Analysis of Deviance Table
diff --git a/bs/.development/Regression.qmd b/bs/.development/004GeneralisedLinearModel.qmd
similarity index 95%
rename from bs/.development/Regression.qmd
rename to bs/.development/004GeneralisedLinearModel.qmd
index ef57cf6..a93c4f4 100644
--- a/bs/.development/Regression.qmd
+++ b/bs/.development/004GeneralisedLinearModel.qmd
@@ -3,7 +3,7 @@ title: "Regression: maximum likelihood by hand"
output: html_document
---
-# Maximum likelihood estimation
+# Regression & Maximum likelihood estimation
We calculate for each entry of the response variable the probability that this value
is taken from a distribution with specific parameters. For example we can calculate the
@@ -13,6 +13,9 @@ This sum is called log-likelihood. The goal is to maximize this sum.
```{r Data, include = TRUE}
+library(FAwR)
+library(ggplot2)
+library(MASS)
data(InsectSprays)
summary(InsectSprays)
head(InsectSprays)
diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap-icons.css b/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap-icons.css
new file mode 100644
index 0000000..94f1940
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap-icons.css
@@ -0,0 +1,2018 @@
+@font-face {
+ font-display: block;
+ font-family: "bootstrap-icons";
+ src:
+url("./bootstrap-icons.woff?2ab2cbbe07fcebb53bdaa7313bb290f2") format("woff");
+}
+
+.bi::before,
+[class^="bi-"]::before,
+[class*=" bi-"]::before {
+ display: inline-block;
+ font-family: bootstrap-icons !important;
+ font-style: normal;
+ font-weight: normal !important;
+ font-variant: normal;
+ text-transform: none;
+ line-height: 1;
+ vertical-align: -.125em;
+ -webkit-font-smoothing: antialiased;
+ -moz-osx-font-smoothing: grayscale;
+}
+
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diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap-icons.woff b/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap-icons.woff
new file mode 100644
index 0000000..18d21d4
Binary files /dev/null and b/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap-icons.woff differ
diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap.min.css b/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap.min.css
new file mode 100644
index 0000000..a87b434
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap.min.css
@@ -0,0 +1,10 @@
+/*!
+ * Bootstrap v5.1.3 (https://getbootstrap.com/)
+ * Copyright 2011-2021 The Bootstrap Authors
+ * Copyright 2011-2021 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
+ */:root{--bs-blue: #0d6efd;--bs-indigo: #6610f2;--bs-purple: #6f42c1;--bs-pink: #d63384;--bs-red: #dc3545;--bs-orange: #fd7e14;--bs-yellow: #ffc107;--bs-green: #198754;--bs-teal: #20c997;--bs-cyan: #0dcaf0;--bs-white: #ffffff;--bs-gray: #6c757d;--bs-gray-dark: #343a40;--bs-gray-100: #f8f9fa;--bs-gray-200: #e9ecef;--bs-gray-300: #dee2e6;--bs-gray-400: #ced4da;--bs-gray-500: #adb5bd;--bs-gray-600: #6c757d;--bs-gray-700: #495057;--bs-gray-800: #343a40;--bs-gray-900: #212529;--bs-default: #dee2e6;--bs-primary: #0d6efd;--bs-secondary: #6c757d;--bs-success: #198754;--bs-info: #0dcaf0;--bs-warning: #ffc107;--bs-danger: #dc3545;--bs-light: #f8f9fa;--bs-dark: #212529;--bs-default-rgb: 222, 226, 230;--bs-primary-rgb: 13, 110, 253;--bs-secondary-rgb: 108, 117, 125;--bs-success-rgb: 25, 135, 84;--bs-info-rgb: 13, 202, 240;--bs-warning-rgb: 255, 193, 7;--bs-danger-rgb: 220, 53, 69;--bs-light-rgb: 248, 249, 250;--bs-dark-rgb: 33, 37, 41;--bs-white-rgb: 255, 255, 255;--bs-black-rgb: 0, 0, 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diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap.min.js b/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap.min.js
new file mode 100644
index 0000000..cc0a255
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap.min.js
@@ -0,0 +1,7 @@
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0===i&&(i={x:0,y:0}),{top:t.top-e.height-i.y,right:t.right-e.width+i.x,bottom:t.bottom-e.height+i.y,left:t.left-e.width-i.x}}function Se(t){return[mt,_t,gt,bt].some((function(e){return t[e]>=0}))}const Ne={name:"hide",enabled:!0,phase:"main",requiresIfExists:["preventOverflow"],fn:function(t){var e=t.state,i=t.name,n=e.rects.reference,s=e.rects.popper,o=e.modifiersData.preventOverflow,r=ke(e,{elementContext:"reference"}),a=ke(e,{altBoundary:!0}),l=De(r,n),c=De(a,s,o),h=Se(l),d=Se(c);e.modifiersData[i]={referenceClippingOffsets:l,popperEscapeOffsets:c,isReferenceHidden:h,hasPopperEscaped:d},e.attributes.popper=Object.assign({},e.attributes.popper,{"data-popper-reference-hidden":h,"data-popper-escaped":d})}},Ie={name:"offset",enabled:!0,phase:"main",requires:["popperOffsets"],fn:function(t){var e=t.state,i=t.options,n=t.name,s=i.offset,o=void 0===s?[0,0]:s,r=Lt.reduce((function(t,i){return t[i]=function(t,e,i){var n=Ut(t),s=[bt,mt].indexOf(n)>=0?-1:1,o="function"==typeof 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0===p?0:p,g=ke(e,{boundary:l,rootBoundary:c,padding:d,altBoundary:h}),_=Ut(e.placement),b=ce(e.placement),v=!b,y=ee(_),w="x"===y?"y":"x",E=e.modifiersData.popperOffsets,A=e.rects.reference,T=e.rects.popper,O="function"==typeof m?m(Object.assign({},e.rects,{placement:e.placement})):m,C={x:0,y:0};if(E){if(o||a){var k="y"===y?mt:bt,L="y"===y?gt:_t,x="y"===y?"height":"width",D=E[y],S=E[y]+g[k],N=E[y]-g[L],I=f?-T[x]/2:0,P=b===wt?A[x]:T[x],j=b===wt?-T[x]:-A[x],M=e.elements.arrow,H=f&&M?Kt(M):{width:0,height:0},B=e.modifiersData["arrow#persistent"]?e.modifiersData["arrow#persistent"].padding:{top:0,right:0,bottom:0,left:0},R=B[k],W=B[L],$=oe(0,A[x],H[x]),z=v?A[x]/2-I-$-R-O:P-$-R-O,q=v?-A[x]/2+I+$+W+O:j+$+W+O,F=e.elements.arrow&&te(e.elements.arrow),U=F?"y"===y?F.clientTop||0:F.clientLeft||0:0,V=e.modifiersData.offset?e.modifiersData.offset[e.placement][y]:0,K=E[y]+z-V-U,X=E[y]+q-V;if(o){var Y=oe(f?ne(S,K):S,D,f?ie(N,X):N);E[y]=Y,C[y]=Y-D}if(a){var Q="x"===y?mt:bt,G="x"===y?gt:_t,Z=E[w],J=Z+g[Q],tt=Z-g[G],et=oe(f?ne(J,K):J,Z,f?ie(tt,X):tt);E[w]=et,C[w]=et-Z}}e.modifiersData[n]=C}},requiresIfExists:["offset"]};function Me(t,e,i){void 0===i&&(i=!1);var n=zt(e);zt(e)&&function(t){var e=t.getBoundingClientRect();e.width,t.offsetWidth,e.height,t.offsetHeight}(e);var s,o,r=Gt(e),a=Vt(t),l={scrollLeft:0,scrollTop:0},c={x:0,y:0};return(n||!n&&!i)&&(("body"!==Rt(e)||we(r))&&(l=(s=e)!==Wt(s)&&zt(s)?{scrollLeft:(o=s).scrollLeft,scrollTop:o.scrollTop}:ve(s)),zt(e)?((c=Vt(e)).x+=e.clientLeft,c.y+=e.clientTop):r&&(c.x=ye(r))),{x:a.left+l.scrollLeft-c.x,y:a.top+l.scrollTop-c.y,width:a.width,height:a.height}}function He(t){var e=new Map,i=new Set,n=[];function s(t){i.add(t.name),[].concat(t.requires||[],t.requiresIfExists||[]).forEach((function(t){if(!i.has(t)){var n=e.get(t);n&&s(n)}})),n.push(t)}return t.forEach((function(t){e.set(t.name,t)})),t.forEach((function(t){i.has(t.name)||s(t)})),n}var Be={placement:"bottom",modifiers:[],strategy:"absolute"};function Re(){for(var t=arguments.length,e=new Array(t),i=0;ij.on(t,"mouseover",d))),this._element.focus(),this._element.setAttribute("aria-expanded",!0),this._menu.classList.add(Je),this._element.classList.add(Je),j.trigger(this._element,"shown.bs.dropdown",t)}hide(){if(c(this._element)||!this._isShown(this._menu))return;const t={relatedTarget:this._element};this._completeHide(t)}dispose(){this._popper&&this._popper.destroy(),super.dispose()}update(){this._inNavbar=this._detectNavbar(),this._popper&&this._popper.update()}_completeHide(t){j.trigger(this._element,"hide.bs.dropdown",t).defaultPrevented||("ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>j.off(t,"mouseover",d))),this._popper&&this._popper.destroy(),this._menu.classList.remove(Je),this._element.classList.remove(Je),this._element.setAttribute("aria-expanded","false"),U.removeDataAttribute(this._menu,"popper"),j.trigger(this._element,"hidden.bs.dropdown",t))}_getConfig(t){if(t={...this.constructor.Default,...U.getDataAttributes(this._element),...t},a(Ue,t,this.constructor.DefaultType),"object"==typeof t.reference&&!o(t.reference)&&"function"!=typeof t.reference.getBoundingClientRect)throw new TypeError(`${Ue.toUpperCase()}: Option "reference" provided type "object" without a required "getBoundingClientRect" method.`);return t}_createPopper(t){if(void 0===Fe)throw new TypeError("Bootstrap's dropdowns require Popper (https://popper.js.org)");let e=this._element;"parent"===this._config.reference?e=t:o(this._config.reference)?e=r(this._config.reference):"object"==typeof this._config.reference&&(e=this._config.reference);const i=this._getPopperConfig(),n=i.modifiers.find((t=>"applyStyles"===t.name&&!1===t.enabled));this._popper=qe(e,this._menu,i),n&&U.setDataAttribute(this._menu,"popper","static")}_isShown(t=this._element){return t.classList.contains(Je)}_getMenuElement(){return V.next(this._element,ei)[0]}_getPlacement(){const t=this._element.parentNode;if(t.classList.contains("dropend"))return ri;if(t.classList.contains("dropstart"))return ai;const e="end"===getComputedStyle(this._menu).getPropertyValue("--bs-position").trim();return t.classList.contains("dropup")?e?ni:ii:e?oi:si}_detectNavbar(){return null!==this._element.closest(".navbar")}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_getPopperConfig(){const t={placement:this._getPlacement(),modifiers:[{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"offset",options:{offset:this._getOffset()}}]};return"static"===this._config.display&&(t.modifiers=[{name:"applyStyles",enabled:!1}]),{...t,..."function"==typeof this._config.popperConfig?this._config.popperConfig(t):this._config.popperConfig}}_selectMenuItem({key:t,target:e}){const i=V.find(".dropdown-menu .dropdown-item:not(.disabled):not(:disabled)",this._menu).filter(l);i.length&&v(i,e,t===Ye,!i.includes(e)).focus()}static jQueryInterface(t){return this.each((function(){const e=hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}static clearMenus(t){if(t&&(2===t.button||"keyup"===t.type&&"Tab"!==t.key))return;const e=V.find(ti);for(let i=0,n=e.length;ie+t)),this._setElementAttributes(di,"paddingRight",(e=>e+t)),this._setElementAttributes(ui,"marginRight",(e=>e-t))}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t)[e];t.style[e]=`${i(Number.parseFloat(s))}px`}))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,"paddingRight"),this._resetElementAttributes(di,"paddingRight"),this._resetElementAttributes(ui,"marginRight")}_saveInitialAttribute(t,e){const i=t.style[e];i&&U.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=U.getDataAttribute(t,e);void 0===i?t.style.removeProperty(e):(U.removeDataAttribute(t,e),t.style[e]=i)}))}_applyManipulationCallback(t,e){o(t)?e(t):V.find(t,this._element).forEach(e)}isOverflowing(){return this.getWidth()>0}}const pi={className:"modal-backdrop",isVisible:!0,isAnimated:!1,rootElement:"body",clickCallback:null},mi={className:"string",isVisible:"boolean",isAnimated:"boolean",rootElement:"(element|string)",clickCallback:"(function|null)"},gi="show",_i="mousedown.bs.backdrop";class bi{constructor(t){this._config=this._getConfig(t),this._isAppended=!1,this._element=null}show(t){this._config.isVisible?(this._append(),this._config.isAnimated&&u(this._getElement()),this._getElement().classList.add(gi),this._emulateAnimation((()=>{_(t)}))):_(t)}hide(t){this._config.isVisible?(this._getElement().classList.remove(gi),this._emulateAnimation((()=>{this.dispose(),_(t)}))):_(t)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_getConfig(t){return(t={...pi,..."object"==typeof t?t:{}}).rootElement=r(t.rootElement),a("backdrop",t,mi),t}_append(){this._isAppended||(this._config.rootElement.append(this._getElement()),j.on(this._getElement(),_i,(()=>{_(this._config.clickCallback)})),this._isAppended=!0)}dispose(){this._isAppended&&(j.off(this._element,_i),this._element.remove(),this._isAppended=!1)}_emulateAnimation(t){b(t,this._getElement(),this._config.isAnimated)}}const vi={trapElement:null,autofocus:!0},yi={trapElement:"element",autofocus:"boolean"},wi=".bs.focustrap",Ei="backward";class Ai{constructor(t){this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}activate(){const{trapElement:t,autofocus:e}=this._config;this._isActive||(e&&t.focus(),j.off(document,wi),j.on(document,"focusin.bs.focustrap",(t=>this._handleFocusin(t))),j.on(document,"keydown.tab.bs.focustrap",(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,j.off(document,wi))}_handleFocusin(t){const{target:e}=t,{trapElement:i}=this._config;if(e===document||e===i||i.contains(e))return;const n=V.focusableChildren(i);0===n.length?i.focus():this._lastTabNavDirection===Ei?n[n.length-1].focus():n[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?Ei:"forward")}_getConfig(t){return t={...vi,..."object"==typeof t?t:{}},a("focustrap",t,yi),t}}const Ti="modal",Oi="Escape",Ci={backdrop:!0,keyboard:!0,focus:!0},ki={backdrop:"(boolean|string)",keyboard:"boolean",focus:"boolean"},Li="hidden.bs.modal",xi="show.bs.modal",Di="resize.bs.modal",Si="click.dismiss.bs.modal",Ni="keydown.dismiss.bs.modal",Ii="mousedown.dismiss.bs.modal",Pi="modal-open",ji="show",Mi="modal-static";class Hi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._dialog=V.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._ignoreBackdropClick=!1,this._isTransitioning=!1,this._scrollBar=new fi}static get Default(){return Ci}static get NAME(){return Ti}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||j.trigger(this._element,xi,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isAnimated()&&(this._isTransitioning=!0),this._scrollBar.hide(),document.body.classList.add(Pi),this._adjustDialog(),this._setEscapeEvent(),this._setResizeEvent(),j.on(this._dialog,Ii,(()=>{j.one(this._element,"mouseup.dismiss.bs.modal",(t=>{t.target===this._element&&(this._ignoreBackdropClick=!0)}))})),this._showBackdrop((()=>this._showElement(t))))}hide(){if(!this._isShown||this._isTransitioning)return;if(j.trigger(this._element,"hide.bs.modal").defaultPrevented)return;this._isShown=!1;const t=this._isAnimated();t&&(this._isTransitioning=!0),this._setEscapeEvent(),this._setResizeEvent(),this._focustrap.deactivate(),this._element.classList.remove(ji),j.off(this._element,Si),j.off(this._dialog,Ii),this._queueCallback((()=>this._hideModal()),this._element,t)}dispose(){[window,this._dialog].forEach((t=>j.off(t,".bs.modal"))),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new bi({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_getConfig(t){return t={...Ci,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Ti,t,ki),t}_showElement(t){const e=this._isAnimated(),i=V.findOne(".modal-body",this._dialog);this._element.parentNode&&this._element.parentNode.nodeType===Node.ELEMENT_NODE||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0,i&&(i.scrollTop=0),e&&u(this._element),this._element.classList.add(ji),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,j.trigger(this._element,"shown.bs.modal",{relatedTarget:t})}),this._dialog,e)}_setEscapeEvent(){this._isShown?j.on(this._element,Ni,(t=>{this._config.keyboard&&t.key===Oi?(t.preventDefault(),this.hide()):this._config.keyboard||t.key!