Minor edit

mrc-ide · Mar 6, 2024 · d338de1 · d338de1
1 parent 9389c1a
commit d338de1
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Showing 9 changed files with 51 additions and 5 deletions.
diff --git a/R/cpp11.R b/R/cpp11.R
@@ -20,6 +20,10 @@ dust_cpu_SEIRV_Model_simulate <- function(ptr, time_end) {
   .Call(`_YEP_dust_cpu_SEIRV_Model_simulate`, ptr, time_end)
 }
 
+dust_cpu_SEIRV_Model_run_adjoint <- function(ptr) {
+  .Call(`_YEP_dust_cpu_SEIRV_Model_run_adjoint`, ptr)
+}
+
 dust_cpu_SEIRV_Model_set_index <- function(ptr, r_index) {
   .Call(`_YEP_dust_cpu_SEIRV_Model_set_index`, ptr, r_index)
 }

diff --git a/R/dust.R b/R/dust.R
@@ -1,4 +1,4 @@
-## Generated by dust (version 0.14.10) - do not edit
+## Generated by dust (version 0.15.1) - do not edit
 SEIRV_Model <- R6::R6Class(
   "dust",
   cloneable = FALSE,
@@ -47,6 +47,7 @@ SEIRV_Model <- R6::R6Class(
            alloc = dust_cpu_SEIRV_Model_alloc,
            run = dust_cpu_SEIRV_Model_run,
            simulate = dust_cpu_SEIRV_Model_simulate,
+           run_adjoint = dust_cpu_SEIRV_Model_run_adjoint,
            set_index = dust_cpu_SEIRV_Model_set_index,
            n_state = dust_cpu_SEIRV_Model_n_state,
            update_state = dust_cpu_SEIRV_Model_update_state,
@@ -105,6 +106,19 @@ SEIRV_Model <- R6::R6Class(
       m
     },
 
+    run_adjoint = function() {
+      res <- private$methods_$run_adjoint(private$ptr_)
+      ## This approach may want to change, because it won't cope well
+      ## with cases where are gradient is structured with respect to
+      ## some parameters, but perhaps it's still a reasonable thing to
+      ## do? While we have array-free models it's fine though.
+      nms <- private$info_$adjoint
+      if (!is.null(nms) && length(nms) == length(res$gradient)) {
+        names(res$gradient) <- nms
+      }
+      res
+    },
+
     set_index = function(index) {
       private$methods_$set_index(private$ptr_, index)
       private$index_ <- index
@@ -267,7 +281,7 @@ SEIRV_Model <- R6::R6Class(
     }
   ))
 class(SEIRV_Model) <- c("dust_generator", class(SEIRV_Model))
-## Generated by odin.dust (version 0.3.8) - do not edit
+## Generated by odin.dust (version 0.3.10) - do not edit
 SEIRV_Model$set("public", "transform_variables", function(y) {
     info <- self$info()
     set_dim <- function(x, dimx) {

diff --git a/inst/dust/SEIRV_Model.cpp b/inst/dust/SEIRV_Model.cpp
@@ -1,8 +1,13 @@
-// Generated by odin.dust (version 0.3.8) - do not edit
+// Generated by odin.dust (version 0.3.10) - do not edit
 template <typename real_type, typename container>
 __host__ __device__ real_type odin_sum1(const container x, size_t from, size_t to);
 template <typename real_type, typename container>
 __host__ __device__ real_type odin_sum2(const container x, int from_i, int to_i, int from_j, int to_j, int dim_x_1);
+template <typename real_type, typename T, typename U>
+__host__ __device__ real_type fintdiv(T x, U y) {
+  return std::floor(x / y);
+}
+
 template <typename real_type, typename T, typename U>
 __host__ __device__ real_type fmodr(T x, U y) {
   real_type tmp = std::fmod(static_cast<real_type>(x),

diff --git a/inst/odin/SEIRV_Model.R b/inst/odin/SEIRV_Model.R
@@ -65,6 +65,7 @@ inv_P_nV[1:N_age] <- 1.0/P_nV[i]
 P[1:N_age] <- P_nV[i] + V[i] #Total population by age group (excluding E+I)
 P_tot <- sum(P) #Total overall population (excluding E+I)
 inv_P[1:N_age] <- 1.0/P[i]
+
 vacc_rate[1:N_age] <- vacc_rate_daily[i,as.integer(year_i)]*vaccine_efficacy*dt*P[i] #Total no. vaccinations by age
 
 
@@ -133,6 +134,7 @@ dim(R_new) <- N_age
 
 
 
+
 dim(P_nV) <- N_age
 dim(inv_P_nV) <- N_age
 dim(P) <- N_age
@@ -151,3 +153,4 @@ dim(dP2_all) <- c(N_age, n_years)
 dim(vacc_rate_daily) <- c(N_age, n_years)
 
 
+
diff --git a/src/SEIRV_Model.cpp b/src/SEIRV_Model.cpp
@@ -1,4 +1,4 @@
-// Generated by dust (version 0.14.10) - do not edit
+// Generated by dust (version 0.15.1) - do not edit
 #include <cpp11.hpp>
 
