mathbiol · wilkinson · Sep 5, 2011 · Sep 5, 2011 · Sep 5, 2011 · Sep 5, 2011
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,19 @@
+#-  Git configuration file
+
+#-  .gitignore ~~
+#                                                   ~~ last updated 08 Oct 2012
+
+#-  Mercurial repository itself (if present)
+.hg/
+
+#-  Vim swap files
+*.swp
+
+#-  OS generated files
+.DS_Store*
+ehthumbs.db
+Icon\?
+.localized
+Thumbs.db
+
+#-  vim:set syntax=gitconfig:
diff --git a/23andme.html b/23andme.html
@@ -0,0 +1,10 @@
+<html>
+<head>
+<script src="//ajax.googleapis.com/ajax/libs/jquery/1.8.2/jquery.min.js"></script>
+<script src="https://api.23andme.com/res/js/ttam-0.1.js"></script>
+</head>
+<body>
+Experimenting with 23andme
+<script src='https://dl.dropbox.com/s/19vygxl13daeor2/23andme.js?dl=1'></script>
+</body>
+</html>
diff --git a/23andme.js b/23andme.js
@@ -0,0 +1,33 @@
+//https://api.23andme.com/authorize/?redirect_uri=http://jmat.googlecode.com/git/23andme.html&response_type=code&client_id=09568fd79aa7911dad7727a024936f8d&scope=basic
+// response directed to http://jmat.googlecode.com/git/23andme.html, alternative URL:
+//https://dl-web.dropbox.com/get/http/jmat/23andme.html?w=bba1484b&code={borrow from above}
+//
+UAB={ // 23and me application document object model
+	code:null,
+	parms:{},
+	search4parms:function(){ // gets parameters from call and pushes them to .parms
+		var parms = window.document.location.search.slice(1).split('&');
+		parms.map(function(x){
+			xx = x.split('=');
+			UAB.parms[xx[0]]=xx[1]
+		})
+
+		//
+	}
+}
+
+
+
+// find out what is being provided and push it to parms
+UAB.search4parms();
+if(!!UAB.parms.code){
+	UAB.code=UAB.parms.code;
+	console.log('code = '+UAB.code);
+}
+else if (!!localStorage.getItem('code')){ // find out if there is one in the localstorage
+	UAB.code = localStorage.getItem('code');
+	console.log('code = '+UAB.code);
+}
+else{
+	throw('23andme access code not found :-(')
+}
diff --git a/f.png b/f.png
diff --git a/fminsearch.html b/fminsearch.html
@@ -0,0 +1,23 @@
+<html>
+<head>
+<script src="fminsearch.js"></script>
+<script type="text/javascript" src="https://www.google.com/jsapi"></script>
+</head>
+<body>
+<div>
+	<h2 style="color:maroon;font-family:verdana"><i>fminsearch</i> </h2>
+	<p style="color:navy;font-family:verdana;font-size:small">This page: <a href="http://jmat.googlecode.com/git/fminsearch.html">http://jmat.googlecode.com/git/fminsearch.html</a>, [<a href="https://code.google.com/p/jmat/source/browse/fminsearch.js">source code</a>]<br>
+	In the browser's console you could, for example, <button style="color:blue;font-family:verdana" onclick=fminsearch.demo()>try</button>:<br>
+	<ol style="color:green;font-family:verdana;font-size:small">
+	<li> <span style="color:blue;font-family:verdana;font-size:small">x=[32,37,42,47,52,57,62,67,72,77,82,87,92];y=[0,34,59,77,99,114,121,133,146,159,165,173,170];</span> // some data</li>
+	<li> <span style="color:blue;font-family:verdana;font-size:small">fun = function(x,P){return x.map(function(xi){return (1/(1/(P[0]*(xi-P[1]))+1/P[2]))})};</span> // some model</li>
+	<li> <span style="color:blue;font-family:verdana;font-size:small">P=fminsearch(fun,[34.6,32,173],x,y);</span> // the regression with some starting values</li> 
+	</ol>
+	</p>	
+</div>	
+<div id="plot"></div>
+<script>
+google.load("visualization", "1", {packages:["corechart"]});