==Oi||this._triggerBackdropTransition()})):j.off(this._element,Ni)}_setResizeEvent(){this._isShown?j.on(window,Di,(()=>this._adjustDialog())):j.off(window,Di)}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(Pi),this._resetAdjustments(),this._scrollBar.reset(),j.trigger(this._element,Li)}))}_showBackdrop(t){j.on(this._element,Si,(t=>{this._ignoreBackdropClick?this._ignoreBackdropClick=!1:t.target===t.currentTarget&&(!0===this._config.backdrop?this.hide():"static"===this._config.backdrop&&this._triggerBackdropTransition())})),this._backdrop.show(t)}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(j.trigger(this._element,"hidePrevented.bs.modal").defaultPrevented)return;const{classList:t,scrollHeight:e,style:i}=this._element,n=e>document.documentElement.clientHeight;!n&&"hidden"===i.overflowY||t.contains(Mi)||(n||(i.overflowY="hidden"),t.add(Mi),this._queueCallback((()=>{t.remove(Mi),n||this._queueCallback((()=>{i.overflowY=""}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;(!i&&t&&!m()||i&&!t&&m())&&(this._element.style.paddingLeft=`${e}px`),(i&&!t&&!m()||!i&&t&&m())&&(this._element.style.paddingRight=`${e}px`)}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=Hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}j.on(document,"click.bs.modal.data-api",'[data-bs-toggle="modal"]',(function(t){const e=n(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),j.one(e,xi,(t=>{t.defaultPrevented||j.one(e,Li,(()=>{l(this)&&this.focus()}))}));const i=V.findOne(".modal.show");i&&Hi.getInstance(i).hide(),Hi.getOrCreateInstance(e).toggle(this)})),R(Hi),g(Hi);const Bi="offcanvas",Ri={backdrop:!0,keyboard:!0,scroll:!1},Wi={backdrop:"boolean",keyboard:"boolean",scroll:"boolean"},$i="show",zi=".offcanvas.show",qi="hidden.bs.offcanvas";class Fi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get NAME(){return Bi}static get Default(){return Ri}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||j.trigger(this._element,"show.bs.offcanvas",{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._element.style.visibility="visible",this._backdrop.show(),this._config.scroll||(new fi).hide(),this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add($i),this._queueCallback((()=>{this._config.scroll||this._focustrap.activate(),j.trigger(this._element,"shown.bs.offcanvas",{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(j.trigger(this._element,"hide.bs.offcanvas").defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.remove($i),this._backdrop.hide(),this._queueCallback((()=>{this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._element.style.visibility="hidden",this._config.scroll||(new fi).reset(),j.trigger(this._element,qi)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_getConfig(t){return t={...Ri,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Bi,t,Wi),t}_initializeBackDrop(){return new bi({className:"offcanvas-backdrop",isVisible:this._config.backdrop,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:()=>this.hide()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_addEventListeners(){j.on(this._element,"keydown.dismiss.bs.offcanvas",(t=>{this._config.keyboard&&"Escape"===t.key&&this.hide()}))}static jQueryInterface(t){return this.each((function(){const e=Fi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}j.on(document,"click.bs.offcanvas.data-api",'[data-bs-toggle="offcanvas"]',(function(t){const e=n(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),c(this))return;j.one(e,qi,(()=>{l(this)&&this.focus()}));const i=V.findOne(zi);i&&i!==e&&Fi.getInstance(i).hide(),Fi.getOrCreateInstance(e).toggle(this)})),j.on(window,"load.bs.offcanvas.data-api",(()=>V.find(zi).forEach((t=>Fi.getOrCreateInstance(t).show())))),R(Fi),g(Fi);const Ui=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Vi=/^(?:(?:https?|mailto|ftp|tel|file|sms):|[^#&/:?]*(?:[#/?]|$))/i,Ki=/^data:(?:image\/(?:bmp|gif|jpeg|jpg|png|tiff|webp)|video\/(?:mpeg|mp4|ogg|webm)|audio\/(?:mp3|oga|ogg|opus));base64,[\d+/a-z]+=*$/i,Xi=(t,e)=>{const i=t.nodeName.toLowerCase();if(e.includes(i))return!Ui.has(i)||Boolean(Vi.test(t.nodeValue)||Ki.test(t.nodeValue));const n=e.filter((t=>t instanceof RegExp));for(let t=0,e=n.length;t{Xi(t,r)||i.removeAttribute(t.nodeName)}))}return n.body.innerHTML}const Qi="tooltip",Gi=new Set(["sanitize","allowList","sanitizeFn"]),Zi={animation:"boolean",template:"string",title:"(string|element|function)",trigger:"string",delay:"(number|object)",html:"boolean",selector:"(string|boolean)",placement:"(string|function)",offset:"(array|string|function)",container:"(string|element|boolean)",fallbackPlacements:"array",boundary:"(string|element)",customClass:"(string|function)",sanitize:"boolean",sanitizeFn:"(null|function)",allowList:"object",popperConfig:"(null|object|function)"},Ji={AUTO:"auto",TOP:"top",RIGHT:m()?"left":"right",BOTTOM:"bottom",LEFT:m()?"right":"left"},tn={animation:!0,template:'',trigger:"hover focus",title:"",delay:0,html:!1,selector:!1,placement:"top",offset:[0,0],container:!1,fallbackPlacements:["top","right","bottom","left"],boundary:"clippingParents",customClass:"",sanitize:!0,sanitizeFn:null,allowList:{"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},popperConfig:null},en={HIDE:"hide.bs.tooltip",HIDDEN:"hidden.bs.tooltip",SHOW:"show.bs.tooltip",SHOWN:"shown.bs.tooltip",INSERTED:"inserted.bs.tooltip",CLICK:"click.bs.tooltip",FOCUSIN:"focusin.bs.tooltip",FOCUSOUT:"focusout.bs.tooltip",MOUSEENTER:"mouseenter.bs.tooltip",MOUSELEAVE:"mouseleave.bs.tooltip"},nn="fade",sn="show",on="show",rn="out",an=".tooltip-inner",ln=".modal",cn="hide.bs.modal",hn="hover",dn="focus";class un extends B{constructor(t,e){if(void 0===Fe)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t),this._isEnabled=!0,this._timeout=0,this._hoverState="",this._activeTrigger={},this._popper=null,this._config=this._getConfig(e),this.tip=null,this._setListeners()}static get Default(){return tn}static get NAME(){return Qi}static get Event(){return en}static get DefaultType(){return Zi}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(t){if(this._isEnabled)if(t){const e=this._initializeOnDelegatedTarget(t);e._activeTrigger.click=!e._activeTrigger.click,e._isWithActiveTrigger()?e._enter(null,e):e._leave(null,e)}else{if(this.getTipElement().classList.contains(sn))return void 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t=this.getTipElement();if(j.trigger(this._element,this.constructor.Event.HIDE).defaultPrevented)return;t.classList.remove(sn),"ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>j.off(t,"mouseover",d))),this._activeTrigger.click=!1,this._activeTrigger.focus=!1,this._activeTrigger.hover=!1;const e=this.tip.classList.contains(nn);this._queueCallback((()=>{this._isWithActiveTrigger()||(this._hoverState!==on&&t.remove(),this._cleanTipClass(),this._element.removeAttribute("aria-describedby"),j.trigger(this._element,this.constructor.Event.HIDDEN),this._disposePopper())}),this.tip,e),this._hoverState=""}update(){null!==this._popper&&this._popper.update()}isWithContent(){return Boolean(this.getTitle())}getTipElement(){if(this.tip)return this.tip;const t=document.createElement("div");t.innerHTML=this._config.template;const e=t.children[0];return this.setContent(e),e.classList.remove(nn,sn),this.tip=e,this.tip}setContent(t){this._sanitizeAndSetContent(t,this.getTitle(),an)}_sanitizeAndSetContent(t,e,i){const n=V.findOne(i,t);e||!n?this.setElementContent(n,e):n.remove()}setElementContent(t,e){if(null!==t)return o(e)?(e=r(e),void(this._config.html?e.parentNode!==t&&(t.innerHTML="",t.append(e)):t.textContent=e.textContent)):void(this._config.html?(this._config.sanitize&&(e=Yi(e,this._config.allowList,this._config.sanitizeFn)),t.innerHTML=e):t.textContent=e)}getTitle(){const t=this._element.getAttribute("data-bs-original-title")||this._config.title;return this._resolvePossibleFunction(t)}updateAttachment(t){return"right"===t?"end":"left"===t?"start":t}_initializeOnDelegatedTarget(t,e){return e||this.constructor.getOrCreateInstance(t.delegateTarget,this._getDelegateConfig())}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof 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t in this._activeTrigger)if(this._activeTrigger[t])return!0;return!1}_getConfig(t){const e=U.getDataAttributes(this._element);return Object.keys(e).forEach((t=>{Gi.has(t)&&delete e[t]})),(t={...this.constructor.Default,...e,..."object"==typeof t&&t?t:{}}).container=!1===t.container?document.body:r(t.container),"number"==typeof t.delay&&(t.delay={show:t.delay,hide:t.delay}),"number"==typeof t.title&&(t.title=t.title.toString()),"number"==typeof t.content&&(t.content=t.content.toString()),a(Qi,t,this.constructor.DefaultType),t.sanitize&&(t.template=Yi(t.template,t.allowList,t.sanitizeFn)),t}_getDelegateConfig(){const t={};for(const e in this._config)this.constructor.Default[e]!==this._config[e]&&(t[e]=this._config[e]);return t}_cleanTipClass(){const t=this.getTipElement(),e=new RegExp(`(^|\\s)${this._getBasicClassPrefix()}\\S+`,"g"),i=t.getAttribute("class").match(e);null!==i&&i.length>0&&i.map((t=>t.trim())).forEach((e=>t.classList.remove(e)))}_getBasicClassPrefix(){return"bs-tooltip"}_handlePopperPlacementChange(t){const{state:e}=t;e&&(this.tip=e.elements.popper,this._cleanTipClass(),this._addAttachmentClass(this._getAttachment(e.placement)))}_disposePopper(){this._popper&&(this._popper.destroy(),this._popper=null)}static jQueryInterface(t){return this.each((function(){const e=un.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}g(un);const fn={...un.Default,placement:"right",offset:[0,8],trigger:"click",content:"",template:''},pn={...un.DefaultType,content:"(string|element|function)"},mn={HIDE:"hide.bs.popover",HIDDEN:"hidden.bs.popover",SHOW:"show.bs.popover",SHOWN:"shown.bs.popover",INSERTED:"inserted.bs.popover",CLICK:"click.bs.popover",FOCUSIN:"focusin.bs.popover",FOCUSOUT:"focusout.bs.popover",MOUSEENTER:"mouseenter.bs.popover",MOUSELEAVE:"mouseleave.bs.popover"};class gn extends un{static get Default(){return fn}static get NAME(){return"popover"}static get Event(){return mn}static get DefaultType(){return pn}isWithContent(){return this.getTitle()||this._getContent()}setContent(t){this._sanitizeAndSetContent(t,this.getTitle(),".popover-header"),this._sanitizeAndSetContent(t,this._getContent(),".popover-body")}_getContent(){return this._resolvePossibleFunction(this._config.content)}_getBasicClassPrefix(){return"bs-popover"}static jQueryInterface(t){return this.each((function(){const 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t=this._scrollElement===this._scrollElement.window?"offset":En,e="auto"===this._config.method?t:this._config.method,n=e===En?this._getScrollTop():0;this._offsets=[],this._targets=[],this._scrollHeight=this._getScrollHeight(),V.find(wn,this._config.target).map((t=>{const s=i(t),o=s?V.findOne(s):null;if(o){const t=o.getBoundingClientRect();if(t.width||t.height)return[U[e](o).top+n,s]}return null})).filter((t=>t)).sort(((t,e)=>t[0]-e[0])).forEach((t=>{this._offsets.push(t[0]),this._targets.push(t[1])}))}dispose(){j.off(this._scrollElement,".bs.scrollspy"),super.dispose()}_getConfig(t){return(t={...bn,...U.getDataAttributes(this._element),..."object"==typeof t&&t?t:{}}).target=r(t.target)||document.documentElement,a(_n,t,vn),t}_getScrollTop(){return this._scrollElement===window?this._scrollElement.pageYOffset:this._scrollElement.scrollTop}_getScrollHeight(){return this._scrollElement.scrollHeight||Math.max(document.body.scrollHeight,document.documentElement.scrollHeight)}_getOffsetHeight(){return this._scrollElement===window?window.innerHeight:this._scrollElement.getBoundingClientRect().height}_process(){const t=this._getScrollTop()+this._config.offset,e=this._getScrollHeight(),i=this._config.offset+e-this._getOffsetHeight();if(this._scrollHeight!==e&&this.refresh(),t>=i){const t=this._targets[this._targets.length-1];this._activeTarget!==t&&this._activate(t)}else{if(this._activeTarget&&t0)return this._activeTarget=null,void this._clear();for(let e=this._offsets.length;e--;)this._activeTarget!==this._targets[e]&&t>=this._offsets[e]&&(void 0===this._offsets[e+1]||t`${e}[data-bs-target="${t}"],${e}[href="${t}"]`)),i=V.findOne(e.join(","),this._config.target);i.classList.add(yn),i.classList.contains("dropdown-item")?V.findOne(".dropdown-toggle",i.closest(".dropdown")).classList.add(yn):V.parents(i,".nav, .list-group").forEach((t=>{V.prev(t,".nav-link, .list-group-item").forEach((t=>t.classList.add(yn))),V.prev(t,".nav-item").forEach((t=>{V.children(t,".nav-link").forEach((t=>t.classList.add(yn)))}))})),j.trigger(this._scrollElement,"activate.bs.scrollspy",{relatedTarget:t})}_clear(){V.find(wn,this._config.target).filter((t=>t.classList.contains(yn))).forEach((t=>t.classList.remove(yn)))}static jQueryInterface(t){return this.each((function(){const e=An.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}j.on(window,"load.bs.scrollspy.data-api",(()=>{V.find('[data-bs-spy="scroll"]').forEach((t=>new An(t)))})),g(An);const Tn="active",On="fade",Cn="show",kn=".active",Ln=":scope > li > .active";class xn extends B{static get NAME(){return"tab"}show(){if(this._element.parentNode&&this._element.parentNode.nodeType===Node.ELEMENT_NODE&&this._element.classList.contains(Tn))return;let t;const e=n(this._element),i=this._element.closest(".nav, .list-group");if(i){const e="UL"===i.nodeName||"OL"===i.nodeName?Ln:kn;t=V.find(e,i),t=t[t.length-1]}const s=t?j.trigger(t,"hide.bs.tab",{relatedTarget:this._element}):null;if(j.trigger(this._element,"show.bs.tab",{relatedTarget:t}).defaultPrevented||null!==s&&s.defaultPrevented)return;this._activate(this._element,i);const o=()=>{j.trigger(t,"hidden.bs.tab",{relatedTarget:this._element}),j.trigger(this._element,"shown.bs.tab",{relatedTarget:t})};e?this._activate(e,e.parentNode,o):o()}_activate(t,e,i){const n=(!e||"UL"!==e.nodeName&&"OL"!==e.nodeName?V.children(e,kn):V.find(Ln,e))[0],s=i&&n&&n.classList.contains(On),o=()=>this._transitionComplete(t,n,i);n&&s?(n.classList.remove(Cn),this._queueCallback(o,t,!0)):o()}_transitionComplete(t,e,i){if(e){e.classList.remove(Tn);const t=V.findOne(":scope > .dropdown-menu 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Dn="toast",Sn="hide",Nn="show",In="showing",Pn={animation:"boolean",autohide:"boolean",delay:"number"},jn={animation:!0,autohide:!0,delay:5e3};class Mn extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._timeout=null,this._hasMouseInteraction=!1,this._hasKeyboardInteraction=!1,this._setListeners()}static get DefaultType(){return Pn}static get Default(){return jn}static get NAME(){return Dn}show(){j.trigger(this._element,"show.bs.toast").defaultPrevented||(this._clearTimeout(),this._config.animation&&this._element.classList.add("fade"),this._element.classList.remove(Sn),u(this._element),this._element.classList.add(Nn),this._element.classList.add(In),this._queueCallback((()=>{this._element.classList.remove(In),j.trigger(this._element,"shown.bs.toast"),this._maybeScheduleHide()}),this._element,this._config.animation))}hide(){this._element.classList.contains(Nn)&&(j.trigger(this._element,"hide.bs.toast").defaultPrevented||(this._element.classList.add(In),this._queueCallback((()=>{this._element.classList.add(Sn),this._element.classList.remove(In),this._element.classList.remove(Nn),j.trigger(this._element,"hidden.bs.toast")}),this._element,this._config.animation)))}dispose(){this._clearTimeout(),this._element.classList.contains(Nn)&&this._element.classList.remove(Nn),super.dispose()}_getConfig(t){return t={...jn,...U.getDataAttributes(this._element),..."object"==typeof t&&t?t:{}},a(Dn,t,this.constructor.DefaultType),t}_maybeScheduleHide(){this._config.autohide&&(this._hasMouseInteraction||this._hasKeyboardInteraction||(this._timeout=setTimeout((()=>{this.hide()}),this._config.delay)))}_onInteraction(t,e){switch(t.type){case"mouseover":case"mouseout":this._hasMouseInteraction=e;break;case"focusin":case"focusout":this._hasKeyboardInteraction=e}if(e)return void this._clearTimeout();const i=t.relatedTarget;this._element===i||this._element.contains(i)||this._maybeScheduleHide()}_setListeners(){j.on(this._element,"mouseover.bs.toast",(t=>this._onInteraction(t,!0))),j.on(this._element,"mouseout.bs.toast",(t=>this._onInteraction(t,!1))),j.on(this._element,"focusin.bs.toast",(t=>this._onInteraction(t,!0))),j.on(this._element,"focusout.bs.toast",(t=>this._onInteraction(t,!1)))}_clearTimeout(){clearTimeout(this._timeout),this._timeout=null}static jQueryInterface(t){return this.each((function(){const e=Mn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}return R(Mn),g(Mn),{Alert:W,Button:z,Carousel:st,Collapse:pt,Dropdown:hi,Modal:Hi,Offcanvas:Fi,Popover:gn,ScrollSpy:An,Tab:xn,Toast:Mn,Tooltip:un}}));
+//# sourceMappingURL=bootstrap.bundle.min.js.map
\ No newline at end of file
diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/clipboard/clipboard.min.js b/bs/.development/004GeneralisedLinearModel_files/libs/clipboard/clipboard.min.js
new file mode 100644
index 0000000..1103f81
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/clipboard/clipboard.min.js
@@ -0,0 +1,7 @@
+/*!
