Remove custom C++ functions

cleanup.win

@@ -3,5 +3,4 @@
 # Note to Windows users: This is not actually platform specific.
 "${R_HOME}/bin/R" --vanilla --slave -e 'roxygen2::roxygenize(load_code = roxygen2::load_source, clean = TRUE)'
 cp -r src/stan_files tests/testthat/stan_files
-cp -r inst/include tests/testthat/include
 exit $?

dev-notes/rstanarm_dev_notes.md

@@ -268,12 +268,6 @@ A brief description of what (generally) goes into each the various files/folders
 
 For example, `continuous.stan` contains all the models that can be declared by `stan_glm` (as well as some others). You can view the compiled model in R by executing `rstanarm:::stanmodels$continuous`.
 
-**`inst/include/` **
-
-This folder can include separate header files (ending with `.hpp`) that implement custom C++
-functions. If you add something, be sure to include it in `meta_header.hpp` and test it inside
-`tests.cpp`.
-
 **`data`**
 
 * Example data used in the examples/tests.

src/stan_files/continuous.stan

@@ -23,22 +23,6 @@ functions {
     return -0.5 * (quad_form(XtX, coeff - OLS) + SSR) / square(sigma)
             - N * (log(sigma) + log(sqrt(2 * pi())));
   }
-
-  /** 
-  * test function for csr_matrix_times_vector
-  *
-  * @param m Integer number of rows
-  * @param n Integer number of columns
-  * @param w Vector (see reference manual)
-  * @param v Integer array (see reference manual)
-  * @param u Integer array (see reference manual)
-  * @param b Vector that is multiplied from the left by the CSR matrix
-  * @return A vector that is the product of the CSR matrix and b
-  */
-  vector test_csr_matrix_times_vector(int m, int n, vector w, 
-                                      int[] v, int[] u, vector b) {
-    return csr_matrix_times_vector(m, n, w, v, u, b); 
-  }
 }
 data {
   // declares N, K, X, xbar, dense_X, nnz_x, w_x, v_x, u_x

src/stan_files/functions/common_functions.stan

@@ -247,21 +247,6 @@
     return V;
   }
 
-  /** 
-  * faster version of csr_matrix_times_vector
-  * declared here and defined in C++
-  *
-  * @param m Integer number of rows
-  * @param n Integer number of columns
-  * @param w Vector (see reference manual)
-  * @param v Integer array (see reference manual)
-  * @param u Integer array (see reference manual)
-  * @param b Vector that is multiplied from the left by the CSR matrix
-  * @return A vector that is the product of the CSR matrix and b
-  */
-  vector csr_matrix_times_vector2(int m, int n, vector w, 
-                                  int[] v, int[] u, vector b);
-
   /**
    * Calculate lower bound on intercept
    *

src/stan_files/model/eta_add_Zb.stan

@@ -1,2 +1,2 @@
     if (special_case) for (i in 1:t) eta += b[V[i]];
-    else eta += csr_matrix_times_vector2(N, q, w, v, u, b);
+    else eta += csr_matrix_times_vector(N, q, w, v, u, b);

src/stan_files/model/make_eta.stan

@@ -1,7 +1,7 @@
   vector[N] eta;  // linear predictor
   if (K > 0) {
     if (dense_X) eta = X[1] * beta;
-    else eta = csr_matrix_times_vector2(N, K, w_X, v_X, u_X, beta);
+    else eta = csr_matrix_times_vector(N, K, w_X, v_X, u_X, beta);
   }
   else eta = rep_vector(0.0, N);
   if (has_offset == 1) eta += offset_;

src/stan_files/model/make_eta_bern.stan

@@ -6,8 +6,8 @@
       eta1 = N[2] > 0 ? X1[1] * beta : rep_vector(0.0, 0);
     }
     else {
-      eta0 = csr_matrix_times_vector2(N[1], K, w_X0, v_X0, u_X0, beta);
-      eta1 = csr_matrix_times_vector2(N[2], K, w_X1, v_X1, u_X1, beta);
+      eta0 = csr_matrix_times_vector(N[1], K, w_X0, v_X0, u_X0, beta);
+      eta1 = csr_matrix_times_vector(N[2], K, w_X1, v_X1, u_X1, beta);
     }
   }
   else {
@@ -31,6 +31,6 @@
     if (N[1] > 0) eta0 += b[V0[i]];
     if (N[2] > 0) eta1 += b[V1[i]];
   } else if (t > 0) {
-    if (N[1] > 0) eta0 += csr_matrix_times_vector2(N[1], q, w0, v0, u0, b);
-    if (N[2] > 0) eta1 += csr_matrix_times_vector2(N[2], q, w1, v1, u1, b);
+    if (N[1] > 0) eta0 += csr_matrix_times_vector(N[1], q, w0, v0, u0, b);
+    if (N[2] > 0) eta1 += csr_matrix_times_vector(N[2], q, w1, v1, u1, b);
   }

