diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..160951a --- /dev/null +++ b/.gitignore @@ -0,0 +1,6 @@ +.Rproj.user +.Rhistory +.RData +.Ruserdata +.DS_Store +*.Rproj diff --git a/01-introduction.Rmd b/01-introduction.Rmd new file mode 100644 index 0000000..330dc5b --- /dev/null +++ b/01-introduction.Rmd @@ -0,0 +1,19 @@ +# Introduction {#intro} + +You can label chapter and section titles using `{#label}` after them, e.g., we can reference Chapter \@ref(intro). If you do not manually label them, there will be automatic labels anyway, e.g., Chapter \@ref(methods). + +Figures and tables with captions will be placed in `figure` and `table` environments, respectively. + +```{r nice-fig, fig.cap='Here is a nice figure!', out.width='80%', fig.asp=.75, fig.align='center'} +par(mar = c(4, 4, .1, .1)) +plot(pressure, type = 'b', pch = 19) +``` + +Reference a figure by its code chunk label with the `fig:` prefix, e.g., see Figure \@ref(fig:nice-fig). Similarly, you can reference tables generated from `knitr::kable()`, e.g., see Table \@ref(tab:nice-tab). + +```{r nice-tab, tidy=FALSE} +knitr::kable( + head(iris, 20), caption = 'Here is a nice table!', + booktabs = TRUE +) +``` diff --git a/_bookdown.yml b/_bookdown.yml new file mode 100644 index 0000000..7313cb9 --- /dev/null +++ b/_bookdown.yml @@ -0,0 +1,6 @@ +output_dir: "docs" +book_filename: "a_new_instrument_for_microbial_epidemiology" +language: + ui: + chapter_name: "Chapter " +delete_merged_file: true diff --git a/_bookdown_files/a_new_instrument_for_microbial_epidemiology_files/figure-html/nice-fig-1.png b/_bookdown_files/a_new_instrument_for_microbial_epidemiology_files/figure-html/nice-fig-1.png new file mode 100644 index 0000000..04cb1da Binary files /dev/null and b/_bookdown_files/a_new_instrument_for_microbial_epidemiology_files/figure-html/nice-fig-1.png differ diff --git a/_output.yml b/_output.yml new file mode 100644 index 0000000..d2c1a5f --- /dev/null +++ b/_output.yml @@ -0,0 +1,22 @@ +bookdown::gitbook: + css: style.css + config: + toc: + before: | +
  • A New Instrument for Microbial Epidemiology
  • + after: | +
  • Published with bookdown
  • +# edit: https://github.com/msberends/a_new_instrument_for_microbial_epidemiology/edit/master/%s + download: ["pdf", "epub"] + +bookdown::pdf_book: + includes: + in_header: preamble.tex + latex_engine: xelatex + citation_package: natbib + keep_tex: yes + +bookdown::epub_book: default + +# no bootstrap 4 for now +# bookdown::bs4_book: default diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 0000000..0328e4a --- /dev/null +++ b/docs/404.html @@ -0,0 +1,230 @@ + + + + + + + Page not found | A New Instrument for Microbial Epidemiology + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    The page you requested cannot be found (perhaps it was moved or renamed).

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    You may want to try searching to find the page's new location, or use +the table of contents to find the page you are looking for.

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    + + + + + + + + + + + + + diff --git a/docs/a_new_instrument_for_microbial_epidemiology_files/figure-html/nice-fig-1.png b/docs/a_new_instrument_for_microbial_epidemiology_files/figure-html/nice-fig-1.png new file mode 100644 index 0000000..04cb1da Binary files /dev/null and b/docs/a_new_instrument_for_microbial_epidemiology_files/figure-html/nice-fig-1.png differ diff --git a/docs/index.html b/docs/index.html new file mode 100644 index 0000000..b0403b1 --- /dev/null +++ b/docs/index.html @@ -0,0 +1,235 @@ + + + + + + + A New Instrument for Microbial Epidemiology + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    +

    Prerequisites

    +

    txt

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    + + + + + + + + + + + + + diff --git a/docs/intro.html b/docs/intro.html new file mode 100644 index 0000000..f93d3dc --- /dev/null +++ b/docs/intro.html @@ -0,0 +1,397 @@ + + + + + + + 1 Introduction | A New Instrument for Microbial Epidemiology + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + +
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    +

    1 Introduction

    +

    You can label chapter and section titles using {#label} after them, e.g., we can reference Chapter 1. If you do not manually label them, there will be automatic labels anyway, e.g., Chapter ??.

    +

    Figures and tables with captions will be placed in figure and table environments, respectively.

    +
    par(mar = c(4, 4, .1, .1))
    +plot(pressure, type = 'b', pch = 19)
    +
    +Here is a nice figure! +

    +Figure 1.1: Here is a nice figure! +

    +
    +

    Reference a figure by its code chunk label with the fig: prefix, e.g., see Figure 1.1. Similarly, you can reference tables generated from knitr::kable(), e.g., see Table 1.1.

