 14))
+  # Identical results if the self method called or non-self 
+  out1 <- mrgsim(mod, param = list(mode = 13))
+  out2 <- mrgsim(mod, param = list(mode = 14))
   
   expect_identical(out1@data, out3@data)
-  expect_identical(out2@data, out4@data)
 })

From 9c16013694aaf305dcb1891458500ad2e72e7551 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Fri, 2 Aug 2024 07:10:37 -0500
Subject: [PATCH 4/6] fix evid problem with reset and dose

---
 inst/base/mrgsolve-evtools.h | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/inst/base/mrgsolve-evtools.h b/inst/base/mrgsolve-evtools.h
index 98272135..0de765dd 100644
--- a/inst/base/mrgsolve-evtools.h
+++ b/inst/base/mrgsolve-evtools.h
@@ -58,10 +58,12 @@ mrgsolve::evdata reset() {
 
 mrgsolve::evdata reset(const double amt, const int cmt, 
                        const double rate = 0) {
-  mrgsolve::evdata ev = evt::reset();
-  ev.cmt = cmt;
+  mrgsolve::evdata ev(0, 4);
   ev.amt = amt;
+  ev.cmt = cmt;
   ev.rate = rate;
+  ev.now = true;
+  ev.check_unique = false;
   return ev;
 }
 
@@ -73,10 +75,7 @@ void reset(databox& self) {
 
 void reset(databox& self, const double amt, const int cmt, 
            const double rate = 0) {
-  mrgsolve::evdata ev = evt::reset();
-  ev.cmt = cmt;
-  ev.amt = amt;
-  ev.rate = rate;
+  mrgsolve::evdata ev = evt::reset(amt, cmt, rate);
   self.mevector.push_back(ev);
   return;
 }

From 0411a429d547c47c4ebbe82c90a92812d652d78c Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Fri, 2 Aug 2024 07:33:19 -0500
Subject: [PATCH 5/6] refactor / improve tests

---
 inst/maintenance/unit-cpp/test-evtools.R | 58 +++++++++++++++++++-----
 1 file changed, 46 insertions(+), 12 deletions(-)

diff --git a/inst/maintenance/unit-cpp/test-evtools.R b/inst/maintenance/unit-cpp/test-evtools.R
index 43c84737..e17abe80 100644
--- a/inst/maintenance/unit-cpp/test-evtools.R
+++ b/inst/maintenance/unit-cpp/test-evtools.R
@@ -163,61 +163,95 @@ test_that("evtools - replace", {
 })
 
 test_that("evtools - reset", {
+  # Reset the system
   mod <- param(mod, dosetime = 5, B0 = 50, mode = 9)
+  mod <- update(mod, rtol = 1e-10, delta = 0.25)
   out <- mrgsim(mod)
   expect_true(all(out$A==0))
   expect_true(all(out$C==0))
+  
   # B starts at 50 and then is reset at time==5
   x <- filter(out, time %in% c(0, 5))
   expect_true(all(x$B==50))
+  
   # Verify value of B just before reset
   x <- filter(out, time==4)
   expect_equal(x$B, 50*exp(-0.1*4), tolerance = 1e-2)
   mod <- param(mod, mode = 10)
+
   # Identical results if the self or non-self function is called
   out1 <- mrgsim(mod, param = list(mode = 9))
   out2 <- mrgsim(mod, param = list(mode = 10))
-  expect_equal(out1@data, out2@data)
+  expect_identical(as.data.frame(out1), as.data.frame(out2))
+    
+  # Do an equivalent simulation with no evtools
+  e <- ev(amt = 100, time = 5, evid = 3)
+  out3 <- mrgsim(mod, e, param = list(mode = 0), obsonly = TRUE, recsort = 3)
+  expect_identical(as.data.frame(out1), as.data.frame(out3))
 })
 
 test_that("evtools - reset with bolus", {
+  # This resets the system and boluses 100 mg into C
   mod <- param(mod, dosetime = 5, B0 = 50, mode = 11)
+  mod <- update(mod, rtol = 1e-10, delta = 0.25)
   out <- mrgsim(mod)
+  
+  # Bolus into C; will check 
+  expect_equal(sort(unique(out$C)), c(0, 100))
+  
+  # At the reset time, B is back to the initial and we have dosed into C
   x <- filter(out, time==5)
   expect_equal(x$A, 0)
   expect_equal(x$B, 50)
   expect_equal(x$C, 100)
+  
+  # Check values just before reset
   x <- filter(out, time==4.75)
   expect_equal(x$C, 0)
-  x <- filter(out, time > 5)
-  expect_true(all(x$C==100))
+  expect_equal(x$B, 50*exp(-0.1*4.75), tolerance = 1e-2)
   
