Welcome to TiddlyWiki created by Jeremy Ruston, Copyright © 2007 UnaMesa Association
The ''Bland-Altman'' or known also as ''Tukey-mean difference'' plot is a graphical tool to measure agreement between two methods. Published in Lancet (1986), the Bland-Altman plot has been a popular method in clinical research to compare a new diagnostic tool with the already established one. The reason behind this method is that the linear regression cannot explain whether two methods differ. Linear regression can only describe a linear relationship between two or more variables.
!!Dataset
For a better understanding, let us use the same dataset as Bland and Altman used in their 1986 paper. Two Wright peak flow meter devices were used to measure peak expiratory flow rate (PEFR): Normal Wright and Mini Wright. For each device, two assessments were made.
The ~RData file is here: [[Bland-Altman_PEFR.RData|http://avan.suinesiaputra.googlepages.com/Bland-Altman_PEFR.RData]], and the contents are shown below:
{{{
> PEFR
Normal1 Normal2 Mini1 Mini2
1 494 490 512 525
2 395 397 430 415
3 516 512 520 508
4 434 401 428 444
5 476 470 500 500
6 557 611 600 625
7 413 415 364 460
8 442 431 380 390
9 650 638 658 642
10 433 429 445 432
11 417 420 432 420
12 656 633 626 605
13 267 275 260 227
14 478 492 477 467
15 178 165 259 268
16 423 372 350 370
17 427 421 451 443
}}}
!!The disagreement plot
[<img(40%,auto)[http://upload.wikimedia.org/wikipedia/commons/b/bc/Bland-altman_plot.png]]
The function:
{{{
> bland_altman_plot <- function(method1,method2,
xlab="Average", ylab="Difference")
{
avgMean <- stack(mean(as.data.frame(t(cbind(method1,
method2)))))$values
diff <- method1 - method2
plot(diff ~ avgMean,pch=16,
ylim=c(-100,100),xlab=xlab,ylab=ylab)
abline(h=mean(diff)-c(-2,0,2)*sd(diff),lty=2)
}
}}}
Call the function:
{{{
> bland_altman_plot(PEFR$Normal1,PEFR$Mini1,
xlab="Average PEFR by two meters (l/min)",
ylab="Difference PEFR (normal-mini) (l/min)")
}}}
The disagreement plot shows the difference between two methods against the average of the methods' values for each sample. The middle line is the mean difference and the two extreme lines are the +2 and -2 standard deviation.
!!Precision of the agreement
The standard error, which is defined as
$$ SE = \sqrt{\frac{s^2}{n}} $$
where $s^2$ and $n$ are the variance of the difference and the number of samples respectively, can be calculated as follows
{{{
> diff <- PEFR$Normal1 - PEFR$Mini1
> sqrt(var(diff)/length(diff))
[1] 9.401925
}}}
The 95% confidence interval of the +2 and -2 standard deviation lines can be calculated as follows:
{{{
> se_limit <- sqrt(2*var(diff)/length(diff))
> mean(diff) + 2*sd(diff) + c(-1,1) * qt(0.975, df=length(diff)-1) * se_limit
[1] 47.22565 103.59957
> mean(diff) - 2*sd(diff) + c(-1,1) * qt(0.975, df=length(diff)-1) * se_limit
[1] -107.83487 -51.46095
}}}
!!References
# Altman DG, Bland JM. (1983). Measurement in medicine: the analysis of method comparison studies. The Statistician 32, 307-317. (//the first paper//)
# Bland JM, Altman DG. (1986). Statistical methods for assessing agreement between two methods of clinical measurement. Lancet, i, 307-310. (//practical paper intended for clinicians//)
# Bland JM, Altman DG. (1987). Statistical methods for assessing agreement between measurement. Biochimica Clinica, 11, 399-404. (//revised version with some small numerical corrections//)
# Bland JM, Altman DG. (1992) This week's citation classic: Comparing methods of clinical measurement. Current Contents, CM20(40) Oct 5, 8. (//declared as Citation Classics due to huge amount of citations by ISI//)
!!Links
* [[A copy of the Lancet (1986) publication complete with the corrections.|http://www-users.york.ac.uk/%7Emb55/meas/ba.htm]]
<!--{{{-->
PrimaryPale: #fff
PrimaryLight: #aaa
PrimaryMid: #222
PrimaryDark: #000
<!--}}}-->
R comes with many pre-defined datasets, most of which are taken from a well-known study and being repeatedly used in many statistical analysis. To show what data are available, call this function:
{{{
> data()
}}}
Some of the datasets that I've been using with:
# [[iris and iris3|Iris dataset]]
[img(20%,auto)[pairs|http://upload.wikimedia.org/wikipedia/commons/e/ea/Anderson%27s_Iris_data_set.png][pairs]][img(20%,auto)[Bland-Altman plot|http://upload.wikimedia.org/wikipedia/commons/b/bc/Bland-altman_plot.png][Bland-Altman]][img(20%,auto)[3D plot|http://upload.wikimedia.org/wikipedia/commons/e/e3/Perspective_3D_Plot.png][Matlab 3D plot logo]]
/***
|Name|ImageSizePlugin|
|Source|http://www.TiddlyTools.com/#ImageSizePlugin|
|Version|1.1.0|
|Author|Eric Shulman - ELS Design Studios|
|License|http://www.TiddlyTools.com/#LegalStatements <br>and [[Creative Commons Attribution-ShareAlike 2.5 License|http://creativecommons.org/licenses/by-sa/2.5/]]|
|~CoreVersion|2.1|
|Type|plugin,formatter|
|Requires||
|Overrides|'image' formatter|
|Description|extends image syntax to add optional CSS width/height values|
!!!!!Usage
<<<
Extends standard TiddlyWiki image syntax, ''{{{[img[...]]}}}'', so you can specify CSS width/height values.
The extended syntax is:
>''{{{[img(x,y)[...]]}}}''
>where x and y are the desired width and height of the image, specified using CSS units of measurement (e.g., px, em, cm, in, or %). Use ''auto'' for either the width or height to scale image proportionally (i.e., maintain aspect ratio). You may also calculate a CSS value on-the-fly by using //evaluated javascript//, enclosed between """{{""" and """}}""", e.g, {{{({{widthFunction()}},{{heightFunction()}})}}}.
Note: this plugin also includes enhancements to support:
*[[AttachFilePluginFormatters]] (embed image files as text-encoded tiddlers)
* [[ImagePathPlugin]] (fallback locations for missing images)
Please refer to those plugins for details...
<<<
!!!!!Examples
<<<
{{{
[<img(34%,auto)[images/meow.gif]]
[<img(21%,auto)[images/meow.gif]]
[<img(13%,auto)[images/meow.gif]]
[<img(8%,auto)[images/meow.gif]]
[<img(5%,auto)[images/meow.gif]]
[<img(3%,auto)[images/meow.gif]]
[<img(2%,auto)[images/meow.gif]]
[img(1%,auto)[images/meow.gif]]
}}}
[<img(34%,auto)[images/meow.gif]]
[<img(21%,auto)[images/meow.gif]]
[<img(13%,auto)[images/meow.gif]]
[<img(8%,auto)[images/meow.gif]]
[<img(5%,auto)[images/meow.gif]]
[<img(3%,auto)[images/meow.gif]]
[<img(2%,auto)[images/meow.gif]]
[img(1%,auto)[images/meow.gif]]
{{clear block{}}}
<<<
!!!!!Revisions
<<<
2008.01.19 [1.1.0] added support for evaluated width/height values!!
2008.01.18 [1.0.1] code cleanup plus improved regexp for matching "(width,height)" by eliminating hard-coded recognition of [px,em,cm,in,%] CSS units. Syntax now accepts ANY values for width/height, and leaves it to the browser's CSS processing to handle any invalid values.
