1 files changed, 63 insertions, 3 deletions
diff --git a/utilities/Rips_complex/ripscomplex.md b/utilities/Rips_complex/ripscomplex.md
index 4291fae7..6df49310 100644
--- a/utilities/Rips_complex/ripscomplex.md
+++ b/utilities/Rips_complex/ripscomplex.md
@@ -1,7 +1,15 @@
+---
+layout: page
+title: "Rips complex"
+meta_title: "Rips complex"
+teaser: ""
+permalink: /ripscomplex/
+---
+{::comment}
+Leave the lines above as it is required by the web site generator 'Jekyll'
+{:/comment}
 
 
-# Rips complex #
-
 ## rips_persistence ##
 This program computes the persistent homology with coefficient field *Z/pZ* of a Rips complex defined on a set of input points, using Euclidean distance. The output diagram contains one bar per line, written with the convention:
 
@@ -39,11 +47,63 @@ Same as `rips_persistence` but taking a distance matrix as input.
 
 **Usage**
 
-`rips_persistence [options] <CSV input file>`
+`rips_distance_matrix_persistence [options] <CSV input file>`
 
 where
 `<CSV input file>` is the path to the file containing a distance matrix. Can be square or lower triangular matrix. Separator is ';'.
+The code do not check if it is dealing with a distance matrix. It is the user responsibility to provide a valid input.
+Please refer to data/distance_matrix/lower_triangular_distance_matrix.csv for an example of a file.
 
 **Example**
 
 `rips_distance_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0`
+
+
+## rips_correlation_matrix_persistence ##
+
+Same as `rips_distance_matrix_persistence` but taking a correlation matrix as input.
+
+**Usage**
+
+`rips_correlation_matrix_persistence [options] <CSV input file>`
+
+where
+`<CSV input file>` is the path to the file containing a correlation matrix. Can be square or lower triangular matrix. Separator is ';'.
+Note that no check is performed if the matrix given as the input is a correlation matrix.
+It is the user responsibility to ensure that this is the case.
+Please refer to data/correlation_matrix/lower_triangular_correlation_matrix.csv for an example of a file.
+
+**Example**
+
+`rips_correlation_matrix_persistence data/distance_matrix/full_square_distance_matrix.csv -r 15 -d 3 -p 3 -m 0`
+
+**Warning**
+
+As persistence diagrams points will be under the diagonal, bottleneck distance and persistence graphical tool will not work
+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:
+
+`p dim birth death`
+
+where `dim` is the dimension of the homological feature, `birth` and `death` are respectively the birth and death of the feature, and `p` is the characteristic of the field *Z/pZ* used for homology coefficients (`p` must be a prime number).
+
+**Usage**
+
+`sparse_rips_persistence [options] <OFF input file>`
+
+**Allowed options**
+
+* `-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.
+* `-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.
+
+**Example with Z/2Z coefficients**
+
+`sparse_rips_persistence ../../data/points/tore3D_1307.off -e .5 -m .2 -d 3 -p 2`