+ * clipboard.js v2.0.11
+ * https://clipboardjs.com/
+ *
+ * Licensed MIT © Zeno Rocha
+ */
+!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return b}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),r=n.n(e);function c(t){try{return document.execCommand(t)}catch(t){return}}var a=function(t){t=r()(t);return c("cut"),t};function o(t,e){var n,o,t=(n=t,o="rtl"===document.documentElement.getAttribute("dir"),(t=document.createElement("textarea")).style.fontSize="12pt",t.style.border="0",t.style.padding="0",t.style.margin="0",t.style.position="absolute",t.style[o?"right":"left"]="-9999px",o=window.pageYOffset||document.documentElement.scrollTop,t.style.top="".concat(o,"px"),t.setAttribute("readonly",""),t.value=n,t);return e.container.appendChild(t),e=r()(t),c("copy"),t.remove(),e}var f=function(t){var e=1.anchorjs-link,.anchorjs-link:focus{opacity:1}",u.sheet.cssRules.length),u.sheet.insertRule("[data-anchorjs-icon]::after{content:attr(data-anchorjs-icon)}",u.sheet.cssRules.length),u.sheet.insertRule('@font-face{font-family:anchorjs-icons;src:url(data:n/a;base64,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) format("truetype")}',u.sheet.cssRules.length)),u=document.querySelectorAll("[id]"),t=[].map.call(u,function(A){return A.id}),i=0;i\]./()*\\\n\t\b\v\u00A0]/g,"-").replace(/-{2,}/g,"-").substring(0,this.options.truncate).replace(/^-+|-+$/gm,"").toLowerCase()},this.hasAnchorJSLink=function(A){var e=A.firstChild&&-1<(" "+A.firstChild.className+" ").indexOf(" anchorjs-link "),A=A.lastChild&&-1<(" "+A.lastChild.className+" ").indexOf(" anchorjs-link ");return e||A||!1}}});
+// @license-end
\ No newline at end of file
diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/popper.min.js b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/popper.min.js
new file mode 100644
index 0000000..2269d66
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/popper.min.js
@@ -0,0 +1,6 @@
+/**
+ * @popperjs/core v2.11.4 - MIT License
+ */
+
+!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?t(exports):"function"==typeof define&&define.amd?define(["exports"],t):t((e="undefined"!=typeof globalThis?globalThis:e||self).Popper={})}(this,(function(e){"use strict";function t(e){if(null==e)return window;if("[object Window]"!==e.toString()){var t=e.ownerDocument;return t&&t.defaultView||window}return e}function n(e){return e instanceof t(e).Element||e instanceof Element}function r(e){return e instanceof t(e).HTMLElement||e instanceof HTMLElement}function o(e){return"undefined"!=typeof ShadowRoot&&(e instanceof t(e).ShadowRoot||e instanceof ShadowRoot)}var i=Math.max,a=Math.min,s=Math.round;function f(e,t){void 0===t&&(t=!1);var n=e.getBoundingClientRect(),o=1,i=1;if(r(e)&&t){var a=e.offsetHeight,f=e.offsetWidth;f>0&&(o=s(n.width)/f||1),a>0&&(i=s(n.height)/a||1)}return{width:n.width/o,height:n.height/i,top:n.top/i,right:n.right/o,bottom:n.bottom/i,left:n.left/o,x:n.left/o,y:n.top/i}}function c(e){var 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+
diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/quarto-syntax-highlighting.css b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/quarto-syntax-highlighting.css
new file mode 100644
index 0000000..d9fd98f
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/quarto-syntax-highlighting.css
@@ -0,0 +1,203 @@
+/* quarto syntax highlight colors */
+:root {
+ --quarto-hl-ot-color: #003B4F;
+ --quarto-hl-at-color: #657422;
+ --quarto-hl-ss-color: #20794D;
+ --quarto-hl-an-color: #5E5E5E;
+ --quarto-hl-fu-color: #4758AB;
+ --quarto-hl-st-color: #20794D;
+ --quarto-hl-cf-color: #003B4F;
+ --quarto-hl-op-color: #5E5E5E;
+ --quarto-hl-er-color: #AD0000;
+ --quarto-hl-bn-color: #AD0000;
+ --quarto-hl-al-color: #AD0000;
+ --quarto-hl-va-color: #111111;
+ --quarto-hl-bu-color: inherit;
+ --quarto-hl-ex-color: inherit;
+ --quarto-hl-pp-color: #AD0000;
+ --quarto-hl-in-color: #5E5E5E;
+ --quarto-hl-vs-color: #20794D;
+ --quarto-hl-wa-color: #5E5E5E;
+ --quarto-hl-do-color: #5E5E5E;
+ --quarto-hl-im-color: #00769E;
+ --quarto-hl-ch-color: #20794D;
+ --quarto-hl-dt-color: #AD0000;
+ --quarto-hl-fl-color: #AD0000;
+ --quarto-hl-co-color: #5E5E5E;
+ --quarto-hl-cv-color: #5E5E5E;
+ --quarto-hl-cn-color: #8f5902;
+ --quarto-hl-sc-color: #5E5E5E;
+ --quarto-hl-dv-color: #AD0000;
+ --quarto-hl-kw-color: #003B4F;
+}
+
+/* other quarto variables */
+:root {
+ --quarto-font-monospace: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace;
+}
+
+pre > code.sourceCode > span {
+ color: #003B4F;
+}
+
+code span {
+ color: #003B4F;
+}
+
+code.sourceCode > span {
+ color: #003B4F;
+}
+
+div.sourceCode,
+div.sourceCode pre.sourceCode {
+ color: #003B4F;
+}
+
+code span.ot {
+ color: #003B4F;
+ font-style: inherit;
+}
+
+code span.at {
+ color: #657422;
+ font-style: inherit;
+}
+
+code span.ss {
+ color: #20794D;
+ font-style: inherit;
+}
+
+code span.an {
+ color: #5E5E5E;
+ font-style: inherit;
+}
+
+code span.fu {
+ color: #4758AB;
+ font-style: inherit;
+}
+
+code span.st {
+ color: #20794D;
+ font-style: inherit;
+}
+
+code span.cf {
+ color: #003B4F;
+ font-style: inherit;
+}
+
+code span.op {
+ color: #5E5E5E;
+ font-style: inherit;
+}
+
+code span.er {
+ color: #AD0000;
+ font-style: inherit;
+}
+
+code span.bn {
+ color: #AD0000;
+ font-style: inherit;
+}
+
+code span.al {
+ color: #AD0000;
+ font-style: inherit;
+}
+
+code span.va {
+ color: #111111;
+ font-style: inherit;
+}
+
+code span.bu {
+ font-style: inherit;
+}
+
+code span.ex {
+ font-style: inherit;
+}
+
+code span.pp {
+ color: #AD0000;
+ font-style: inherit;
+}
+
+code span.in {
+ color: #5E5E5E;
+ font-style: inherit;
+}
+
+code span.vs {
+ color: #20794D;
+ font-style: inherit;
+}
+
+code span.wa {
+ color: #5E5E5E;
+ font-style: italic;
+}
+
+code span.do {
+ color: #5E5E5E;
+ font-style: italic;
+}
+
+code span.im {
+ color: #00769E;
+ font-style: inherit;
+}
+
+code span.ch {
+ color: #20794D;
+ font-style: inherit;
+}
+
+code span.dt {
+ color: #AD0000;
+ font-style: inherit;
+}
+
+code span.fl {
+ color: #AD0000;
+ font-style: inherit;
+}
+
+code span.co {
+ color: #5E5E5E;
+ font-style: inherit;
+}
+
+code span.cv {
+ color: #5E5E5E;
+ font-style: italic;
+}
+
+code span.cn {
+ color: #8f5902;
+ font-style: inherit;
+}
+
+code span.sc {
+ color: #5E5E5E;
+ font-style: inherit;
+}
+
+code span.dv {
+ color: #AD0000;
+ font-style: inherit;
+}
+
+code span.kw {
+ color: #003B4F;
+ font-style: inherit;
+}
+
+.prevent-inlining {
+ content: "";
+}
+
+/*# sourceMappingURL=debc5d5d77c3f9108843748ff7464032.css.map */
diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/quarto.js b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/quarto.js
new file mode 100644
index 0000000..c3935c7
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/quarto.js
@@ -0,0 +1,902 @@
+const sectionChanged = new CustomEvent("quarto-sectionChanged", {
+ detail: {},
+ bubbles: true,
+ cancelable: false,
+ composed: false,
+});
+
+const layoutMarginEls = () => {
+ // Find any conflicting margin elements and add margins to the
+ // top to prevent overlap
+ const marginChildren = window.document.querySelectorAll(
+ ".column-margin.column-container > * "
+ );
+
+ let lastBottom = 0;
+ for (const marginChild of marginChildren) {
+ if (marginChild.offsetParent !== null) {
+ // clear the top margin so we recompute it
+ marginChild.style.marginTop = null;
+ const top = marginChild.getBoundingClientRect().top + window.scrollY;
+ console.log({
+ childtop: marginChild.getBoundingClientRect().top,
+ scroll: window.scrollY,
+ top,
+ lastBottom,
+ });
+ if (top < lastBottom) {
+ const margin = lastBottom - top;
+ marginChild.style.marginTop = `${margin}px`;
+ }
+ const styles = window.getComputedStyle(marginChild);
+ const marginTop = parseFloat(styles["marginTop"]);
+
+ console.log({
+ top,
+ height: marginChild.getBoundingClientRect().height,
+ marginTop,
+ total: top + marginChild.getBoundingClientRect().height + marginTop,
+ });
+ lastBottom = top + marginChild.getBoundingClientRect().height + marginTop;
+ }
+ }
+};
+
+window.document.addEventListener("DOMContentLoaded", function (_event) {
+ // Recompute the position of margin elements anytime the body size changes
+ if (window.ResizeObserver) {
+ const resizeObserver = new window.ResizeObserver(
+ throttle(layoutMarginEls, 50)
+ );
+ resizeObserver.observe(window.document.body);
+ }
+
+ const tocEl = window.document.querySelector('nav.toc-active[role="doc-toc"]');
+ const sidebarEl = window.document.getElementById("quarto-sidebar");
+ const leftTocEl = window.document.getElementById("quarto-sidebar-toc-left");
+ const marginSidebarEl = window.document.getElementById(
+ "quarto-margin-sidebar"
+ );
+ // function to determine whether the element has a previous sibling that is active
+ const prevSiblingIsActiveLink = (el) => {
+ const sibling = el.previousElementSibling;
+ if (sibling && sibling.tagName === "A") {
+ return sibling.classList.contains("active");
+ } else {
+ return false;
+ }
+ };
+
+ // fire slideEnter for bootstrap tab activations (for htmlwidget resize behavior)
+ function fireSlideEnter(e) {
+ const event = window.document.createEvent("Event");
+ event.initEvent("slideenter", true, true);
+ window.document.dispatchEvent(event);
+ }
+ const tabs = window.document.querySelectorAll('a[data-bs-toggle="tab"]');
+ tabs.forEach((tab) => {
+ tab.addEventListener("shown.bs.tab", fireSlideEnter);
+ });
+
+ // fire slideEnter for tabby tab activations (for htmlwidget resize behavior)
+ document.addEventListener("tabby", fireSlideEnter, false);
+
+ // Track scrolling and mark TOC links as active
+ // get table of contents and sidebar (bail if we don't have at least one)
+ const tocLinks = tocEl
+ ? [...tocEl.querySelectorAll("a[data-scroll-target]")]
+ : [];
+ const makeActive = (link) => tocLinks[link].classList.add("active");
+ const removeActive = (link) => tocLinks[link].classList.remove("active");
+ const removeAllActive = () =>
+ [...Array(tocLinks.length).keys()].forEach((link) => removeActive(link));
+
+ // activate the anchor for a section associated with this TOC entry
+ tocLinks.forEach((link) => {
+ link.addEventListener("click", () => {
+ if (link.href.indexOf("#") !== -1) {
+ const anchor = link.href.split("#")[1];
+ const heading = window.document.querySelector(
+ `[data-anchor-id=${anchor}]`
+ );
+ if (heading) {
+ // Add the class
+ heading.classList.add("reveal-anchorjs-link");
+
+ // function to show the anchor
+ const handleMouseout = () => {
+ heading.classList.remove("reveal-anchorjs-link");
+ heading.removeEventListener("mouseout", handleMouseout);
+ };
+
+ // add a function to clear the anchor when the user mouses out of it
+ heading.addEventListener("mouseout", handleMouseout);
+ }
+ }
+ });
+ });
+
+ const sections = tocLinks.map((link) => {
+ const target = link.getAttribute("data-scroll-target");
+ if (target.startsWith("#")) {
+ return window.document.getElementById(decodeURI(`${target.slice(1)}`));
+ } else {
+ return window.document.querySelector(decodeURI(`${target}`));
+ }
+ });
+
+ const sectionMargin = 200;
+ let currentActive = 0;
+ // track whether we've initialized state the first time
+ let init = false;
+
+ const updateActiveLink = () => {
+ // The index from bottom to top (e.g. reversed list)
+ let sectionIndex = -1;
+ if (
+ window.innerHeight + window.pageYOffset >=
+ window.document.body.offsetHeight
+ ) {
+ sectionIndex = 0;
+ } else {
+ sectionIndex = [...sections].reverse().findIndex((section) => {
+ if (section) {
+ return window.pageYOffset >= section.offsetTop - sectionMargin;
+ } else {
+ return false;
+ }
+ });
+ }
+ if (sectionIndex > -1) {
+ const current = sections.length - sectionIndex - 1;
+ if (current !== currentActive) {
+ removeAllActive();
+ currentActive = current;
+ makeActive(current);
+ if (init) {
+ window.dispatchEvent(sectionChanged);
+ }
+ init = true;
+ }
+ }
+ };
+
+ const inHiddenRegion = (top, bottom, hiddenRegions) => {
+ for (const region of hiddenRegions) {
+ if (top <= region.bottom && bottom >= region.top) {
+ return true;
+ }
+ }
+ return false;
+ };
+
+ const categorySelector = "header.quarto-title-block .quarto-category";
+ const activateCategories = (href) => {
+ // Find any categories
+ // Surround them with a link pointing back to:
+ // #category=Authoring
+ try {
+ const categoryEls = window.document.querySelectorAll(categorySelector);
+ for (const categoryEl of categoryEls) {
+ const categoryText = categoryEl.textContent;
+ if (categoryText) {
+ const link = `${href}#category=${encodeURIComponent(categoryText)}`;
+ const linkEl = window.document.createElement("a");
+ linkEl.setAttribute("href", link);
+ for (const child of categoryEl.childNodes) {
+ linkEl.append(child);
+ }
+ categoryEl.appendChild(linkEl);
+ }
+ }
+ } catch {
+ // Ignore errors
+ }
+ };
+ function hasTitleCategories() {
+ return window.document.querySelector(categorySelector) !== null;
+ }
+
+ function offsetRelativeUrl(url) {
+ const offset = getMeta("quarto:offset");
+ return offset ? offset + url : url;
+ }
+
+ function offsetAbsoluteUrl(url) {
+ const offset = getMeta("quarto:offset");
+ const baseUrl = new URL(offset, window.location);
+
+ const projRelativeUrl = url.replace(baseUrl, "");
+ if (projRelativeUrl.startsWith("/")) {
+ return projRelativeUrl;
+ } else {
+ return "/" + projRelativeUrl;
+ }
+ }
+
+ // read a meta tag value
+ function getMeta(metaName) {
+ const metas = window.document.getElementsByTagName("meta");
+ for (let i = 0; i < metas.length; i++) {
+ if (metas[i].getAttribute("name") === metaName) {
+ return metas[i].getAttribute("content");
+ }
+ }
+ return "";
+ }
+
+ async function findAndActivateCategories() {
+ const currentPagePath = offsetAbsoluteUrl(window.location.href);
+ const response = await fetch(offsetRelativeUrl("listings.json"));
+ if (response.status == 200) {
+ return response.json().then(function (listingPaths) {
+ const listingHrefs = [];
+ for (const listingPath of listingPaths) {
+ const pathWithoutLeadingSlash = listingPath.listing.substring(1);
+ for (const item of listingPath.items) {
+ if (
+ item === currentPagePath ||
+ item === currentPagePath + "index.html"
+ ) {
+ // Resolve this path against the offset to be sure
+ // we already are using the correct path to the listing
+ // (this adjusts the listing urls to be rooted against
+ // whatever root the page is actually running against)
+ const relative = offsetRelativeUrl(pathWithoutLeadingSlash);
+ const baseUrl = window.location;
+ const resolvedPath = new URL(relative, baseUrl);
+ listingHrefs.push(resolvedPath.pathname);
+ break;
+ }
+ }
+ }
+
+ // Look up the tree for a nearby linting and use that if we find one
+ const nearestListing = findNearestParentListing(
+ offsetAbsoluteUrl(window.location.pathname),
+ listingHrefs
+ );
+ if (nearestListing) {
+ activateCategories(nearestListing);
+ } else {
+ // See if the referrer is a listing page for this item
+ const referredRelativePath = offsetAbsoluteUrl(document.referrer);
+ const referrerListing = listingHrefs.find((listingHref) => {
+ const isListingReferrer =
+ listingHref === referredRelativePath ||
+ listingHref === referredRelativePath + "index.html";
+ return isListingReferrer;
+ });
+
+ if (referrerListing) {
+ // Try to use the referrer if possible
+ activateCategories(referrerListing);
+ } else if (listingHrefs.length > 0) {
+ // Otherwise, just fall back to the first listing
+ activateCategories(listingHrefs[0]);
+ }
+ }
+ });
+ }
+ }
