Fill out evtools function set for dosing

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: mrgsolve
 Title: Simulate from ODE-Based Models
-Version: 1.5.1
+Version: 1.5.1.9000
 Authors@R: 
     c(person(given = "Kyle T", family = "Baron",
              role = c("aut", "cre"),

NEWS.md

@@ -1,3 +1,5 @@
+# mrgsolve (development version)
+
 # mrgsolve 1.5.1
 
 - Fixed `yaml_to_cpp()` example code to prevent saving the file to the working 

inst/base/mrgsolv.h

@@ -53,6 +53,9 @@ struct evdata {
     cmt = 1;
     amt = 0.0;
     rate = 0.0;
+    ii = 0.0;
+    ss = 0; 
+    addl = 0;
     now = false;
     check_unique = false;
   } 
@@ -61,6 +64,9 @@ struct evdata {
   int cmt;
   double amt; 
   double rate;
+  double ii; 
+  int ss; 
+  int addl;
   bool now;
   bool check_unique;
 }; 

inst/base/mrgsolve-evtools.h

@@ -86,6 +86,36 @@ void retime(mrgsolve::evdata& ev, const double time) {
   return;
 }
 
+void addl(mrgsolve::evdata& ev, const int addl) {
+  ev.addl = addl;
+  return;
+}
+
+void ii(mrgsolve::evdata& ev, const double ii) {
+  ev.ii = ii;
+  return;
+}
+
+void ss(mrgsolve::evdata& ev, const int ss) {
+  ev.ss = ss;
+  return;
+}
+
+void amt(mrgsolve::evdata& ev, const double amt) {
+  ev.amt = amt; 
+  return;
+}
+
+void rate(mrgsolve::evdata& ev, const double rate) {
+  ev.rate = rate; 
+  return;
+}
+
+void cmt(mrgsolve::evdata& ev, const int cmt) {
+  ev.cmt = cmt;
+  return;
+}
+
 void now(mrgsolve::evdata& ev) {
   ev.now = true;
   return;

inst/maintenance/tests.R

@@ -9,7 +9,10 @@ a$result <- NULL
 message("\ninst/maintenance/unit")
 b <- test_dir("inst/maintenance/unit/")
 b$result <- NULL
-results <- dplyr::bind_rows(as_tibble(a),as_tibble(b))
+c <- test_dir("inst/maintenance/unit-cpp/")
+c$result <- NULL
+
+results <- dplyr::bind_rows(as_tibble(a),as_tibble(b),as_tibble(c))
 results$user <- NULL
 results$system <- NULL
 results$real <- NULL