2008.01.17 [1.0.0] initial release
<<<
!!!!!Code
***/
//{{{
version.extensions.imageSize = {major: 1, minor: 1, revision: 0, date: new Date(2008,1,19)};
// replace standard handler for image formatter
// note: includes modifications for [[AttachFilePluginFormatters]] AND [[ImagePathPlugin]]
var f=config.formatters.findByField("name","image");
config.formatters[f].match="\\[[<>]?[Ii][Mm][Gg](?:\\([^,]*,[^\\)]*\\))?\\[";
config.formatters[f].lookaheadRegExp=/\[([<]?)(>?)[Ii][Mm][Gg](\([^,]*,[^\)]*\))?\[(?:([^\|\]]+)\|)?([^\[\]\|]+)\](?:\[([^\]]*)\])?\]/mg;
config.formatters[f].handler=function(w) {
this.lookaheadRegExp.lastIndex = w.matchStart;
var lookaheadMatch = this.lookaheadRegExp.exec(w.source)
if(lookaheadMatch && lookaheadMatch.index == w.matchStart) {
var floatLeft=lookaheadMatch[1];
var floatRight=lookaheadMatch[2];
var XY=lookaheadMatch[3];
var tooltip=lookaheadMatch[4];
var src=lookaheadMatch[5];
var link=lookaheadMatch[6];
// Simple bracketted link
var e = w.output;
if(link) { // LINKED IMAGE
if (config.formatterHelpers.isExternalLink(link)) {
if (config.macros.attach && config.macros.attach.isAttachment(link)) {
// see [[AttachFilePluginFormatters]]
e = createExternalLink(w.output,link);
e.href=config.macros.attach.getAttachment(link);
e.title = config.macros.attach.linkTooltip + link;
} else
e = createExternalLink(w.output,link);
} else
e = createTiddlyLink(w.output,link,false,null,w.isStatic);
addClass(e,"imageLink");
}
var img = createTiddlyElement(e,"img");
if(floatLeft) img.align="left"; else if(floatRight) img.align="right"; // FLOAT LEFT/RIGHT
if(XY) { // CUSTOM SIZE with optional EVAL'ED width/height ({{...}},{{...}})
var parts=XY.replace(/[\(\)]/g,'').split(","); var x=parts[0]; var y=parts[1];
if (x.substr(0,2)=="{{") {
try{img.style.width=eval(x.substr(2,x.length-4));}
catch(e){displayMessage(e.description||e.toString())}
} else img.style.width=x;
if (y.substr(0,2)=="{{") {
try{img.style.height=eval(y.substr(2,y.length-4));}
catch(e){displayMessage(e.description||e.toString())}
} else img.style.height=y;
}
if(tooltip) img.title = tooltip; // TOOLTIP
// GET IMAGE SOURCE (get attachment or resolve fallback path as needed)
if (config.macros.attach && config.macros.attach.isAttachment(src))
src=config.macros.attach.getAttachment(src); // see [[AttachFilePluginFormatters]]
else if (config.formatterHelpers.resolvePath) { // see [[ImagePathPlugin]]
// Note: IE and Safari use onError to call resolvePath() only if initial lookup fails
// (avoids security messages for initial filesystem access)... otherwise, attempt to
// resolve the original path/file before initial rendering
if (config.browser.isIE || config.browser.isSafari) {
img.onerror=(function(){
this.src=config.formatterHelpers.resolvePath(this.src,false);
return false;
});
} else
src=config.formatterHelpers.resolvePath(lookaheadMatch[5],true);
}
img.src=src; // RENDER IMAGE
w.nextMatch = this.lookaheadRegExp.lastIndex;
}
}
//}}}
The {{{iris}}} and {{{iris3}}}, known as ''Iris flower data set'', or ''Fisher's Iris data set'', or ''Edgar Anderson's Iris data set'', are data set of measurements of three species of //Iris// flowers (//I. setosa//, //I. versicolor//, and //I. virginica//). There are 50 samples for each species, each of which have four measurements: septal length, septal width, petal length and petal width.
The {{{iris}}} data is a data frame of 150 samples, where the columns are:
{{{
> names(iris)
[1] "Sepal.Length" "Sepal.Width" "Petal.Length" "Petal.Width" "Species"
}}}
The {{{iris3}}} is the same as {{{iris}}}, but it is stored as matrix of three dimensions:
{{{
> dim(iris3)
[1] 50 4 3
}}}
where the last dimension is the species. For instances, to get measurements of the 15th sample of //I. versicolor//:
{{{
> iris3[15,,'Versicolor']
Sepal L. Sepal W. Petal L. Petal W.
5.6 2.9 3.6 1.3
}}}
! Presentations
As a scatterplot:
{{{
> pairs(iris[1:4],main="Iris Data (red=setosa,green=versicolor,blue=virginica)", pch=21,
+ bg = c("red", "green3", "blue")[unclass(iris$Species)])
}}}
[img(50%,auto)[http://upload.wikimedia.org/wikipedia/commons/e/ea/Anderson%27s_Iris_data_set.png][pairs]]
! Appearances
The Fisher's iris data set has been used extensively in the pattern recognition / machine learning community since its first appearance in 1936. The data was collected by Edgar Anderson in 1935. Common analysis is predicting the species of Iris based on the four measurements.
# Edgar Anderson (1935). "The irises of the Gaspé Peninsula". Bulletin of the American Iris Society 59: 2–5.
# Fisher, R.A. (1936). "[[The Use of Multiple Measurements in Taxonomic Problems|http://digital.library.adelaide.edu.au/coll/special//fisher/138.pdf]]". Annals of Eugenics 7: 179–188.
# Duda,R.O., & Hart,P.E. (1973) Pattern Classification and Scene Analysis. John Wiley & Sons. ISBN 0-471-22361-1. (see page 218)
/***
|''Name:''|LoadRemoteFileThroughProxy (previous LoadRemoteFileHijack)|
|''Description:''|When the TiddlyWiki file is located on the web (view over http) the content of [[SiteProxy]] tiddler is added in front of the file url. If [[SiteProxy]] does not exist "/proxy/" is added. |
|''Version:''|1.1.0|
|''Date:''|mar 17, 2007|
|''Source:''|http://tiddlywiki.bidix.info/#LoadRemoteFileHijack|
|''Author:''|BidiX (BidiX (at) bidix (dot) info)|
|''License:''|[[BSD open source license|http://tiddlywiki.bidix.info/#%5B%5BBSD%20open%20source%20license%5D%5D ]]|
|''~CoreVersion:''|2.2.0|
***/
//{{{
version.extensions.LoadRemoteFileThroughProxy = {
major: 1, minor: 1, revision: 0,
date: new Date("mar 17, 2007"),
source: "http://tiddlywiki.bidix.info/#LoadRemoteFileThroughProxy"};
if (!window.bidix) window.bidix = {}; // bidix namespace
if (!bidix.core) bidix.core = {};
bidix.core.loadRemoteFile = loadRemoteFile;
loadRemoteFile = function(url,callback,params)
{
if ((document.location.toString().substr(0,4) == "http") && (url.substr(0,4) == "http")){
url = store.getTiddlerText("SiteProxy", "/proxy/") + url;
}
return bidix.core.loadRemoteFile(url,callback,params);
}
//}}}
[[Data]]
[[Methods]]
[[Graphics]]
A funny example of producing Matlab-like logo with R:
{{{
x <- seq(-10, 10, length= 30)
y <- x
f <- function(x,y) {
r <- sqrt(x^2+y^2);
10 * sin(r)/r
}
z <- outer(x, y, f)
z[is.na(z)] <- 1
par(mar=c(5.1, 4.1, 4.1, 2.1), lwd=1)
persp(x, y, z, theta = 30, phi = 30, expand = 0.5)
}}}
Source: http://www.stat.auckland.ac.nz/~paul/RGraphics/chapter1.html
{{third{[img(100%,auto)[Matlab 3D Plot|http://upload.wikimedia.org/wikipedia/commons/e/e3/Perspective_3D_Plot.png][Matlab 3D Plot]]}}}
# [[Bland-Altman plot|Bland-Altman]]
<!--{{{-->
<div class='header' background=[[ColorPalette::PrimaryMid]]>
<div class='headerShadow'>
<div id='siteTitle' refresh='content' tiddler='SiteTitle'></div>
</div></div>
<div id='topMenu' refresh='content' tiddler='MainMenu'></div>
<div id='sidebar'>
<div id='sidebarOptions' refresh='content' tiddler='SideBarOptions'></div>
<div id='sidebarTabs' refresh='content' force='true' tiddler='SideBarTabs'></div>
</div>
<div id='displayArea'>
<div id='messageArea'></div>
<div id='tiddlerDisplay'></div>
</div>
<!--}}}-->
/***
|Name|Plugin: jsMath|
|Created by|BobMcElrath|
|Email|my first name at my last name dot org|
|Location|http://bob.mcelrath.org/tiddlyjsmath.html|
|Version|1.5.1|
|Requires|[[TiddlyWiki|http://www.tiddlywiki.com]] ≥ 2.0.3, [[jsMath|http://www.math.union.edu/~dpvc/jsMath/]] ≥ 3.0|
!Description
LaTeX is the world standard for specifying, typesetting, and communicating mathematics among scientists, engineers, and mathematicians. For more information about LaTeX itself, visit the [[LaTeX Project|http://www.latex-project.org/]]. This plugin typesets math using [[jsMath|http://www.math.union.edu/~dpvc/jsMath/]], which is an implementation of the TeX math rules and typesetting in javascript, for your browser. Notice the small button in the lower right corner which opens its control panel.