+ if (hasTitleCategories()) {
+ findAndActivateCategories();
+ }
+
+ const findNearestParentListing = (href, listingHrefs) => {
+ if (!href || !listingHrefs) {
+ return undefined;
+ }
+ // Look up the tree for a nearby linting and use that if we find one
+ const relativeParts = href.substring(1).split("/");
+ while (relativeParts.length > 0) {
+ const path = relativeParts.join("/");
+ for (const listingHref of listingHrefs) {
+ if (listingHref.startsWith(path)) {
+ return listingHref;
+ }
+ }
+ relativeParts.pop();
+ }
+
+ return undefined;
+ };
+
+ const manageSidebarVisiblity = (el, placeholderDescriptor) => {
+ let isVisible = true;
+ let elRect;
+
+ return (hiddenRegions) => {
+ if (el === null) {
+ return;
+ }
+
+ // Find the last element of the TOC
+ const lastChildEl = el.lastElementChild;
+
+ if (lastChildEl) {
+ // Converts the sidebar to a menu
+ const convertToMenu = () => {
+ for (const child of el.children) {
+ child.style.opacity = 0;
+ child.style.overflow = "hidden";
+ }
+
+ nexttick(() => {
+ const toggleContainer = window.document.createElement("div");
+ toggleContainer.style.width = "100%";
+ toggleContainer.classList.add("zindex-over-content");
+ toggleContainer.classList.add("quarto-sidebar-toggle");
+ toggleContainer.classList.add("headroom-target"); // Marks this to be managed by headeroom
+ toggleContainer.id = placeholderDescriptor.id;
+ toggleContainer.style.position = "fixed";
+
+ const toggleIcon = window.document.createElement("i");
+ toggleIcon.classList.add("quarto-sidebar-toggle-icon");
+ toggleIcon.classList.add("bi");
+ toggleIcon.classList.add("bi-caret-down-fill");
+
+ const toggleTitle = window.document.createElement("div");
+ const titleEl = window.document.body.querySelector(
+ placeholderDescriptor.titleSelector
+ );
+ if (titleEl) {
+ toggleTitle.append(
+ titleEl.textContent || titleEl.innerText,
+ toggleIcon
+ );
+ }
+ toggleTitle.classList.add("zindex-over-content");
+ toggleTitle.classList.add("quarto-sidebar-toggle-title");
+ toggleContainer.append(toggleTitle);
+
+ const toggleContents = window.document.createElement("div");
+ toggleContents.classList = el.classList;
+ toggleContents.classList.add("zindex-over-content");
+ toggleContents.classList.add("quarto-sidebar-toggle-contents");
+ for (const child of el.children) {
+ if (child.id === "toc-title") {
+ continue;
+ }
+
+ const clone = child.cloneNode(true);
+ clone.style.opacity = 1;
+ clone.style.display = null;
+ toggleContents.append(clone);
+ }
+ toggleContents.style.height = "0px";
+ const positionToggle = () => {
+ // position the element (top left of parent, same width as parent)
+ if (!elRect) {
+ elRect = el.getBoundingClientRect();
+ }
+ toggleContainer.style.left = `${elRect.left}px`;
+ toggleContainer.style.top = `${elRect.top}px`;
+ toggleContainer.style.width = `${elRect.width}px`;
+ };
+ positionToggle();
+
+ toggleContainer.append(toggleContents);
+ el.parentElement.prepend(toggleContainer);
+
+ // Process clicks
+ let tocShowing = false;
+ // Allow the caller to control whether this is dismissed
+ // when it is clicked (e.g. sidebar navigation supports
+ // opening and closing the nav tree, so don't dismiss on click)
+ const clickEl = placeholderDescriptor.dismissOnClick
+ ? toggleContainer
+ : toggleTitle;
+
+ const closeToggle = () => {
+ if (tocShowing) {
+ toggleContainer.classList.remove("expanded");
+ toggleContents.style.height = "0px";
+ tocShowing = false;
+ }
+ };
+
+ // Get rid of any expanded toggle if the user scrolls
+ window.document.addEventListener(
+ "scroll",
+ throttle(() => {
+ closeToggle();
+ }, 50)
+ );
+
+ // Handle positioning of the toggle
+ window.addEventListener(
+ "resize",
+ throttle(() => {
+ elRect = undefined;
+ positionToggle();
+ }, 50)
+ );
+
+ window.addEventListener("quarto-hrChanged", () => {
+ elRect = undefined;
+ });
+
+ // Process the click
+ clickEl.onclick = () => {
+ if (!tocShowing) {
+ toggleContainer.classList.add("expanded");
+ toggleContents.style.height = null;
+ tocShowing = true;
+ } else {
+ closeToggle();
+ }
+ };
+ });
+ };
+
+ // Converts a sidebar from a menu back to a sidebar
+ const convertToSidebar = () => {
+ for (const child of el.children) {
+ child.style.opacity = 1;
+ child.style.overflow = null;
+ }
+
+ const placeholderEl = window.document.getElementById(
+ placeholderDescriptor.id
+ );
+ if (placeholderEl) {
+ placeholderEl.remove();
+ }
+
+ el.classList.remove("rollup");
+ };
+
+ if (isReaderMode()) {
+ convertToMenu();
+ isVisible = false;
+ } else {
+ // Find the top and bottom o the element that is being managed
+ const elTop = el.offsetTop;
+ const elBottom =
+ elTop + lastChildEl.offsetTop + lastChildEl.offsetHeight;
+
+ if (!isVisible) {
+ // If the element is current not visible reveal if there are
+ // no conflicts with overlay regions
+ if (!inHiddenRegion(elTop, elBottom, hiddenRegions)) {
+ convertToSidebar();
+ isVisible = true;
+ }
+ } else {
+ // If the element is visible, hide it if it conflicts with overlay regions
+ // and insert a placeholder toggle (or if we're in reader mode)
+ if (inHiddenRegion(elTop, elBottom, hiddenRegions)) {
+ convertToMenu();
+ isVisible = false;
+ }
+ }
+ }
+ }
+ };
+ };
+
+ const tabEls = document.querySelectorAll('a[data-bs-toggle="tab"]');
+ for (const tabEl of tabEls) {
+ const id = tabEl.getAttribute("data-bs-target");
+ if (id) {
+ const columnEl = document.querySelector(
+ `${id} .column-margin, .tabset-margin-content`
+ );
+ if (columnEl)
+ tabEl.addEventListener("shown.bs.tab", function (event) {
+ const el = event.srcElement;
+ if (el) {
+ const visibleCls = `${el.id}-margin-content`;
+ // walk up until we find a parent tabset
+ let panelTabsetEl = el.parentElement;
+ while (panelTabsetEl) {
+ if (panelTabsetEl.classList.contains("panel-tabset")) {
+ break;
+ }
+ panelTabsetEl = panelTabsetEl.parentElement;
+ }
+
+ if (panelTabsetEl) {
+ const prevSib = panelTabsetEl.previousElementSibling;
+ if (
+ prevSib &&
+ prevSib.classList.contains("tabset-margin-container")
+ ) {
+ const childNodes = prevSib.querySelectorAll(
+ ".tabset-margin-content"
+ );
+ for (const childEl of childNodes) {
+ if (childEl.classList.contains(visibleCls)) {
+ childEl.classList.remove("collapse");
+ } else {
+ childEl.classList.add("collapse");
+ }
+ }
+ }
+ }
+ }
+
+ layoutMarginEls();
+ });
+ }
+ }
+
+ // Manage the visibility of the toc and the sidebar
+ const marginScrollVisibility = manageSidebarVisiblity(marginSidebarEl, {
+ id: "quarto-toc-toggle",
+ titleSelector: "#toc-title",
+ dismissOnClick: true,
+ });
+ const sidebarScrollVisiblity = manageSidebarVisiblity(sidebarEl, {
+ id: "quarto-sidebarnav-toggle",
+ titleSelector: ".title",
+ dismissOnClick: false,
+ });
+ let tocLeftScrollVisibility;
+ if (leftTocEl) {
+ tocLeftScrollVisibility = manageSidebarVisiblity(leftTocEl, {
+ id: "quarto-lefttoc-toggle",
+ titleSelector: "#toc-title",
+ dismissOnClick: true,
+ });
+ }
+
+ // Find the first element that uses formatting in special columns
+ const conflictingEls = window.document.body.querySelectorAll(
+ '[class^="column-"], [class*=" column-"], aside, [class*="margin-caption"], [class*=" margin-caption"], [class*="margin-ref"], [class*=" margin-ref"]'
+ );
+
+ // Filter all the possibly conflicting elements into ones
+ // the do conflict on the left or ride side
+ const arrConflictingEls = Array.from(conflictingEls);
+ const leftSideConflictEls = arrConflictingEls.filter((el) => {
+ if (el.tagName === "ASIDE") {
+ return false;
+ }
+ return Array.from(el.classList).find((className) => {
+ return (
+ className !== "column-body" &&
+ className.startsWith("column-") &&
+ !className.endsWith("right") &&
+ !className.endsWith("container") &&
+ className !== "column-margin"
+ );
+ });
+ });
+ const rightSideConflictEls = arrConflictingEls.filter((el) => {
+ if (el.tagName === "ASIDE") {
+ return true;
+ }
+
+ const hasMarginCaption = Array.from(el.classList).find((className) => {
+ return className == "margin-caption";
+ });
+ if (hasMarginCaption) {
+ return true;
+ }
+
+ return Array.from(el.classList).find((className) => {
+ return (
+ className !== "column-body" &&
+ !className.endsWith("container") &&
+ className.startsWith("column-") &&
+ !className.endsWith("left")
+ );
+ });
+ });
+
+ const kOverlapPaddingSize = 10;
+ function toRegions(els) {
+ return els.map((el) => {
+ const boundRect = el.getBoundingClientRect();
+ const top =
+ boundRect.top +
+ document.documentElement.scrollTop -
+ kOverlapPaddingSize;
+ return {
+ top,
+ bottom: top + el.scrollHeight + 2 * kOverlapPaddingSize,
+ };
+ });
+ }
+
+ let hasObserved = false;
+ const visibleItemObserver = (els) => {
+ let visibleElements = [...els];
+ const intersectionObserver = new IntersectionObserver(
+ (entries, _observer) => {
+ entries.forEach((entry) => {
+ if (entry.isIntersecting) {
+ if (visibleElements.indexOf(entry.target) === -1) {
+ visibleElements.push(entry.target);
+ }
+ } else {
+ visibleElements = visibleElements.filter((visibleEntry) => {
+ return visibleEntry !== entry;
+ });
+ }
+ });
+
+ if (!hasObserved) {
+ hideOverlappedSidebars();
+ }
+ hasObserved = true;
+ },
+ {}
+ );
+ els.forEach((el) => {
+ intersectionObserver.observe(el);
+ });
+
+ return {
+ getVisibleEntries: () => {
+ return visibleElements;
+ },
+ };
+ };
+
+ const rightElementObserver = visibleItemObserver(rightSideConflictEls);
+ const leftElementObserver = visibleItemObserver(leftSideConflictEls);
+
+ const hideOverlappedSidebars = () => {
+ marginScrollVisibility(toRegions(rightElementObserver.getVisibleEntries()));
+ sidebarScrollVisiblity(toRegions(leftElementObserver.getVisibleEntries()));
+ if (tocLeftScrollVisibility) {
+ tocLeftScrollVisibility(
+ toRegions(leftElementObserver.getVisibleEntries())
+ );
+ }
+ };
+
+ window.quartoToggleReader = () => {
+ // Applies a slow class (or removes it)
+ // to update the transition speed
+ const slowTransition = (slow) => {
+ const manageTransition = (id, slow) => {
+ const el = document.getElementById(id);
+ if (el) {
+ if (slow) {
+ el.classList.add("slow");
+ } else {
+ el.classList.remove("slow");
+ }
+ }
+ };
+
+ manageTransition("TOC", slow);
+ manageTransition("quarto-sidebar", slow);
+ };
+ const readerMode = !isReaderMode();
+ setReaderModeValue(readerMode);
+
+ // If we're entering reader mode, slow the transition
+ if (readerMode) {
+ slowTransition(readerMode);
+ }
+ highlightReaderToggle(readerMode);
+ hideOverlappedSidebars();
+
+ // If we're exiting reader mode, restore the non-slow transition
+ if (!readerMode) {
+ slowTransition(!readerMode);
+ }
+ };
+
+ const highlightReaderToggle = (readerMode) => {
+ const els = document.querySelectorAll(".quarto-reader-toggle");
+ if (els) {
+ els.forEach((el) => {
+ if (readerMode) {
+ el.classList.add("reader");
+ } else {
+ el.classList.remove("reader");
+ }
+ });
+ }
+ };
+
+ const setReaderModeValue = (val) => {
+ if (window.location.protocol !== "file:") {
+ window.localStorage.setItem("quarto-reader-mode", val);
+ } else {
+ localReaderMode = val;
+ }
+ };
+
+ const isReaderMode = () => {
+ if (window.location.protocol !== "file:") {
+ return window.localStorage.getItem("quarto-reader-mode") === "true";
+ } else {
+ return localReaderMode;
+ }
+ };
+ let localReaderMode = null;
+
+ const tocOpenDepthStr = tocEl?.getAttribute("data-toc-expanded");
+ const tocOpenDepth = tocOpenDepthStr ? Number(tocOpenDepthStr) : 1;
+
+ // Walk the TOC and collapse/expand nodes
+ // Nodes are expanded if:
+ // - they are top level
+ // - they have children that are 'active' links
+ // - they are directly below an link that is 'active'
+ const walk = (el, depth) => {
+ // Tick depth when we enter a UL
+ if (el.tagName === "UL") {
+ depth = depth + 1;
+ }
+
+ // It this is active link
+ let isActiveNode = false;
+ if (el.tagName === "A" && el.classList.contains("active")) {
+ isActiveNode = true;
+ }
+
+ // See if there is an active child to this element
+ let hasActiveChild = false;
+ for (child of el.children) {
+ hasActiveChild = walk(child, depth) || hasActiveChild;
+ }
+
+ // Process the collapse state if this is an UL
+ if (el.tagName === "UL") {
+ if (tocOpenDepth === -1 && depth > 1) {
+ el.classList.add("collapse");
+ } else if (
+ depth <= tocOpenDepth ||
+ hasActiveChild ||
+ prevSiblingIsActiveLink(el)
+ ) {
+ el.classList.remove("collapse");
+ } else {
+ el.classList.add("collapse");
+ }
+
+ // untick depth when we leave a UL
+ depth = depth - 1;
+ }
+ return hasActiveChild || isActiveNode;
+ };
+
+ // walk the TOC and expand / collapse any items that should be shown
+
+ if (tocEl) {
+ walk(tocEl, 0);
+ updateActiveLink();
+ }
+
+ // Throttle the scroll event and walk peridiocally
+ window.document.addEventListener(
+ "scroll",
+ throttle(() => {
+ if (tocEl) {
+ updateActiveLink();
+ walk(tocEl, 0);
+ }
+ if (!isReaderMode()) {
+ hideOverlappedSidebars();
+ }
+ }, 5)
+ );
+ window.addEventListener(
+ "resize",
+ throttle(() => {
+ if (!isReaderMode()) {
+ hideOverlappedSidebars();
+ }
+ }, 10)
+ );
+ hideOverlappedSidebars();
+ highlightReaderToggle(isReaderMode());
+});
+
+// grouped tabsets
+window.addEventListener("pageshow", (_event) => {
+ function getTabSettings() {
+ const data = localStorage.getItem("quarto-persistent-tabsets-data");
+ if (!data) {
+ localStorage.setItem("quarto-persistent-tabsets-data", "{}");
+ return {};
+ }
+ if (data) {
+ return JSON.parse(data);
+ }
+ }
+
+ function setTabSettings(data) {
+ localStorage.setItem(
+ "quarto-persistent-tabsets-data",
+ JSON.stringify(data)
+ );
+ }
+
+ function setTabState(groupName, groupValue) {
+ const data = getTabSettings();
+ data[groupName] = groupValue;
+ setTabSettings(data);
+ }
+
+ function toggleTab(tab, active) {
+ const tabPanelId = tab.getAttribute("aria-controls");
+ const tabPanel = document.getElementById(tabPanelId);
+ if (active) {
+ tab.classList.add("active");
+ tabPanel.classList.add("active");
+ } else {
+ tab.classList.remove("active");
+ tabPanel.classList.remove("active");
+ }
+ }
+
+ function toggleAll(selectedGroup, selectorsToSync) {
+ for (const [thisGroup, tabs] of Object.entries(selectorsToSync)) {
+ const active = selectedGroup === thisGroup;
+ for (const tab of tabs) {
+ toggleTab(tab, active);
+ }
+ }
+ }
+
+ function findSelectorsToSyncByLanguage() {
+ const result = {};
+ const tabs = Array.from(
+ document.querySelectorAll(`div[data-group] a[id^='tabset-']`)
+ );
+ for (const item of tabs) {
+ const div = item.parentElement.parentElement.parentElement;
+ const group = div.getAttribute("data-group");
+ if (!result[group]) {
+ result[group] = {};
+ }
+ const selectorsToSync = result[group];
+ const value = item.innerHTML;
+ if (!selectorsToSync[value]) {
+ selectorsToSync[value] = [];
+ }
+ selectorsToSync[value].push(item);
+ }
+ return result;
+ }
+
+ function setupSelectorSync() {
+ const selectorsToSync = findSelectorsToSyncByLanguage();
+ Object.entries(selectorsToSync).forEach(([group, tabSetsByValue]) => {
+ Object.entries(tabSetsByValue).forEach(([value, items]) => {
+ items.forEach((item) => {
+ item.addEventListener("click", (_event) => {
+ setTabState(group, value);
+ toggleAll(value, selectorsToSync[group]);
+ });
+ });
+ });
+ });
+ return selectorsToSync;
+ }
+
+ const selectorsToSync = setupSelectorSync();
+ for (const [group, selectedName] of Object.entries(getTabSettings())) {
+ const selectors = selectorsToSync[group];
+ // it's possible that stale state gives us empty selections, so we explicitly check here.