    +
    knitr::kable(
    +  head(iris, 20), caption = 'Here is a nice table!',
    +  booktabs = TRUE
    +)
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Table 1.1: Here is a nice table!
    Sepal.LengthSepal.WidthPetal.LengthPetal.WidthSpecies
    5.13.51.40.2setosa
    4.93.01.40.2setosa
    4.73.21.30.2setosa
    4.63.11.50.2setosa
    5.03.61.40.2setosa
    5.43.91.70.4setosa
    4.63.41.40.3setosa
    5.03.41.50.2setosa
    4.42.91.40.2setosa
    4.93.11.50.1setosa
    5.43.71.50.2setosa
    4.83.41.60.2setosa
    4.83.01.40.1setosa
    4.33.01.10.1setosa
    5.84.01.20.2setosa
    5.74.41.50.4setosa
    5.43.91.30.4setosa
    5.13.51.40.3setosa
    5.73.81.70.3setosa
    5.13.81.50.3setosa
    + +
    +
    + +
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    +
    + + +
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#73553c; + background: none; +} +.book.color-theme-1 .book-header h1 { + color: #704214; +} +.book.color-theme-2 .book-header { + color: #7e888b; + background: transparent; +} +.book.color-theme-2 .book-header .btn { + color: #3b3f54; +} +.book.color-theme-2 .book-header .btn:hover { + color: #fffff5; + background: none; +} +.book.color-theme-2 .book-header h1 { + color: #bdcadb; +} +.book.color-theme-1 .book-body .navigation { + color: #afa790; +} +.book.color-theme-1 .book-body .navigation:hover { + color: #73553c; +} +.book.color-theme-2 .book-body .navigation { + color: #383f52; +} +.book.color-theme-2 .book-body .navigation:hover { + color: #fffff5; +} +/* + * Theme 1 + */ +.book.color-theme-1 .book-summary { + color: #afa790; + background: #111111; + border-right: 1px solid rgba(0, 0, 0, 0.07); +} +.book.color-theme-1 .book-summary .book-search { + background: transparent; +} +.book.color-theme-1 .book-summary .book-search input, +.book.color-theme-1 .book-summary .book-search input:focus { + border: 1px solid transparent; +} +.book.color-theme-1 .book-summary ul.summary li.divider { + background: #7e888b; + box-shadow: none; +} +.book.color-theme-1 .book-summary ul.summary li i.fa-check { + color: #33cc33; +} +.book.color-theme-1 .book-summary ul.summary li.done > a { + color: #877f6a; +} +.book.color-theme-1 .book-summary ul.summary li a, +.book.color-theme-1 .book-summary ul.summary li span { + color: #877f6a; + background: transparent; + font-weight: normal; +} +.book.color-theme-1 .book-summary ul.summary li.active > a, +.book.color-theme-1 .book-summary ul.summary li a:hover { + color: #704214; + background: transparent; + font-weight: normal; +} +/* + * Theme 2 + */ +.book.color-theme-2 .book-summary { + color: #bcc1d2; + background: #2d3143; + border-right: none; +} +.book.color-theme-2 .book-summary .book-search { + background: transparent; +} +.book.color-theme-2 .book-summary .book-search input, +.book.color-theme-2 .book-summary .book-search input:focus { + border: 1px solid transparent; +} +.book.color-theme-2 .book-summary ul.summary li.divider { + background: #272a3a; + box-shadow: none; +} +.book.color-theme-2 .book-summary ul.summary li i.fa-check { + color: #33cc33; +} +.book.color-theme-2 .book-summary ul.summary li.done > a { + color: #62687f; +} +.book.color-theme-2 .book-summary ul.summary li a, +.book.color-theme-2 .book-summary ul.summary li span { + color: #c1c6d7; + background: transparent; + font-weight: 600; +} +.book.color-theme-2 .book-summary ul.summary li.active > a, +.book.color-theme-2 .book-summary ul.summary li a:hover { + color: #f4f4f5; + background: #252737; + font-weight: 600; +} diff --git a/docs/libs/gitbook-2.6.7/css/plugin-highlight.css b/docs/libs/gitbook-2.6.7/css/plugin-highlight.css new file mode 100644 index 0000000..2aabd3d --- /dev/null +++ b/docs/libs/gitbook-2.6.7/css/plugin-highlight.css @@ -0,0 +1,426 @@ +.book .book-body .page-wrapper .page-inner section.normal pre, +.book 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isObj=isObject(source),props=isObj?keys(source):undefined,methodNames=props&&props.length?baseFunctions(source,props):undefined;if(!(methodNames?methodNames.length:isObj)){methodNames=false;options=source;source=object;object=this}}if(!methodNames){methodNames=baseFunctions(source,keys(source))}var chain=true,index=-1,isFunc=isFunction(object),length=methodNames.length;if(options===false){chain=false}else if(isObject(options)&&"chain"in options){chain=options.chain}while(++index0||end<0)){return new LazyWrapper(result)}if(start<0){result=result.takeRight(-start)}else if(start){result=result.drop(start)}if(end!==undefined){end=+end||0;result=end<0?result.dropRight(-end):result.take(end-start)}return result};LazyWrapper.prototype.takeRightWhile=function(predicate,thisArg){return this.reverse().takeWhile(predicate,thisArg).reverse()};LazyWrapper.prototype.toArray=function(){return this.take(POSITIVE_INFINITY)};baseForOwn(LazyWrapper.prototype,function(func,methodName){var 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if(freeExports&&freeModule){if(moduleExports){(freeModule.exports=_)._=_}else{freeExports._=_}}else{root._=_}}).call(this)}).call(this,typeof global!