!Installation
In addition to this plugin, you must also [[install jsMath|http://www.math.union.edu/~dpvc/jsMath/download/jsMath.html]] on the same server as your TiddlyWiki html file. If you're using TiddlyWiki without a web server, then the jsMath directory must be placed in the same location as the TiddlyWiki html file.
I also recommend modifying your StyleSheet use serif fonts that are slightly larger than normal, so that the math matches surrounding text, and \\small fonts are not unreadable (as in exponents and subscripts).
{{{
.viewer {
line-height: 125%;
font-family: serif;
font-size: 12pt;
}
}}}
If you had used a previous version of [[Plugin: jsMath]], it is no longer necessary to edit the main tiddlywiki.html file to add the jsMath <script> tag. [[Plugin: jsMath]] now uses ajax to load jsMath.
!History
* 11-Nov-05, version 1.0, Initial release
* 22-Jan-06, version 1.1, updated for ~TW2.0, tested with jsMath 3.1, editing tiddlywiki.html by hand is no longer necessary.
* 24-Jan-06, version 1.2, fixes for Safari, Konqueror
* 27-Jan-06, version 1.3, improved error handling, detect if ajax was already defined (used by ZiddlyWiki)
* 12-Jul-06, version 1.4, fixed problem with not finding image fonts
* 26-Feb-07, version 1.5, fixed problem with Mozilla "unterminated character class".
* 27-Feb-07, version 1.5.1, Runs compatibly with TW 2.1.0+, by Bram Chen
!Examples
|!Source|!Output|h
|{{{The variable $x$ is real.}}}|The variable $x$ is real.|
|{{{The variable \(y\) is complex.}}}|The variable \(y\) is complex.|
|{{{This \[\int_a^b x = \frac{1}{2}(b^2-a^2)\] is an easy integral.}}}|This \[\int_a^b x = \frac{1}{2}(b^2-a^2)\] is an easy integral.|
|{{{This $$\int_a^b \sin x = -(\cos b - \cos a)$$ is another easy integral.}}}|This $$\int_a^b \sin x = -(\cos b - \cos a)$$ is another easy integral.|
|{{{Block formatted equations may also use the 'equation' environment \begin{equation} \int \tan x = -\ln \cos x \end{equation} }}}|Block formatted equations may also use the 'equation' environment \begin{equation} \int \tan x = -\ln \cos x \end{equation}|
|{{{Equation arrays are also supported \begin{eqnarray} a &=& b \\ c &=& d \end{eqnarray} }}}|Equation arrays are also supported \begin{eqnarray} a &=& b \\ c &=& d \end{eqnarray} |
|{{{I spent \$7.38 on lunch.}}}|I spent \$7.38 on lunch.|
|{{{I had to insert a backslash (\\) into my document}}}|I had to insert a backslash (\\) into my document|
!Code
***/
//{{{
// AJAX code adapted from http://timmorgan.org/mini
// This is already loaded by ziddlywiki...
if(typeof(window["ajax"]) == "undefined") {
ajax = {
x: function(){try{return new ActiveXObject('Msxml2.XMLHTTP')}catch(e){try{return new ActiveXObject('Microsoft.XMLHTTP')}catch(e){return new XMLHttpRequest()}}},
gets: function(url){var x=ajax.x();x.open('GET',url,false);x.send(null);return x.responseText}
}
}
// Load jsMath
jsMath = {
Setup: {inited: 1}, // don't run jsMath.Setup.Body() yet
Autoload: {root: new String(document.location).replace(/[^\/]*$/,'jsMath/')} // URL to jsMath directory, change if necessary
};
var jsMathstr;
try {
jsMathstr = ajax.gets(jsMath.Autoload.root+"jsMath.js");
} catch(e) {
alert("jsMath was not found: you must place the 'jsMath' directory in the same place as this file. "
+"The error was:\n"+e.name+": "+e.message);
throw(e); // abort eval
}
try {
window.eval(jsMathstr);
} catch(e) {
alert("jsMath failed to load. The error was:\n"+e.name + ": " + e.message + " on line " + e.lineNumber);
}
jsMath.Setup.inited=0; // allow jsMath.Setup.Body() to run again
// Define wikifers for latex
config.formatterHelpers.mathFormatHelper = function(w) {
var e = document.createElement(this.element);
e.className = this.className;
var endRegExp = new RegExp(this.terminator, "mg");
endRegExp.lastIndex = w.matchStart+w.matchLength;
var matched = endRegExp.exec(w.source);
if(matched) {
var txt = w.source.substr(w.matchStart+w.matchLength,
matched.index-w.matchStart-w.matchLength);
if(this.keepdelim) {
txt = w.source.substr(w.matchStart, matched.index+matched[0].length-w.matchStart);
}
e.appendChild(document.createTextNode(txt));
w.output.appendChild(e);
w.nextMatch = endRegExp.lastIndex;
}
}
config.formatters.push({
name: "displayMath1",
match: "\\\$\\\$",
terminator: "\\\$\\\$\\n?", // 2.0 compatability
termRegExp: "\\\$\\\$\\n?",
element: "div",
className: "math",
handler: config.formatterHelpers.mathFormatHelper
});
config.formatters.push({
name: "inlineMath1",
match: "\\\$",
terminator: "\\\$", // 2.0 compatability
termRegExp: "\\\$",
element: "span",
className: "math",
handler: config.formatterHelpers.mathFormatHelper
});
var backslashformatters = new Array(0);
backslashformatters.push({
name: "inlineMath2",
match: "\\\\\\\(",
terminator: "\\\\\\\)", // 2.0 compatability
termRegExp: "\\\\\\\)",
element: "span",
className: "math",
handler: config.formatterHelpers.mathFormatHelper
});
backslashformatters.push({
name: "displayMath2",
match: "\\\\\\\[",
terminator: "\\\\\\\]\\n?", // 2.0 compatability
termRegExp: "\\\\\\\]\\n?",
element: "div",
className: "math",
handler: config.formatterHelpers.mathFormatHelper
});
backslashformatters.push({
name: "displayMath3",
match: "\\\\begin\\{equation\\}",
terminator: "\\\\end\\{equation\\}\\n?", // 2.0 compatability
termRegExp: "\\\\end\\{equation\\}\\n?",
element: "div",
className: "math",
handler: config.formatterHelpers.mathFormatHelper
});
// These can be nested. e.g. \begin{equation} \begin{array}{ccc} \begin{array}{ccc} ...
backslashformatters.push({
name: "displayMath4",
match: "\\\\begin\\{eqnarray\\}",
terminator: "\\\\end\\{eqnarray\\}\\n?", // 2.0 compatability
termRegExp: "\\\\end\\{eqnarray\\}\\n?",
element: "div",
className: "math",
keepdelim: true,
handler: config.formatterHelpers.mathFormatHelper
});
// The escape must come between backslash formatters and regular ones.
