1.1 Basic node, edge, and layer properties +href="mammult_docse1.html#x4-30001.1">Basic node, edge, and layer properties
  1.1.1 Node and layer activity +href="mammult_docsu1.html#x5-40001.1.1">Node and layer activity
  1.1.2 Layer aggregation +href="mammult_docsu11.html#x15-140001.1.2">Layer aggregation
  1.1.3 Node degree, participation coefficient, cartography +href="mammult_docsu14.html#x18-170001.1.3">Node degree, participation coefficient, cartography
  1.1.4 Edge overlap, reinforcement +href="mammult_docsu19.html#x23-220001.1.4">Edge overlap, reinforcement
1.2 Inter-layer degree correlations +href="mammult_docse2.html#x27-260001.2">Inter-layer degree correlations
  1.2.1 Node ranking +href="mammult_docsu23.html#x28-270001.2.1">Node ranking
  1.2.2 Interlayer degree correlation coefficients +href="mammult_docsu27.html#x32-310001.2.2">Interlayer degree correlation coefficients
  1.2.3 Interlayer degree correlation functions - - - +href="mammult_docsu31.html#x36-350001.2.3">Interlayer degree correlation functions

[

[next] [prev] [prev-tail] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docch2.html b/doc/html/mammult_docch2.html index 3981763..1f2f5e5 100644 --- a/doc/html/mammult_docch2.html +++ b/doc/html/mammult_docch2.html @@ -7,47 +7,47 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

Chapter 2
Models of multi-layer networks

+ id="x41-400002">Models of multi-layer networks

2.1 Null models +href="mammult_docse3.html#x42-410002.1">Null models
  2.1.1 Null-models of node and layer activity +href="mammult_docsu36.html#x43-420002.1.1">Null-models of node and layer activity
2.2 Growing multiplex networks +href="mammult_docse4.html#x48-470002.2">Growing multiplex networks
  2.2.1 Linear preferential attachment +href="mammult_docsu41.html#x49-480002.2.1">Linear preferential attachment
  2.2.2 Non-linear preferential attachment +href="mammult_docsu46.html#x54-530002.2.2">Non-linear preferential attachment
  2.2.3 Utilities +href="mammult_docsu48.html#x56-550002.2.3">Utilities
2.3 Multiplex networks with inter-layer degree correlations +href="mammult_docse5.html#x58-570002.3">Multiplex networks with inter-layer degree correlations
  2.3.1 Models based on simulated annealing +href="mammult_docsu50.html#x59-580002.3.1">Models based on simulated annealing

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docch3.html b/doc/html/mammult_docch3.html index 64e26b3..9f1bb31 100644 --- a/doc/html/mammult_docch3.html +++ b/doc/html/mammult_docch3.html @@ -7,38 +7,38 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

Chapter 3
Dynamics on multi-layer networks

+ id="x62-610003">Dynamics on multi-layer networks

3.1 Interacting opinions - Multilayer ising model +href="mammult_docse6.html#x63-620003.1">Interacting opinions - Multilayer ising model
3.2 Biased random walks +href="mammult_docse7.html#x65-640003.2">Biased random walks
3.2.1 Stationary distribution +href="mammult_docsu54.html#x66-650003.2.1">Stationary distribution
3.2.2 Entropy rate +href="mammult_docsu56.html#x68-670003.2.2">Entropy rate

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docli1.html b/doc/html/mammult_docli1.html new file mode 100644 index 0000000..1bcc41e --- /dev/null +++ b/doc/html/mammult_docli1.html @@ -0,0 +1,86 @@ + + +Contents + + + + + + + + +

[next] [prev] [prev-tail] [tail] [up]

+ 1 Structural descriptors +
1.1 Basic node, edge, and layer properties +
  1.1.1 Node and layer activity + + + +
  1.1.2 Layer aggregation +
  1.1.3 Node degree, participation coefficient, cartography +
  1.1.4 Edge overlap, reinforcement +
1.2 Inter-layer degree correlations +
  1.2.1 Node ranking +
  1.2.2 Interlayer degree correlation coefficients +
  1.2.3 Interlayer degree correlation functions +
2 Models of multi-layer networks +
2.1 Null models +
  2.1.1 Null-models of node and layer activity +
2.2 Growing multiplex networks +
  2.2.1 Linear preferential attachment +
  2.2.2 Non-linear preferential attachment +
  2.2.3 Utilities +
2.3 Multiplex networks with inter-layer degree correlations +
  2.3.1 Models based on simulated annealing +
3 Dynamics on multi-layer networks +
3.1 Interacting opinions - Multilayer ising model +
3.2 Biased random walks +
  3.2.1 Stationary distribution +
  3.2.2 Entropy rate +

+ + + +

[next] [prev] [prev-tail] [front] [up]

+ diff --git a/doc/html/mammult_docse1.html b/doc/html/mammult_docse1.html index 6b2da86..8b1be3b 100644 --- a/doc/html/mammult_docse1.html +++ b/doc/html/mammult_docse1.html @@ -7,109 +7,112 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