src/stan_files/polr.stan

@@ -122,20 +122,6 @@ functions {
     else reject("invalid link");
     return ystar;
   }
-
-  /** 
-  * faster version of csr_matrix_times_vector
-  * declared here and defined in C++
-  *
-  * @param m Integer number of rows
-  * @param n Integer number of columns
-  * @param w Vector (see reference manual)
-  * @param v Integer array (see reference manual)
-  * @param u Integer array (see reference manual)
-  * @param b Vector that is multiplied from the left by the CSR matrix
-  * @return A vector that is the product of the CSR matrix and b
-  */
-  vector csr_matrix_times_vector2(int m, int n, vector w, int[] v, int[] u, vector b);
 }
 data {
   // declares N, K, X, xbar, dense_X, nnz_x, w_x, v_x, u_x

tests/testthat/test_stan_functions.R

@@ -50,9 +50,6 @@ functions <- sapply(dir(MODELS_HOME, pattern = "stan$", full.names = TRUE), func
   } else return(as.character(NULL))
 })
 names(functions) <- basename(names(functions))
-functions$polr.stan <- grep("csr_matrix_times_vector2", 
-                            functions$polr.stan, 
-                            value = TRUE, fixed = TRUE, invert = TRUE)
 functions <- c(unlist(lapply(file.path(MODELS_HOME, "functions", 
                              c("common_functions.stan",
                                "bernoulli_likelihoods.stan",
@@ -65,7 +62,6 @@ model_code <- paste(c("functions {", functions, "}"), collapse = "\n")
 stanc_ret <- stanc(model_code = model_code, model_name = "Stan Functions",
                    allow_undefined = TRUE)
 expose_stan_functions(stanc_ret, rebuild = TRUE, verbose = TRUE)
-Rcpp::sourceCpp(file.path(INCLUDE_DIR, "tests.cpp"), rebuild = TRUE, verbose = TRUE)
 N <- 99L
 
 # bernoulli
@@ -399,16 +395,13 @@ if (require(lme4) && require(HSAUR3)) test_that("the Stan equivalent of lme4's Z
                  tol = 1e-14)
 
     parts <- extract_sparse_parts(Z)
-    Zb <- csr_matrix_times_vector2_test(nrow(Z), ncol(Z), parts$w, 
-                                        parts$v - 1L, parts$u - 1L, b)
     expect_equal(Zb, as.vector(Z %*% b), tol = 1e-14)
     if (all(sapply(group$cnms, FUN = function(x) {
         length(x) == 1 && x == "(Intercept)"
       })) ) {
       V <- matrix(parts$v, nrow = sum(p), ncol = nrow(Z))
       expect_true(all(V == 
                       t(as.matrix(as.data.frame(make_V(nrow(Z), nrow(V), parts$v - 1L))))))
-      expect_equal(Zb, apply(V, 2, FUN = function(v) sum(b[v])))
     }
   }
   test_lme4(glFormula(Reaction ~ Days + (Days | Subject), data = sleepstudy)$reTrms)

tools/make_cc.R

@@ -21,8 +21,6 @@ make_cc <- function(file) {
   file <- sub("\\.cc$", ".stan", file)
   cppcode <- rstan::stanc(file, allow_undefined = TRUE,
                           obfuscate_model_name = FALSE)$cppcode
-  cppcode <- sub("(class[[:space:]][A-Za-z_][A-Za-z0-9_]*[[:space:]])",
-                 paste("#include <meta_header.hpp>\n", "\\1"), cppcode)
 
   cat(readLines(dir("stan_files", pattern = "license.stan", recursive = TRUE, full.names = TRUE)),
       "#ifndef MODELS_HPP", "#define MODELS_HPP", "#define STAN__SERVICES__COMMAND_HPP",