// So any latex-like \commands must be added to the beginning of
// backslashformatters here.
backslashformatters.push({
name: "escape",
match: "\\\\.",
handler: function(w) {
w.output.appendChild(document.createTextNode(w.source.substr(w.matchStart+1,1)));
w.nextMatch = w.matchStart+2;
}
});
config.formatters=backslashformatters.concat(config.formatters);
window.wikify = function(source,output,highlightRegExp,tiddler)
{
if(source && source != "") {
if(version.major == 2 && version.minor > 0) {
var wikifier = new Wikifier(source,getParser(tiddler),highlightRegExp,tiddler);
wikifier.subWikifyUnterm(output);
} else {
var wikifier = new Wikifier(source,formatter,highlightRegExp,tiddler);
wikifier.subWikify(output,null);
}
jsMath.ProcessBeforeShowing();
}
}
//}}}
[img(75px,auto)[http://upload.wikimedia.org/wikipedia/commons/c/c1/Rlogo.png]] Statistics
/*{{{*/
/*Blackicity Theme for TiddlyWiki*/
/*Design and CSS by Saq Imtiaz*/
/*Version 1.0*/
/*}}}*/
/*{{{*/
body{ font-family: "Neue Helvetica", Helvetica, "Lucida Grande", Verdana, sans-serif;
background-color: #fff;
color: #333;}
#siteTitle { color:#fff; font-family:'Lucida Grande', Verdana, Sans-Serif; font-size: 2em; font-weight: bold; }
#topMenu {position:relative; background:#222; padding:10px; color:#fff;font-family:'Lucida Grande', Verdana, Sans-Serif;}
#topMenu br {display:none;}
#topMenu a{ color: #999;
padding: 0px 8px 0px 8px;
border-right: 1px solid #444;}
#topMenu a:hover {color:#fff; background:transparent;}
#displayArea {margin-left:1em; margin-bottom:2em; margin-top:0.5em;}
a, a:hover{
color:#333;
text-decoration: none; background:transparent;
}
.viewer a, .viewer a:hover {border-bottom:1px dotted #333; font-weight:bold;}
.viewer .button, .editorFooter .button{
color: #333;
border: 1px solid #333;
}
.viewer .button:hover,
.editorFooter .button:hover, .viewer .button:active, .viewer .highlight,.editorFooter .button:active, .editorFooter .highlight{
color: #fff;
background: #333;
border-color: #333;
}
.tiddler .viewer {line-height:1.45em;}
.title {color:#222; border-bottom:1px solid#222; font-family:'Lucida Grande', Verdana, Sans-Serif; font-size:1.5em;}
.subtitle, .subtitle a { color: #999999; font-size: 0.95em;margin:0.2em;}
.shadow .title{color:#999;}
.toolbar {font-size:90%;}
.selected .toolbar a {color:#999999;}
.selected .toolbar a:hover {color:#333; background:transparent;border:1px solid #fff;}
.toolbar .button:hover, .toolbar .highlight, .toolbar .marked, .toolbar a.button:active{color:#333; background:transparent;border:1px solid #fff;}
/***
!Sidebar
***/
#sidebar { margin-bottom:2em !important; margin-bottom:1em; right:0;
}
/***
!SidebarOptions
***/
#sidebarOptions { padding-top:2em;background:#f3f3f3;padding-left:0.5em;}
#sidebarOptions a {
color:#333;
background:#f3f3f3;
border:1px solid #f3f3f3;
text-decoration: none;
}
#sidebarOptions a:hover, #sidebarOptions a:active {
color:#222;
background-color:#fff;border:1px solid #fff;
}
#sidebarOptions input {border:1px solid #ccc; }
#sidebarOptions .sliderPanel {
background: #f3f3f3; font-size: .9em;
}
#sidebarOptions .sliderPanel input {border:1px solid #999;}
#sidebarOptions .sliderPanel .txtOptionInput {border:1px solid #999;width:9em;}
#sidebarOptions .sliderPanel a {font-weight:normal; color:#555;background-color: #f3f3f3; border-bottom:1px dotted #333;}
#sidebarOptions .sliderPanel a:hover {
color:#111;
background-color: #f3f3f3;
border:none;
border-bottom:1px dotted #111;
}
/***
!SidebarTabs
***/
.listTitle {color:#222;}
#sidebarTabs {background:#f3f3f3;}
#sidebarTabs .tabContents {background:#cfcfcf;}
#sidebarTabs .tabUnselected:hover {color:#999;}
#sidebarTabs .tabSelected{background:#cfcfcf;}
#sidebarTabs .tabContents .tiddlyLink, #sidebarTabs .tabContents .button{color:#666;}
#sidebarTabs .tabContents .tiddlyLink:hover,#sidebarTabs .tabContents .button:hover{color:#222;background:transparent; text-decoration:none;border:none;}
#sidebarTabs .tabContents .button:hover, #sidebarTabs .tabContents .highlight, #sidebarTabs .tabContents .marked, #sidebarTabs .tabContents a.button:active{color:#222;background:transparent;}
#sidebarTabs .txtMoreTab .tabSelected,
#sidebarTabs .txtMoreTab .tab:hover,
#sidebarTabs .txtMoreTab .tabContents{
color: #111;
background: #f3f3f3; border:1px solid #f3f3f3;
}
#sidebarTabs .txtMoreTab .tabUnselected {
color: #555;
background: #AFAFAF;
}
/***
!Tabs
***/
.tabSelected{color:#fefefe; background:#999; padding-bottom:1px;}
.tabSelected, .tabSelected:hover {
color: #111;
background: #fefefe;
border: solid 1px #cfcfcf;
}
.tabUnselected {
color: #999;
background: #eee;
border: solid 1px #cfcfcf;
padding-bottom:1px;
}
.tabUnselected:hover {text-decoration:none; border:1px solid #cfcfcf;}
.tabContents {background:#fefefe;}
.tagging, .tagged {
border: 1px solid #eee;
background-color: #F7F7F7;
}
.selected .tagging, .selected .tagged {
background-color: #f3f3f3;
border: 1px solid #ccc;
}
.tagging .listTitle, .tagged .listTitle {
color: #bbb;
}
.selected .tagging .listTitle, .selected .tagged .listTitle {
color: #333;
}
.tagging .button, .tagged .button {
color:#ccc;
}
.selected .tagging .button, .selected .tagged .button {
color:#aaa;
}
.highlight, .marked {background:transparent; color:#111; border:none; text-decoration:underline;}
.tagging .button:hover, .tagged .button:hover, .tagging .button:active, .tagged .button:active {
border: none; background:transparent; text-decoration:underline; color:#333;
}
.popup {
background: #cfcfcf;
border: 1px solid #333;
}
.popup li.disabled {
color: #000;
}
.popup li a, .popup li a:visited {
color: #555;
border: none;
}
.popup li a:hover {
background: #f3f3f3;
color: #555;
border: none;
}
#messageArea {
border: 4px dotted #282826;
background: #F3F3F3;
color: #333;
font-size:90%;
}
#messageArea a:hover { background:#f5f5f5; border:none;}
#messageArea .button{
color: #333;
border: 1px solid #282826;
}
#messageArea .button:hover {
color: #fff;
background: #282826;
border-color: #282826;
}
.tiddler {padding-bottom:10px;}
.viewer blockquote {
border-left: 5px solid #282826;
}
.viewer table, .viewer td {
border: 1px solid #282826;
}
.viewer th, thead td {
background: #282826;
border: 1px solid #282826;
color: #fff;
}
.viewer pre {
border: 1px solid #ccc;
background: #f5f5f5;
}
.viewer code {
color: #111; background:#f5f5f5;
}
.viewer hr {
border-top: dashed 1px #222; margin:0 1em;
}
.editor input {
border: 1px solid #ccc; margin-top:5px;
}
.editor textarea {
border: 1px solid #ccc;
}
h1,h2,h3,h4,h5 { color: #282826; background: transparent; padding-bottom:2px; font-family: Arial, Helvetica, sans-serif; }
h1 {font-size:18px;}
h2 {font-size:16px;}
h3 {font-size: 14px;}
/*}}}*/
/***
Contains the stuff you need to use Tiddlyspot
Note you must also have UploadPlugin installed
***/
//{{{
// edit this if you are migrating sites or retrofitting an existing TW
config.tiddlyspotSiteId = 'rstats';
// make it so you can by default see edit controls via http
config.options.chkHttpReadOnly = false;
window.readOnly = false; // make sure of it (for tw 2.2)
window.showBackstage = true; // show backstage too
// disable autosave in d3
if (window.location.protocol != "file:")
config.options.chkGTDLazyAutoSave = false;
// tweak shadow tiddlers to add upload button, password entry box etc
with (config.shadowTiddlers) {
SiteUrl = 'http://'+config.tiddlyspotSiteId+'.tiddlyspot.com';