+ if (selectors) {
+ toggleAll(selectedName, selectors);
+ }
+ }
+});
+
+function throttle(func, wait) {
+ let waiting = false;
+ return function () {
+ if (!waiting) {
+ func.apply(this, arguments);
+ waiting = true;
+ setTimeout(function () {
+ waiting = false;
+ }, wait);
+ }
+ };
+}
+
+function nexttick(func) {
+ return setTimeout(func, 0);
+}
diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/tippy.css b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/tippy.css
new file mode 100644
index 0000000..e6ae635
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/tippy.css
@@ -0,0 +1 @@
+.tippy-box[data-animation=fade][data-state=hidden]{opacity:0}[data-tippy-root]{max-width:calc(100vw - 10px)}.tippy-box{position:relative;background-color:#333;color:#fff;border-radius:4px;font-size:14px;line-height:1.4;white-space:normal;outline:0;transition-property:transform,visibility,opacity}.tippy-box[data-placement^=top]>.tippy-arrow{bottom:0}.tippy-box[data-placement^=top]>.tippy-arrow:before{bottom:-7px;left:0;border-width:8px 8px 0;border-top-color:initial;transform-origin:center top}.tippy-box[data-placement^=bottom]>.tippy-arrow{top:0}.tippy-box[data-placement^=bottom]>.tippy-arrow:before{top:-7px;left:0;border-width:0 8px 8px;border-bottom-color:initial;transform-origin:center bottom}.tippy-box[data-placement^=left]>.tippy-arrow{right:0}.tippy-box[data-placement^=left]>.tippy-arrow:before{border-width:8px 0 8px 8px;border-left-color:initial;right:-7px;transform-origin:center left}.tippy-box[data-placement^=right]>.tippy-arrow{left:0}.tippy-box[data-placement^=right]>.tippy-arrow:before{left:-7px;border-width:8px 8px 8px 0;border-right-color:initial;transform-origin:center right}.tippy-box[data-inertia][data-state=visible]{transition-timing-function:cubic-bezier(.54,1.5,.38,1.11)}.tippy-arrow{width:16px;height:16px;color:#333}.tippy-arrow:before{content:"";position:absolute;border-color:transparent;border-style:solid}.tippy-content{position:relative;padding:5px 9px;z-index:1}
\ No newline at end of file
diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/tippy.umd.min.js b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/tippy.umd.min.js
new file mode 100644
index 0000000..ca292be
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/tippy.umd.min.js
@@ -0,0 +1,2 @@
+!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?module.exports=t(require("@popperjs/core")):"function"==typeof define&&define.amd?define(["@popperjs/core"],t):(e=e||self).tippy=t(e.Popper)}(this,(function(e){"use strict";var t={passive:!0,capture:!0},n=function(){return document.body};function r(e,t,n){if(Array.isArray(e)){var r=e[t];return null==r?Array.isArray(n)?n[t]:n:r}return e}function o(e,t){var n={}.toString.call(e);return 0===n.indexOf("[object")&&n.indexOf(t+"]")>-1}function i(e,t){return"function"==typeof e?e.apply(void 0,t):e}function a(e,t){return 0===t?e:function(r){clearTimeout(n),n=setTimeout((function(){e(r)}),t)};var n}function s(e,t){var n=Object.assign({},e);return t.forEach((function(e){delete n[e]})),n}function u(e){return[].concat(e)}function c(e,t){-1===e.indexOf(t)&&e.push(t)}function p(e){return e.split("-")[0]}function f(e){return[].slice.call(e)}function l(e){return Object.keys(e).reduce((function(t,n){return void 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+
diff --git a/bs/.development/DiagnosticPlots.R b/bs/.development/DiagnosticPlots.R
deleted file mode 100644
index c0d6856..0000000
--- a/bs/.development/DiagnosticPlots.R
+++ /dev/null
@@ -1,181 +0,0 @@
-library(car)
-library(ggplot2)
-library(cowplot)
-
-diagnosticPlots <- function(df, formula) {
- model <- lm(formula, data = df)
- resids <- residuals(model)
- fitted <- fitted(model)
-
- # Identify influential points
- p <- length(coef(model))
- n <- length(resids)
- leverage <- hatvalues(model)
- cooks_dist <- cooks.distance(model)
- high_leverage_threshold <- (2 * (p + 1)) / n
- high_cooks_threshold <- 4 / n
- influential_points <- which(
- leverage > high_leverage_threshold | cooks_dist > high_cooks_threshold
- )
-
- # resids vs fitted
- line_data <- lowess(fitted, resids) |> as.data.frame()
- resids_fitted_df <- data.frame(fitted = fitted, residuals = resids, index = 1:n)
- resids_vs_fitted <- ggplot(
- data = resids_fitted_df,
- aes(x = fitted, y = residuals)
- ) +
- geom_point() +
- geom_hline(yintercept = 0,
- linetype = "dashed",
- color = "black",
- size = 0.25
- ) +
- geom_line(
- data = line_data,
- aes(x = x, y = y)
- ) +
- geom_text(data = resids_fitted_df[influential_points, ],
- aes(label = index),
- vjust = -1,
- color = "black",
- size = 3) +
- labs(
- y = "Residuals", x = "Fitted values",
- title = "Residuals vs Fitted values"
- )
-
- # qq norm plot
- standardized_resids <- resids / sd(resids)
- sqrt_resids <- sqrt(abs(standardized_resids))
- ordered_resids <- sort(standardized_resids)
- theoretical_quantiles <- qnorm((1:n) / (n + 1))
- resids_quantiles_df <- data.frame(
- quantiles = theoretical_quantiles, residuals = ordered_resids,
- index = 1:n
- )
- slope <- sd(ordered_resids)
- intercept <- mean(ordered_resids)
- resids_vs_quantiles <- ggplot(
- data = resids_quantiles_df,
- aes(x = quantiles, y = residuals)
- ) +
- geom_point() +
- geom_abline(
- aes(
- slope = slope,
- intercept = intercept
- )
- ) +
- geom_text(data = resids_quantiles_df[influential_points, ],
- aes(label = index),
- vjust = -1,
- color = "black",
- size = 3) +
- labs(
- y = "Standardized residuals", x = "Theoretical Quantiles",
- title = "Q-Q Residuals"
- )
-
- # Manual Scale-Location Plot
- line_data <- lowess(fitted, sqrt_resids) |> as.data.frame()
- sqrt_resids_fitted_df <- data.frame(
- fitted = fitted, residuals = sqrt_resids,
- index = 1:n
- )
- sqrt_resids_vs_fitted <- ggplot(
- data = sqrt_resids_fitted_df,
- aes(x = fitted, y = residuals)
- ) +
- geom_point() +
- geom_line(
- data = line_data,
- aes(x = x, y = y),
- colour = "black"
- ) +
- geom_text(data = sqrt_resids_fitted_df[influential_points, ],
- aes(label = index),
- vjust = -1,
- color = "black",
- size = 3) +
- labs(
- y = expression(sqrt("Standardized residuals")),
- x = "Fitted values",
- title = "Scale-Location"
- )
-
- # Residuals vs Leverage
- line_data <- lowess(leverage, standardized_resids) |> as.data.frame()
- residuals_leverage_df <- data.frame(
- residuals = standardized_resids, leverage = leverage,
- index = 1:n
- )
- residuals_vs_leverage <- ggplot(
- data = residuals_leverage_df,
- aes(x = leverage, y = residuals)
- ) +
- geom_point() +
- geom_line(
- data = line_data,
- aes(x = x, y = y)
- ) +
- geom_hline(yintercept = 0,
- linetype = "dashed",
- color = "black",
- size = 0.25
- ) +
- geom_text(data = residuals_leverage_df[influential_points, ],
- aes(label = index),
- vjust = -1,
- color = "black",
- size = 3) +
- labs(
- y = "Standardized residuals", x = "Leverage",
- title = "Residuals vs Leverage"
- )
-
- plot_grid(
- resids_vs_fitted,
- resids_vs_quantiles,
- sqrt_resids_vs_fitted,
- residuals_vs_leverage
- )
-}
-
-df <- CO2
-f <- formula(uptake ~ conc)
-p <- diagnosticPlots(df, f)
-print(p)
-
-model <- lm(f, data = df)
-par(mfrow = c(3, 2))
-plot(model)
-plot(model, 4)
-
-CooksDistance <- function(df, formula) {
- # https://rpubs.com/DragonflyStats/Cooks-Distance
- model <- lm(formula, data = df)
- cd <- cooks.distance(model)
- cd <- data.frame(CooksDistance = cd,
- Index = 1:length(cd))
- n <- nrow(df)
- # NOTE: number of predictors -1 (remove intercept via -1)
- k <- length(coef(model)) - 1
- cutoff <- 4 / (n - k - 1)
- ggplot(data = cd, aes(Index, CooksDistance)) +
- geom_point() +
- geom_line() +
- geom_hline(yintercept = cutoff,
- linetype = "dashed",
- color = "black",
- size = 0.25
- ) +
- geom_text(data = cd[cd$CooksDistance >= cutoff, ],
- aes(label = Index),
- vjust = -1,
- color = "black",
- size = 3)
-}
-
-CooksDistance(df, f)
-
diff --git a/bs/.development/Distris.R b/bs/.development/Distris.R
deleted file mode 100644
index 61b717f..0000000
--- a/bs/.development/Distris.R
+++ /dev/null
@@ -1,28 +0,0 @@
-dnorm(0.25, mean = 0, sd = 1)
-dnorm(0.5, mean = 0, sd = 1)
-dnorm(0.005, mean = 0, sd = 1)
-dnorm(5, mean = 0, sd = 1)
-dnorm(0.01, mean = 0, sd = 1)
-
-mean <- 0
-sd <- 1
-set.seed(123) # For reproducibility
-samples <- rnorm(1000, mean, sd)
-hist(samples,
- breaks = 30, probability = TRUE, col = "lightgray",
- main = "Histogram of Random Samples with PDF Overlay",
- xlab = "x", ylab = "Density", ylim = c(0, 1.25)
-)
-
-x <- seq(-4, 4, length.out = 100)
-lines(x, dnorm(x, mean, sd), col = "blue", lwd = 2)
-
-x <- seq(-4, 4, length.out = 100)
-lines(x, pnorm(x, mean, sd), type = "l", lwd = 2, col = "red")
-
-lines(density(samples), col = "green", lwd = 2)
-
-legend("topright",
- legend = c("PDF (dnorm)", "CDF (pnorm)", "Empirical Density", "Histogram of Samples"),
- col = c("blue", "red", "green", "lightgray"), lwd = 2, fill = c(NA, NA, NA, "lightgray")
-)
diff --git a/bs/.development/Distris_files/figure-html/Likelihood-1.png b/bs/.development/Distris_files/figure-html/Likelihood-1.png
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diff --git a/bs/.development/Distris_files/figure-html/Regressions-2.png b/bs/.development/Distris_files/figure-html/Regressions-2.png
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diff --git a/bs/.development/Distris_files/figure-html/plot-histogram-2.png b/bs/.development/Distris_files/figure-html/plot-histogram-2.png
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diff --git a/bs/.development/Distris_files/libs/bootstrap/bootstrap-icons.woff b/bs/.development/Distris_files/libs/bootstrap/bootstrap-icons.woff
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diff --git a/bs/.development/Distris_files/libs/bootstrap/bootstrap.min.js b/bs/.development/Distris_files/libs/bootstrap/bootstrap.min.js
deleted file mode 100644
index e8f21f7..0000000
--- a/bs/.development/Distris_files/libs/bootstrap/bootstrap.min.js
+++ /dev/null
@@ -1,7 +0,0 @@
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- */
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m?m(Object.assign({},e.rects,{placement:e.placement})):m,O="number"==typeof C?{mainAxis:C,altAxis:C}:Object.assign({mainAxis:0,altAxis:0},C),x=e.modifiersData.offset?e.modifiersData.offset[e.placement]:null,k={x:0,y:0};if(A){if(o){var L,S="y"===y?zt:Vt,D="y"===y?Rt:qt,$="y"===y?"height":"width",I=A[y],N=I+g[S],P=I-g[D],M=f?-T[$]/2:0,j=b===Xt?E[$]:T[$],F=b===Xt?-T[$]:-E[$],H=e.elements.arrow,W=f&&H?Ce(H):{width:0,height:0},B=e.modifiersData["arrow#persistent"]?e.modifiersData["arrow#persistent"].padding:{top:0,right:0,bottom:0,left:0},z=B[S],R=B[D],q=Ne(0,E[$],W[$]),V=v?E[$]/2-M-q-z-O.mainAxis:j-q-z-O.mainAxis,K=v?-E[$]/2+M+q+R+O.mainAxis:F+q+R+O.mainAxis,Q=e.elements.arrow&&$e(e.elements.arrow),X=Q?"y"===y?Q.clientTop||0:Q.clientLeft||0:0,Y=null!=(L=null==x?void 0:x[y])?L:0,U=I+K-Y,G=Ne(f?ye(N,I+V-Y-X):N,I,f?ve(P,U):P);A[y]=G,k[y]=G-I}if(a){var J,Z="x"===y?zt:Vt,tt="x"===y?Rt:qt,et=A[w],it="y"===w?"height":"width",nt=et+g[Z],st=et-g[tt],ot=-1!==[zt,Vt].indexOf(_),rt=null!=(J=null==x?void 0:x[w])?J:0,at=ot?nt:et-E[it]-T[it]-rt+O.altAxis,lt=ot?et+E[it]+T[it]-rt-O.altAxis:st,ct=f&&ot?function(t,e,i){var n=Ne(t,e,i);return n>i?i:n}(at,et,lt):Ne(f?at:nt,et,f?lt:st);A[w]=ct,k[w]=ct-et}e.modifiersData[n]=k}},requiresIfExists:["offset"]};function di(t,e,i){void 0===i&&(i=!1);var n,s,o=me(e),r=me(e)&&function(t){var e=t.getBoundingClientRect(),i=we(e.width)/t.offsetWidth||1,n=we(e.height)/t.offsetHeight||1;return 1!==i||1!==n}(e),a=Le(e),l=Te(t,r,i),c={scrollLeft:0,scrollTop:0},h={x:0,y:0};return(o||!o&&!i)&&(("body"!==ue(e)||Ue(a))&&(c=(n=e)!==fe(n)&&me(n)?{scrollLeft:(s=n).scrollLeft,scrollTop:s.scrollTop}:Xe(n)),me(e)?((h=Te(e,!0)).x+=e.clientLeft,h.y+=e.clientTop):a&&(h.x=Ye(a))),{x:l.left+c.scrollLeft-h.x,y:l.top+c.scrollTop-h.y,width:l.width,height:l.height}}function ui(t){var e=new Map,i=new Set,n=[];function s(t){i.add(t.name),[].concat(t.requires||[],t.requiresIfExists||[]).forEach((function(t){if(!i.has(t)){var n=e.get(t);n&&s(n)}})),n.push(t)}return t.forEach((function(t){e.set(t.name,t)})),t.forEach((function(t){i.has(t.name)||s(t)})),n}var fi={placement:"bottom",modifiers:[],strategy:"absolute"};function pi(){for(var t=arguments.length,e=new Array(t),i=0;iNumber.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_getPopperConfig(){const t={placement:this._getPlacement(),modifiers:[{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"offset",options:{offset:this._getOffset()}}]};return(this._inNavbar||"static"===this._config.display)&&(F.setDataAttribute(this._menu,"popper","static"),t.modifiers=[{name:"applyStyles",enabled:!1}]),{...t,...g(this._config.popperConfig,[t])}}_selectMenuItem({key:t,target:e}){const i=z.find(".dropdown-menu 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e=/input|textarea/i.test(t.target.tagName),i="Escape"===t.key,n=[Ei,Ti].includes(t.key);if(!n&&!i)return;if(e&&!i)return;t.preventDefault();const s=this.matches(Ii)?this:z.prev(this,Ii)[0]||z.next(this,Ii)[0]||z.findOne(Ii,t.delegateTarget.parentNode),o=qi.getOrCreateInstance(s);if(n)return t.stopPropagation(),o.show(),void o._selectMenuItem(t);o._isShown()&&(t.stopPropagation(),o.hide(),s.focus())}}N.on(document,Si,Ii,qi.dataApiKeydownHandler),N.on(document,Si,Pi,qi.dataApiKeydownHandler),N.on(document,Li,qi.clearMenus),N.on(document,Di,qi.clearMenus),N.on(document,Li,Ii,(function(t){t.preventDefault(),qi.getOrCreateInstance(this).toggle()})),m(qi);const Vi="backdrop",Ki="show",Qi=`mousedown.bs.${Vi}`,Xi={className:"modal-backdrop",clickCallback:null,isAnimated:!1,isVisible:!0,rootElement:"body"},Yi={className:"string",clickCallback:"(function|null)",isAnimated:"boolean",isVisible:"boolean",rootElement:"(element|string)"};class Ui extends H{constructor(t){super(),this._config=this._getConfig(t),this._isAppended=!1,this._element=null}static get Default(){return Xi}static get DefaultType(){return Yi}static get NAME(){return Vi}show(t){if(!this._config.isVisible)return void g(t);this._append();const e=this._getElement();this._config.isAnimated&&d(e),e.classList.add(Ki),this._emulateAnimation((()=>{g(t)}))}hide(t){this._config.isVisible?(this._getElement().classList.remove(Ki),this._emulateAnimation((()=>{this.dispose(),g(t)}))):g(t)}dispose(){this._isAppended&&(N.off(this._element,Qi),this._element.remove(),this._isAppended=!1)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_configAfterMerge(t){return t.rootElement=r(t.rootElement),t}_append(){if(this._isAppended)return;const t=this._getElement();this._config.rootElement.append(t),N.on(t,Qi,(()=>{g(this._config.clickCallback)})),this._isAppended=!0}_emulateAnimation(t){_(t,this._getElement(),this._config.isAnimated)}}const Gi=".bs.focustrap",Ji=`focusin${Gi}`,Zi=`keydown.tab${Gi}`,tn="backward",en={autofocus:!0,trapElement:null},nn={autofocus:"boolean",trapElement:"element"};class sn extends H{constructor(t){super(),this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}static get Default(){return en}static get DefaultType(){return nn}static get NAME(){return"focustrap"}activate(){this._isActive||(this._config.autofocus&&this._config.trapElement.focus(),N.off(document,Gi),N.on(document,Ji,(t=>this._handleFocusin(t))),N.on(document,Zi,(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,N.off(document,Gi))}_handleFocusin(t){const{trapElement:e}=this._config;if(t.target===document||t.target===e||e.contains(t.target))return;const i=z.focusableChildren(e);0===i.length?e.focus():this._lastTabNavDirection===tn?i[i.length-1].focus():i[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?tn:"forward")}}const on=".fixed-top, .fixed-bottom, .is-fixed, .sticky-top",rn=".sticky-top",an="padding-right",ln="margin-right";class cn{constructor(){this._element=document.body}getWidth(){const t=document.documentElement.clientWidth;return Math.abs(window.innerWidth-t)}hide(){const t=this.getWidth();this._disableOverFlow(),this._setElementAttributes(this._element,an,(e=>e+t)),this._setElementAttributes(on,an,(e=>e+t)),this._setElementAttributes(rn,ln,(e=>e-t))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,an),this._resetElementAttributes(on,an),this._resetElementAttributes(rn,ln)}isOverflowing(){return this.getWidth()>0}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t).getPropertyValue(e);t.style.setProperty(e,`${i(Number.parseFloat(s))}px`)}))}_saveInitialAttribute(t,e){const i=t.style.getPropertyValue(e);i&&F.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=F.getDataAttribute(t,e);null!==i?