1.1 Basic node, edge, and layer properties

+ id="x4-30001.1">Basic node, edge, and layer properties +

  1.1.1 Node and layer activity +href="mammult_docsu1.html#x5-40001.1.1">Node and layer activity
   node_activity.py
   layer_activity.py
   node_activity_vectors.py
   layer_activity_vectors.py
   multiplexity.py
   hamming_dist.py
   node_degree_vectors.py
   degs_to_binary.py
   degs_to_activity_overlap.py
  1.1.2 Layer aggregation +href="mammult_docsu11.html#x15-140001.1.2">Layer aggregation
   aggregate_layers_w.py
   intersect_layers.py
  1.1.3 Node degree, participation coefficient, cartography +href="mammult_docsu14.html#x18-170001.1.3">Node degree, participation coefficient, cartography
   overlap_degree.py
   cartography_from_layers.py
   cartography_from_deg_vectors.py
   cartography_from_columns.py
  1.1.4 Edge overlap, reinforcement +href="mammult_docsu19.html#x23-220001.1.4">Edge overlap, reinforcement
   edge_overlap.py + + +
   avg_edge_overlap.py
   reinforcement.py

@@ -118,12 +121,12 @@ class="cmtt-10x-x-109">reinforcement.py -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docse2.html b/doc/html/mammult_docse2.html index 3f56105..4def360 100644 --- a/doc/html/mammult_docse2.html +++ b/doc/html/mammult_docse2.html @@ -7,70 +7,70 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

1.2 Inter-layer degree correlations

+ id="x27-260001.2">Inter-layer degree correlations +

  1.2.1 Node ranking +href="mammult_docsu23.html#x28-270001.2.1">Node ranking
   rank_nodes.py
   rank_nodes_thresh.py
   rank_occurrence.py
  1.2.2 Interlayer degree correlation coefficients +href="mammult_docsu27.html#x32-310001.2.2">Interlayer degree correlation coefficients
   compute_pearson.py
   compute_rho.py
   compute_tau.py
  1.2.3 Interlayer degree correlation functions +href="mammult_docsu31.html#x36-350001.2.3">Interlayer degree correlation functions
   dump_k_q
   knn_q_from_layers.py
   knn_q_from_degrees.py
   fit_knn

@@ -79,12 +79,12 @@ class="cmtt-10x-x-109">_knn -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docse3.html b/doc/html/mammult_docse3.html index 3c7a57d..51390cf 100644 --- a/doc/html/mammult_docse3.html +++ b/doc/html/mammult_docse3.html @@ -7,36 +7,36 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

2.1 Null models

+ id="x42-410002.1">Null models +

  2.1.1 Null-models of node and layer activity +href="mammult_docsu36.html#x43-420002.1.1">Null-models of node and layer activity
   model_hypergeometric.py
   model_MDM.py
   model_MSM.py
   model_layer_growth.py @@ -44,12 +44,12 @@ class="cmtt-10x-x-109">_growth.py -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docse4.html b/doc/html/mammult_docse4.html index c7f96fa..b2f804d 100644 --- a/doc/html/mammult_docse4.html +++ b/doc/html/mammult_docse4.html @@ -7,54 +7,54 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

2.2 Growing multiplex networks

+ id="x48-470002.2">Growing multiplex networks +

  2.2.1 Linear preferential attachment +href="mammult_docsu41.html#x49-480002.2.1">Linear preferential attachment
   nibilab_linear_delta
   nibilab_linear_delay
   nibilab_linear_delay_mix
   nibilab_linear_random_times
  2.2.2 Non-linear preferential attachment +href="mammult_docsu46.html#x54-530002.2.2">Non-linear preferential attachment
   nibilab_nonlinear
  2.2.3 Utilities +href="mammult_docsu48.html#x56-550002.2.3">Utilities
   node_deg_over_time.py -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docse5.html b/doc/html/mammult_docse5.html index 65b7d82..6f61c57 100644 --- a/doc/html/mammult_docse5.html +++ b/doc/html/mammult_docse5.html @@ -7,28 +7,28 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

2.3 Multiplex networks with inter-layer degree correlations

+ id="x58-570002.3">Multiplex networks with inter-layer degree correlations +

  2.3.1 Models based on simulated annealing +href="mammult_docsu50.html#x59-580002.3.1">Models based on simulated annealing
   tune_rho
   tune_qnn_adaptive @@ -36,12 +36,12 @@ class="cmtt-10x-x-109">_adaptive -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docse6.html b/doc/html/mammult_docse6.html index 36d0a33..c0109c6 100644 --- a/doc/html/mammult_docse6.html +++ b/doc/html/mammult_docse6.html @@ -7,34 +7,34 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

3.1 Interacting opinions - Multilayer ising model

+ id="x63-620003.1">Interacting opinions - Multilayer ising model

multiplex_ising

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docse7.html b/doc/html/mammult_docse7.html index 9c46101..05a3257 100644 --- a/doc/html/mammult_docse7.html +++ b/doc/html/mammult_docse7.html @@ -7,43 +7,43 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