SideBarOptions = SideBarOptions.replace(/(<<saveChanges>>)/,"$1<<tiddler TspotSidebar>>");
OptionsPanel = OptionsPanel.replace(/^/,"<<tiddler TspotOptions>>");
DefaultTiddlers = DefaultTiddlers.replace(/^/,"[[WelcomeToTiddlyspot]] ");
MainMenu = MainMenu.replace(/^/,"[[WelcomeToTiddlyspot]] ");
}
// create some shadow tiddler content
merge(config.shadowTiddlers,{
'WelcomeToTiddlyspot':[
"This document is a ~TiddlyWiki from tiddlyspot.com. A ~TiddlyWiki is an electronic notebook that is great for managing todo lists, personal information, and all sorts of things.",
"",
"@@font-weight:bold;font-size:1.3em;color:#444; //What now?// @@ Before you can save any changes, you need to enter your password in the form below. Then configure privacy and other site settings at your [[control panel|http://" + config.tiddlyspotSiteId + ".tiddlyspot.com/controlpanel]] (your control panel username is //" + config.tiddlyspotSiteId + "//).",
"<<tiddler TspotControls>>",
"See also GettingStarted.",
"",
"@@font-weight:bold;font-size:1.3em;color:#444; //Working online// @@ You can edit this ~TiddlyWiki right now, and save your changes using the \"save to web\" button in the column on the right.",
"",
"@@font-weight:bold;font-size:1.3em;color:#444; //Working offline// @@ A fully functioning copy of this ~TiddlyWiki can be saved onto your hard drive or USB stick. You can make changes and save them locally without being connected to the Internet. When you're ready to sync up again, just click \"upload\" and your ~TiddlyWiki will be saved back to tiddlyspot.com.",
"",
"@@font-weight:bold;font-size:1.3em;color:#444; //Help!// @@ Find out more about ~TiddlyWiki at [[TiddlyWiki.com|http://tiddlywiki.com]]. Also visit [[TiddlyWiki.org|http://tiddlywiki.org]] for documentation on learning and using ~TiddlyWiki. New users are especially welcome on the [[TiddlyWiki mailing list|http://groups.google.com/group/TiddlyWiki]], which is an excellent place to ask questions and get help. If you have a tiddlyspot related problem email [[tiddlyspot support|mailto:support@tiddlyspot.com]].",
"",
"@@font-weight:bold;font-size:1.3em;color:#444; //Enjoy :)// @@ We hope you like using your tiddlyspot.com site. Please email [[feedback@tiddlyspot.com|mailto:feedback@tiddlyspot.com]] with any comments or suggestions."
].join("\n"),
'TspotControls':[
"| tiddlyspot password:|<<option pasUploadPassword>>|",
"| site management:|<<upload http://" + config.tiddlyspotSiteId + ".tiddlyspot.com/store.cgi index.html . . " + config.tiddlyspotSiteId + ">>//(requires tiddlyspot password)//<br>[[control panel|http://" + config.tiddlyspotSiteId + ".tiddlyspot.com/controlpanel]], [[download (go offline)|http://" + config.tiddlyspotSiteId + ".tiddlyspot.com/download]]|",
"| links:|[[tiddlyspot.com|http://tiddlyspot.com/]], [[FAQs|http://faq.tiddlyspot.com/]], [[blog|http://tiddlyspot.blogspot.com/]], email [[support|mailto:support@tiddlyspot.com]] & [[feedback|mailto:feedback@tiddlyspot.com]], [[donate|http://tiddlyspot.com/?page=donate]]|"
].join("\n"),
'TspotSidebar':[
"<<upload http://" + config.tiddlyspotSiteId + ".tiddlyspot.com/store.cgi index.html . . " + config.tiddlyspotSiteId + ">><html><a href='http://" + config.tiddlyspotSiteId + ".tiddlyspot.com/download' class='button'>download</a></html>"
].join("\n"),
'TspotOptions':[
"tiddlyspot password:",
"<<option pasUploadPassword>>",
""
].join("\n")
});
//}}}
| !date | !user | !location | !storeUrl | !uploadDir | !toFilename | !backupdir | !origin |
| 31/07/2008 00:48:47 | avan | [[/|http://rstats.tiddlyspot.com/]] | [[store.cgi|http://rstats.tiddlyspot.com/store.cgi]] | . | [[index.html | http://rstats.tiddlyspot.com/index.html]] | . |
| 02/08/2008 01:30:43 | avan | [[/|http://rstats.tiddlyspot.com/]] | [[store.cgi|http://rstats.tiddlyspot.com/store.cgi]] | . | [[index.html | http://rstats.tiddlyspot.com/index.html]] | . |
| 02/08/2008 04:49:33 | avan | [[/|http://rstats.tiddlyspot.com/#Bland-Altman]] | [[store.cgi|http://rstats.tiddlyspot.com/store.cgi]] | . | [[index.html | http://rstats.tiddlyspot.com/index.html]] | . | failed |
| 02/08/2008 04:49:55 | avan | [[/|http://rstats.tiddlyspot.com/#Bland-Altman]] | [[store.cgi|http://rstats.tiddlyspot.com/store.cgi]] | . | [[index.html | http://rstats.tiddlyspot.com/index.html]] | . | ok |
| 02/08/2008 05:02:09 | avan | [[/|http://rstats.tiddlyspot.com/#Bland-Altman]] | [[store.cgi|http://rstats.tiddlyspot.com/store.cgi]] | . | [[index.html | http://rstats.tiddlyspot.com/index.html]] | . | ok |
| 02/08/2008 05:07:02 | avan | [[/|http://rstats.tiddlyspot.com/#Bland-Altman]] | [[store.cgi|http://rstats.tiddlyspot.com/store.cgi]] | . | [[index.html | http://rstats.tiddlyspot.com/index.html]] | . | ok |
| 02/08/2008 05:10:05 | avan | [[/|http://rstats.tiddlyspot.com/#Bland-Altman]] | [[store.cgi|http://rstats.tiddlyspot.com/store.cgi]] | . | [[index.html | http://rstats.tiddlyspot.com/index.html]] | . |
| 02/08/2008 05:17:20 | avan | [[/|http://rstats.tiddlyspot.com/#Bland-Altman]] | [[store.cgi|http://rstats.tiddlyspot.com/store.cgi]] | . | [[index.html | http://rstats.tiddlyspot.com/index.html]] | . |
| 02/08/2008 16:35:55 | avan | [[/|http://rstats.tiddlyspot.com/]] | [[store.cgi|http://rstats.tiddlyspot.com/store.cgi]] | . | [[index.html | http://rstats.tiddlyspot.com/index.html]] | . |
| 16/06/2009 14:38:16 | YourName | [[/|http://rstats.tiddlyspot.com/]] | [[store.cgi|http://rstats.tiddlyspot.com/store.cgi]] | . | [[index.html | http://rstats.tiddlyspot.com/index.html]] | . |
/***
|''Name:''|PasswordOptionPlugin|
|''Description:''|Extends TiddlyWiki options with non encrypted password option.|
|''Version:''|1.0.2|
|''Date:''|Apr 19, 2007|
|''Source:''|http://tiddlywiki.bidix.info/#PasswordOptionPlugin|
|''Author:''|BidiX (BidiX (at) bidix (dot) info)|
|''License:''|[[BSD open source license|http://tiddlywiki.bidix.info/#%5B%5BBSD%20open%20source%20license%5D%5D ]]|
|''~CoreVersion:''|2.2.0 (Beta 5)|
***/
//{{{
version.extensions.PasswordOptionPlugin = {
major: 1, minor: 0, revision: 2,
date: new Date("Apr 19, 2007"),
source: 'http://tiddlywiki.bidix.info/#PasswordOptionPlugin',
author: 'BidiX (BidiX (at) bidix (dot) info',
license: '[[BSD open source license|http://tiddlywiki.bidix.info/#%5B%5BBSD%20open%20source%20license%5D%5D]]',
coreVersion: '2.2.0 (Beta 5)'
};
config.macros.option.passwordCheckboxLabel = "Save this password on this computer";
config.macros.option.passwordInputType = "password"; // password | text
setStylesheet(".pasOptionInput {width: 11em;}\n","passwordInputTypeStyle");
merge(config.macros.option.types, {
'pas': {
elementType: "input",
valueField: "value",
eventName: "onkeyup",
className: "pasOptionInput",
typeValue: config.macros.option.passwordInputType,
create: function(place,type,opt,className,desc) {
// password field
config.macros.option.genericCreate(place,'pas',opt,className,desc);
// checkbox linked with this password "save this password on this computer"
config.macros.option.genericCreate(place,'chk','chk'+opt,className,desc);
// text savePasswordCheckboxLabel
place.appendChild(document.createTextNode(config.macros.option.passwordCheckboxLabel));
},
onChange: config.macros.option.genericOnChange
}
});
merge(config.optionHandlers['chk'], {
get: function(name) {
// is there an option linked with this chk ?
