GENENET8 update

1 files changed, 200 insertions, 0 deletions

diff --git a/sourcecodes/parameter_learning/writeSettings.m b/sourcecodes/parameter_learning/writeSettings.m
new file mode 100644
index 00000000..0c5ad865
--- /dev/null
+++ b/sourcecodes/parameter_learning/writeSettings.m
@@ -0,0 +1,200 @@
+function writeSettings(pre)
+  %function to write tables of settings used in structure learning
+  % so they can be reviewed by users
+
+
+parfile = strcat(pre,'parent.txt');
+paropen = fopen(parfile,'r');
+par_val = fscanf(paropen,'%i');
+
+kfile = strcat(pre,'k.txt');
+kopen = fopen(kfile,'r');
+k_val = fscanf(kopen,'%i');
+
+thrfile = strcat(pre,'thr.txt');
+thropen = fopen(thrfile,'r');
+thr_val = fscanf(thropen,'%f');
+
+filename = strcat(pre,'slsettings.txt');
+fileID = fopen(filename,'w');
+fprintf(fileID,'Structure learning settings\n');
+fprintf(fileID,'Parameter\tValue\n');
+fprintf(fileID,'Maximum number of parents\t%i\n',par_val);
+fprintf(fileID,'Number of structures for model averaging\t%i\n',k_val);
+fprintf(fileID,'Model averaging selection threshold\t%6.3f\n',thr_val);
+fprintf(fileID,'\n');
+
+tierfile = strcat(pre,'tier.txt');
+if exist(tierfile,'file') == 2
+	tieropen = fopen(tierfile,'r');
+	tiers = fscanf(tieropen,'%s');
+	tiers = strsplit(",",tiers);
+	tiers(size(tiers,2)) = [];
+	fprintf(fileID,'Tier assignments\n');
+	fprintf(fileID,'Variable\tTier\n');
+	notiers = str2num(tiers{1});
+	i = 1;
+        for j = 1:notiers
+		i = i + 1;
+		tiername = tiers{i};
+		i = i + 1;
+		novars = str2num(tiers{i});
+                if novars == 0
+                   fprintf(fileID,'No variables\t%s\n',tiername);
+                else
+		   for k = 1:novars
+		       i = i + 1;
+		       fprintf(fileID,'%s\t%s\n',tiers{i},tiername);
+                   end
+                end
+        end
+fprintf(fileID,"\n");
+end
+
+
+descfile = strcat(pre,'tierdesc.txt');
+%format of ???tierdesc.txt is:
+%% Assume that there are n tiers:
+%% For Tier i:
+%%   within tier interactions allowed: 
+%%       (i-1)*n+1 true/false for yes,
+%%       (i-1)*n+2 true/false for no;  (not needed, opposite of above)
+%%   Tier j (for 1 to n, with i != j)
+%%       Can j be parent of Tier i
+%%       Can j be child of Tier i
+if exist(descfile,'file') == 2
+        %%I am going to assume that if ???tierdesc.txt exists, then
+        %%%  ???tiers.txt exists and notiers has been defined.
