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diff --git a/src/Rips_complex/utilities/ripscomplex.md b/src/Rips_complex/utilities/ripscomplex.md index 421caa7d..84f40cc1 100644 --- a/src/Rips_complex/utilities/ripscomplex.md +++ b/src/Rips_complex/utilities/ripscomplex.md @@ -1,3 +1,13 @@ +--- +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 # @@ -35,20 +45,46 @@ Beware: this program may use a lot of RAM and take a lot of time if `max-edge-le ## rips_distance_matrix_persistence ## -Same as `rips_persistence` but taking a distance matrix as input. +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: |