var opt = name.substr(3);
if (config.options[opt])
saveOptionCookie(opt);
return config.options[name] ? "true" : "false";
}
});
merge(config.optionHandlers, {
'pas': {
get: function(name) {
if (config.options["chk"+name]) {
return encodeCookie(config.options[name].toString());
} else {
return "";
}
},
set: function(name,value) {config.options[name] = decodeCookie(value);}
}
});
// need to reload options to load passwordOptions
loadOptionsCookie();
/*
if (!config.options['pasPassword'])
config.options['pasPassword'] = '';
merge(config.optionsDesc,{
pasPassword: "Test password"
});
*/
//}}}
/***
|''Name:''|UploadPlugin|
|''Description:''|Save to web a TiddlyWiki|
|''Version:''|4.1.0|
|''Date:''|May 5, 2007|
|''Source:''|http://tiddlywiki.bidix.info/#UploadPlugin|
|''Documentation:''|http://tiddlywiki.bidix.info/#UploadPluginDoc|
|''Author:''|BidiX (BidiX (at) bidix (dot) info)|
|''License:''|[[BSD open source license|http://tiddlywiki.bidix.info/#%5B%5BBSD%20open%20source%20license%5D%5D ]]|
|''~CoreVersion:''|2.2.0 (#3125)|
|''Requires:''|PasswordOptionPlugin|
***/
//{{{
version.extensions.UploadPlugin = {
major: 4, minor: 1, revision: 0,
date: new Date("May 5, 2007"),
source: 'http://tiddlywiki.bidix.info/#UploadPlugin',
author: 'BidiX (BidiX (at) bidix (dot) info',
coreVersion: '2.2.0 (#3125)'
};
//
// Environment
//
if (!window.bidix) window.bidix = {}; // bidix namespace
bidix.debugMode = false; // true to activate both in Plugin and UploadService
//
// Upload Macro
//
config.macros.upload = {
// default values
defaultBackupDir: '', //no backup
defaultStoreScript: "store.php",
defaultToFilename: "index.html",
defaultUploadDir: ".",
authenticateUser: true // UploadService Authenticate User
};
config.macros.upload.label = {
promptOption: "Save and Upload this TiddlyWiki with UploadOptions",
promptParamMacro: "Save and Upload this TiddlyWiki in %0",
saveLabel: "save to web",
saveToDisk: "save to disk",
uploadLabel: "upload"
};
config.macros.upload.messages = {
noStoreUrl: "No store URL in parmeters or options",
usernameOrPasswordMissing: "Username or password missing"
};
config.macros.upload.handler = function(place,macroName,params) {
if (readOnly)
return;
var label;
if (document.location.toString().substr(0,4) == "http")
label = this.label.saveLabel;
else
label = this.label.uploadLabel;
var prompt;
if (params[0]) {
prompt = this.label.promptParamMacro.toString().format([this.destFile(params[0],
(params[1] ? params[1]:bidix.basename(window.location.toString())), params[3])]);
} else {
prompt = this.label.promptOption;
}
createTiddlyButton(place, label, prompt, function() {config.macros.upload.action(params);}, null, null, this.accessKey);
};
config.macros.upload.action = function(params)
{
// for missing macro parameter set value from options
var storeUrl = params[0] ? params[0] : config.options.txtUploadStoreUrl;
var toFilename = params[1] ? params[1] : config.options.txtUploadFilename;
var backupDir = params[2] ? params[2] : config.options.txtUploadBackupDir;
var uploadDir = params[3] ? params[3] : config.options.txtUploadDir;
var username = params[4] ? params[4] : config.options.txtUploadUserName;
var password = config.options.pasUploadPassword; // for security reason no password as macro parameter
// for still missing parameter set default value
if ((!storeUrl) && (document.location.toString().substr(0,4) == "http"))
storeUrl = bidix.dirname(document.location.toString())+'/'+config.macros.upload.defaultStoreScript;
if (storeUrl.substr(0,4) != "http")
storeUrl = bidix.dirname(document.location.toString()) +'/'+ storeUrl;
if (!toFilename)
toFilename = bidix.basename(window.location.toString());
if (!toFilename)
toFilename = config.macros.upload.defaultToFilename;
if (!uploadDir)
uploadDir = config.macros.upload.defaultUploadDir;
if (!backupDir)
backupDir = config.macros.upload.defaultBackupDir;
// report error if still missing
if (!storeUrl) {
alert(config.macros.upload.messages.noStoreUrl);
clearMessage();
return false;
}
if (config.macros.upload.authenticateUser && (!username || !password)) {
alert(config.macros.upload.messages.usernameOrPasswordMissing);
clearMessage();
return false;
}
bidix.upload.uploadChanges(false,null,storeUrl, toFilename, uploadDir, backupDir, username, password);
return false;
};
config.macros.upload.destFile = function(storeUrl, toFilename, uploadDir)
{
if (!storeUrl)
return null;
var dest = bidix.dirname(storeUrl);
if (uploadDir && uploadDir != '.')