=="undefined"?global:typeof self!=="undefined"?self:typeof window!=="undefined"?window:{})},{}],3:[function(require,module,exports){(function(window,document,undefined){var _MAP={8:"backspace",9:"tab",13:"enter",16:"shift",17:"ctrl",18:"alt",20:"capslock",27:"esc",32:"space",33:"pageup",34:"pagedown",35:"end",36:"home",37:"left",38:"up",39:"right",40:"down",45:"ins",46:"del",91:"meta",93:"meta",224:"meta"};var _KEYCODE_MAP={106:"*",107:"+",109:"-",110:".",111:"/",186:";",187:"=",188:",",189:"-",190:".",191:"/",192:"`",219:"[",220:"\\",221:"]",222:"'"};var _SHIFT_MAP={"~":"`","!":"1","@":"2","#":"3",$:"4","%":"5","^":"6","&":"7","*":"8","(":"9",")":"0",_:"-","+":"=",":":";",'"':"'","<":",",">":".","?":"/","|":"\\"};var _SPECIAL_ALIASES={option:"alt",command:"meta",return:"enter",escape:"esc",plus:"+",mod:/Mac|iPod|iPhone|iPad/.test(navigator.platform)?"meta":"ctrl"};var _REVERSE_MAP;for(var i=1;i<20;++i){_MAP[111+i]="f"+i}for(i=0;i<=9;++i){_MAP[i+96]=i}function _addEvent(object,type,callback){if(object.addEventListener){object.addEventListener(type,callback,false);return}object.attachEvent("on"+type,callback)}function _characterFromEvent(e){if(e.type=="keypress"){var character=String.fromCharCode(e.which);if(!e.shiftKey){character=character.toLowerCase()}return character}if(_MAP[e.which]){return _MAP[e.which]}if(_KEYCODE_MAP[e.which]){return _KEYCODE_MAP[e.which]}return String.fromCharCode(e.which).toLowerCase()}function _modifiersMatch(modifiers1,modifiers2){return modifiers1.sort().join(",")===modifiers2.sort().join(",")}function _eventModifiers(e){var modifiers=[];if(e.shiftKey){modifiers.push("shift")}if(e.altKey){modifiers.push("alt")}if(e.ctrlKey){modifiers.push("ctrl")}if(e.metaKey){modifiers.push("meta")}return modifiers}function _preventDefault(e){if(e.preventDefault){e.preventDefault();return}e.returnValue=false}function _stopPropagation(e){if(e.stopPropagation){e.stopPropagation();return}e.cancelBubble=true}function _isModifier(key){return key=="shift"||key=="ctrl"||key=="alt"||key=="meta"}function _getReverseMap(){if(!_REVERSE_MAP){_REVERSE_MAP={};for(var key in _MAP){if(key>95&&key<112){continue}if(_MAP.hasOwnProperty(key)){_REVERSE_MAP[_MAP[key]]=key}}}return _REVERSE_MAP}function _pickBestAction(key,modifiers,action){if(!action){action=_getReverseMap()[key]?"keydown":"keypress"}if(action=="keypress"&&modifiers.length){action="keydown"}return action}function _keysFromString(combination){if(combination==="+"){return["+"]}combination=combination.replace(/\+{2}/g,"+plus");return combination.split("+")}function _getKeyInfo(combination,action){var keys;var key;var i;var modifiers=[];keys=_keysFromString(combination);for(i=0;i1){_bindSequence(combination,sequence,callback,action);return}info=_getKeyInfo(combination,action);self._callbacks[info.key]=self._callbacks[info.key]||[];_getMatches(info.key,info.modifiers,{type:info.action},sequenceName,combination,level);self._callbacks[info.key][sequenceName?"unshift":"push"]({callback:callback,modifiers:info.modifiers,action:info.action,seq:sequenceName,level:level,combo:combination})}self._bindMultiple=function(combinations,callback,action){for(var i=0;i-1){return false}if(_belongsTo(element,self.target)){return false}return element.tagName=="INPUT"||element.tagName=="SELECT"||element.tagName=="TEXTAREA"||element.isContentEditable};Mousetrap.prototype.handleKey=function(){var self=this;return self._handleKey.apply(self,arguments)};Mousetrap.init=function(){var documentMousetrap=Mousetrap(document);for(var method in documentMousetrap){if(method.charAt(0)!=="_"){Mousetrap[method]=function(method){return function(){return documentMousetrap[method].apply(documentMousetrap,arguments)}}(method)}}};Mousetrap.init();window.Mousetrap=Mousetrap;if(typeof module!=="undefined"&&module.exports){module.exports=Mousetrap}if(typeof define==="function"&&define.amd){define(function(){return Mousetrap})}})(window,document)},{}],4:[function(require,module,exports){(function(process){function normalizeArray(parts,allowAboveRoot){var up=0;for(var i=parts.length-1;i>=0;i--){var last=parts[i];if(last==="."){parts.splice(i,1)}else if(last===".."){parts.splice(i,1);up++}else if(up){parts.splice(i,1);up--}}if(allowAboveRoot){for(;up--;up){parts.unshift("..")}}return parts}var splitPathRe=/^(\/?|)([\s\S]*?)((?:\.{1,2}|[^\/]+?|)(\.[^.\/]*|))(?:[\/]*)$/;var splitPath=function(filename){return splitPathRe.exec(filename).slice(1)};exports.resolve=function(){var resolvedPath="",resolvedAbsolute=false;for(var i=arguments.length-1;i>=-1&&!resolvedAbsolute;i--){var path=i>=0?arguments[i]:process.cwd();if(typeof path!