3.2 Biased random walks

+ id="x65-640003.2">Biased random walks +

  3.2.1 Stationary distribution +href="mammult_docsu54.html#x66-650003.2.1">Stationary distribution
   statdistr2
  3.2.2 Entropy rate +href="mammult_docsu56.html#x68-670003.2.2">Entropy rate
   entropyrate2add
   entropyrate2mult
   entropyrate2int

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu1.html b/doc/html/mammult_docsu1.html index 47a6c51..2114571 100644 --- a/doc/html/mammult_docsu1.html +++ b/doc/html/mammult_docsu1.html @@ -7,63 +7,60 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

1.1.1 Node and layer activity

This section includes programs related to the computation of node and layer + id="x5-40001.1.1">Node and layer activity +

This section includes programs related to the computation of node and layer activity, activity vectors, pairwise multiplexity, pairwise normalised Hamming distance, node degree vectors.

   node_activity.py - - -
   layer_activity.py
   node_activity_vectors.py
   layer_activity_vectors.py
   multiplexity.py
   hamming_dist.py
   node_degree_vectors.py
   degs_to_binary.py
   degs_to_activity_overlap.py -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu10.html b/doc/html/mammult_docsu10.html index deea403..fc37d72 100644 --- a/doc/html/mammult_docsu10.html +++ b/doc/html/mammult_docsu10.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu9.html#tailmammult_docsu9.html" >prev-tail] [tail] [up]

degs_to_activityhttp://journals.aps.org/pre/abstract/10.1103/PhysRevE.92. -
[
[next] [prev] [prev-tail] [front] [up]
-

diff --git a/doc/html/mammult_docsu11.html b/doc/html/mammult_docsu11.html index b504286..75e7e47 100644 --- a/doc/html/mammult_docsu11.html +++ b/doc/html/mammult_docsu11.html @@ -7,29 +7,29 @@ - + -
[
[next] [prev] [prev-tail] [tail] [up]

1.1.2 Layer aggregation
-
This section includes programs to obtain various single-layer aggregated graphs + id="x15-140001.1.2">Layer aggregation

This section includes programs to obtain various single-layer aggregated graphs associated to a multiplex network.

aggregate_layers_w.py
intersect_layers.py

@@ -37,12 +37,12 @@ class="cmtt-10x-x-109">_layers.py -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu12.html b/doc/html/mammult_docsu12.html index 24166d2..ee927e2 100644 --- a/doc/html/mammult_docsu12.html +++ b/doc/html/mammult_docsu12.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu11.html#tailmammult_docsu11.html" >prev-tail] [tail] [up]

aggregate_layers_w.py

diff --git a/doc/html/mammult_docsu13.html b/doc/html/mammult_docsu13.html index aa6075c..036a144 100644 --- a/doc/html/mammult_docsu13.html +++ b/doc/html/mammult_docsu13.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu12.html#tailmammult_docsu12.html" >prev-tail] [tail] [up]

intersect_layers.py

http://journals.aps.org/pre/abstract/10.1103/PhysRevE.92. -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu14.html b/doc/html/mammult_docsu14.html index 59bb308..198035c 100644 --- a/doc/html/mammult_docsu14.html +++ b/doc/html/mammult_docsu14.html @@ -7,39 +7,39 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

1.1.3 Node degree, participation coefficient, cartography

This section includes programs to compute the total degree and participation + id="x18-170001.1.3">Node degree, participation coefficient, cartography +

This section includes programs to compute the total degree and participation coefficient of each node, and to draw the cartography diagram of a multiplex.

   overlap_degree.py
   cartography_from_layers.py
   cartography_from_deg_vectors.py
   cartography_from_columns.py @@ -50,12 +50,12 @@ class="cmtt-10x-x-109">_columns.py -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu15.html b/doc/html/mammult_docsu15.html index 217dbc3..3d11f56 100644 --- a/doc/html/mammult_docsu15.html +++ b/doc/html/mammult_docsu15.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu14.html#tailmammult_docsu14.html" >prev-tail] [tail] [up]

overlap_degree.py

- + @@ -18,7 +18,7 @@ href="mammult_docsu15.html#tailmammult_docsu15.html" >prev-tail] [tail] [up]

cartography_from_layers.py

diff --git a/doc/html/mammult_docsu17.html b/doc/html/mammult_docsu17.html index 9399878..49f4aff 100644 --- a/doc/html/mammult_docsu17.html +++ b/doc/html/mammult_docsu17.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu16.html#tailmammult_docsu16.html" >prev-tail] [tail] [up]

cartography_from_deg - + @@ -18,7 +18,7 @@ href="mammult_docsu17.html#tailmammult_docsu17.html" >prev-tail] [tail] [up]

cartography_from_columns.py

@@ -91,12 +91,15 @@ class="cmtt-10x-x-109">http://journals.aps.org/pre/abstract/10.1103/PhysRevE.92. -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu19.html b/doc/html/mammult_docsu19.html index 0d431f5..d3f75c8 100644 --- a/doc/html/mammult_docsu19.html +++ b/doc/html/mammult_docsu19.html @@ -7,33 +7,33 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