+  # Dose in to C at time==5
+  x <- filter(out, time >= 5)
+  expect_true(all(x$C==100))
+
   # Identical results if the self method called or non-self 
   out1 <- mrgsim(mod, param = list(mode = 11))
-  out2 <- mrgsim(mod, param = list(mode = 12))
-  
-  expect_identical(out1@data, out3@data)
+  out2 <- mrgsim(mod, param = list(mode = 13))
+  expect_identical(as.data.frame(out1), as.data.frame(out2))
+    
+  # Do an equivalent simulation with no evtools
+  e <- ev(amt = 100, time = 5, evid = 4, cmt = "C")
+  out3 <- mrgsim(mod, e, param = list(mode = 0), obsonly = TRUE, recsort = 3)
+  expect_identical(as.data.frame(out1), as.data.frame(out3))
 })
 
-
 test_that("evtools - reset with infusion", {
+  # This resets the system and starts an infusion into A lasting 5 hours
   mod <- param(mod, dosetime = 5, B0 = 50, mode = 12)
-  out <- mrgsim(mod, rtol = 1e-12, delta = 0.25)
+  mod <- update(mod, rtol = 1e-10, delta = 0.25)
+  out <- mrgsim(mod)
+  
   # B should be 50 to start and the reset time
   x <- filter(out, time %in% c(0, 5))
   expect_true(all(x$B==50))
   expect_true(all(x$A==0))
+  
   # Check values of A and B just before reset
   x <- filter(out, time == 4.75)
   expect_equal(x$A, 0)
   expect_equal(x$B, 50*exp(-0.1*4.75), tolerance = 1e-2)
+  
   # Check the infusion; Amax should be at the end of the 5 hr infusion
   x <- filter(out, A==max(A))
   expect_equal(x$time, 10)
-  
+
   # Identical results if the self method called or non-self 
-  out1 <- mrgsim(mod, param = list(mode = 13))
+  out1 <- mrgsim(mod, param = list(mode = 12))
   out2 <- mrgsim(mod, param = list(mode = 14))
-  
-  expect_identical(out1@data, out3@data)
+  expect_identical(as.data.frame(out1), as.data.frame(out2))
+    
+  # Do an equivalent simulation with no evtools 
+  e <- ev(amt = 100, time = 5, evid = 4, cmt = "A", rate = 100/5)
+  out3 <- mrgsim(mod, e, param = list(mode = 0), obsonly = TRUE, recsort = 3)
+  expect_identical(as.data.frame(out1), as.data.frame(out3))
 })

From 54708e72d686423eeed0d603b20acf83ade26d65 Mon Sep 17 00:00:00 2001
From: Kyle Baron <kyleb@metrumrg.com>
Date: Fri, 2 Aug 2024 07:36:00 -0500
Subject: [PATCH 6/6] finish out comment in test

---
 inst/maintenance/unit-cpp/test-evtools.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/maintenance/unit-cpp/test-evtools.R b/inst/maintenance/unit-cpp/test-evtools.R
index e17abe80..62c703f2 100644
--- a/inst/maintenance/unit-cpp/test-evtools.R
+++ b/inst/maintenance/unit-cpp/test-evtools.R
@@ -196,7 +196,7 @@ test_that("evtools - reset with bolus", {
   mod <- update(mod, rtol = 1e-10, delta = 0.25)
   out <- mrgsim(mod)
   
-  # Bolus into C; will check 
+  # Bolus into C; will check when this happens next 
   expect_equal(sort(unique(out$C)), c(0, 100))
   
   # At the reset time, B is back to the initial and we have dosed into C