=="string"){throw new TypeError("Arguments to path.resolve must be strings")}else if(!path){continue}resolvedPath=path+"/"+resolvedPath;resolvedAbsolute=path.charAt(0)==="/"}resolvedPath=normalizeArray(filter(resolvedPath.split("/"),function(p){return!!p}),!resolvedAbsolute).join("/");return(resolvedAbsolute?"/":"")+resolvedPath||"."};exports.normalize=function(path){var isAbsolute=exports.isAbsolute(path),trailingSlash=substr(path,-1)==="/";path=normalizeArray(filter(path.split("/"),function(p){return!!p}),!isAbsolute).join("/");if(!path&&!isAbsolute){path="."}if(path&&trailingSlash){path+="/"}return(isAbsolute?"/":"")+path};exports.isAbsolute=function(path){return path.charAt(0)==="/"};exports.join=function(){var paths=Array.prototype.slice.call(arguments,0);return exports.normalize(filter(paths,function(p,index){if(typeof p!=="string"){throw new TypeError("Arguments to path.join must be strings")}return p}).join("/"))};exports.relative=function(from,to){from=exports.resolve(from).substr(1);to=exports.resolve(to).substr(1);function trim(arr){var start=0;for(;start=0;end--){if(arr[end]!=="")break}if(start>end)return[];return arr.slice(start,end-start+1)}var fromParts=trim(from.split("/"));var toParts=trim(to.split("/"));var length=Math.min(fromParts.length,toParts.length);var samePartsLength=length;for(var i=0;i1){for(var i=1;i= 0x80 (not a basic code point)","invalid-input":"Invalid input"},baseMinusTMin=base-tMin,floor=Math.floor,stringFromCharCode=String.fromCharCode,key;function error(type){throw RangeError(errors[type])}function map(array,fn){var length=array.length;var result=[];while(length--){result[length]=fn(array[length])}return result}function mapDomain(string,fn){var parts=string.split("@");var result="";if(parts.length>1){result=parts[0]+"@";string=parts[1]}string=string.replace(regexSeparators,".");var labels=string.split(".");var encoded=map(labels,fn).join(".");return result+encoded}function ucs2decode(string){var output=[],counter=0,length=string.length,value,extra;while(counter=55296&&value<=56319&&counter65535){value-=65536;output+=stringFromCharCode(value>>>10&1023|55296);value=56320|value&1023}output+=stringFromCharCode(value);return output}).join("")}function basicToDigit(codePoint){if(codePoint-48<10){return codePoint-22}if(codePoint-65<26){return codePoint-65}if(codePoint-97<26){return codePoint-97}return base}function digitToBasic(digit,flag){return digit+22+75*(digit<26)-((flag!=0)<<5)}function adapt(delta,numPoints,firstTime){var k=0;delta=firstTime?floor(delta/damp):delta>>1;delta+=floor(delta/numPoints);for(;delta>baseMinusTMin*tMax>>1;k+=base){delta=floor(delta/baseMinusTMin)}return floor(k+(baseMinusTMin+1)*delta/(delta+skew))}function decode(input){var output=[],inputLength=input.length,out,i=0,n=initialN,bias=initialBias,basic,j,index,oldi,w,k,digit,t,baseMinusT;basic=input.lastIndexOf(delimiter);if(basic<0){basic=0}for(j=0;j=128){error("not-basic")}output.push(input.charCodeAt(j))}for(index=basic>0?basic+1:0;index=inputLength){error("invalid-input")}digit=basicToDigit(input.charCodeAt(index++));if(digit>=base||digit>floor((maxInt-i)/w)){error("overflow")}i+=digit*w;t=k<=bias?tMin:k>=bias+tMax?tMax:k-bias;if(digitfloor(maxInt/baseMinusT)){error("overflow")}w*=baseMinusT}out=output.length+1;bias=adapt(i-oldi,out,oldi==0);if(floor(i/out)>maxInt-n){error("overflow")}n+=floor(i/out);i%=out;output.splice(i++,0,n)}return ucs2encode(output)}function encode(input){var n,delta,handledCPCount,basicLength,bias,j,m,q,k,t,currentValue,output=[],inputLength,handledCPCountPlusOne,baseMinusT,qMinusT;input=ucs2decode(input);inputLength=input.length;n=initialN;delta=0;bias=initialBias;for(j=0;j=n&¤tValuefloor((maxInt-delta)/handledCPCountPlusOne)){error("overflow")}delta+=(m-n)*handledCPCountPlusOne;n=m;for(j=0;jmaxInt){error("overflow")}if(currentValue==n){for(q=delta,k=base;;k+=base){t=k<=bias?tMin:k>=bias+tMax?tMax:k-bias;if(q0&&len>maxKeys){len=maxKeys}for(var i=0;i=0){kstr=x.substr(0,idx);vstr=x.substr(idx+1)}else{kstr=x;vstr=""}k=decodeURIComponent(kstr);v=decodeURIComponent(vstr);if(!hasOwnProperty(obj,k)){obj[k]=v}else if(isArray(obj[k])){obj[k].push(v)}else{obj[k]=[obj[k],v]}}return obj};var isArray=Array.isArray||function(xs){return Object.prototype.toString.call(xs)==="[object Array]"}},{}],8:[function(require,module,exports){"use strict";var stringifyPrimitive=function(v){switch(typeof v){case"string":return v;case"boolean":return v?"true":"false";case"number":return isFinite(v)?v:"";default:return""}};module.exports=function(obj,sep,eq,name){sep=sep||"&";eq=eq||"=";if(obj===null){obj=undefined}if(typeof obj==="object"){return map(objectKeys(obj),function(k){var ks=encodeURIComponent(stringifyPrimitive(k))+eq;if(isArray(obj[k])){return map(obj[k],function(v){return ks+encodeURIComponent(stringifyPrimitive(v))}).join(sep)}else{return ks+encodeURIComponent(stringifyPrimitive(obj[k]))}}).join(sep)}if(!name)return"";return encodeURIComponent(stringifyPrimitive(name))+eq+encodeURIComponent(stringifyPrimitive(obj))};var isArray=Array.isArray||function(xs){return Object.prototype.toString.call(xs)==="[object Array]"};function map(xs,f){if(xs.map)return xs.map(f);var res=[];for(var i=0;i",'"',"`"," ","\r","\n","\t"],unwise=["{","}","|","\\","^","`"].concat(delims),autoEscape=["'"].concat(unwise),nonHostChars=["%","/","?",";","#"].concat(autoEscape),hostEndingChars=["/","?","#"],hostnameMaxLen=255,hostnamePartPattern=/^[a-z0-9A-Z_-]{0,63}$/,hostnamePartStart=/^([a-z0-9A-Z_-]{0,63})(.