(F.removeDataAttribute(t,e),t.style.setProperty(e,i)):t.style.removeProperty(e)}))}_applyManipulationCallback(t,e){if(o(t))e(t);else for(const i of z.find(t,this._element))e(i)}}const hn=".bs.modal",dn=`hide${hn}`,un=`hidePrevented${hn}`,fn=`hidden${hn}`,pn=`show${hn}`,mn=`shown${hn}`,gn=`resize${hn}`,_n=`click.dismiss${hn}`,bn=`mousedown.dismiss${hn}`,vn=`keydown.dismiss${hn}`,yn=`click${hn}.data-api`,wn="modal-open",An="show",En="modal-static",Tn={backdrop:!0,focus:!0,keyboard:!0},Cn={backdrop:"(boolean|string)",focus:"boolean",keyboard:"boolean"};class On extends W{constructor(t,e){super(t,e),this._dialog=z.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._isTransitioning=!1,this._scrollBar=new cn,this._addEventListeners()}static get Default(){return Tn}static get DefaultType(){return Cn}static get NAME(){return"modal"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||N.trigger(this._element,pn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isTransitioning=!0,this._scrollBar.hide(),document.body.classList.add(wn),this._adjustDialog(),this._backdrop.show((()=>this._showElement(t))))}hide(){this._isShown&&!this._isTransitioning&&(N.trigger(this._element,dn).defaultPrevented||(this._isShown=!1,this._isTransitioning=!0,this._focustrap.deactivate(),this._element.classList.remove(An),this._queueCallback((()=>this._hideModal()),this._element,this._isAnimated())))}dispose(){N.off(window,hn),N.off(this._dialog,hn),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new Ui({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_showElement(t){document.body.contains(this._element)||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0;const e=z.findOne(".modal-body",this._dialog);e&&(e.scrollTop=0),d(this._element),this._element.classList.add(An),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,N.trigger(this._element,mn,{relatedTarget:t})}),this._dialog,this._isAnimated())}_addEventListeners(){N.on(this._element,vn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():this._triggerBackdropTransition())})),N.on(window,gn,(()=>{this._isShown&&!this._isTransitioning&&this._adjustDialog()})),N.on(this._element,bn,(t=>{N.one(this._element,_n,(e=>{this._element===t.target&&this._element===e.target&&("static"!==this._config.backdrop?this._config.backdrop&&this.hide():this._triggerBackdropTransition())}))}))}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(wn),this._resetAdjustments(),this._scrollBar.reset(),N.trigger(this._element,fn)}))}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(N.trigger(this._element,un).defaultPrevented)return;const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._element.style.overflowY;"hidden"===e||this._element.classList.contains(En)||(t||(this._element.style.overflowY="hidden"),this._element.classList.add(En),this._queueCallback((()=>{this._element.classList.remove(En),this._queueCallback((()=>{this._element.style.overflowY=e}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;if(i&&!t){const t=p()?"paddingLeft":"paddingRight";this._element.style[t]=`${e}px`}if(!i&&t){const t=p()?"paddingRight":"paddingLeft";this._element.style[t]=`${e}px`}}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const 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W{constructor(t,e){super(t,e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get Default(){return zn}static get DefaultType(){return Rn}static get NAME(){return"offcanvas"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||N.trigger(this._element,Nn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._backdrop.show(),this._config.scroll||(new cn).hide(),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add(Dn),this._queueCallback((()=>{this._config.scroll&&!this._config.backdrop||this._focustrap.activate(),this._element.classList.add(Sn),this._element.classList.remove(Dn),N.trigger(this._element,Pn,{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(N.trigger(this._element,Mn).defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.add($n),this._backdrop.hide(),this._queueCallback((()=>{this._element.classList.remove(Sn,$n),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._config.scroll||(new cn).reset(),N.trigger(this._element,Fn)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_initializeBackDrop(){const t=Boolean(this._config.backdrop);return new Ui({className:"offcanvas-backdrop",isVisible:t,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:t?()=>{"static"!==this._config.backdrop?this.hide():N.trigger(this._element,jn)}:null})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_addEventListeners(){N.on(this._element,Bn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():N.trigger(this._element,jn))}))}static jQueryInterface(t){return this.each((function(){const e=qn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}N.on(document,Wn,'[data-bs-toggle="offcanvas"]',(function(t){const e=z.getElementFromSelector(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),l(this))return;N.one(e,Fn,(()=>{a(this)&&this.focus()}));const i=z.findOne(In);i&&i!==e&&qn.getInstance(i).hide(),qn.getOrCreateInstance(e).toggle(this)})),N.on(window,Ln,(()=>{for(const t of z.find(In))qn.getOrCreateInstance(t).show()})),N.on(window,Hn,(()=>{for(const t of z.find("[aria-modal][class*=show][class*=offcanvas-]"))"fixed"!==getComputedStyle(t).position&&qn.getOrCreateInstance(t).hide()})),R(qn),m(qn);const Vn={"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},Kn=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Qn=/^(?!javascript:)(?:[a-z0-9+.-]+:|[^&:/?#]*(?:[/?#]|$))/i,Xn=(t,e)=>{const i=t.nodeName.toLowerCase();return e.includes(i)?!Kn.has(i)||Boolean(Qn.test(t.nodeValue)):e.filter((t=>t instanceof RegExp)).some((t=>t.test(i)))},Yn={allowList:Vn,content:{},extraClass:"",html:!1,sanitize:!0,sanitizeFn:null,template:"
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i=this._getTipElement();this._element.setAttribute("aria-describedby",i.getAttribute("id"));const{container:n}=this._config;if(this._element.ownerDocument.documentElement.contains(this.tip)||(n.append(i),N.trigger(this._element,this.constructor.eventName("inserted"))),this._popper=this._createPopper(i),i.classList.add(es),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.on(t,"mouseover",h);this._queueCallback((()=>{N.trigger(this._element,this.constructor.eventName("shown")),!1===this._isHovered&&this._leave(),this._isHovered=!1}),this.tip,this._isAnimated())}hide(){if(this._isShown()&&!N.trigger(this._element,this.constructor.eventName("hide")).defaultPrevented){if(this._getTipElement().classList.remove(es),"ontouchstart"in document.documentElement)for(const t 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Map,this._observableSections=new Map;const t=z.find(bs,this._config.target);for(const e of t){if(!e.hash||l(e))continue;const t=z.findOne(decodeURI(e.hash),this._element);a(t)&&(this._targetLinks.set(decodeURI(e.hash),e),this._observableSections.set(e.hash,t))}}_process(t){this._activeTarget!==t&&(this._clearActiveClass(this._config.target),this._activeTarget=t,t.classList.add(_s),this._activateParents(t),N.trigger(this._element,ps,{relatedTarget:t}))}_activateParents(t){if(t.classList.contains("dropdown-item"))z.findOne(".dropdown-toggle",t.closest(".dropdown")).classList.add(_s);else for(const e of z.parents(t,".nav, .list-group"))for(const t of z.prev(e,ys))t.classList.add(_s)}_clearActiveClass(t){t.classList.remove(_s);const e=z.find(`${bs}.${_s}`,t);for(const t of e)t.classList.remove(_s)}static jQueryInterface(t){return this.each((function(){const e=Es.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t]()}}))}}N.on(window,gs,(()=>{for(const t of z.find('[data-bs-spy="scroll"]'))Es.getOrCreateInstance(t)})),m(Es);const Ts=".bs.tab",Cs=`hide${Ts}`,Os=`hidden${Ts}`,xs=`show${Ts}`,ks=`shown${Ts}`,Ls=`click${Ts}`,Ss=`keydown${Ts}`,Ds=`load${Ts}`,$s="ArrowLeft",Is="ArrowRight",Ns="ArrowUp",Ps="ArrowDown",Ms="Home",js="End",Fs="active",Hs="fade",Ws="show",Bs=":not(.dropdown-toggle)",zs='[data-bs-toggle="tab"], [data-bs-toggle="pill"], [data-bs-toggle="list"]',Rs=`.nav-link${Bs}, .list-group-item${Bs}, [role="tab"]${Bs}, ${zs}`,qs=`.${Fs}[data-bs-toggle="tab"], .${Fs}[data-bs-toggle="pill"], .${Fs}[data-bs-toggle="list"]`;class Vs extends W{constructor(t){super(t),this._parent=this._element.closest('.list-group, .nav, [role="tablist"]'),this._parent&&(this._setInitialAttributes(this._parent,this._getChildren()),N.on(this._element,Ss,(t=>this._keydown(t))))}static get NAME(){return"tab"}show(){const t=this._element;if(this._elemIsActive(t))return;const e=this._getActiveElem(),i=e?N.trigger(e,Cs,{relatedTarget:t}):null;N.trigger(t,xs,{relatedTarget:e}).defaultPrevented||i&&i.defaultPrevented||(this._deactivate(e,t),this._activate(t,e))}_activate(t,e){t&&(t.classList.add(Fs),this._activate(z.getElementFromSelector(t)),this._queueCallback((()=>{"tab"===t.getAttribute("role")?(t.removeAttribute("tabindex"),t.setAttribute("aria-selected",!0),this._toggleDropDown(t,!0),N.trigger(t,ks,{relatedTarget:e})):t.classList.add(Ws)}),t,t.classList.contains(Hs)))}_deactivate(t,e){t&&(t.classList.remove(Fs),t.blur(),this._deactivate(z.getElementFromSelector(t)),this._queueCallback((()=>{"tab"===t.getAttribute("role")?(t.setAttribute("aria-selected",!1),t.setAttribute("tabindex","-1"),this._toggleDropDown(t,!1),N.trigger(t,Os,{relatedTarget:e})):t.classList.remove(Ws)}),t,t.classList.contains(Hs)))}_keydown(t){if(![$s,Is,Ns,Ps,Ms,js].includes(t.key))return;t.stopPropagation(),t.preventDefault();const e=this._getChildren().filter((t=>!l(t)));let 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"${t}"`);e[t]()}}))}}N.on(document,Ls,zs,(function(t){["A","AREA"].includes(this.tagName)&&t.preventDefault(),l(this)||Vs.getOrCreateInstance(this).show()})),N.on(window,Ds,(()=>{for(const t of z.find(qs))Vs.getOrCreateInstance(t)})),m(Vs);const Ks=".bs.toast",Qs=`mouseover${Ks}`,Xs=`mouseout${Ks}`,Ys=`focusin${Ks}`,Us=`focusout${Ks}`,Gs=`hide${Ks}`,Js=`hidden${Ks}`,Zs=`show${Ks}`,to=`shown${Ks}`,eo="hide",io="show",no="showing",so={animation:"boolean",autohide:"boolean",delay:"number"},oo={animation:!0,autohide:!0,delay:5e3};class ro extends W{constructor(t,e){super(t,e),this._timeout=null,this._hasMouseInteraction=!1,this._hasKeyboardInteraction=!1,this._setListeners()}static get Default(){return oo}static get DefaultType(){return so}static get NAME(){return"toast"}show(){N.trigger(this._element,Zs).defaultPrevented||(this._clearTimeout(),this._config.animation&&this._element.classList.add("fade"),this._element.classList.remove(eo),d(this._element),this._element.classList.add(io,no),this._queueCallback((()=>{this._element.classList.remove(no),N.trigger(this._element,to),this._maybeScheduleHide()}),this._element,this._config.animation))}hide(){this.isShown()&&(N.trigger(this._element,Gs).defaultPrevented||(this._element.classList.add(no),this._queueCallback((()=>{this._element.classList.add(eo),this._element.classList.remove(no,io),N.trigger(this._element,Js)}),this._element,this._config.animation)))}dispose(){this._clearTimeout(),this.isShown()&&this._element.classList.remove(io),super.dispose()}isShown(){return this._element.classList.contains(io)}_maybeScheduleHide(){this._config.autohide&&(this._hasMouseInteraction||this._hasKeyboardInteraction||(this._timeout=setTimeout((()=>{this.hide()}),this._config.delay)))}_onInteraction(t,e){switch(t.type){case"mouseover":case"mouseout":this._hasMouseInteraction=e;break;case"focusin":case"focusout":this._hasKeyboardInteraction=e}if(e)return void this._clearTimeout();const i=t.relatedTarget;this._element===i||this._element.contains(i)||this._maybeScheduleHide()}_setListeners(){N.on(this._element,Qs,(t=>this._onInteraction(t,!0))),N.on(this._element,Xs,(t=>this._onInteraction(t,!1))),N.on(this._element,Ys,(t=>this._onInteraction(t,!0))),N.on(this._element,Us,(t=>this._onInteraction(t,!1)))}_clearTimeout(){clearTimeout(this._timeout),this._timeout=null}static jQueryInterface(t){return this.each((function(){const e=ro.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}return 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\ No newline at end of file
diff --git a/bs/.development/Distris_files/libs/quarto-html/anchor.min.js b/bs/.development/Distris_files/libs/quarto-html/anchor.min.js
deleted file mode 100644
index 5ac814d..0000000
--- a/bs/.development/Distris_files/libs/quarto-html/anchor.min.js
+++ /dev/null
@@ -1,9 +0,0 @@
-// @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&dn=expat.txt Expat
-//
-// AnchorJS - v5.0.0 - 2023-01-18
-// https://www.bryanbraun.com/anchorjs/
-// Copyright (c) 2023 Bryan Braun; Licensed MIT
-//
-// @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&dn=expat.txt Expat
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-// @license-end
\ No newline at end of file
diff --git a/bs/.development/Distris_files/libs/quarto-html/popper.min.js b/bs/.development/Distris_files/libs/quarto-html/popper.min.js
deleted file mode 100644
index e3726d7..0000000
--- a/bs/.development/Distris_files/libs/quarto-html/popper.min.js
+++ /dev/null
@@ -1,6 +0,0 @@
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- */
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t=e.state,n=e.name,r=t.rects.reference,o=t.rects.popper,i=t.modifiersData.preventOverflow,a=J(t,{elementContext:"reference"}),s=J(t,{altBoundary:!0}),f=ve(a,r),c=ve(s,o,i),p=ye(f),u=ye(c);t.modifiersData[n]={referenceClippingOffsets:f,popperEscapeOffsets:c,isReferenceHidden:p,hasPopperEscaped:u},t.attributes.popper=Object.assign({},t.attributes.popper,{"data-popper-reference-hidden":p,"data-popper-escaped":u})}},be=Z({defaultModifiers:[ee,te,oe,ie]}),xe=[ee,te,oe,ie,ae,le,he,me,ge],we=Z({defaultModifiers:xe});e.applyStyles=ie,e.arrow=me,e.computeStyles=oe,e.createPopper=we,e.createPopperLite=be,e.defaultModifiers=xe,e.detectOverflow=J,e.eventListeners=ee,e.flip=le,e.hide=ge,e.offset=ae,e.popperGenerator=Z,e.popperOffsets=te,e.preventOverflow=he,Object.defineProperty(e,"__esModule",{value:!0})}));
-
diff --git a/bs/.development/FormulaHelper.R b/bs/.development/FormulaHelper.R
deleted file mode 100644
index a206f64..0000000
--- a/bs/.development/FormulaHelper.R
+++ /dev/null
@@ -1,18 +0,0 @@
-get_formula <- function(model) {
- call <- model$call |> as.character()
- e <- try(
- {
- as.formula(call[2])
- },
- silent = TRUE
- )
- if (inherits(e, "try-error")) {
- return(get(call[2]) |> knitr::kable())
- } else {
- return(knitr::kable(call[2]))
- }
-}
-
-show <- function(model) {
- knitr::kable(broom::tidy(model))
-}
diff --git a/bs/.development/Regression_linear_model_files/figure-html/Regressions-1.png b/bs/.development/Regression_linear_model_files/figure-html/Regressions-1.png
deleted file mode 100644
index 1afa818..0000000
Binary files a/bs/.development/Regression_linear_model_files/figure-html/Regressions-1.png and /dev/null differ
diff --git a/bs/.development/Rplots.pdf b/bs/.development/Rplots.pdf
deleted file mode 100644
index ea7f0ef..0000000
Binary files a/bs/.development/Rplots.pdf and /dev/null differ
diff --git a/bs/.development/deploy.R b/bs/.development/deploy.R
deleted file mode 100644
index 3cbafb4..0000000
--- a/bs/.development/deploy.R
+++ /dev/null
@@ -1,4 +0,0 @@
-setwd("/home/konrad/Documents/Biostats")
-
-shinylive::export("./bs/inst/serverless_app/", "docs")
-httpuv::runStaticServer("docs/")
diff --git a/bs/.development/minimalApp.R b/bs/.development/minimalApp.R
deleted file mode 100644
index f233de6..0000000
--- a/bs/.development/minimalApp.R
+++ /dev/null
@@ -1,56 +0,0 @@
-library(shiny)
-
-ui <- fluidPage(
- # JavaScript to initialize the popover with interactive content on click
- tags$script(HTML("
- $(document).ready(function() {
- // Initialize the popover on click instead of hover
- $('#aovTest').popover({
- trigger: 'click', // Opens on click
- html: true,
- content: 'Go to ANOVA Info ',
- placement: 'bottom'
- });
-
- // Set up click event for the button inside the popover
- $(document).on('click', '#popoverBtn', function() {
- Shiny.setInputValue('go_to_tab', 'infoTab');
- $('#aovTest').popover('hide'); // Hide the popover after clicking the button
- });
-
- // Close the popover if clicking outside of it
- $(document).on('click', function(e) {
- if (!$(e.target).closest('#aovTest').length) {
- $('#aovTest').popover('hide');
- }
- });
- });
- ")),
-
- # UI with tab layout
- tabsetPanel(
- id = "mainTabset",
- tabPanel("Main",
- # Action button with popover for interactive tooltip
- actionButton(
- "aovTest", "ANOVA"
- ),
- p("This is the Main tab.")
