function?[SWPdelta_Cdelta_L]?=?small_world_propensity（A?varargin）

%?a?function?for?calculating?the?small?world?propensity?of
%?a?given?network?-?assumes?that?matrix?is?undirected?（symmeteric）?and?if
%?not?creates?a?symmetric?matrix?which?is?used?for?the?calculations

%NOTE:??This?code?requires?the?Bioinformatics?Toolbox?to?be?installed
%????????（uses?graphallshortestpaths.m）

%Inputs:
%???A???????????the?connectivity?matrix?weighted?or?binary
%???varargin????a?string?corresponding?to?the?method?of?clustering
%???????????????to?be?used?where?‘O‘?is?Onnela?‘Z‘?is?Zhang?
%???????????????‘B‘?is?Barrat?‘bin‘?is?binary?（default?is?Onnela）.
%???????????????If?the?user?specifies?binary?analysis?a?
%???????????????weighted?matrix?will?be?converted?to?a?binary?matrix?
%???????????????before?proceeding.
%????????

%Outputs:
%???SWP?????????the?small?world?propensity?of?the?matrix
%???delta_C?????the?fractional?deviation?from?the?expected?culstering?coefficient?of?a
%???????????????????random?network
%???delta_L?????the?fractional?deviation?from?the?expected?path?length?of?a
%???????????????????random?network

%written?by?Eric?Bridgeford?and?modified?by?Sarah?F.?Muldoon

%?Reference:?Muldoon?Bridgeford?and?Bassett?（2015）?“Small-World?Propensity?in?Weighted?
%???????????????Real-World?Networks“?http://arxiv.org/abs/1505.02194

if?isempty（varargin）
????varargin{1}?=?‘O‘;
end

if?sum（sum（A））?>?0
????
bin_matrix?=?0;
if?strcmp（varargin{1}‘bin‘）?==?1
???bin_matrix?=?1;
???A?=?A?>?0;
end

%check?to?see?if?matrix?is?symmeteric
symcheck=abs（A-A‘）;
if?sum（sum（symcheck））?>?0
????%?adjust?the?input?matrix?to?symmeterize
????disp（‘Input?matrix?is?not?symmetric.?Symmetrizing.‘）
????W?=?symm_matrix（A?bin_matrix）;
else
????W=A;
end

%calculate?the?number?of?nodes
n?=?length（W）;??
%compute?the?weighted?density?of?the?network
dens_net?=?sum（sum（W））/（max（max（W））*n*（n-1））;

%compute?the?average?degree?of?the?unweighted?network?to?give
%the?approximate?radius
numb_connections?=?length（find（W>0））;
avg_deg_unw?=?numb_connections/n;
avg_rad_unw?=?avg_deg_unw/2;
avg_rad_eff?=?ceil（avg_rad_unw）;


%compute?the?regular?and?random?matrix?for?the?network?W
W_reg?=?regular_matrix_generator（W?avg_rad_eff）;
W_rand?=?randomize_matrix（W）;

%compute?all?path?length?calculations?for?the?network
reg_path?=?avg_path_matrix（1./W_reg）;??????%path?of?the?regular?network
rand_path?=?avg_path_matrix（1./W_rand）;????%path?of?the?random?netowork
net_path?=?avg_path_matrix（1./W）;??????????%path?of?the?network

A?=?（net_path?-?rand_path）;
if?A?????A?=?0;
end
diff_path?=??A/?（reg_path?-?rand_path）;
if?net_path?==?Inf?||?rand_path?==?Inf?||?reg_path?==?Inf
????diff_path?=?1;
end
if?diff_path?>?1
????diff_path?=?1;
end


%compute?all?clustering?calculations?for?the?network
reg_clus?=?avg_clus_matrix（W_regvarargin{1}）;
rand_clus?=?avg_clus_matrix（W_randvarargin{1}）;
net_clus?=?avg_clus_matrix（W