*)$/,unsafeProtocol={javascript:true,"javascript:":true},hostlessProtocol={javascript:true,"javascript:":true},slashedProtocol={http:true,https:true,ftp:true,gopher:true,file:true,"http:":true,"https:":true,"ftp:":true,"gopher:":true,"file:":true},querystring=require("querystring");function urlParse(url,parseQueryString,slashesDenoteHost){if(url&&isObject(url)&&url instanceof Url)return url;var u=new Url;u.parse(url,parseQueryString,slashesDenoteHost);return u}Url.prototype.parse=function(url,parseQueryString,slashesDenoteHost){if(!isString(url)){throw new TypeError("Parameter 'url' must be a string, not "+typeof url)}var rest=url;rest=rest.trim();var proto=protocolPattern.exec(rest);if(proto){proto=proto[0];var lowerProto=proto.toLowerCase();this.protocol=lowerProto;rest=rest.substr(proto.length)}if(slashesDenoteHost||proto||rest.match(/^\/\/[^@\/]+@[^@\/]+/)){var slashes=rest.substr(0,2)==="//";if(slashes&&!(proto&&hostlessProtocol[proto])){rest=rest.substr(2);this.slashes=true}}if(!hostlessProtocol[proto]&&(slashes||proto&&!slashedProtocol[proto])){var hostEnd=-1;for(var i=0;i127){newpart+="x"}else{newpart+=part[j]}}if(!newpart.match(hostnamePartPattern)){var validParts=hostparts.slice(0,i);var notHost=hostparts.slice(i+1);var bit=part.match(hostnamePartStart);if(bit){validParts.push(bit[1]);notHost.unshift(bit[2])}if(notHost.length){rest="/"+notHost.join(".")+rest}this.hostname=validParts.join(".");break}}}}if(this.hostname.length>hostnameMaxLen){this.hostname=""}else{this.hostname=this.hostname.toLowerCase()}if(!ipv6Hostname){var domainArray=this.hostname.split(".");var newOut=[];for(var i=0;i0?result.host.split("@"):false;if(authInHost){result.auth=authInHost.shift();result.host=result.hostname=authInHost.shift()}}result.search=relative.search;result.query=relative.query;if(!isNull(result.pathname)||!isNull(result.search)){result.path=(result.pathname?result.pathname:"")+(result.search?result.search:"")}result.href=result.format();return result}if(!srcPath.length){result.pathname=null;if(result.search){result.path="/"+result.search}else{result.path=null}result.href=result.format();return result}var last=srcPath.slice(-1)[0];var hasTrailingSlash=(result.host||relative.host)&&(last==="."||last==="..")||last==="";var up=0;for(var i=srcPath.length;i>=0;i--){last=srcPath[i];if(last=="."){srcPath.splice(i,1)}else if(last===".."){srcPath.splice(i,1);up++}else if(up){srcPath.splice(i,1);up--}}if(!mustEndAbs&&!removeAllDots){for(;up--;up){srcPath.unshift("..")}}if(mustEndAbs&&srcPath[0]!==""&&(!srcPath[0]||srcPath[0].charAt(0)!=="/")){srcPath.unshift("")}if(hasTrailingSlash&&srcPath.join("/").substr(-1)!=="/"){srcPath.push("")}var isAbsolute=srcPath[0]===""||srcPath[0]&&srcPath[0].charAt(0)==="/";if(psychotic){result.hostname=result.host=isAbsolute?"":srcPath.length?srcPath.shift():"";var authInHost=result.host&&result.host.indexOf("@")>0?result.host.split("@"):false;if(authInHost){result.auth=authInHost.shift();result.host=result.hostname=authInHost.shift()}}mustEndAbs=mustEndAbs||result.host&&srcPath.length;if(mustEndAbs&&!isAbsolute){srcPath.unshift("")}if(!srcPath.length){result.pathname=null;result.path=null}else{result.pathname=srcPath.join("/")}if(!isNull(result.pathname)||!isNull(result.search)){result.path=(result.pathname?result.pathname:"")+(result.search?result.search:"")}result.auth=relative.auth||result.auth;result.slashes=result.slashes||relative.slashes;result.href=result.format();return result};Url.prototype.parseHost=function(){var host=this.host;var port=portPattern.exec(host);if(port){port=port[0];if(port!==":"){this.port=port.substr(1)}host=host.substr(0,host.length-port.length)}if(host)this.hostname=host};function isString(arg){return typeof arg==="string"}function isObject(arg){return typeof arg==="object"&&arg!