- ),
- tabPanel("Info",
- value = "infoTab", # This is the ID to match in JavaScript
- h3("ANOVA Information"),
- p("Here are more details about ANOVA...")
- )
- )
-)
-
-server <- function(input, output, session) {
- # Observe the JavaScript input and update the selected tab
- observeEvent(input$go_to_tab, {
- updateTabsetPanel(session, "mainTabset", selected = input$go_to_tab)
- })
-}
-
-shinyApp(ui, server)
-
diff --git a/bs/.development/remove_buttons.R b/bs/.development/remove_buttons.R
deleted file mode 100644
index c62235b..0000000
--- a/bs/.development/remove_buttons.R
+++ /dev/null
@@ -1,55 +0,0 @@
-library(shiny)
-
-ui <- fluidPage(
- titlePanel("Dynamic List with Remove Buttons"),
- sidebarLayout(
- sidebarPanel(
- numericInput("num_input", "Enter a number:", value = 0),
- actionButton("add_btn", "Add to List")
- ),
- mainPanel(
- uiOutput("dynamic_list")
- )
- )
-)
-
-server <- function(input, output, session) {
- listValues <- reactiveVal(list())
- observeEvent(input$add_btn, {
- current_list <- listValues()
- new_item_name <- paste0("item_", length(current_list) + 1)
- current_list[[new_item_name]] <- input$num_input
- listValues(current_list)
- })
-
- # Dynamically render the list UI
- output$dynamic_list <- renderUI({
- current_list <- listValues()
- if (length(current_list) == 0) {
- return("No items in the list.")
- }
- # Create UI elements for each item in the list
- tagList(lapply(names(current_list), function(name) {
- div(
- style = "margin-bottom: 10px;",
- span(paste(name, ":", current_list[[name]]), style = "margin-right: 10px;"),
- actionButton(name, "Remove", class = "btn-danger btn-sm")
- )
- }))
- })
-
- # Observe and handle remove buttons dynamically
- observe({
- current_list <- listValues()
- lapply(names(current_list), function(name) {
- observeEvent(input[[name]], {
- current_list <- listValues()
- current_list[[name]] <- NULL # Remove the item
- listValues(current_list)
- }, ignoreInit = TRUE)
- })
- })
-}
-
-shinyApp(ui, server)
-
diff --git a/bs/R/DoseResponse.R b/bs/R/DoseResponse.R
index c156520..8c18ae5 100644
--- a/bs/R/DoseResponse.R
+++ b/bs/R/DoseResponse.R
@@ -17,8 +17,16 @@ DoseResponseSidebarUI <- function(id) {
),
br(),
uiOutput(NS(id, "substanceNamesUI")),
- uiOutput(NS(id, "negIdentifierUI")),
- uiOutput(NS(id, "posIdentifierUI")),
+ checkboxInput(
+ NS(id, "xTransform"),
+ label = "Log transform x-axis",
+ value = FALSE
+ ),
+ checkboxInput(
+ NS(id, "yTransform"),
+ label = "Log transform y-axis",
+ value = FALSE
+ ),
actionButton(NS(id, "ic50"), "Conduct analysis")
)
)
@@ -41,9 +49,13 @@ DoseResponseUI <- function(id) {
tabPanel(
"Results Plot",
uiOutput(NS(id, "dropdown_plots")),
- plotOutput(NS(id, "dr_result_plot")),
+ plotOutput(
+ NS(id, "dr_result_plot"),
+ click = NS(id, "plot_click")
+ ),
actionButton(NS(id, "previousPage"), "Previous plot"),
- actionButton(NS(id, "nextPage"), "Next plot")
+ actionButton(NS(id, "nextPage"), "Next plot"),
+ p("Click on the plot to mark outliers")
)
)
)
@@ -56,10 +68,11 @@ DoseResponseServer <- function(id, data, listResults) {
names = NULL, # For dropdown_plots
overview_plots = NULL,
currentPage = 1,
- currentPageOverview = 1
+ currentPageOverview = 1,
+ outliers = NULL
)
- # Render names, conc and abs column
+ # Render names of substances
output[["substanceNamesUI"]] <- renderUI({
req(!is.null(data$df))
req(is.data.frame(data$df))
@@ -81,52 +94,6 @@ DoseResponseServer <- function(id, data, listResults) {
)
})
- output[["negIdentifierUI"]] <- renderUI({
- req(!is.null(data$df))
- req(is.data.frame(data$df))
- req(input$`substanceNames`)
- choices <- unique(data$df[[input$substanceNames]])
- req(length(choices) >= 1)
- tooltip <- "Select the name used for the negative control"
- div(
- tags$label(
- "Dependent Variable",
- class = "tooltip",
- title = tooltip,
- `data-toggle` = "tooltip"
- ),
- selectInput(
- inputId = paste0("DOSERESPONSE-negIdentifier"),
- label = "Name of the negative control",
- choices = choices[1:length(choices)],
- selected = NULL
- )
- )
- })
-
- output[["posIdentifierUI"]] <- renderUI({
- req(!is.null(data$df))
- req(is.data.frame(data$df))
- req(input$`substanceNames`)
- choices <- unique(data$df[[input$substanceNames]])
- req(length(choices) >= 1)
- tooltip <- "Select the name used for the positive control"
- div(
- tags$label(
- "Dependent Variable",
- class = "tooltip",
- title = tooltip,
- `data-toggle` = "tooltip"
- ),
- selectInput(
- inputId = paste0("DOSERESPONSE-posIdentifier"),
- label = "Name of the positive control",
- choices = choices[1:length(choices)],
- selected = NULL
- )
- )
- })
-
# Render split by group
output[["open_split_by_group"]] <- renderUI({
actionButton(NS(id, "open_split_by_group"),
@@ -206,15 +173,11 @@ DoseResponseServer <- function(id, data, listResults) {
})
})
- drFct <- function() {
+ drFct <- function(reset_outliers = TRUE) {
req(is.data.frame(data$df))
df <- data$df
req(input$substanceNames)
names <- input$substanceNames
- req(input$negIdentifier)
- neg <- input$negIdentifier
- req(input$posIdentifier)
- pos <- input$posIdentifier
print_noti(!is.null(data$formula), "You have to set a formula")
req(!is.null(data$formula))
r_vals$plots <- NULL # reset
@@ -222,51 +185,73 @@ DoseResponseServer <- function(id, data, listResults) {
r_vals$currentPage <- 1 # reset
r_vals$overview_plots <- NULL # reset
r_vals$currentPageOverview <- 1 # reset
+ if (reset_outliers) {
+ r_vals$outliers <- NULL
+ }
+ is_xlog <- input$xTransform
+ is_ylog <- input$yTransform
f <- as.character(data$formula)
+ formula <- data$formula
dep <- f[2]
indep <- f[3]
err <- NULL
resDF <- NULL
resPlot <- NULL
- e <- try({
- check_ast(str2lang(indep), colnames(df))
- check_ast(str2lang(dep), colnames(df))
- res <- ic50(df, dep, indep, names, neg, pos)
- stopifnot(!inherits(res, "errorClass"))
- resDF <- lapply(res, function(x) {
- if (inherits(x, "errorClass")) {
- return(NULL)
- }
- return(x[[1]])
- })
- resDF <- resDF[!is.null(resDF)]
- resDF <- resDF[!sapply(resDF, is.null)]
- resDF <- Reduce(rbind, resDF)
- resP <- lapply(res, function(x) {
- if (inherits(x, "errorClass")) {
- return(NULL)
+ e <- try(
+ {
+ check_formula(formula)
+ check_ast(str2lang(indep), colnames(df))
+ check_ast(str2lang(dep), colnames(df))
+ res <- ic50(
+ df, dep,
+ indep, names, r_vals$outliers,
+ is_xlog, is_ylog
+ )
+ if (inherits(res, "errorClass")) {
+ stop(res$error_message)
}
- return(x[[2]])
- })
- resP <- resP[!is.null(resP)]
- resP <- resP[!sapply(resP, is.null)]
- r_vals$plots <- resP
- r_vals$names <- resDF$name
- resPlot <- resP
- overviewPlots <- create_plot_pages(resPlot)
- r_vals$overview_plots <- overviewPlots
- })
+ resDF <- lapply(res, function(x) {
+ if (inherits(x, "errorClass")) {
+ return(NULL)
+ }
+ return(x[[1]])
+ })
+ resDF <- resDF[!is.null(resDF)]
+ resDF <- resDF[!sapply(resDF, is.null)]
+ resDF <- Reduce(rbind, resDF)
+ resP <- lapply(res, function(x) {
+ if (inherits(x, "errorClass")) {
+ return(NULL)
+ }
+ return(x[[2]])
+ })
+ resP <- resP[!is.null(resP)]
+ resP <- resP[!sapply(resP, is.null)]
+ r_vals$plots <- resP
+ r_vals$names <- resDF$name
+ resPlot <- resP
+ overviewPlots <- create_plot_pages(resPlot)
+ r_vals$overview_plots <- overviewPlots
+ },
+ silent = TRUE
+ )
if (inherits(e, "try-error")) {
err <- conditionMessage(attr(e, "condition"))
print_noti(FALSE, err)
} else {
listResults$curr_data <- new("doseResponse", df = resDF, p = resPlot)
- listResults$curr_name <- paste("Test Nr", length(listResults$all_names) + 1, "Conducted dose response analysis")
+ listResults$curr_name <- paste(
+ "Test Nr", length(listResults$all_names) + 1,
+ "Conducted dose response analysis"
+ )
output$dr_result <- renderTable(resDF, digits = 6)
listResults$counter <- listResults$counter + 1
new_result_name <- paste0("DoseResponseNr", listResults$counter)
- listResults$all_data[[new_result_name]] <- new("doseResponse", df = resDF, p = resPlot)
+ listResults$all_data[[new_result_name]] <- new(
+ "doseResponse",
+ df = resDF, p = resPlot
+ )
exportTestValues(
doseresponse_res = listResults$curr_data
@@ -326,6 +311,47 @@ DoseResponseServer <- function(id, data, listResults) {
}
})
+ observeEvent(input$plot_click, {
+ req(!is.null(input$plot_click))
+ req(is.data.frame(data$df))
+ print_noti(!is.null(data$formula), "You have to set a formula")
+ try({
+ click <- input$plot_click
+ df <- data$df
+ indices <- which(df$names == r_vals$names[r_vals$currentPage])
+ indices <- data.frame(
+ original_indices = indices,
+ new_indices = seq_along(indices)
+ )
+ sub_df <- df[df$names == r_vals$names[r_vals$currentPage], ]
+ f <- as.character(data$formula)
+ formula <- data$formula
+ check_formula(formula)
+ dep <- f[2]
+ indep <- f[3]
+ x <- as.numeric(sub_df[, indep])
+ y <- as.numeric(sub_df[, dep])
+ x <- x[!is.na(x)]
+ y <- y[!is.na(y)]
+ distances <- sqrt((x - click$x)^2 + (y - click$y)^2)
+ nearest <- which.min(distances)
+ if (distances[nearest] < 0.1) {
+ nearest <- indices[indices$new_indices == nearest, "original_indices"]
+ if (nearest %in% r_vals$outliers) {
+ r_vals$outliers <- r_vals$outliers[r_vals$outliers != nearest]
+ } else {
+ r_vals$outliers <- c(
+ r_vals$outliers,
+ nearest
+ )
+ }
+ old_current_page <- r_vals$currentPage
+ drFct(FALSE)
+ r_vals$currentPage <- old_current_page
+ }
+ })
+ })
+
# Display overview plots
observe({
req(!is.null(r_vals$overview_plots))
diff --git a/bs/R/lc50.r b/bs/R/lc50.r
index 3f95f3e..d15409b 100644
--- a/bs/R/lc50.r
+++ b/bs/R/lc50.r
@@ -3,10 +3,10 @@ errorClass <- R6::R6Class("errorClass",
error_message = NULL,
object = NULL,
initialize = function(error_message = NULL) {
- self$error_message = error_message
+ self$error_message <- error_message
},
isNull = function() {
- if(is.null(self$error_message)) {
+ if (is.null(self$error_message)) {
return(TRUE)
}
return(FALSE)
@@ -14,285 +14,365 @@ errorClass <- R6::R6Class("errorClass",
)
)
-shapenumber <- function (my.number) {
- if (is.finite(my.number)) {
- my.result <- signif(my.number,3)
- } else {
- my.result <- NA
- }
- return (my.result)
+shapenumber <- function(num) {
+ if (is.finite(num)) {
+ res <- signif(num)
+ } else {
+ res <- NA
+ }
+ return(res)
}
-#calculates the robust 68th percentile of the residuals
-#adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123
-robust_68_percentile <- function (residuals) {
+# calculates the robust 68th percentile of the residuals
+# adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123
+robust_68_percentile <- function(residuals) {
res <- abs(residuals)
res_sorted <- sort(res)
- res_percentiles <- (seq(1:length(res_sorted))/length(res_sorted))*100
- index <- min(which(res_percentiles > 68.25))
- x <- c(res_percentiles[index-1],res_percentiles[index])
- y <- c(res_sorted[index-1],res_sorted[index])
- m <- lm(y~x)
- x <- c(68.25)
+ res_percentiles <- (seq_len(length(res_sorted)) / length(res_sorted))
+ index <- min(which(res_percentiles > 0.6825))
+ x <- c(res_percentiles[index - 1], res_percentiles[index])
+ y <- c(res_sorted[index - 1], res_sorted[index])
+ m <- lm(y ~ x)
+ x <- 0.6825
y <- predict(m, as.data.frame(x))
return(y)
}
-#calculates the robust standard deviation of the residuals (RSDR) with correction for degrees of freedom
-#adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123
-robust_standard_deviation_residuals <- function(residuals, number_of_coefficients_fitted) {
- my_residuals <- as.numeric(residuals)
- my_residuals <- na.omit(residuals)
- N <- length(my_residuals) #the number of data points fitted
- K <- number_of_coefficients_fitted #for ic50, 4 coefficients are fitted
- result <- robust_68_percentile(residuals) * N/(N-K)
- return (result)
+# calculates the robust standard deviation of the residuals (RSDR)
+# with correction for degrees of freedom
+# adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123
+# robust_standard_deviation_residuals = rsdr
+rsdr <- function(residuals, number_of_coefficients_fitted) {
+ resids <- as.numeric(residuals)
+ resids <- na.omit(residuals)
+ N <- length(resids)
+ robust_68_percentile(residuals) *
+ N / (N - number_of_coefficients_fitted)
}
-#false discovery rate (FDR) approach, returns a T/F vector for selection of valid data points
-#adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123
+# false discovery rate (FDR) approach,
+# returns a T/F vector for selection of valid data points
+# adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123
false_discovery_rate <- function(res) {
- N <- length(res)
- Q <- 0.01 #Q=1%
- K <- 4 #number of coefficients in the fitted LL.4 model
- R <- robust_standard_deviation_residuals(res,K) #the robust standard deviation of the residuals
- id <- seq(1:length(res))
- df <- data.frame(id,res)
+ N <- length(res)
+ # Q=1%
+ Q <- 0.01
+ # number of coefficients in the fitted LL.4 model
+ K <- 4
+ R <- rsdr(res, K)
+ id <- seq_len(length(res))
+ df <- data.frame(id, res)
df$res_abs <- abs(df$res)
- df <- df[order(df$res_abs),]
+ df <- df[order(df$res_abs), ]
df$i <- seq(1:N)
df$i_fraction <- df$i / N
- df$alpha <- Q*(N-(df$i-1))/N
+ df$alpha <- Q * (N - (df$i - 1)) / N
df$t <- df$res_abs / R
- df$P <- dt(df$t, N-K)
+ df$P <- dt(df$t, N - K)
df$include <- ifelse(df$P < df$alpha & df$i_fraction >= 0.7, FALSE, TRUE)
df2 <- df[order(df$id), ]
- return (df2$include)
+ return(df2$include)
}
-check_fit <- function(model, min_conc, max_conc, min_abs, max_abs, substance_name) {
- if(model$fit$convergence != TRUE) return(errorClass$new(paste(substance_name,
- "Model did not converge")))
- b <- coefficients(model)[1] #Hill coefficient
- c <- coefficients(model)[2] #asymptote 1
- d <- coefficients(model)[3] #asymptote 2
- e <- coefficients(model)[4] #IC50
- RSE <- summary(model)$rseMat[1] #residual standard error estimated
- Response_lowestdose_predicted <- predict(model, data.frame(concentration = min_conc), se.fit = FALSE)[1]
- Response_highestdose_predicted <- predict(model, data.frame(concentration = max_conc), se.fit = FALSE)[1]
- Response_difference <- 100 * abs(Response_lowestdose_predicted - Response_highestdose_predicted)
+check_fit <- function(model, min_conc, max_conc,
+ min_abs, max_abs, substance_name) {
+ if (model$fit$convergence != TRUE) {
+ return(errorClass$new(paste(
+ substance_name,
+ "Model did not converge"
+ )))
+ }
+ b <- coefficients(model)[1] # Hill coefficient
+ c <- coefficients(model)[2] # asymptote 1
+ d <- coefficients(model)[3] # asymptote 2
+ e <- coefficients(model)[4] # IC50
+ RSE <- summary(model)$rseMat[1] # residual standard error estimated
+ Response_lowestdose_predicted <- predict(
+ model, data.frame(concentration = min_conc),
+ se.fit = FALSE
+ )[1]
+ Response_highestdose_predicted <- predict(
+ model, data.frame(concentration = max_conc),
+ se.fit = FALSE
+ )[1]
+ Response_difference <- abs(
+ Response_lowestdose_predicted - Response_highestdose_predicted
+ )
HillCoefficient <- b
- IC50_relative <- e
- pIC50 <- -log10(e/1000000)
+ IC50_relative <- e
Problems <- ""
- if (Response_difference < 25) {
- Problems <- paste(Problems, "Response Difference lower than 25%", collapse = " , ")