1.1.4 Edge overlap, reinforcement

This section includes programs to compute the egde overlap and to evaulate the + id="x23-220001.1.4">Edge overlap, reinforcement +

This section includes programs to compute the egde overlap and to evaulate the edge reinforcement effect.

   edge_overlap.py
   avg_edge_overlap.py
   reinforcement.py

@@ -41,12 +41,12 @@ class="cmtt-10x-x-109">reinforcement.py -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu2.html b/doc/html/mammult_docsu2.html index b28c5ff..17fc922 100644 --- a/doc/html/mammult_docsu2.html +++ b/doc/html/mammult_docsu2.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu1.html#tailmammult_docsu1.html" >prev-tail] [tail] [up]

node_activity.py

_ID and dest_ID are the IDs of the two endpoints of an edge. + + +

OUTPUT

A list of lines, where the n-th line is the value of activity of the n-th node, diff --git a/doc/html/mammult_docsu20.html b/doc/html/mammult_docsu20.html index b1336c1..de348ae 100644 --- a/doc/html/mammult_docsu20.html +++ b/doc/html/mammult_docsu20.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu19.html#tailmammult_docsu19.html" >prev-tail] [tail] [up]

edge_overlap.py

- + @@ -18,7 +18,7 @@ href="mammult_docsu20.html#tailmammult_docsu20.html" >prev-tail] [tail] [up]

avg_edge_overlap.py

diff --git a/doc/html/mammult_docsu22.html b/doc/html/mammult_docsu22.html index 2647158..ab98c61 100644 --- a/doc/html/mammult_docsu22.html +++ b/doc/html/mammult_docsu22.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu21.html#tailmammult_docsu21.html" >prev-tail] [tail] [up]

reinforcement.py

NAME @@ -81,12 +81,15 @@ class="cmtt-10x-x-109">http://journals.aps.org/pre/abstract/10.1103/PhysRevE.89. -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu23.html b/doc/html/mammult_docsu23.html index 432b1fc..b4ccd93 100644 --- a/doc/html/mammult_docsu23.html +++ b/doc/html/mammult_docsu23.html @@ -7,34 +7,34 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

1.2.1 Node ranking

This section includes various utilities to compute and compare node rankings + id="x28-270001.2.1">Node ranking +

This section includes various utilities to compute and compare node rankings induced by any generic structural node property, including degree at different layers.

   rank_nodes.py
   rank_nodes_thresh.py
   rank_occurrence.py

@@ -43,12 +43,12 @@ class="cmtt-10x-x-109">_occurrence.py -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu24.html b/doc/html/mammult_docsu24.html index efdd3bb..ade7f9e 100644 --- a/doc/html/mammult_docsu24.html +++ b/doc/html/mammult_docsu24.html @@ -7,7 +7,7 @@ - + @@ -21,7 +21,7 @@ href="mammult_docsu23.html#mammult_docsu24.html" >up]

rank_nodes.py

- + @@ -18,7 +18,7 @@ href="mammult_docsu24.html#tailmammult_docsu24.html" >prev-tail] [tail] [up]

rank_nodes_thresh.py

diff --git a/doc/html/mammult_docsu26.html b/doc/html/mammult_docsu26.html index 196d267..1d7aad5 100644 --- a/doc/html/mammult_docsu26.html +++ b/doc/html/mammult_docsu26.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu25.html#tailmammult_docsu25.html" >prev-tail] [tail] [up]

rank_occurrence.py

http://journals.aps.org/pre/abstract/10.1103/PhysRevE.92. -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu27.html b/doc/html/mammult_docsu27.html index caa7357..0c4a19d 100644 --- a/doc/html/mammult_docsu27.html +++ b/doc/html/mammult_docsu27.html @@ -7,32 +7,32 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

1.2.2 Interlayer degree correlation coefficients

This section includes programs for the computation of various inter-layer degree + id="x32-310001.2.2">Interlayer degree correlation coefficients +

This section includes programs for the computation of various inter-layer degree correlation coefficients.

   compute_pearson.py
   compute_rho.py
   compute_tau.py

@@ -41,12 +41,12 @@ class="cmtt-10x-x-109">_tau.py -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu28.html b/doc/html/mammult_docsu28.html index bd4ed03..0444079 100644 --- a/doc/html/mammult_docsu28.html +++ b/doc/html/mammult_docsu28.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu27.html#tailmammult_docsu27.html" >prev-tail] [tail] [up]

compute_pearson.py

- + @@ -18,7 +18,7 @@ href="mammult_docsu28.html#tailmammult_docsu28.html" >prev-tail] [tail] [up]

compute_rho.py

- + @@ -18,7 +18,7 @@ href="mammult_docsu2.html#tailmammult_docsu2.html" >prev-tail] [tail] [up]

layer_activity.py

- + @@ -18,7 +18,7 @@ href="mammult_docsu29.html#tailmammult_docsu29.html" >prev-tail] [tail] [up]

compute_tau.py

http://journals.aps.org/pre/abstract/10.1103/PhysRevE.90. -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu31.html b/doc/html/mammult_docsu31.html index 0aad436..eb66846 100644 --- a/doc/html/mammult_docsu31.html +++ b/doc/html/mammult_docsu31.html @@ -7,41 +7,41 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