==null}function isNull(arg){return arg===null}function isNullOrUndefined(arg){return arg==null}},{punycode:6,querystring:9}],11:[function(require,module,exports){var $=require("jquery");function toggleDropdown(e){var $dropdown=$(e.currentTarget).parent().find(".dropdown-menu");$dropdown.toggleClass("open");e.stopPropagation();e.preventDefault()}function closeDropdown(e){$(".dropdown-menu").removeClass("open")}function init(){$(document).on("click",".toggle-dropdown",toggleDropdown);$(document).on("click",".dropdown-menu",function(e){e.stopPropagation()});$(document).on("click",closeDropdown)}module.exports={init:init}},{jquery:1}],12:[function(require,module,exports){var $=require("jquery");module.exports=$({})},{jquery:1}],13:[function(require,module,exports){var $=require("jquery");var _=require("lodash");var storage=require("./storage");var dropdown=require("./dropdown");var events=require("./events");var state=require("./state");var keyboard=require("./keyboard");var navigation=require("./navigation");var sidebar=require("./sidebar");var toolbar=require("./toolbar");function start(config){sidebar.init();keyboard.init();dropdown.init();navigation.init();toolbar.createButton({index:0,icon:"fa fa-align-justify",label:"Toggle Sidebar",onClick:function(e){e.preventDefault();sidebar.toggle()}});events.trigger("start",config);navigation.notify()}var gitbook={start:start,events:events,state:state,toolbar:toolbar,sidebar:sidebar,storage:storage,keyboard:keyboard};var MODULES={gitbook:gitbook,jquery:$,lodash:_};window.gitbook=gitbook;window.$=$;window.jQuery=$;gitbook.require=function(mods,fn){mods=_.map(mods,function(mod){mod=mod.toLowerCase();if(!MODULES[mod]){throw new Error("GitBook module "+mod+" doesn't exist")}return MODULES[mod]});fn.apply(null,mods)};module.exports={}},{"./dropdown":11,"./events":12,"./keyboard":14,"./navigation":16,"./sidebar":18,"./state":19,"./storage":20,"./toolbar":21,jquery:1,lodash:2}],14:[function(require,module,exports){var Mousetrap=require("mousetrap");var navigation=require("./navigation");var sidebar=require("./sidebar");function bindShortcut(keys,fn){Mousetrap.bind(keys,function(e){fn();return false})}function init(){bindShortcut(["right"],function(e){navigation.goNext()});bindShortcut(["left"],function(e){navigation.goPrev()});bindShortcut(["s"],function(e){sidebar.toggle()})}module.exports={init:init,bind:bindShortcut}},{"./navigation":16,"./sidebar":18,mousetrap:3}],15:[function(require,module,exports){var state=require("./state");function showLoading(p){state.$book.addClass("is-loading");p.always(function(){state.$book.removeClass("is-loading")});return p}module.exports={show:showLoading}},{"./state":19}],16:[function(require,module,exports){var $=require("jquery");var url=require("url");var events=require("./events");var state=require("./state");var loading=require("./loading");var usePushState=typeof history.pushState!=="undefined";function handleNavigation(relativeUrl,push){var uri=url.resolve(window.location.pathname,relativeUrl);notifyPageChange();location.href=relativeUrl;return}function updateNavigationPosition(){var bodyInnerWidth,pageWrapperWidth;bodyInnerWidth=parseInt($(".body-inner").css("width"),10);pageWrapperWidth=parseInt($(".page-wrapper").css("width"),10);$(".navigation-next").css("margin-right",bodyInnerWidth-pageWrapperWidth+"px")}function notifyPageChange(){events.trigger("page.change")}function preparePage(notify){var $bookBody=$(".book-body");var $bookInner=$bookBody.find(".body-inner");var $pageWrapper=$bookInner.find(".page-wrapper");updateNavigationPosition();$bookInner.scrollTop(0);$bookBody.scrollTop(0);if(notify!==false)notifyPageChange()}function isLeftClickEvent(e){return e.button===0}function isModifiedEvent(e){return!!(e.metaKey||e.altKey||e.ctrlKey||e.shiftKey)}function handlePagination(e){if(isModifiedEvent(e)||!isLeftClickEvent(e)){return}e.stopPropagation();e.preventDefault();var url=$(this).attr("href");if(url)handleNavigation(url,true)}function goNext(){var url=$(".navigation-next").attr("href");if(url)handleNavigation(url,true)}function goPrev(){var url=$(".navigation-prev").attr("href");if(url)handleNavigation(url,true)}function init(){$.ajaxSetup({});if(location.protocol!=="file:"){history.replaceState({path:window.location.href},"")}window.onpopstate=function(event){if(event.state===null){return}return handleNavigation(event.state.path,false)};$(document).on("click",".navigation-prev",handlePagination);$(document).on("click",".navigation-next",handlePagination);$(document).on("click",".summary [data-path] a",handlePagination);$(window).resize(updateNavigationPosition);preparePage(false)}module.exports={init:init,goNext:goNext,goPrev:goPrev,notify:notifyPageChange}},{"./events":12,"./loading":15,"./state":19,jquery:1,url:10}],17:[function(require,module,exports){module.exports={isMobile:function(){return document.body.clientWidth<=600}}},{}],18:[function(require,module,exports){var $=require("jquery");var _=require("lodash");var storage=require("./storage");var platform=require("./platform");var state=require("./state");function toggleSidebar(_state,animation){if(state!=null&&isOpen()==_state)return;if(animation==null)animation=true;state.$book.toggleClass("without-animation",!animation);state.$book.toggleClass("with-summary",_state);storage.set("sidebar",isOpen())}function isOpen(){return state.