- } else if(IC50_relative > max_conc) {
- Problems <- paste(Problems, "IC50 larger than highest measured concentration", collapse = " , ")
- } else if(IC50_relative < min_conc) {
- Problems <- paste(Problems, "IC50 lower than lowest measured concentration", collapse = " , ")
- }
-
+ if (Response_difference < 0.25) {
+ Problems <- paste(Problems,
+ "Response Difference lower than 25%",
+ collapse = " , "
+ )
+ } else if (IC50_relative > max_conc) {
+ Problems <- paste(Problems,
+ "IC50 larger than highest measured concentration",
+ collapse = " , "
+ )
+ } else if (IC50_relative < min_conc) {
+ Problems <- paste(Problems,
+ "IC50 lower than lowest measured concentration",
+ collapse = " , "
+ )
+ }
confidence_interval <- confint(model, parm = c("e"), level = 0.95)
- IC50_relative_lower <- confidence_interval[1]
+ IC50_relative_lower <- confidence_interval[1]
IC50_relative_higher <- confidence_interval[2]
p_value <- noEffect(model)[3]
Response_lowestdose_predicted <- shapenumber(Response_lowestdose_predicted)
Response_highestdose_predicted <- shapenumber(Response_highestdose_predicted)
- HillCoefficient <- shapenumber(HillCoefficient)
+ HillCoefficient <- shapenumber(HillCoefficient)
IC50_relative <- shapenumber(IC50_relative)
IC50_relative_lower <- shapenumber(IC50_relative_lower)
IC50_relative_higher <- shapenumber(IC50_relative_higher)
- pIC50 <- shapenumber( -log10(IC50_relative/1000000))
+ pIC50 <- shapenumber(-log10(IC50_relative))
p_value <- shapenumber(p_value)
- ylim_low = 0
- ylim_high = 125
- if (min_abs < ylim_low) ylim_low <- min_abs
- if (max_abs > ylim_high) ylim_high <- max_abs
- outvar <- data.frame(name = substance_name,
- Response_lowestdose_predicted = Response_lowestdose_predicted,
- Response_highestdose_predicted = Response_highestdose_predicted,
- HillCoefficient = HillCoefficient,
- asymptote_one = c, asymptote_two = d,
- IC50_relative = IC50_relative, IC50_relative_lower = IC50_relative_lower,
- IC50_relative_higher = IC50_relative_higher, pIC50 = pIC50,
- RSE = RSE, p_value = p_value, Problems = Problems)
- return (outvar)
+ outvar <- data.frame(
+ name = substance_name,
+ Response_lowestdose_predicted = Response_lowestdose_predicted,
+ Response_highestdose_predicted = Response_highestdose_predicted,
+ HillCoefficient = HillCoefficient,
+ asymptote_one = c, asymptote_two = d,
+ IC50_relative = IC50_relative, IC50_relative_lower = IC50_relative_lower,
+ IC50_relative_higher = IC50_relative_higher, pIC50 = pIC50,
+ RSE = RSE, p_value = p_value, Problems = Problems
+ )
+ return(outvar)
+}
+
+drawplotOnlyRawData <- function(df, abs_col, conc_col, title) {
+ data_measured <- data.frame(conc = df[, conc_col], abs = df[, abs_col])
+ p <- ggplot() +
+ geom_boxplot(
+ data = data_measured,
+ aes(x = conc, y = abs, group = conc)
+ ) +
+ geom_point(
+ data = data_measured,
+ aes(x = conc, y = abs)
+ ) +
+ xlab("Concentration") + # Concentration in µM
+ ylab("Viability") + # Viaibility [%]
+ ggtitle(title)
+ return(p)
+}
+
+addOutlierLayer <- function(df_outlier, abs_col, conc_col, p) {
+ if (nrow(df_outlier) == 0) {
+ return(p)
+ }
+ p <- p +
+ geom_point(
+ data = df_outlier,
+ aes(
+ x = df_outlier[, conc_col],
+ y = df_outlier[, abs_col], color = "Outlier"
+ )
+ ) +
+ scale_color_manual(
+ name = "",
+ values = "darkorange"
+ )
}
drawplot <- function(df, abs_col, conc_col, model, valid_points, title,
- IC50_relative, IC50_relative_lower, IC50_relative_higher) {
+ IC50_relative, IC50_relative_lower, IC50_relative_higher,
+ df_outlier) {
min_conc <- min(df[, conc_col])
max_conc <- max(df[, conc_col])
grid <- seq(min_conc, max_conc, 0.1)
plotFct <- (model$curve)[[1]]
res <- plotFct(grid)
- data <- data.frame(abs = res,
- conc = grid)
- data_measured <- data.frame(conc = df[, conc_col], abs = df[, abs_col])
- p <- ggplot() +
- geom_boxplot(data = data_measured, aes(x = conc, y = abs*100, group = conc)) +
- geom_line(data = data, aes(x = conc, y = abs*100)) +
- xlab("Concentration [µM]") +
- ylab("Viability [%]") +
- ggtitle(title)
-
- max_conc <- max(df[, conc_col]) + 10
- min_conc <- -10
+ data <- data.frame(
+ abs = res,
+ conc = grid
+ )
+ p <- drawplotOnlyRawData(df, abs_col, conc_col, title) +
+ geom_line(data = data, aes(x = conc, y = abs))
+ p <- addOutlierLayer(df_outlier, abs_col, conc_col, p)
+ max_conc <- max(df[, conc_col]) +
+ 0.1 * (max(df[, conc_col]) - min(df[, conc_col]))
+ min_conc <- min(df[, conc_col]) - 0.1 * min(df[, conc_col])
xmin <- IC50_relative - IC50_relative_lower
xmax <- IC50_relative + IC50_relative_higher
- if (!is.na(xmin) & !is.na(xmax)) {
- ymin <- min(df[, abs_col]) * 100
- ymax <- max(df[, abs_col]) * 100
+ if (!is.na(xmin) && !is.na(xmax)) {
+ ymin <- min(df[, abs_col])
+ ymax <- max(df[, abs_col])
yrange <- ymax - ymin
butt_height <- yrange * 0.1
- ymedian <- median(df[, abs_col]) * 100
- if (xmin > min_conc && xmax < max_conc ) {
- p <- p + geom_errorbarh(aes(xmin = xmin,
- xmax = xmax, y = ymedian),
- colour = "darkred", end = "butt", height = butt_height)
+ ymedian <- median(df[, abs_col])
+ if (xmin > min_conc && xmax < max_conc) {
+ p <- p + geom_errorbarh(
+ aes(
+ xmin = xmin,
+ xmax = xmax, y = ymedian
+ ),
+ colour = "darkred", end = "butt", height = butt_height
+ )
} else {
p <- p + labs(caption = "Confidence intervall not in conc. range") +
- theme(plot.caption = element_text(color = "darkred", face = "italic", size = 7))
- }
+ theme(
+ plot.caption =
+ element_text(color = "darkred", face = "italic", size = 8)
+ )
+ }
} else {
p <- p + labs(caption = "Confidence intervall could not be calculated") +
- theme(plot.caption = element_text(color = "darkred", face = "italic", size = 7))
+ theme(
+ plot.caption =
+ element_text(color = "darkred", face = "italic", size = 8)
+ )
}
-
+
return(p)
}
-ic50_internal <- function(df, abs, conc, title) {
- model <- drm(abs ~ conc, data = df , fct = LL.4(), robust = "median")
+ic50_internal <- function(df, abs, conc, title, df_outlier) {
+ model <- drm(abs ~ conc,
+ data = df, fct = LL.4(),
+ robust = "median"
+ )
valid_points <- false_discovery_rate(residuals(model))
- model <- drm(abs ~ conc, data = df , subset = valid_points, start = model$coefficients, fct = LL.4(), robust = "mean")
- res <- check_fit(model, min(df[, conc]), max(df[, conc]), min(df[, abs]), max(df[, abs]), title)
- p <- drawplot(df, abs, conc, model, valid_points, title, res$IC50_relative,
- res$IC50_relative_lower, res$IC50_relative_higher)
+ model <- drm(abs ~ conc,
+ data = df,
+ subset = valid_points,
+ start = model$coefficients,
+ fct = LL.4(), robust = "mean",
+ )
+ res <- check_fit(
+ model, min(df[, conc]),
+ max(df[, conc]), min(df[, abs]), max(df[, abs]), title
+ )
+ p <- drawplot(
+ df, abs, conc, model, valid_points, title, res$IC50_relative,
+ res$IC50_relative_lower, res$IC50_relative_higher, df_outlier
+ )
return(list(res, p))
}
-drawplotOnlyRawData <- function(df, abs_col, conc_col, title) {
- min_conc <- min(df[, conc_col])
- max_conc <- max(df[, conc_col])
- data_measured <- data.frame(conc = df[, conc_col], abs = df[, abs_col])
- p <- ggplot() +
- geom_boxplot(data = data_measured, aes(x = conc, y = abs*100, group = conc)) +
- xlab("Concentration [µM]") +
- ylab("Viability [%]") +
- ggtitle(title)
- return(p)
+check_dr_df <- function(df, abs_col,
+ conc_col, substance_name_col) {
+ if (!is.character(df[, substance_name_col]) &&
+ !is.factor(df[, substance_name_col])) {
+ return(errorClass$new("The substance names are not character"))
+ }
+ substances <- unique(df[, substance_name_col])
+ if (length(substances) < 1) {
+ return(errorClass$new("The data for compounds seems to be missing"))
+ }
+ if (!is.numeric(df[, abs_col])) {
+ return(errorClass$new("The absorbance data is not numerical"))
+ }
+ return(NULL)
}
-#' Calculates the ic50 values
-#' @export
-#' @import drc
-#' @import ggplot2
-#' @param df a data.frame which contains all the data
-#' @param abs_col the name of the column in df which contains the dependent variable
-#' @param conc_col the name of the column in df which contains the different concentrations
-#' @param substance_name_col the name of the column in df which contains the different names of the compounds
-#' @param negative_identifier a character defining the name to identify the negative control within conc_col
-#' @param positive_identifier a character defining the name to identify the positive control within conc_col
-#' @return a list is returned containing the ic50 value the fitted plots and other parameters
-#' @examples
-#' path <- system.file("data", package = "MTT")
-#' df <- read.csv(paste0(path, "/ExampleData.txt"))
-#' ic50(df, "abs", "conc", "names", "neg", "pos")
-ic50 <- function(df, abs_col, conc_col, substance_name_col, negative_identifier, positive_identifier) {
- substances <- unique(df$names)
-
- if(!(negative_identifier %in% substances)) {
- return(errorClass$new("the string for the negative control was not found!"))
+transform_conc_dr <- function(conc_col) {
+ temp_conc <- as.numeric(conc_col)
+ if (all(is.na(temp_conc))) {
+ return(errorClass$new(
+ "The concentration data cannot be converted to numerical"
+ ))
}
- if(!(positive_identifier %in% substances)) {
- return(errorClass$new("the string for the positive control was not found!"))
+ if (!is.numeric(temp_conc)) {
+ return(errorClass$new("The concentration data is not numerical"))
}
- substances <- substances[substances != negative_identifier]
- substances <- substances[substances != positive_identifier]
- if(length(substances) < 1) {
- return(errorClass$new("The data for compounds seems to be missing"))
+ return(temp_conc)
+}
+
+log_dr <- function(df, islog_x, islog_y) {
+ if (islog_x) {
+ df$conc <- log(df$conc)
}
- if(!is.numeric(df[, abs_col])) {
- return(errorClass$new("The absorbance data is not numerical"))
+ if (islog_y) {
+ df$abs <- log(df$abs)
}
- temp_conc <- df[, conc_col]
- temp_conc[temp_conc == negative_identifier] <- -1
- temp_conc[temp_conc == positive_identifier] <- -2
- temp_conc <- as.numeric(temp_conc)
- if(any(is.na(temp_conc))) {
- return(errorClass$new("The concentration data cannot be converted to numerical"))
+ return(df)
+}
+
+#' @examples
+#' path <- system.file("data", package = "MTT")
+#' df <- read.csv(paste0(path, "/ExampleData.txt"))
+#' ic50(df, "abs", "conc", "names", NULL, FALSE, FALSE)
+ic50 <- function(df, abs_col, conc_col,
+ substance_name_col, outliers,
+ islog_x, islog_y) {
+ # Checks
+ err <- check_dr_df(df, abs_col, conc_col, substance_name_col)
+ if (inherits(err, "errorClass")) {
+ return(err)
+ }
+ substances <- unique(df[, substance_name_col])
+ # Data preparation
+ temp_conc <- transform_conc_dr(df[, conc_col])
+ if (inherits(temp_conc, "errorClass")) {
+ return(temp_conc)
}
df[, conc_col] <- temp_conc
- if(!is.numeric(df[, conc_col])) {
- return(errorClass$new("The concentration data is not numerical"))
+ df <- data.frame(
+ abs = df[, abs_col],
+ conc = df[, conc_col],
+ names = df[, substance_name_col]
+ )
+ df <- log_dr(df, islog_x, islog_y)
+ df_outlier <- data.frame()
+ if (length(outliers) >= 1) {
+ df_outlier <- df[outliers, ]
+ df <- df[-outliers, ]
}
- neg_mean <- mean(df[df[ , substance_name_col] == negative_identifier, abs_col])
- pos_mean <- mean(df[df[ , substance_name_col] == positive_identifier, abs_col])
- df[, abs_col] <- (df[, abs_col] - pos_mean) / neg_mean
+ df <- df[!sapply(df$conc, is.na), ]
res <- list()
- for(i in seq_along(substances)) {
+ for (i in seq_along(substances)) {
df_temp <- df[df$names == substances[i], ]
- m <- tryCatch({
- m <- ic50_internal(df_temp, abs_col, conc_col, substances[i])
- },
- error = function(err) {
- retval <- errorClass$new(paste("A warning occurred: ", conditionMessage(err)))
- retval$object <- drawplotOnlyRawData(df_temp, abs_col, conc_col, substances[i])
- return(retval)
- })
+ df_temp_outlier <- df_outlier[df_outlier$names == substances[i], ]
+ m <- tryCatch(
+ {
+ m <- ic50_internal(
+ df_temp,
+ "abs", "conc",
+ substances[i], df_temp_outlier
+ )
+ },
+ error = function(err) {
+ retval <- errorClass$new(
+ paste("A warning occurred: ", conditionMessage(err))
+ )
+ retval$object <- drawplotOnlyRawData(
+ df_temp, "abs", "conc", substances[i]
+ )
+ return(retval)
+ }
+ )
res[[i]] <- m
}
-
return(res)
}
-report_plots <- function(ic50List) {
- p3 <- ggdraw() +
- draw_line(x = c(0, 1), y = c(0.5, 0.5), color = "black", size = 1) +
- theme_void()
- for(i in seq_along(ic50List)) {
- if(is(ic50List[[i]], "errorClass")) {
- p <- ic50List[[i]]$object
- p <- p +
- annotate("text", x = -Inf, y = -Inf,
- hjust = -0.2, vjust = -1, label = ic50List[[i]]$error_message)
- #print(p)
- #print(p3)
- next
- }
- p1 <- ic50List[[i]][[2]]
- a <- ic50List[[i]][[1]] |> t() |> as.data.frame()
- a <- data.frame(names = row.names(a), Predicition = a)
- a[a$names == "Response_lowestdose_predicted", 1] <- "Response_lowestdose"
- a[a$names == "Response_highestdose_predicted", 1] <- "Response_highestdose"
- problem <- a[a$names == "Problems", 2]
- a <- a[(a$names != "Problems") & (a$names != "name"), ]
- p2 <- ggplot(a, aes(x = 0, y = factor(names), label = Prediction)) +
- geom_line(size = 0) +
- geom_text(position = position_nudge(x = -1.1), hjust = 0, size = 3) +
- theme_minimal() +
- theme(axis.text.x = element_blank(),
- axis.ticks.x = element_blank(),
- panel.grid.major.x = element_blank(),
- panel.grid.minor.x = element_blank(),
- panel.grid.major.y = element_blank(),
- panel.grid.minor.y = element_blank(),
- axis.title.x = element_blank(),
- axis.title.y = element_blank(),
- axis.text.y = element_text(hjust = 0, face = "bold"),
- axis.line.y = element_line(),
- plot.caption = element_text(hjust = 1, face = "italic", colour = "darkred",
- size = 7) )
- if(problem != "") {
- p2 <- p2 + labs(caption = paste("Note:", as.character(problem)) )
- }
-
- p <- ggdraw() +
- draw_plot(p2, x = 0, y = 0, width = 0.5, height = 0.5) +
- draw_plot(p1, x = 0.5, y = 0, width = 0.5, height = 0.5)
- #print(p)
- #print(p3)
+df <- read.csv("/home/konrad/Documents/Biostats/test_data/Biostats_2.csv")
+library(ggplot2)
+library(drc)
+
+l <- ic50(
+ df,
+ "Activity_SpotTotalIntensity",
+ "concentration", "ColumnValues",
+ NULL, FALSE, TRUE
+)
+pf <- function(l, idx) {
+ p <- l[[idx]]
+ if (inherits(p, "errorClass")) {
+ print(p$error_message)
+ return(p$object)
}
+ p[[2]] + scale_x_log10()
}
+pl <- lapply(1:20, function(i) pf(l, i))
+cowplot::plot_grid(plotlist = pl)
+pl <- lapply(21:40, function(i) pf(l, i))
+cowplot::plot_grid(plotlist = pl)
+pl <- lapply(41:60, function(i) pf(l, i))
+cowplot::plot_grid(plotlist = pl)
+
+rm(list = ls())
+head(df)
diff --git a/test_data/Biostats_2.csv b/test_data/Biostats_2.csv
new file mode 100644
index 0000000..2fa039b
--- /dev/null
+++ b/test_data/Biostats_2.csv
@@ -0,0 +1,1537 @@
+"PlateId/Barcode","PlateNumber","WellId","Row","Column","Status","Zposition","ColumnValues","Activity_ValidObjectCount","Activity_SpotTotalAreaCh2","Activity_SpotTotalIntensity","concentration"
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