record censored death values as missing rather than infinite

NEWS.md

@@ -2,6 +2,11 @@
 
 ## Vietoris-Rips PH
 
+## censored death values
+
+This version addresses #39 by encoding deaths that exceed the threshold as undefined (`NaN`) rather than infinite (`Inf`) then converting these values to missing (`NA_REAL`) while populating the `Rcpp::NumericMatrix` returned to R.
+A single infinite degree-0 feature for the connected component is retained.
+
 ### sliding window embeddings of multivariable time series (breaking change)
 
 Previously only univariable time series could be passed to `vietoris_rips()` via the sliding window embedding (used for quasi-attractor detection).

R/data.r

@@ -27,7 +27,7 @@
 #' acre_coord <- aegypti[aegypti$state_code == "AC", c("x", "y"), drop = FALSE]
 #' acre_rips <- vietoris_rips(acre_coord)
 #' plot.new()
-#' xymax <- max(setdiff(acre_rips$death, Inf))
+#' xymax <- max(setdiff(acre_rips$death, Inf), na.rm = TRUE)
 #' plot.window(
 #'   xlim = c(0, xymax),
 #'   ylim = c(0, xymax),

src/ripser.cpp

@@ -671,8 +671,10 @@ template <typename DistanceMatrix> class ripser {
 #endif
 		  // ripserq: Accumulate pairs in an object to be returned to the user.
 #ifdef COLLECT_PERSISTENCE_PAIRS
-    for (index_t i = 0; i < n; ++i)
-      if (dset.find(i) == i) persistence_pairs[0].emplace_back(0.0, std::numeric_limits<value_t>::infinity());
+		for (index_t i = 0; i < n - 1; ++i)
+		  // ripserq: `quiet_NaN()` for deaths that subceed threshold.
+		  if (dset.find(i) == i) persistence_pairs[0].emplace_back(0.0, std::numeric_limits<value_t>::quiet_NaN());
+	  if (dset.find(n - 1) == n - 1) persistence_pairs[0].emplace_back(0.0, std::numeric_limits<value_t>::infinity());
 #endif
 	}
 
@@ -863,7 +865,8 @@ template <typename DistanceMatrix> class ripser {
 #endif
 				  // ripserq: Accumulate pairs in an object to be returned to the user.
 #ifdef COLLECT_PERSISTENCE_PAIRS
-				  persistence_pairs[dim].emplace_back(diameter, std::numeric_limits<value_t>::infinity());
+				  // ripserq: `quiet_NaN()` for deaths that subceed threshold.
+				  persistence_pairs[dim].emplace_back(diameter, std::numeric_limits<value_t>::quiet_NaN());
 #endif
 					break;
 				}
@@ -1404,7 +1407,10 @@ Rcpp::List ripser_cpp_dist(const Rcpp::NumericVector &dataset, int dim, double t
     Rcpp::NumericMatrix mat(pairs.size(), 2);
     for (size_t i = 0; i < pairs.size(); ++i) {
       mat(i, 0) = pairs[i].first;
-      mat(i, 1) = pairs[i].second;
+      if (std::isnan(pairs[i].second))
+        mat(i, 1) = NA_REAL;
+      else
+        mat(i, 1) = pairs[i].second;
     }
     output[d] = mat;
   }