$book.hasClass("with-summary")}function init(){if(platform.isMobile()){toggleSidebar(false,false)}else{toggleSidebar(storage.get("sidebar",true),false)}$(document).on("click",".book-summary li.chapter a",function(e){if(platform.isMobile())toggleSidebar(false,false)})}function filterSummary(paths){var $summary=$(".book-summary");$summary.find("li").each(function(){var path=$(this).data("path");var st=paths==null||_.contains(paths,path);$(this).toggle(st);if(st)$(this).parents("li").show()})}module.exports={init:init,isOpen:isOpen,toggle:toggleSidebar,filter:filterSummary}},{"./platform":17,"./state":19,"./storage":20,jquery:1,lodash:2}],19:[function(require,module,exports){var $=require("jquery");var url=require("url");var path=require("path");var state={};state.update=function(dom){var $book=$(dom.find(".book"));state.$book=$book;state.level=$book.data("level");state.basePath=$book.data("basepath");state.innerLanguage=$book.data("innerlanguage");state.revision=$book.data("revision");state.filepath=$book.data("filepath");state.chapterTitle=$book.data("chapter-title");state.root=url.resolve(location.protocol+"//"+location.host,path.dirname(path.resolve(location.pathname.replace(/\/$/,"/index.html"),state.basePath))).replace(/\/?$/,"/");state.bookRoot=state.innerLanguage?url.resolve(state.root,".."):state.root};state.update($);module.exports=state},{jquery:1,path:4,url:10}],20:[function(require,module,exports){var baseKey="";module.exports={setBaseKey:function(key){baseKey=key},set:function(key,value){key=baseKey+":"+key;try{sessionStorage[key]=JSON.stringify(value)}catch(e){}},get:function(key,def){key=baseKey+":"+key;if(sessionStorage[key]===undefined)return def;try{var v=JSON.parse(sessionStorage[key]);return v==null?def:v}catch(err){return 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    ",{class:"buttons"});var sizeClass="size-"+group.length;_.each(group,function(btn){btn=_.defaults(btn||{},{text:"",className:"",onClick:defaultOnClick});var $btn=$("'; + var clipboard; + + gitbook.events.bind("page.change", function() { + + if (!ClipboardJS.isSupported()) return; + + // the page.change event is thrown twice: before and after the page changes + if (clipboard) { + // clipboard is already defined + // we can deduct that we are before page changes + clipboard.destroy(); // destroy the previous events listeners + clipboard = undefined; // reset the clipboard object + return; + } + + $(copyButton).prependTo("div.sourceCode"); + + clipboard = new ClipboardJS(".copy-to-clipboard-button", { + text: function(trigger) { + return trigger.parentNode.textContent; + } + }); + + }); + +}); diff --git a/docs/libs/gitbook-2.6.7/js/plugin-fontsettings.js b/docs/libs/gitbook-2.6.7/js/plugin-fontsettings.js new file mode 100644 index 0000000..a70f0fb --- /dev/null +++ b/docs/libs/gitbook-2.6.7/js/plugin-fontsettings.js @@ -0,0 +1,152 @@ +gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) { + var fontState; + + var THEMES = { + "white": 0, + "sepia": 1, + "night": 2 + }; + + var FAMILY = { + "serif": 0, + "sans": 1 + }; + + // Save current font settings + function saveFontSettings() { + gitbook.storage.set("fontState", fontState); + update(); + } + + // Increase font size + function enlargeFontSize(e) { + e.preventDefault(); + if (fontState.size >= 4) return; + + fontState.size++; + saveFontSettings(); + }; + + // Decrease font size + function reduceFontSize(e) { + e.preventDefault(); + if (fontState.size <= 0) return; + + fontState.size--; + saveFontSettings(); + }; + + // Change font family + function changeFontFamily(index, e) { + e.preventDefault(); + + fontState.family = index; + saveFontSettings(); + }; + + // Change type of color + function changeColorTheme(index, e) { + e.preventDefault(); + + var $book = $(".book"); + + if (fontState.theme !== 0) + $book.removeClass("color-theme-"+fontState.theme); + + fontState.theme = index; + if (fontState.theme !== 0) + $book.addClass("color-theme-"+fontState.theme); + + saveFontSettings(); + }; + + function update() { + var $book = gitbook.state.$book; + + $(".font-settings .font-family-list li").removeClass("active"); + $(".font-settings .font-family-list li:nth-child("+(fontState.family+1)+")").addClass("active"); + + $book[0].className = $book[0].className.replace(/\bfont-\S+/g, ''); + $book.addClass("font-size-"+fontState.size); + $book.addClass("font-family-"+fontState.family); + + if(fontState.theme !== 0) { + $book[0].className = $book[0].className.replace(/\bcolor-theme-\S+/g, ''); + $book.addClass("color-theme-"+fontState.theme); + } + }; + + function init(config) { + var $bookBody, $book; + + //Find DOM elements. + $book = gitbook.state.