 [[cpp11::register]]
@@ -18,6 +18,9 @@ SEXP dust_cpu_SEIRV_Model_run(SEXP ptr, cpp11::sexp r_time_end);
 [[cpp11::register]]
 SEXP dust_cpu_SEIRV_Model_simulate(SEXP ptr, cpp11::sexp time_end);
 
+[[cpp11::register]]
+SEXP dust_cpu_SEIRV_Model_run_adjoint(SEXP ptr);
+
 [[cpp11::register]]
 SEXP dust_cpu_SEIRV_Model_set_index(SEXP ptr, cpp11::sexp r_index);
 
@@ -69,11 +72,16 @@ void dust_cpu_SEIRV_Model_set_stochastic_schedule(SEXP ptr, SEXP time);
 SEXP dust_cpu_SEIRV_Model_ode_statistics(SEXP ptr);
 #include <dust/r/dust.hpp>
 
-// Generated by odin.dust (version 0.3.8) - do not edit
+// Generated by odin.dust (version 0.3.10) - do not edit
 template <typename real_type, typename container>
 __host__ __device__ real_type odin_sum1(const container x, size_t from, size_t to);
 template <typename real_type, typename container>
 __host__ __device__ real_type odin_sum2(const container x, int from_i, int to_i, int from_j, int to_j, int dim_x_1);
+template <typename real_type, typename T, typename U>
+__host__ __device__ real_type fintdiv(T x, U y) {
+  return std::floor(x / y);
+}
+
 template <typename real_type, typename T, typename U>
 __host__ __device__ real_type fmodr(T x, U y) {
   real_type tmp = std::fmod(static_cast<real_type>(x),
@@ -702,6 +710,10 @@ SEXP dust_cpu_SEIRV_Model_simulate(SEXP ptr, cpp11::sexp r_time_end) {
   return dust::r::dust_simulate<model_cpu>(ptr, r_time_end);
 }
 
+SEXP dust_cpu_SEIRV_Model_run_adjoint(SEXP ptr) {
+  return dust::r::dust_run_adjoint<model_cpu>(ptr);
+}
+
 SEXP dust_cpu_SEIRV_Model_set_index(SEXP ptr, cpp11::sexp r_index) {
   dust::r::dust_set_index<model_cpu>(ptr, r_index);
   return R_NilValue;

diff --git a/src/SEIRV_Model.o b/src/SEIRV_Model.o
diff --git a/src/YEP.dll b/src/YEP.dll
diff --git a/src/cpp11.cpp b/src/cpp11.cpp
@@ -41,6 +41,13 @@ extern "C" SEXP _YEP_dust_cpu_SEIRV_Model_simulate(SEXP ptr, SEXP time_end) {
   END_CPP11
 }
 // SEIRV_Model.cpp
+SEXP dust_cpu_SEIRV_Model_run_adjoint(SEXP ptr);
+extern "C" SEXP _YEP_dust_cpu_SEIRV_Model_run_adjoint(SEXP ptr) {
+  BEGIN_CPP11
+    return cpp11::as_sexp(dust_cpu_SEIRV_Model_run_adjoint(cpp11::as_cpp<cpp11::decay_t<SEXP>>(ptr)));
+  END_CPP11
+}
+// SEIRV_Model.cpp
 SEXP dust_cpu_SEIRV_Model_set_index(SEXP ptr, cpp11::sexp r_index);
 extern "C" SEXP _YEP_dust_cpu_SEIRV_Model_set_index(SEXP ptr, SEXP r_index) {
   BEGIN_CPP11
@@ -162,6 +169,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_YEP_dust_cpu_SEIRV_Model_resample",                (DL_FUNC) &_YEP_dust_cpu_SEIRV_Model_resample,                2},
     {"_YEP_dust_cpu_SEIRV_Model_rng_state",               (DL_FUNC) &_YEP_dust_cpu_SEIRV_Model_rng_state,               3},
     {"_YEP_dust_cpu_SEIRV_Model_run",                     (DL_FUNC) &_YEP_dust_cpu_SEIRV_Model_run,                     2},
+    {"_YEP_dust_cpu_SEIRV_Model_run_adjoint",             (DL_FUNC) &_YEP_dust_cpu_SEIRV_Model_run_adjoint,             1},
     {"_YEP_dust_cpu_SEIRV_Model_set_data",                (DL_FUNC) &_YEP_dust_cpu_SEIRV_Model_set_data,                3},
     {"_YEP_dust_cpu_SEIRV_Model_set_index",               (DL_FUNC) &_YEP_dust_cpu_SEIRV_Model_set_index,               2},
     {"_YEP_dust_cpu_SEIRV_Model_set_n_threads",           (DL_FUNC) &_YEP_dust_cpu_SEIRV_Model_set_n_threads,           2},

diff --git a/src/cpp11.o b/src/cpp11.o