1.2.3 Interlayer degree correlation functions

This section includes programs to compute intra-layer and inter-layer degree + id="x36-350001.2.3">Interlayer degree correlation functions +

This section includes programs to compute intra-layer and inter-layer degree correlation functions, and to fit those functions with a power-law.

   dump_k_q
   knn_q_from_layers.py
   knn_q_from_degrees.py
   fit_knn

@@ -51,12 +51,12 @@ class="cmtt-10x-x-109">_knn -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu32.html b/doc/html/mammult_docsu32.html index bc169c9..646d34d 100644 --- a/doc/html/mammult_docsu32.html +++ b/doc/html/mammult_docsu32.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu31.html#tailmammult_docsu31.html" >prev-tail] [tail] [up]

dump_k_q

diff --git a/doc/html/mammult_docsu33.html b/doc/html/mammult_docsu33.html index 039a355..c4526d4 100644 --- a/doc/html/mammult_docsu33.html +++ b/doc/html/mammult_docsu33.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu32.html#tailmammult_docsu32.html" >prev-tail] [tail] [up]

knn_q_from - + @@ -18,7 +18,7 @@ href="mammult_docsu33.html#tailmammult_docsu33.html" >prev-tail] [tail] [up]

knn_q_from - + @@ -18,7 +18,7 @@ href="mammult_docsu34.html#tailmammult_docsu34.html" >prev-tail] [tail] [up]

fit_knn

http://journals.aps.org/pre/abstract/10.1103/PhysRevE.90. -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu36.html b/doc/html/mammult_docsu36.html index 773fe1b..5db6778 100644 --- a/doc/html/mammult_docsu36.html +++ b/doc/html/mammult_docsu36.html @@ -7,34 +7,34 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

2.1.1 Null-models of node and layer activity

+ id="x43-420002.1.1">Null-models of node and layer activity

   model_hypergeometric.py
   model_MDM.py
   model_MSM.py
   model_layer_growth.py @@ -45,12 +45,12 @@ class="cmtt-10x-x-109">_growth.py -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu37.html b/doc/html/mammult_docsu37.html index 6de8b25..1b614af 100644 --- a/doc/html/mammult_docsu37.html +++ b/doc/html/mammult_docsu37.html @@ -7,7 +7,7 @@ - + @@ -21,7 +21,7 @@ href="mammult_docsu36.html#tailmammult_docsu36.html" >prev-tail] [tail] [up]

model_hypergeometric.py

- + @@ -18,7 +18,7 @@ href="mammult_docsu37.html#tailmammult_docsu37.html" >prev-tail] [tail] [up]

model_MDM.py

- + @@ -18,7 +18,7 @@ href="mammult_docsu38.html#tailmammult_docsu38.html" >prev-tail] [tail] [up]

model_MSM.py

- + @@ -18,7 +18,7 @@ href="mammult_docsu3.html#tailmammult_docsu3.html" >prev-tail] [tail] [up]

node_activity_vectors.py

diff --git a/doc/html/mammult_docsu40.html b/doc/html/mammult_docsu40.html index a8cccba..9768e54 100644 --- a/doc/html/mammult_docsu40.html +++ b/doc/html/mammult_docsu40.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu39.html#tailmammult_docsu39.html" >prev-tail] [tail] [up]

model_layer_growth.py

@@ -127,12 +127,15 @@ class="cmtt-10x-x-109">http://journals.aps.org/pre/abstract/10.1103/PhysRevE.92. -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu41.html b/doc/html/mammult_docsu41.html index 5e82756..e25e547 100644 --- a/doc/html/mammult_docsu41.html +++ b/doc/html/mammult_docsu41.html @@ -7,38 +7,38 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

2.2.1 Linear preferential attachment

+ id="x49-480002.2.1">Linear preferential attachment

   nibilab_linear_delta
   nibilab_linear_delay
   nibilab_linear_delay_mix
   nibilab_linear_random_times -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu42.html b/doc/html/mammult_docsu42.html index f3f6862..a2f2456 100644 --- a/doc/html/mammult_docsu42.html +++ b/doc/html/mammult_docsu42.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu41.html#tailmammult_docsu41.html" >prev-tail] [tail] [up]

nibilab_linear_delta

diff --git a/doc/html/mammult_docsu43.html b/doc/html/mammult_docsu43.html index 3da9e4a..c92d96c 100644 --- a/doc/html/mammult_docsu43.html +++ b/doc/html/mammult_docsu43.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu42.html#tailmammult_docsu42.html" >prev-tail] [tail] [up]

nibilab_linear_delay

diff --git a/doc/html/mammult_docsu44.html b/doc/html/mammult_docsu44.html index 363edfd..87cb478 100644 --- a/doc/html/mammult_docsu44.html +++ b/doc/html/mammult_docsu44.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu43.html#tailmammult_docsu43.html" >prev-tail] [tail] [up]

nibilab_linear_delay - + @@ -18,7 +18,7 @@ href="mammult_docsu44.html#tailmammult_docsu44.html" >prev-tail] [tail] [up]

nibilab_linear_randomhttp://prl.aps.org/abstract/PRL/v111/i5/e058701
[
[next] [prev] [prev-tail] [front] [up]
-

diff --git a/doc/html/mammult_docsu46.html b/doc/html/mammult_docsu46.html index 8665bf5..53b98df 100644 --- a/doc/html/mammult_docsu46.html +++ b/doc/html/mammult_docsu46.html @@ -7,34 +7,34 @@ - + -
[
[next] [prev] [prev-tail] [tail] [up]