+        within = cell(notiers,1);
+        parents = cell(notiers,notiers);
+        children = cell(notiers,notiers);
+        within(:) = 0;
+        parents(:) = 0;
+        children(:) = 0;
+	descopen = fopen(descfile,'r');
+	desc = fscanf(descopen,'%s');
+	desc = strsplit(",",desc);
+	desc(size(desc,2)) = [];
+        for i = 1:notiers
+            %%Pull out the section of desc array for this tiers
+            desc_current = desc((i-1)*notiers*2+1:i*notiers*2);
+	    for j = 1:notiers
+		if j < i
+                   if strcmp(desc_current{j*2+1},'true')
+                       parents{i,j} = j;
+		   end
+                   if strcmp(desc_current{j*2+2},'true')
+                       children{i,j} = j;
+		   end
+		end
+                if i == j
+                   if strcmp(desc_current{1},'true')
+                      within{i,1} = 1;
+		   end
+		end
+		if j > i
+                   if strcmp(desc_current{(j-1)*2+1},'true')
+                       parents{i,j} = j;
+		   end
+                   if strcmp(desc_current{(j-1)*2+2},'true')
+                       children{i,j} = j;
+		   end
+		end
+	end
+	end
+        fprintf(fileID,"Within tier interactions\n");
+        fprintf(fileID,"Tier\tAre within tier interaction allowed?\n");
+        for i = 1:notiers
+            i1 = sprintf("%i",i);
+            if within{i,1} == 1
+               fprintf(fileID,"Tier%s\tYes\n",i1);
+            else
+               fprintf(fileID,"Tier%s\tNo\n",i1);
+            end
+        end
+        fprintf(fileID,'\n');          
+	fprintf(fileID,'Allowed parents\n');
+	fprintf(fileID,'Tier\tOther tiers containing potential parents\n');
+        for i=1:notiers
+	    lineout = '';
+            for j=1:notiers
+               if parents{i,j} != 0
+                   j1 = sprintf("%i",parents{i,j});
+                   lineout = strcat(lineout,j1,',',{' '});
+               end
+            end
+	    col1 = sprintf("%i",i);
+            col1 = strcat("Tier",col1);
+            if size(lineout,1) > 0
+	       fprintf(fileID,'%s\t%s\n',col1,lineout{1,1}(1:end-2));
+            else 
+	       fprintf(fileID,'%s\tNone\n',col1);
+            end
+        end
+        fprintf(fileID,'\n');          
+	fprintf(fileID,'Allowed children\n');
+	fprintf(fileID,'Tier\tOther tiers containing potential children\n');
+        for i=1:notiers
+	    lineout = '';
+            for j=1:notiers
+               if children{i,j} != 0
+                   j1 = sprintf("%i",children{i,j});
+                   lineout = strcat(lineout,j1,',',{' '});
+               end
+            end
+	    col1 = sprintf("%i",i);
+            col1 = strcat("Tier",col1);
+            if size(lineout,1) > 0
+	       fprintf(fileID,'%s\t%s\n',col1,lineout{1,1}(1:end-2));
+            else 
+	       fprintf(fileID,'%s\tNone\n',col1);
+            end
+        end
+end
+
+banfile = strcat(pre,'ban.txt');
+if exist(banfile,'file') == 2
+	banopen = fopen(banfile,'r');
+	ban = fscanf(banopen,'%s');
+	ban = strsplit(",",ban);
+        ban(end) = [];
+        nban = size(ban,2)/2;
+        if nban > 0
+           fprintf(fileID,'\n');          
+           fprintf(fileID,'Banned edges\n');
+	   fprintf(fileID,'From\tTo\n');
+           for j=1:nban
+              j1 = (j-1)*2 + 1;
+              j2 = (j-1)*2 + 2;
+	      fprintf(fileID,"%s\t%s\n",ban{1,j1},ban{1,j2})
+           end
+        end
+end
+
+
+
+whitefile = strcat(pre,'white.txt');
+if exist(whitefile,'file') == 2
+	whiteopen = fopen(whitefile,'r');
+	white = fscanf(whiteopen,'%s');
+	white = strsplit(",",white);
+        white(end) = [];
+        nwhite = size(white,2)/2;
+        if nwhite > 0
+           fprintf(fileID,'\n');          
+           fprintf(fileID,'Required edges\n');
+	   fprintf(fileID,'From\tTo\n');
+           for j=1:nwhite
+              j1 = (j-1)*2 + 1;
+              j2 = (j-1)*2 + 2;
+	      fprintf(fileID,"%s\t%s\n",white{1,j1},white{1,j2})
+           end
+        end
+end
+
+
+
+
+fclose(fileID);
+
+end
\ No newline at end of file