Merge branch 'master' into toplex_map

4 files changed, 9 insertions, 6 deletions

diff --git a/src/Rips_complex/doc/Intro_rips_complex.h b/src/Rips_complex/doc/Intro_rips_complex.h
index 712d3b6e..a2537036 100644
--- a/src/Rips_complex/doc/Intro_rips_complex.h
+++ b/src/Rips_complex/doc/Intro_rips_complex.h
@@ -39,7 +39,7 @@ namespace rips_complex {
  * <a target="_blank" href="https://en.wikipedia.org/wiki/Vietoris%E2%80%93Rips_complex">(Wikipedia)</a>
  * is an abstract simplicial complex
  * defined on a finite metric space, where each simplex corresponds to a subset
- * of point whose diameter is smaller that some given threshold.
+ * of points whose diameter is smaller that some given threshold.
  * Varying the threshold, we can also see the Rips complex as a filtration of
  * the \f$(n-1)-\f$dimensional simplex, where the filtration value of each
  * simplex is the diameter of the corresponding subset of points.
@@ -53,7 +53,10 @@ namespace rips_complex {
  * The number of simplices in the full Rips complex is exponential in the
  * number of vertices, it is thus usually restricted, by excluding all the
  * simplices with filtration value larger than some threshold, and keeping only
- * the dim_max-skeleton.
+ * the dim_max-skeleton. It may also be a good idea to start by making the
+ * point set sparser, for instance with
+ * `Gudhi::subsampling::sparsify_point_set()`, since small clusters of points
+ * have a disproportionate cost without affecting the persistence diagram much.
  *
  * In order to build this complex, the algorithm first builds the graph.
  * The filtration value of each edge is computed from a user-given distance
diff --git a/src/Rips_complex/include/gudhi/Rips_complex.h b/src/Rips_complex/include/gudhi/Rips_complex.h
index f0fe57f4..e902e52c 100644
--- a/src/Rips_complex/include/gudhi/Rips_complex.h
+++ b/src/Rips_complex/include/gudhi/Rips_complex.h
@@ -59,7 +59,7 @@ class Rips_complex {
   /**
    * \brief Type of the one skeleton graph stored inside the Rips complex structure.
    */
-  typedef typename boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS
+  typedef typename boost::adjacency_list < boost::vecS, boost::vecS, boost::directedS
   , boost::property < vertex_filtration_t, Filtration_value >
   , boost::property < edge_filtration_t, Filtration_value >> OneSkeletonGraph;
 
diff --git a/src/Rips_complex/include/gudhi/Sparse_rips_complex.h b/src/Rips_complex/include/gudhi/Sparse_rips_complex.h
index 4dcc08ed..00da148f 100644
--- a/src/Rips_complex/include/gudhi/Sparse_rips_complex.h
+++ b/src/Rips_complex/include/gudhi/Sparse_rips_complex.h
@@ -55,7 +55,7 @@ template <typename Filtration_value>
 class Sparse_rips_complex {
  private:
   // TODO(MG): use a different graph where we know we can safely insert in parallel.
-  typedef typename boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS,
+  typedef typename boost::adjacency_list<boost::vecS, boost::vecS, boost::directedS,
                                          boost::property<vertex_filtration_t, Filtration_value>,
                                          boost::property<edge_filtration_t, Filtration_value>>
       Graph;
diff --git a/src/Rips_complex/utilities/ripscomplex.md b/src/Rips_complex/utilities/ripscomplex.md
index 6df49310..108cdd50 100644
--- a/src/Rips_complex/utilities/ripscomplex.md
+++ b/src/Rips_complex/utilities/ripscomplex.md
@@ -85,7 +85,7 @@ properly, this is a known issue.
 
 ## sparse_rips_persistence ##
 This program computes the persistent homology with coefficient field *Z/pZ*
-of a sparse (1+epsilon)-approximation of the Rips complex defined on a set of input Euclidean points. The output diagram contains one bar per line, written with the convention:
+of a sparse (1+epsilon)/(1-epsilon)-approximation of the Rips complex defined on a set of input Euclidean points. The output diagram contains one bar per line, written with the convention:
 
 `p dim birth death`
 
@@ -99,7 +99,7 @@ where `dim` is the dimension of the homological feature, `birth` and `death` are
 
 * `-h [ --help ]` Produce help message
 * `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output.
-* `-e [ --approximation ]` (default = .5) Epsilon, where the sparse Rips complex is a (1+epsilon)-approximation of the Rips complex.
+* `-e [ --approximation ]` (default = .5) Epsilon, where the sparse Rips complex is a (1+epsilon)/(1-epsilon)-approximation of the Rips complex.
 * `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Rips complex we want to compute.
 * `-p [ --field-charac ]` (default = 11)     Characteristic p of the coefficient field Z/pZ for computing homology.
 * `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.