+</script>
+</body>
+</html>
diff --git a/fminsearch.js b/fminsearch.js
@@ -0,0 +1,89 @@
+fminsearch=function(fun,Parm0,x,y,Opt){// fun = function(x,Parm)
+	// example
+	//
+	// x = [32,37,42,47,52,57,62,67,72,77,82,87,92];y=[749,1525,1947,2201,2380,2537,2671,2758,2803,2943,3007,2979,2992]
+	// fun = function(x,P){return x.map(function(xi){return (P[0]+1/(1/(P[1]*(xi-P[2]))+1/P[3]))})}
+	// Parms=jmat.fminsearch(fun,[100,30,10,5000],x,y)
+	//
+	// Another test:
+	// x=[32,37,42,47,52,57,62,67,72,77,82,87,92];y=[0,34,59,77,99,114,121,133,146,159,165,173,170];
+	//
+	// Opt is an object will all other parameters, from the objective function (cost function), to the 
+	// number of iterations, initial step vector and the display switch, for example
+	// Parms=fminsearch(fun,[100,30,10,5000],x,y,{maxIter:10000,display:false})
+
+	if(!Opt){Opt={}};
+	if(!Opt.maxIter){Opt.maxIter=1000};
+	if(!Opt.step){// initial step is 1/100 of initial value (remember not to use zero in Parm0)
+		Opt.step=Parm0.map(function(p){return p/100});
+		Opt.step=Opt.step.map(function(si){if(si==0){return 1}else{ return si}}); // convert null steps into 1's
+	};
+	if(typeof(Opt.display)=='undefined'){Opt.display=true};
+	if(!Opt.objFun){Opt.objFun=function(y,yp){return y.map(function(yi,i){return Math.pow((yi-yp[i]),2)}).reduce(function(a,b){return a+b})}} //SSD
+
+	var cloneVector=function(V){return V.map(function(v){return v})};
+	var ya,y0,yb,fP0,fP1;
+	var P0=cloneVector(Parm0),P1=cloneVector(Parm0);
+	var n = P0.length;
+	var step=Opt.step;
+	var funParm=function(P){return Opt.objFun(y,fun(x,P))}//function (of Parameters) to minimize
+	// silly multi-univariate screening
+	for(var i=0;i<Opt.maxIter;i++){
+		for(var j=0;j<n;j++){ // take a step for each parameter
+			P1[j]+=step[j];
+			if(funParm(P1)<funParm(P0)){ // if parm value going in the righ direction
+				step[j]=1.2*step[j]; // then go a little faster
+				P0[j]=P1[j];
+			}
+			else{
+				step[j]=-(0.5*step[j]); // otherwiese reverse and go slower
+				P1[j]=P0[j];
+			}	
+		}
+		if(Opt.display){if(i>(Opt.maxIter-10)){console.log(i+1,funParm(P0),P0)}}
+	}
+	if (!!document.getElementById('plot')){ // if there is then use it
+		fminsearch.plot(x,y,fun(x,P0),P0);
+	}
+	return P0
+};
+
+fminsearch.load=function(src){ // script loading
+	// example: fminsearch.load('http://localhost:8888/jmat/jmat.js')
+	var s = document.createElement('script');
+	s.src = src;
+	document.head.appendChild(s);
+	s.parentElement.removeChild(s);
+};
+
+fminsearch.plot=function(x,y,yp,Parms,id){ // ploting results using <script type="text/javascript" src="https://www.google.com/jsapi"></script>
+	// defaults
+	var titulo='Model fitting';
+	if(!!Parms){titulo='Model parameters: '+Parms};
+	if(!id){var id='plot'}
+	// create Array in Google's format
+	var data = new google.visualization.DataTable();
+	data.addColumn('number', 'X');
+	data.addColumn('number', 'Observed');
+	data.addColumn('number', 'Model fit');
+	var n = x.length;
+	for (var i=0;i<n;i++){
+		data.addRow([x[i],y[i],yp[i]]);
+	};
+	var chart = new google.visualization.ComboChart(
+		document.getElementById(id));
+	    chart.draw(data, {title: titulo,
+	                      width: 600, height: 400,
+	                      vAxis: {title: "Y", titleTextStyle: {color: "black"}},
+	                      hAxis: {title: "X", titleTextStyle: {color: "black"}},
+						  seriesType: "scatter",