inst/maintenance/unit-cpp/test-evtools-dosing.R

@@ -0,0 +1,271 @@
+library(testthat)
+library(mrgsolve)
+library(dplyr)
+
+Sys.setenv(R_TESTS="")
+options("mrgsolve_mread_quiet"=TRUE)
+
+local_edition(3)
+
+code <- '
+$PLUGIN evtools
+
+$PARAM Mdose = 0
+
+$PARAM 
+Lag   =  0
+Ii    =  24
+Ss    =  0
+Addl  =  0
+Rate  =  0
+Dur   =  0
+Amt   =  100
+Cmt2  = -1
+Amt2  = -1
+Rate2 = -1
+Time2 = -1
+
+$CMT B D
+
+$MAIN 
+ALAG_B = Lag;
+D_B = Dur; 
+
+$ODE
+dxdt_D =  -0.3 * D;
+dxdt_B =   0.3 * D - 0.1*B;
+
+$ERROR
+
+if(TIME==0 && Mdose > 0) {
+  evt::ev dose = evt::infuse(Amt, 1, Rate); 
+  evt::ss(dose, Ss); 
+  evt::ii(dose, Ii); 
+  evt::addl(dose, Addl); 
+  if(Rate2 > 0) evt::rate(dose, Rate2);
+  if(Cmt2 > 0) evt::cmt(dose, Cmt2);
+  if(Amt2 > 0) evt::amt(dose, Amt2);
+  if(Time2 > 0) evt::retime(dose, Time2);
+  self.push(dose);
+}
+'
+
+mod1 <- mcode("reset", code, delta = 0.1, end = 96)
+mod2 <- update(mod1, param = list(Mdose = 1))
+
+test_that("Bolus - ss and addl via evt", {
+  d <-   ev(amt = 100, ii = 24, addl = 3)
+  p <- list(Amt = 100, Ii = 24, Addl = 3)
+  out1 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out2 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out1$B, out2$B)
+
+  # same dose, but "later"
+  d <-   mutate(d, time = 3)
+  p$Time2 <- 3
+  out3 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out4 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out3$B, out4$B)
+})
+
+test_that("Bolus, lag - ss and addl via evt", {
+  d <-   ev(amt = 100, ii = 24, addl = 3, Lag = 5)
+  p <- list(Amt = 100, Ii = 24, Addl = 3, Lag = 5)
+  out1 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out2 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out1$B, out2$B)
+
+  # same dose, but "later"
+  d <-   mutate(d, time = 2.5)
+  p$Time2 <- 2.5
+  out3 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out4 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out3$B, out4$B)
+})
+
+test_that("Bolus, ss - ss and addl via evt", {
+  d <-   ev(amt = 100, ii = 24, addl = 3, ss = 1)
+  p <- list(Amt = 100, Ii = 24, Addl = 3, Ss = 1)
+  out1 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out2 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out1$B, out2$B)
+
+  # same dose, but "later"
+  d <-   mutate(d, time = 3.5)
+  p$Time2 <- 3.5
+  out3 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out4 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out3$B, out4$B)
+})
+
+test_that("Bolus, ss, lag - ss and addl via evt", {
+  d <-   ev(amt = 100, ii = 24, addl = 3, ss = 1, Lag = 3)
+  p <- list(Amt = 100, Ii = 24, Addl = 3, Ss = 1, Lag = 3)
+  out1 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out2 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out1$B, out2$B)
+
+  # same dose, but "later"
+  d <- mutate(d, time = 3.1)
+  p$Time2 <- 3.1
+  out3 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out4 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out3$B, out4$B)
+})
+
+test_that("Infusion - ss and addl via evt", {
+  d <-   ev(amt = 100, ii = 12, addl = 3, Dur = 7, rate = -2)
+  p <- list(Amt = 100, Ii = 12, Addl = 3, Dur = 7, Rate = -2)
+  out1 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out2 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out1$B, out2$B)
+
+  # same dose, but "later"
+  d <- mutate(d, time = 2)
+  p$Time2 <- 2
+  out3 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out4 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out3$B, out4$B)
+})
+
+test_that("Infusion, lag - ss and addl via evt", {
+  d <-   ev(amt = 100, ii = 8, addl = 3, Lag = 5, Dur = 5, rate = -2)
+  p <- list(Amt = 100, Ii = 8, Addl = 3, Lag = 5, Dur = 5, Rate = -2)
+  out1 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out2 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out1$B, out2$B)
+
+  # same dose, but "later"
+  d <- mutate(d, time = 4)
+  p$Time2 <- 4
+  out3 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out4 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out3$B, out4$B)
+})
+
+test_that("Infusion, ss - ss and addl via evt", {