2.2.2 Non-linear preferential attachment
+ id="x54-530002.2.2">Non-linear preferential attachment

nibilab_nonlinear

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu47.html b/doc/html/mammult_docsu47.html index f2762fe..b28df01 100644 --- a/doc/html/mammult_docsu47.html +++ b/doc/html/mammult_docsu47.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu46.html#tailmammult_docsu46.html" >prev-tail] [tail] [up]

nibilab_nonlinear

http://prl.aps.org/abstract/PRL/v111/i5/e058701

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu48.html b/doc/html/mammult_docsu48.html index 3b6b027..a1354db 100644 --- a/doc/html/mammult_docsu48.html +++ b/doc/html/mammult_docsu48.html @@ -7,22 +7,22 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

2.2.3 Utilities

+ id="x56-550002.2.3">Utilities

node_deg_over_time.py -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu49.html b/doc/html/mammult_docsu49.html index 8b0c98c..416165c 100644 --- a/doc/html/mammult_docsu49.html +++ b/doc/html/mammult_docsu49.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu48.html#tailmammult_docsu48.html" >prev-tail] [tail] [up]

node_deg_overhttp://prl.aps.org/abstract/PRL/v111/i5/e058701
[
[next] [prev] [prev-tail] [front] [up]
-

diff --git a/doc/html/mammult_docsu5.html b/doc/html/mammult_docsu5.html index d0df370..76dd920 100644 --- a/doc/html/mammult_docsu5.html +++ b/doc/html/mammult_docsu5.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu4.html#tailmammult_docsu4.html" >prev-tail] [tail] [up]

layer_activity_vectors.py
diff --git a/doc/html/mammult_docsu50.html b/doc/html/mammult_docsu50.html index c165edc..a4fa6f0 100644 --- a/doc/html/mammult_docsu50.html +++ b/doc/html/mammult_docsu50.html @@ -7,26 +7,26 @@ - + -
[
[next] [prev] [prev-tail] [tail] [up]

2.3.1 Models based on simulated annealing
+ id="x59-580002.3.1">Models based on simulated annealing

tune_rho
tune_qnn_adaptive @@ -35,12 +35,12 @@ class="cmtt-10x-x-109">_adaptive -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu51.html b/doc/html/mammult_docsu51.html index 7964b96..e1ee9ba 100644 --- a/doc/html/mammult_docsu51.html +++ b/doc/html/mammult_docsu51.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu50.html#tailmammult_docsu50.html" >prev-tail] [tail] [up]

tune_rho

- + @@ -18,7 +18,7 @@ href="mammult_docsu51.html#tailmammult_docsu51.html" >prev-tail] [tail] [up]

tune_qnn_adaptive

@@ -137,12 +137,15 @@ class="cmtt-10x-x-109">http://journals.aps.org/pre/abstract/10.1103/PhysRevE.92. -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu53.html b/doc/html/mammult_docsu53.html index 0f3bf0e..2a2fd27 100644 --- a/doc/html/mammult_docsu53.html +++ b/doc/html/mammult_docsu53.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docse6.html#tailmammult_docse6.html" >prev-tail] [tail] [up]

multiplex_ising

http://arxiv.org/abs/1506.04544 -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu54.html b/doc/html/mammult_docsu54.html index 27a6e41..416234b 100644 --- a/doc/html/mammult_docsu54.html +++ b/doc/html/mammult_docsu54.html @@ -7,33 +7,33 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

3.2.1 Stationary distribution

+ id="x66-650003.2.1">Stationary distribution

statdistr2

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu55.html b/doc/html/mammult_docsu55.html index 8d25965..4a1be72 100644 --- a/doc/html/mammult_docsu55.html +++ b/doc/html/mammult_docsu55.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu54.html#tailmammult_docsu54.html" >prev-tail] [tail] [up]

statdistr2

NAME @@ -110,12 +110,15 @@ class="cmtt-10x-x-109">http://arxiv.org/abs/1505.01378 -

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu56.html b/doc/html/mammult_docsu56.html index 6f3af3b..c45b1bf 100644 --- a/doc/html/mammult_docsu56.html +++ b/doc/html/mammult_docsu56.html @@ -7,37 +7,37 @@ - + -

[

[next] [prev] [prev-tail] [tail] [up]