+						  series: {1: {type: "line"}}}
+	              );
+};
+
+fminsearch.demo=function(){ // demo example in http://jmat.googlecode.com/git/fminsearch.html
+	x=[32,37,42,47,52,57,62,67,72,77,82,87,92];y=[0,34,59,77,99,114,121,133,146,159,165,173,170]; // some data
+	fun = function(x,P){return x.map(function(xi){return (1/(1/(P[0]*(xi-P[1]))+1/P[2]))})}; // some model
+	P=fminsearch(fun,[34.6,32,173],x,y); // the regression with some starting values
+};
+
diff --git a/funTable.html b/funTable.html
@@ -0,0 +1,19 @@
+<html>
+<body>
+	<p>Fun With Tables</p>
+	<input type="file" id="files" multiple onchange="funTable.loadFiles(this.files,'readAsText')"></input>
+
+	<div id='work'>
+	</div>
+
+	<div id="chat">
+	<textarea id='console' style="border:none;color:blue" cols=50>></textarea><button onclick="funTable.clearConsole(this)">(x)</button><br>
+	<textarea id='msg'cols=50 style="border:none;color:navy" rows=10></textarea><button onclick="jmat.gId('msg').textContent='';jmat.gId('console').focus()">(x)</button>
+	</div>
+
+	<iframe id="loadingFrame" style="display:none"></iframe>
+
+	<script src="jmat.js"></script>
+	<script src="funTable.js"></script>
+</body>
+</html>
diff --git a/funTable.js b/funTable.js
@@ -0,0 +1,50 @@
+console.log('fun with tables (funTable) loaded');
+
+funTable={
+	loadFiles:function(files,readAs,callback){
+		//<input type="file" id="files" multiple onchange="funTable.loadFiles(this.files,'readAsText')"></input>
+		if(!readAs){readAs='readAsDataURL'} // default is to read as dataURL
+		for(var i=0;i<files.length;i++){
+			this.readFile(files[i],readAs)
+		}
+		return i
+	},
+	readFile:function(f,readAs,callback){
+		var that = this;
+		if(!callback){callback=function(x){ // DEAFAULT CALLBACK - you may want to write your own
+			console.log('---'+x.file.fileName+'---');console.log(x.result); // comment out if you don't want to track reading in the cnsole
+			if(!that.work){that.work={}};if(!that.work.files){that.work.files=[]} // results stored in .work.files
+			that.work.files[x.file.fileName]={file:x.file,result:x.result}; // array indexed to file name
+			}
+		}
+		var reader = new FileReader();
+		reader.onload=(function(theFile){
+			return function(ev){
+				//if(!funTable.work.Files){funTable.work.Files=[]}
+				//funTable.work.Files[theFile.fileName]={file:theFile,result:ev.target.result};
+				callback({file:theFile,result:ev.target.result})
+				//console.log(ev.target.result,theFile)
+			}
+		})(f)
+		reader[readAs](f);
+	},
+	log:function(x){
+		console.log(x);
+		jmat.gId('msg').textContent+=x+'\n';
+	},
+	clearConsole:function(){
+		var c=jmat.gId('console');
+		c.textContent='>';
+		c.focus();
+	},
+	clearMsg:function(){
+		var m=jmat.gId('msg');
+		m.textContent='';
+		c.focus();
+	},
+	work:{
+		// workspace variables 
+	}
+}
+
+
diff --git a/google24741bc4ba4d02c3.html b/google24741bc4ba4d02c3.html
@@ -0,0 +1 @@
+google-site-verification: google24741bc4ba4d02c3.html
diff --git a/icon128.png b/icon128.png
diff --git a/jmat.html b/jmat.html
@@ -1,5 +1,9 @@
-<html>
- <body> 
- <script src="jmat.js"></script>
- </body>
-</html>
+<html>
+ <head>
+ <meta name="google-site-verification" content="7fcghhoQd8T11z8Sk0to8AoJB_c209X1KJzd-QHKG5U" />
+ </head>
+ <body> 
+ <script src="jmat.js"></script>
+ </body>
+ JMAT
+</html>
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		google-site-verification: google24741bc4ba4d02c3.html