dest = dest + '/' + uploadDir;
dest = dest + '/' + toFilename;
return dest;
};
//
// uploadOptions Macro
//
config.macros.uploadOptions = {
handler: function(place,macroName,params) {
var wizard = new Wizard();
wizard.createWizard(place,this.wizardTitle);
wizard.addStep(this.step1Title,this.step1Html);
var markList = wizard.getElement("markList");
var listWrapper = document.createElement("div");
markList.parentNode.insertBefore(listWrapper,markList);
wizard.setValue("listWrapper",listWrapper);
this.refreshOptions(listWrapper,false);
var uploadCaption;
if (document.location.toString().substr(0,4) == "http")
uploadCaption = config.macros.upload.label.saveLabel;
else
uploadCaption = config.macros.upload.label.uploadLabel;
wizard.setButtons([
{caption: uploadCaption, tooltip: config.macros.upload.label.promptOption,
onClick: config.macros.upload.action},
{caption: this.cancelButton, tooltip: this.cancelButtonPrompt, onClick: this.onCancel}
]);
},
refreshOptions: function(listWrapper) {
var uploadOpts = [
"txtUploadUserName",
"pasUploadPassword",
"txtUploadStoreUrl",
"txtUploadDir",
"txtUploadFilename",
"txtUploadBackupDir",
"chkUploadLog",
"txtUploadLogMaxLine",
]
var opts = [];
for(i=0; i<uploadOpts.length; i++) {
var opt = {};
opts.push()
opt.option = "";
n = uploadOpts[i];
opt.name = n;
opt.lowlight = !config.optionsDesc[n];
opt.description = opt.lowlight ? this.unknownDescription : config.optionsDesc[n];
opts.push(opt);
}
var listview = ListView.create(listWrapper,opts,this.listViewTemplate);
for(n=0; n<opts.length; n++) {
var type = opts[n].name.substr(0,3);
var h = config.macros.option.types[type];
if (h && h.create) {
h.create(opts[n].colElements['option'],type,opts[n].name,opts[n].name,"no");
}
}
},
onCancel: function(e)
{
backstage.switchTab(null);
return false;
},
wizardTitle: "Upload with options",
step1Title: "These options are saved in cookies in your browser",
step1Html: "<input type='hidden' name='markList'></input><br>",
cancelButton: "Cancel",
cancelButtonPrompt: "Cancel prompt",
listViewTemplate: {
columns: [
{name: 'Description', field: 'description', title: "Description", type: 'WikiText'},
{name: 'Option', field: 'option', title: "Option", type: 'String'},
{name: 'Name', field: 'name', title: "Name", type: 'String'}
],
rowClasses: [
{className: 'lowlight', field: 'lowlight'}
]}
}
//
// upload functions
//
if (!bidix.upload) bidix.upload = {};
if (!bidix.upload.messages) bidix.upload.messages = {
//from saving
invalidFileError: "The original file '%0' does not appear to be a valid TiddlyWiki",
backupSaved: "Backup saved",
backupFailed: "Failed to upload backup file",
rssSaved: "RSS feed uploaded",
rssFailed: "Failed to upload RSS feed file",
emptySaved: "Empty template uploaded",
emptyFailed: "Failed to upload empty template file",
mainSaved: "Main TiddlyWiki file uploaded",
mainFailed: "Failed to upload main TiddlyWiki file. Your changes have not been saved",
//specific upload
loadOriginalHttpPostError: "Can't get original file",
aboutToSaveOnHttpPost: 'About to upload on %0 ...',
storePhpNotFound: "The store script '%0' was not found."
};
bidix.upload.uploadChanges = function(onlyIfDirty,tiddlers,storeUrl,toFilename,uploadDir,backupDir,username,password)
{
var callback = function(status,uploadParams,original,url,xhr) {
if (!status) {
displayMessage(bidix.upload.messages.loadOriginalHttpPostError);
return;
}
if (bidix.debugMode)
alert(original.substr(0,500)+"\n...");
// Locate the storeArea div's
var posDiv = locateStoreArea(original);
if((posDiv[0] == -1) || (posDiv[1] == -1)) {
alert(config.messages.invalidFileError.format([localPath]));
return;
}
bidix.upload.uploadRss(uploadParams,original,posDiv);
};
if(onlyIfDirty && !store.isDirty())
return;
clearMessage();
// save on localdisk ?
if (document.location.toString().substr(0,4) == "file") {
var path = document.location.toString();
var localPath = getLocalPath(path);
saveChanges();
}
// get original
var uploadParams = Array(storeUrl,toFilename,uploadDir,backupDir,username,password);
var originalPath = document.location.toString();
// If url is a directory : add index.html
if (originalPath.charAt(originalPath.length-1) == "/")
originalPath = originalPath + "index.html";
var dest = config.macros.upload.destFile(storeUrl,toFilename,uploadDir);
var log = new bidix.UploadLog();
log.startUpload(storeUrl, dest, uploadDir, backupDir);
displayMessage(bidix.upload.messages.aboutToSaveOnHttpPost.format([dest]));
if (bidix.debugMode)
alert("about to execute Http - GET on "+originalPath);
var r = doHttp("GET",originalPath,null,null,null,null,callback,uploadParams,null);
if (typeof r == "string")
displayMessage(r);
return r;
};
bidix.upload.uploadRss = function(uploadParams,original,posDiv)
{
var callback = function(status,params,responseText,url,xhr) {
if(status) {
var destfile = responseText.substring(responseText.indexOf("destfile:")+9,responseText.indexOf("\n", responseText.indexOf("destfile:")));
displayMessage(bidix.upload.messages.rssSaved,bidix.dirname(url)+'/'+destfile);
bidix.upload.uploadMain(params[0],params[1],params[2]);
} else {
displayMessage(bidix.upload.messages.rssFailed);
}
};
// do uploadRss
if(config.options.chkGenerateAnRssFeed) {
var rssPath = uploadParams[1].substr(0,uploadParams[1].lastIndexOf(".")) + ".xml";
var rssUploadParams = Array(uploadParams[0],rssPath,uploadParams[2],'',uploadParams[4],uploadParams[5]);
bidix.upload.httpUpload(rssUploadParams,convertUnicodeToUTF8(generateRss()),callback,Array(uploadParams,original,posDiv));
} else {
bidix.upload.uploadMain(uploadParams,original,posDiv);
}
};
bidix.upload.uploadMain = function(uploadParams,original,posDiv)
{
var callback = function(status,params,responseText,url,xhr) {
var log = new bidix.UploadLog();
if(status) {
// if backupDir specified
if ((params[3]) && (responseText.indexOf("backupfile:") > -1)) {
var backupfile = responseText.substring(responseText.indexOf("backupfile:")+11,responseText.indexOf("\n", responseText.indexOf("backupfile:")));
displayMessage(bidix.upload.messages.backupSaved,bidix.dirname(url)+'/'+backupfile);
}
var destfile = responseText.substring(responseText.indexOf("destfile:")+9,responseText.indexOf("\n", responseText.indexOf("destfile:")));
displayMessage(bidix.upload.messages.mainSaved,bidix.dirname(url)+'/'+destfile);
store.setDirty(false);
log.endUpload("ok");
} else {
alert(bidix.upload.messages.mainFailed);
displayMessage(bidix.upload.messages.mainFailed);
log.endUpload("failed");
}
};
// do uploadMain
var revised = bidix.upload.updateOriginal(original,posDiv);
bidix.upload.httpUpload(uploadParams,revised,callback,uploadParams);
};
bidix.upload.httpUpload = function(uploadParams,data,callback,params)
{
var localCallback = function(status,params,responseText,url,xhr) {
url = (url.indexOf("nocache=") < 0 ? url : url.substring(0,url.indexOf("nocache=")-1));
if (xhr.status == httpStatus.NotFound)
alert(bidix.upload.messages.storePhpNotFound.format([url]));
if ((bidix.debugMode) || (responseText.indexOf("Debug mode") >= 0 )) {
alert(responseText);
if (responseText.indexOf("Debug mode") >= 0 )
responseText = responseText.substring(responseText.indexOf("\n\n")+2);
} else if (responseText.charAt(0) != '0')
alert(responseText);
if (responseText.charAt(0) != '0')
status = null;
callback(status,params,responseText,url,xhr);
};
// do httpUpload
var boundary = "---------------------------"+"AaB03x";
var uploadFormName = "UploadPlugin";
// compose headers data
var sheader = "";