3.2.2 Entropy rate

+ id="x68-670003.2.2">Entropy rate

   entropyrate2add
   entropyrate2mult
   entropyrate2int

[

[next] [prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu57.html b/doc/html/mammult_docsu57.html index 466706d..fbbe555 100644 --- a/doc/html/mammult_docsu57.html +++ b/doc/html/mammult_docsu57.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu56.html#tailmammult_docsu56.html" >prev-tail] [tail] [up]

entropyrate2add

NAME diff --git a/doc/html/mammult_docsu58.html b/doc/html/mammult_docsu58.html index 8e54059..3818d3c 100644 --- a/doc/html/mammult_docsu58.html +++ b/doc/html/mammult_docsu58.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu57.html#tailmammult_docsu57.html" >prev-tail] [tail] [up]

entropyrate2mult

NAME diff --git a/doc/html/mammult_docsu59.html b/doc/html/mammult_docsu59.html index a929784..7dd6bad 100644 --- a/doc/html/mammult_docsu59.html +++ b/doc/html/mammult_docsu59.html @@ -7,7 +7,7 @@ - + @@ -17,7 +17,7 @@ href="mammult_docsu58.html#tailmammult_docsu58.html" >prev-tail] [tail] [up]

entropyrate2int

NAME @@ -93,11 +93,14 @@ class="cmti-10x-x-109">networks”, arxiv:1505.01378 (2015).

Link to paper: http://arxiv.org/abs/1505.01378 -

[

[prev] [prev-tail] [front] [up]

diff --git a/doc/html/mammult_docsu6.html b/doc/html/mammult_docsu6.html index fb2c967..354c8b2 100644 --- a/doc/html/mammult_docsu6.html +++ b/doc/html/mammult_docsu6.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu5.html#tailmammult_docsu5.html" >prev-tail] [tail] [up]

multiplexity.py

NAME diff --git a/doc/html/mammult_docsu7.html b/doc/html/mammult_docsu7.html index 7378d93..f6ca425 100644 --- a/doc/html/mammult_docsu7.html +++ b/doc/html/mammult_docsu7.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu6.html#tailmammult_docsu6.html" >prev-tail] [tail] [up]

hamming_dist.py

- + @@ -18,7 +18,7 @@ href="mammult_docsu7.html#tailmammult_docsu7.html" >prev-tail] [tail] [up]

node_degree_vectors.py

diff --git a/doc/html/mammult_docsu9.html b/doc/html/mammult_docsu9.html index 900e27b..af6b608 100644 --- a/doc/html/mammult_docsu9.html +++ b/doc/html/mammult_docsu9.html @@ -7,7 +7,7 @@ - + @@ -18,7 +18,7 @@ href="mammult_docsu8.html#tailmammult_docsu8.html" >prev-tail] [tail] [up]

degs_to_binary.py

diff --git a/doc/latex/make_doc.sh b/doc/latex/make_doc.sh new file mode 100755 index 0000000..81dea3c --- /dev/null +++ b/doc/latex/make_doc.sh @@ -0,0 +1,6 @@ +#!/bin/bash + +htlatex mammult_doc.tex "html,index=2,3,4,5,next" "" -d../html/ +rm *.html + +pdflatex mammult_doc.tex diff --git a/doc/latex/mammult_doc.pdf b/doc/latex/mammult_doc.pdf new file mode 100644 index 0000000..da74f70 Binary files /dev/null and b/doc/latex/mammult_doc.pdf differ diff --git a/doc/latex/mammult_doc.tex b/doc/latex/mammult_doc.tex index 4d93d88..77f9174 100644 --- a/doc/latex/mammult_doc.tex +++ b/doc/latex/mammult_doc.tex @@ -121,6 +121,7 @@ \begin{document} \maketitle +\tableofcontents \chapter{Structural descriptors} @@ -142,6 +143,8 @@ normalised Hamming distance, node degree vectors. \input{./latex/structure/activity/degs_to_binary.tex} \input{./latex/structure/activity/degs_to_activity_overlap.tex} +\clearpage + \subsection{Layer aggregation} This section includes programs to obtain various single-layer @@ -149,6 +152,7 @@ aggregated graphs associated to a multiplex network. \input{./latex/structure/metrics/aggregate_layers_w.tex} \input{./latex/structure/metrics/intersect_layers.tex} +\clearpage \subsection{Node degree, participation coefficient, cartography} @@ -160,6 +164,7 @@ diagram of a multiplex. \input{./latex/structure/metrics/cartography_from_layers.tex} \input{./latex/structure/metrics/cartography_from_deg_vectors.tex} \input{./latex/structure/metrics/cartography_from_columns.tex} +\clearpage \subsection{Edge overlap, reinforcement} This section includes programs to compute the egde overlap and to @@ -168,6 +173,7 @@ evaulate the edge reinforcement effect. \input{./latex/structure/metrics/edge_overlap.tex} \input{./latex/structure/metrics/avg_edge_overlap.tex} \input{./latex/structure/reinforcement/reinforcement.tex} +\clearpage \section{Inter-layer degree correlations} @@ -180,6 +186,7 @@ degree at different layers. \input{./latex/structure/correlations/rank_nodes.tex} \input{./latex/structure/correlations/rank_nodes_thresh.tex} \input{./latex/structure/correlations/rank_occurrence.tex} +\clearpage \subsection{Interlayer degree correlation coefficients} @@ -189,6 +196,7 @@ inter-layer degree correlation coefficients. \input{./latex/structure/correlations/compute_pearson.tex} \input{./latex/structure/correlations/compute_rho.tex} \input{./latex/structure/correlations/compute_tau.tex} +\clearpage \subsection{Interlayer degree correlation functions} @@ -204,6 +212,7 @@ power-law. \input{./latex/structure/correlations/knn_q_from_degrees.tex} %% \input{./latex/structure/correlations/knn_q_from_degrees_log.tex} \input{./latex/structure/correlations/fit_knn.tex} +\clearpage \chapter{Models of multi-layer networks} @@ -215,6 +224,7 @@ power-law. \input{./latex/models/nullmodels/model_MDM.tex} \input{./latex/models/nullmodels/model_MSM.tex} \input{./latex/models/nullmodels/model_layer_growth.tex} +\clearpage \section{Growing multiplex networks} @@ -226,15 +236,18 @@ power-law. \input{./latex/models/growth/nibilab_linear_delay_mix.tex} \input{./latex/models/growth/nibilab_linear_random_times.tex} %%\input{./latex/models/growth/nibilab_semilinear.tex} +\clearpage \subsection{Non-linear preferential attachment} \input{./latex/models/growth/nibilab_nonlinear.tex} +\clearpage \subsection{Utilities} \input{./latex/models/growth/node_deg_over_time.tex} +\clearpage \section{Multiplex networks with inter-layer degree correlations} @@ -242,6 +255,7 @@ power-law. \input{./latex/models/correlations/tune_rho.tex} \input{./latex/models/correlations/tune_qnn_adaptive.tex} +\clearpage \chapter{Dynamics on multi-layer networks} @@ -249,17 +263,20 @@ power-law. \section{Interacting opinions - Multilayer ising model} \input{./latex/dynamics/Ising/multiplex_ising.tex} +\clearpage \section{Biased random walks} \subsection{Stationary distribution} \input{./latex/dynamics/randomwalks/statdistr2.tex} +\clearpage \subsection{Entropy rate} \input{./latex/dynamics/randomwalks/entropyrate2add.tex} \input{./latex/dynamics/randomwalks/entropyrate2mult.tex} \input{./latex/dynamics/randomwalks/entropyrate2int.tex} +\clearpage \end{document} -- cgit v1.2.3