$book; + $bookBody = $book.find(".book-body"); + + // Instantiate font state object + fontState = gitbook.storage.get("fontState", { + size: config.size || 2, + family: FAMILY[config.family || "sans"], + theme: THEMES[config.theme || "white"] + }); + + update(); + }; + + + gitbook.events.bind("start", function(e, config) { + var opts = config.fontsettings; + if (!opts) return; + + // Create buttons in toolbar + gitbook.toolbar.createButton({ + icon: 'fa fa-font', + label: 'Font Settings', + className: 'font-settings', + dropdown: [ + [ + { + text: 'A', + className: 'font-reduce', + onClick: reduceFontSize + }, + { + text: 'A', + className: 'font-enlarge', + onClick: enlargeFontSize + } + ], + [ + { + text: 'Serif', + onClick: _.partial(changeFontFamily, 0) + }, + { + text: 'Sans', + onClick: _.partial(changeFontFamily, 1) + } + ], + [ + { + text: 'White', + onClick: _.partial(changeColorTheme, 0) + }, + { + text: 'Sepia', + onClick: _.partial(changeColorTheme, 1) + }, + { + text: 'Night', + onClick: _.partial(changeColorTheme, 2) + } + ] + ] + }); + + + // Init current settings + init(opts); + }); +}); + + diff --git a/docs/libs/gitbook-2.6.7/js/plugin-search.js b/docs/libs/gitbook-2.6.7/js/plugin-search.js new file mode 100644 index 0000000..747fcce --- /dev/null +++ b/docs/libs/gitbook-2.6.7/js/plugin-search.js @@ -0,0 +1,270 @@ +gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) { + var index = null; + var fuse = null; + var _search = {engine: 'lunr', opts: {}}; + var $searchInput, $searchLabel, $searchForm; + var $highlighted = [], hi, hiOpts = { className: 'search-highlight' }; + var collapse = false, toc_visible = []; + + function init(config) { + // Instantiate search settings + _search = gitbook.storage.get("search", { + engine: config.search.engine || 'lunr', + opts: config.search.options || {}, + }); + }; + + // Save current search settings + function saveSearchSettings() { + gitbook.storage.set("search", _search); + } + + // Use a specific index + function loadIndex(data) { + // [Yihui] In bookdown, I use a character matrix to store the chapter + // content, and the index is dynamically built on the client side. + // Gitbook prebuilds the index data instead: https://github.com/GitbookIO/plugin-search + // We can certainly do that via R packages V8 and jsonlite, but let's + // see how slow it really is before improving it. On the other hand, + // lunr cannot handle non-English text very well, e.g. the default + // tokenizer cannot deal with Chinese text, so we may want to replace + // lunr with a dumb simple text matching approach. + if (_search.engine === 'lunr') { + index = lunr(function () { + this.ref('url'); + this.field('title', { boost: 10 }); + this.field('body'); + }); + data.map(function(item) { + index.add({ + url: item[0], + title: item[1], + body: item[2] + }); + }); + return; + } + fuse = new Fuse(data.map((_data => { + return { + url: _data[0], + title: _data[1], + body: _data[2] + }; + })), Object.assign( + { + includeScore: true, + threshold: 0.1, + ignoreLocation: true, + keys: ["title", "body"] + }, + _search.opts + )); + } + + // Fetch the search index + function fetchIndex() { + return $.getJSON(gitbook.state.basePath+"/search_index.json") + .then(loadIndex); // [Yihui] we need to use this object later + } + + // Search for a term and return results + function search(q) { + let results = []; + switch (_search.engine) { + case 'fuse': + if (!fuse) return; + results = fuse.search(q).map(function(result) { + var parts = result.item.url.split('#'); + return { + path: parts[0], + hash: parts[1] + }; + }); + break; + case 'lunr': + default: + if (!index) return; + results = _.chain(index.search(q)).map(function(result) { + var parts = result.ref.split("#"); + return { + path: parts[0], + hash: parts[1] + }; + }) + .value(); + } + + // [Yihui] Highlight the search keyword on current page + $highlighted = $('.page-inner') + .unhighlight(hiOpts).highlight(q, hiOpts).find('span.search-highlight'); + scrollToHighlighted(0); + + return results; + } + + // [Yihui] Scroll the chapter body to the i-th highlighted string + function scrollToHighlighted(d) { + var n = $highlighted.length; + hi = hi === undefined ? 0 : hi + d; + // navignate to the previous/next page in the search results if reached the top/bottom + var b = hi < 0; + if (d !== 0 && (b || hi >= n)) { + var path = currentPath(), n2 = toc_visible.length; + if (n2 === 0) return; + for (var i = b ? 0 : n2; (b && i < n2) || (!b && i >= 0); i += b ? 1 : -1) { + if (toc_visible.eq(i).data('path') === path) break; + } + i += b ? -1 : 1; + if (i < 0) i = n2 - 1; + if (i >= n2) i = 0; + var lnk = toc_visible.eq(i).find('a[href$=".html"]'); + if (lnk.length) lnk[0].click(); + return; + } + if (n === 0) return; + var $p = $highlighted.eq(hi); + $p[0].scrollIntoView(); + $highlighted.css('background-color', ''); + // an orange background color on the current item and removed later + $p.css('background-color', 'orange'); + setTimeout(function() { + $p.css('background-color', ''); + }, 2000); + } + + function currentPath() { + var href = window.location.pathname; + href = href.substr(href.lastIndexOf('/') + 1); + return href === '' ? 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