Added TODOs and FIXMEs (#11)

ocbe-uio · Sep 17, 2024 · 59484e3 · 59484e3
1 parent 320bc08
commit 59484e3
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 5 deletions.
diff --git a/src/func_MCMC_graph_cpp.cpp b/src/func_MCMC_graph_cpp.cpp
@@ -26,7 +26,7 @@ arma::mat construct_G_MRF(arma::mat G, arma::vec b, uint S, int p, bool MRF_2b)
     }
   } else {
     // one value for b in MRF prior for all subgraphs
-    G_MRF = b[0] * G;
+    G_MRF = b[0] * G; // TODO: replace [] with () for bound check
   }
   return G_MRF;
 }
@@ -58,7 +58,7 @@ Rcpp::List func_MCMC_graph_cpp(
   Rcpp::List C = Rcpp::as<Rcpp::List>(ini["C.ini"]);
 
   Rcpp::List gamma_ini_list = Rcpp::as<Rcpp::List>(ini["gamma.ini"]);
-  arma::vec gamma_ini = Rcpp::as<arma::vec>(gamma_ini_list[0]); // TODO: Test for S > 1, not sure the results are correct.
+  arma::vec gamma_ini = Rcpp::as<arma::vec>(gamma_ini_list[0]); // FIXME: use list_to_matrix() and change with S
 
   if (MRF_2b) {
     // two different values for b in MRF prior for subgraphs G_ss and G_rs

diff --git a/tests/testthat/test-cpp_translation.R b/tests/testthat/test-cpp_translation.R
@@ -29,7 +29,6 @@ hyperPooled = list(
 )
 hyperPooled_2S <- hyperPooled
 hyperPooled_2S$G <- Matrix::bdiag(simData$G, simData$G)
-hyperPooled_2S$b <- c(0.1, 0.2)
 
 # Run a 'Pooled' Bayesian Cox model with graphical learning
 
@@ -39,7 +38,10 @@ BayesSurvive_wrap <- function(
   MRF_G = TRUE, MRF_2b = FALSE, verbose = FALSE
   ) {
   if (!MRF_G) {
-    if (!is.null(names(data))) data <- list(data)
+    if (!is.null(names(data))) {
+      data <- list(data)
+      # hyper$b <- c(0.1, 0.2) # TODO: uncomment for !MRF_2b cases
+    }
     hyper$lambda <- 3 # TODO: mandatory for !MRG.G? Add validation!
     hyper$nu0 <- 0.05
     hyper$nu1 <- 5
@@ -59,7 +61,7 @@ fit_C_noMRFG <- BayesSurvive_wrap(data, initial, hyperPooled, MRF_G = FALSE, use
 fit_R_2b <- BayesSurvive_wrap(data, initial, hyperPooled, MRF_2b = TRUE)
 fit_C_2b <- BayesSurvive_wrap(data, initial, hyperPooled, MRF_2b = TRUE, use_cpp = TRUE)
 fit_R_2b_no_G <- BayesSurvive_wrap(data_2S, initial, hyperPooled_2S, MRF_2b = TRUE, MRF_G = FALSE, n_iter = 2L)
-# fit_C_2b_no_G <- BayesSurvive_wrap(data_2S, initial, hyperPooled_2S, MRF_2b = TRUE, MRF_G = FALSE, use_cpp = TRUE, n_iter = 2L) // FIXME: broken
+# fit_C_2b_no_G <- BayesSurvive_wrap(data_2S, initial, hyperPooled_2S, MRF_2b = TRUE, MRF_G = FALSE, use_cpp = TRUE, n_iter = 2L) # FIXME: broken
 
 # TODO: reorganize tests so that they come right after each fit_R/fit_C pair
 test_that("R and C++ objects are similar", {