+  d <-   ev(amt = 100, ii = 24, addl = 2, ss = 1, Dur = 8, rate = -2)
+  p <- list(Amt = 100, Ii = 24, Addl = 2, Ss = 1, Dur = 8, Rate = -2)
+  out1 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out2 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out1$B, out2$B)
+
+  # same dose, but "later"
+  d <- mutate(d, time = 1.5)
+  p$Time2 <- 1.5
+  out3 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out4 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out3$B, out4$B)
+})
+
+test_that("Infusion, ss, lag - ss and addl via evt", {
+  d <-   ev(amt = 100, ii = 16, addl = 3, ss = 1, Lag = 3, Dur = 9, rate = -2)
+  p <- list(Amt = 100, Ii = 16, Addl = 3, Ss = 1, Lag = 3, Dur = 9, Rate = -2)
+  out1 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out2 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out1$B, out2$B)
+
+  # same dose, but "later"
+  d <- mutate(d, time = 2.1)
+  p$Time2 <- 2.1
+  out3 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out4 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out3$B, out4$B)
+})
+
+test_that("Alternate infusion - dosing via evt", {
+  # data event passes the rate directly rather than modeled duration
+  d <-   ev(amt = 100, ii = 24, addl = 1, tinf = 4)
+  p <- list(Amt = 100, Ii = 24, Addl = 1, Dur = 4, Rate = -2)
+  out1 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out2 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out1$B, out2$B)
+
+  # Both use direct rate rather than modeled duration
+  d <- ev(amt = 100, ii = 24, addl = 1, rate = 20)
+  p <- list(Amt = 100, Ii = 24, Addl = 1, Rate = 20)
+  out3 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out4 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out3$B, out4$B)
+})
+
+test_that("Steady state continuous infusion - dosing via evt", {
+  d <-   ev(amt = 0, ii = 24, rate = 20, ss = 1)
+  p <- list(Amt = 0, Ii = 24, Rate = 20, Ss = 1)
+  out1 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out2 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out1$B, out2$B)
+  expect_equal(out2$B[1], 20/0.1)
+
+  # same dose at a later time
+  d <- mutate(d, time = 10)
+  p$Time2 <- 10
+  out3 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out4 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out3$B, out4$B)
+  expect_equal(out3$B[out3$time==10], 20/0.1)
+})
+
+test_that("Single dose - dosing via evt", {
+  d <-   ev(amt = 100, ii = 24, tinf = 3)
+  p <- list(Amt = 100, Ii = 24, Addl = 0, Dur = 3, Rate = -2)
+  out1 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out2 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out1$B, out2$B)
+
+  d <- mutate(d, time = 3.3)
+  p$Time2 <- 3.3
+  out3 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out4 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out3$B, out4$B)
+})
+
+test_that("Switch compartment - dosing via evt", {
+  d <-   ev(amt = 100, ii = 24, addl = 2, cmt = 2)
+  p <- list(Amt = 100, Ii = 24, Addl = 2, Cmt2 = 2)
+  out1 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out2 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out1$B, out2$B)
+  expect_identical(out1$D, out2$D)
+})
+
+test_that("Switch dose amount - dosing via evt", {
+  d <-   ev(amt = 200, ii = 24, addl = 2)
+  p <- list(Amt = 100, Ii = 24, Addl = 2, Amt2 = 200)
+  out1 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out2 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out1$B, out2$B)
+})
+
+test_that("Switch infusion rate - dosing via evt", {
+  d <-   ev(amt = 100, ii = 24, addl = 2, tinf = 5)
+  p <- list(Amt = 100, Ii = 24, Addl = 2, Rate2 = 100/5, Rate = -2, Dur = 10)
+  out1 <- mrgsim(mod1, d, recsort = 3, obsonly = TRUE)
+  out2 <- mrgsim(mod2, param = p, obsonly = TRUE, recsort = 3)
+
+  expect_identical(out1$B, out2$B)
+})

inst/maintenance/unit-cpp/test-evtools-regimen.R

@@ -42,7 +42,7 @@ capture ccmt = reg.cmt();
 '
 
 mod1 <- mcode("test-evtools-regimen", code, quiet = TRUE)
-mod2 <- modlib("pk1", quiet = TRUE)
+mod2 <- modlib("pk1", quiet = TRUE, preclean = TRUE)
 mod2 <- param(mod2, as.list(param(mod1)))
 
 test_that("Identical results with pk1", {