sheader += "--" + boundary + "\r\nContent-disposition: form-data; name=\"";
sheader += uploadFormName +"\"\r\n\r\n";
sheader += "backupDir="+uploadParams[3] +
";user=" + uploadParams[4] +
";password=" + uploadParams[5] +
";uploaddir=" + uploadParams[2];
if (bidix.debugMode)
sheader += ";debug=1";
sheader += ";;\r\n";
sheader += "\r\n" + "--" + boundary + "\r\n";
sheader += "Content-disposition: form-data; name=\"userfile\"; filename=\""+uploadParams[1]+"\"\r\n";
sheader += "Content-Type: text/html;charset=UTF-8" + "\r\n";
sheader += "Content-Length: " + data.length + "\r\n\r\n";
// compose trailer data
var strailer = new String();
strailer = "\r\n--" + boundary + "--\r\n";
data = sheader + data + strailer;
if (bidix.debugMode) alert("about to execute Http - POST on "+uploadParams[0]+"\n with \n"+data.substr(0,500)+ " ... ");
var r = doHttp("POST",uploadParams[0],data,"multipart/form-data; boundary="+boundary,uploadParams[4],uploadParams[5],localCallback,params,null);
if (typeof r == "string")
displayMessage(r);
return r;
};
// same as Saving's updateOriginal but without convertUnicodeToUTF8 calls
bidix.upload.updateOriginal = function(original, posDiv)
{
if (!posDiv)
posDiv = locateStoreArea(original);
if((posDiv[0] == -1) || (posDiv[1] == -1)) {
alert(config.messages.invalidFileError.format([localPath]));
return;
}
var revised = original.substr(0,posDiv[0] + startSaveArea.length) + "\n" +
store.allTiddlersAsHtml() + "\n" +
original.substr(posDiv[1]);
var newSiteTitle = getPageTitle().htmlEncode();
revised = revised.replaceChunk("<title"+">","</title"+">"," " + newSiteTitle + " ");
revised = updateMarkupBlock(revised,"PRE-HEAD","MarkupPreHead");
revised = updateMarkupBlock(revised,"POST-HEAD","MarkupPostHead");
revised = updateMarkupBlock(revised,"PRE-BODY","MarkupPreBody");
revised = updateMarkupBlock(revised,"POST-SCRIPT","MarkupPostBody");
return revised;
};
//
// UploadLog
//
// config.options.chkUploadLog :
// false : no logging
// true : logging
// config.options.txtUploadLogMaxLine :
// -1 : no limit
// 0 : no Log lines but UploadLog is still in place
// n : the last n lines are only kept
// NaN : no limit (-1)
bidix.UploadLog = function() {
if (!config.options.chkUploadLog)
return; // this.tiddler = null
this.tiddler = store.getTiddler("UploadLog");
if (!this.tiddler) {
this.tiddler = new Tiddler();
this.tiddler.title = "UploadLog";
this.tiddler.text = "| !date | !user | !location | !storeUrl | !uploadDir | !toFilename | !backupdir | !origin |";
this.tiddler.created = new Date();
this.tiddler.modifier = config.options.txtUserName;
this.tiddler.modified = new Date();
store.addTiddler(this.tiddler);
}
return this;
};
bidix.UploadLog.prototype.addText = function(text) {
if (!this.tiddler)
return;
// retrieve maxLine when we need it
var maxLine = parseInt(config.options.txtUploadLogMaxLine,10);
if (isNaN(maxLine))
maxLine = -1;
// add text
if (maxLine != 0)
this.tiddler.text = this.tiddler.text + text;
// Trunck to maxLine
if (maxLine >= 0) {
var textArray = this.tiddler.text.split('\n');
if (textArray.length > maxLine + 1)
textArray.splice(1,textArray.length-1-maxLine);
this.tiddler.text = textArray.join('\n');
}
// update tiddler fields
this.tiddler.modifier = config.options.txtUserName;
this.tiddler.modified = new Date();
store.addTiddler(this.tiddler);
// refresh and notifiy for immediate update
story.refreshTiddler(this.tiddler.title);
store.notify(this.tiddler.title, true);
};
bidix.UploadLog.prototype.startUpload = function(storeUrl, toFilename, uploadDir, backupDir) {
if (!this.tiddler)
return;
var now = new Date();
var text = "\n| ";
var filename = bidix.basename(document.location.toString());
if (!filename) filename = '/';
text += now.formatString("0DD/0MM/YYYY 0hh:0mm:0ss") +" | ";
text += config.options.txtUserName + " | ";
text += "[["+filename+"|"+location + "]] |";
text += " [[" + bidix.basename(storeUrl) + "|" + storeUrl + "]] | ";
text += uploadDir + " | ";
text += "[[" + bidix.basename(toFilename) + " | " +toFilename + "]] | ";
text += backupDir + " |";
this.addText(text);
};
bidix.UploadLog.prototype.endUpload = function(status) {
if (!this.tiddler)
return;
this.addText(" "+status+" |");
};
//
// Utilities
//
bidix.checkPlugin = function(plugin, major, minor, revision) {
var ext = version.extensions[plugin];
if (!
(ext &&
((ext.major > major) ||
((ext.major == major) && (ext.minor > minor)) ||
((ext.major == major) && (ext.minor == minor) && (ext.revision >= revision))))) {
// write error in PluginManager
if (pluginInfo)
pluginInfo.log.push("Requires " + plugin + " " + major + "." + minor + "." + revision);
eval(plugin); // generate an error : "Error: ReferenceError: xxxx is not defined"
}
};
bidix.dirname = function(filePath) {
if (!filePath)
return;
var lastpos;
if ((lastpos = filePath.lastIndexOf("/")) != -1) {
return filePath.substring(0, lastpos);
} else {
return filePath.substring(0, filePath.lastIndexOf("\\"));
}
};
bidix.basename = function(filePath) {
if (!filePath)
return;
var lastpos;
if ((lastpos = filePath.lastIndexOf("#")) != -1)
filePath = filePath.substring(0, lastpos);
if ((lastpos = filePath.lastIndexOf("/")) != -1) {
return filePath.substring(lastpos + 1);
} else
return filePath.substring(filePath.lastIndexOf("\\")+1);
};
bidix.initOption = function(name,value) {
if (!config.options[name])
config.options[name] = value;
};
//
// Initializations
//
// require PasswordOptionPlugin 1.0.1 or better
bidix.checkPlugin("PasswordOptionPlugin", 1, 0, 1);
// styleSheet
setStylesheet('.txtUploadStoreUrl, .txtUploadBackupDir, .txtUploadDir {width: 22em;}',"uploadPluginStyles");
//optionsDesc
merge(config.optionsDesc,{
txtUploadStoreUrl: "Url of the UploadService script (default: store.php)",
txtUploadFilename: "Filename of the uploaded file (default: in index.html)",
txtUploadDir: "Relative Directory where to store the file (default: . (downloadService directory))",
txtUploadBackupDir: "Relative Directory where to backup the file. If empty no backup. (default: ''(empty))",
txtUploadUserName: "Upload Username",
pasUploadPassword: "Upload Password",
chkUploadLog: "do Logging in UploadLog (default: true)",
txtUploadLogMaxLine: "Maximum of lines in UploadLog (default: 10)"
});
// Options Initializations
bidix.initOption('txtUploadStoreUrl','');
bidix.initOption('txtUploadFilename','');
bidix.initOption('txtUploadDir','');
bidix.initOption('txtUploadBackupDir','');
bidix.initOption('txtUploadUserName','');
bidix.initOption('pasUploadPassword','');
bidix.initOption('chkUploadLog',true);
bidix.initOption('txtUploadLogMaxLine','10');
/* don't want this for tiddlyspot sites
// Backstage
merge(config.tasks,{
uploadOptions: {text: "upload", tooltip: "Change UploadOptions and Upload", content: '<<uploadOptions>>'}
});
config.backstageTasks.push("uploadOptions");
*/
//}}}
{{{pairs}}} is a scatterplot of a matrix.
Examples:
# Scatterplot with colors. Note how the color for each class is decided smartly using {{{unclass}}} function. The {{{unclass}}} function demotes the categorical variable of species in the [[Iris dataset]] from //setosa//, //versicolor// and //virginica// labels into numerics of 1, 2 and 3, which then feeds the background.
{{{
> pairs(iris[1:4],main="Iris Data (red=setosa,green=versicolor,blue=virginica)", pch=21,
+ bg = c("red", "green3", "blue")[unclass(iris$Species)])
}}}
{{third{[img(100%,auto)[pairs|http://upload.wikimedia.org/wikipedia/commons/e/ea/Anderson%27s_Iris_data_set.png][pairs]]}}}