Chapter 1Structural descriptors

Chapter 2Models of multi-layer networks

Chapter 3Dynamics on multi-layer networks

Contents

1.1 Basic node, edge, and layer properties

1.2 Inter-layer degree correlations

2.1 Null models

2.2 Growing multiplex networks

2.3 Multiplex networks with inter-layer degree correlations

3.1 Interacting opinions - Multilayer ising model

3.2 Biased random walks

1.1.1 Node and layer activity

1.1.2 Layer aggregation

aggregate_layers_w.py

intersect_layers.py

1.1.3 Node degree, participation coefficient, cartography

overlap_degree.py

cartography_from_layers.py

cartography_from_deg - + @@ -18,7 +18,7 @@ href="mammult_docsu17.html#tailmammult_docsu17.html" >prev-tail] [tail] [up]

cartography_from_columns.py

1.1.4 Edge overlap, reinforcement

node_activity.py

edge_overlap.py

avg_edge_overlap.py

reinforcement.py

1.2.1 Node ranking

rank_nodes.py

rank_nodes_thresh.py

rank_occurrence.py

1.2.2 Interlayer degree correlation coefficients

compute_pearson.py

compute_rho.py

layer_activity.py

compute_tau.py

1.2.3 Interlayer degree correlation functions

dump_k_q

knn_q_from - + @@ -18,7 +18,7 @@ href="mammult_docsu33.html#tailmammult_docsu33.html" >prev-tail] [tail] [up]

knn_q_from - + @@ -18,7 +18,7 @@ href="mammult_docsu34.html#tailmammult_docsu34.html" >prev-tail] [tail] [up]

fit_knn

2.1.1 Null-models of node and layer activity

model_hypergeometric.py

model_MDM.py

model_MSM.py

node_activity_vectors.py

model_layer_growth.py

2.2.1 Linear preferential attachment

nibilab_linear_delta

nibilab_linear_delay

nibilab_linear_delay - + @@ -18,7 +18,7 @@ href="mammult_docsu44.html#tailmammult_docsu44.html" >prev-tail] [tail] [up]

2.2.2 Non-linear preferential attachment

nibilab_nonlinear

2.2.3 Utilities

layer_activity_vectors.py

2.3.1 Models based on simulated annealing

tune_rho

tune_qnn_adaptive

multiplex_ising

3.2.1 Stationary distribution

statdistr2

3.2.2 Entropy rate

entropyrate2add

entropyrate2mult

entropyrate2int

multiplexity.py

hamming_dist.py

node_degree_vectors.py

degs_to_binary.py

Chapter 1
Structural descriptors

Chapter 2
Models of multi-layer networks

Chapter 3
Dynamics on multi-layer networks