From c50cacee1d798e9cf67a740a20c23916fb347ccf Mon Sep 17 00:00:00 2001
From: Julian Karch <j.d.karch@fsw.leidenuniv.nl>
Date: Mon, 7 Oct 2024 11:21:02 +0200
Subject: [PATCH] added auto.th and auto.delta options

---
 frontend/src/MenuTop/AddMenu.svelte | 20 +++++++++----
 frontend/src/Shiny/toR.js           |  6 ++--
 frontend/src/stores.js              |  2 ++
 inst/www/assets/index-53e5964a.js   | 45 +++++++++++++++++++++++++++++
 inst/www/assets/index-c381e0bd.js   | 43 ---------------------------
 inst/www/index.html                 |  2 +-
 6 files changed, 66 insertions(+), 52 deletions(-)
 create mode 100644 inst/www/assets/index-53e5964a.js
 delete mode 100644 inst/www/assets/index-c381e0bd.js

diff --git a/frontend/src/MenuTop/AddMenu.svelte b/frontend/src/MenuTop/AddMenu.svelte
index ad2084b..86df2cb 100644
--- a/frontend/src/MenuTop/AddMenu.svelte
+++ b/frontend/src/MenuTop/AddMenu.svelte
@@ -29,6 +29,14 @@
       name: "Treat Exogenous Observed Variables as Fixed Variables",
       modelProperty: "fixed_x",
     },
+    {
+      name: "Include Freely Estimated Thresholds for Ordered Variables in the Model",
+      modelProperty: "auto.th",
+    },
+    {
+      name: "Include Freely Estimated Response Scaling Parameters for Ordered Variables in the Model",
+      modelProperty: "auto.delta",
+    },
   ];
 
   const name = "Automatically..";
@@ -42,12 +50,6 @@
 </script>
 
 <Dropdown {name}>
-  {#each menuItems as item}
-    <CheckItem
-      bind:name={item.name}
-      bind:checked={$modelOptions[item.modelProperty]}
-    />
-  {/each}
   <li class="dropdown-submenu">
     <a tabindex="-1" href={"#"}>Add Means?</a>
     <ul class="dropdown-menu">
@@ -70,6 +72,12 @@
     bind:checked={$modelOptions.intLvFree}
     bind:disable={disabledInts}
   />
+  {#each menuItems as item}
+    <CheckItem
+      bind:name={item.name}
+      bind:checked={$modelOptions[item.modelProperty]}
+    />
+  {/each}
 </Dropdown>
 
 <style>
diff --git a/frontend/src/Shiny/toR.js b/frontend/src/Shiny/toR.js
index 6b292f8..3be21b8 100644
--- a/frontend/src/Shiny/toR.js
+++ b/frontend/src/Shiny/toR.js
@@ -358,7 +358,8 @@ function produceLavaanOptions(ordered_labels) {
 \t\t auto.cov.lv.x = ${boolToString(
     modelOpt.auto_cov_lv_x
   )}, auto.cov.y = ${boolToString(modelOpt.auto_cov_y)},
-  \t\t fixed.x = ${boolToString(modelOpt.fixed_x)}`;
+  \t\t fixed.x = ${boolToString(modelOpt.fixed_x)}, auto.th = ${boolToString(modelOpt["auto.th"])}, 
+  \t\t auto.delta = ${boolToString(modelOpt["auto.delta"])}`;
   if (modelOpt.se == "boot") {
     const additional = `, bootstrap = ${modelOpt.n_boot})`;
     options = options + additional;
@@ -368,7 +369,8 @@ function produceLavaanOptions(ordered_labels) {
 
   if (ordered_labels.length > 0) {
     const ordered_arg = 'c("' + ordered_labels.join('", "') + '")'
-    options = `ordered = ${ordered_arg}, ${options}`
+    options = `ordered = ${ordered_arg}, 
+    \t\t ${options}`
   }
   return options;
 }
diff --git a/frontend/src/stores.js b/frontend/src/stores.js
index df65d58..7b9c8a5 100644
--- a/frontend/src/stores.js
+++ b/frontend/src/stores.js
@@ -19,6 +19,8 @@ export let modelOptions = writable({
   auto_cov_y: true,
   fixed_x: true,
   mode: "user model",
+  "auto.th": true,
+  "auto.delta": true,
 });
 
 export let gridViewOptions = writable({
diff --git a/inst/www/assets/index-53e5964a.js b/inst/www/assets/index-53e5964a.js
new file mode 100644
index 0000000..64f2acb
--- /dev/null
+++ b/inst/www/assets/index-53e5964a.js
@@ -0,0 +1,45 @@
+import{d as Cn,w as Te,S as X,i as Z,s as K,c as te,g as W,o as we,e as U,a as E,b as $e,f as O,l as oe,n as ce,h as N,r as Je,j as Y,k as se,m as V,t as xe,p as R,q as Ie,u as _e,v as Re,x as Xe,y as G,z as j,A as Ze,B as Ke,C as Qe,D as M,E as I,F as q,G as Be,H as Ve,I as Sn,J as it,K as lt,L as ae,M as ve,N as ye,O as de}from"./svelte-fdfc2579.js";import{c as H}from"./cytoscape-86e840ae.js";import{g as Ln}from"./cytoscape-grid-guide-eb2f2e88.js";import{e as Mn}from"./cytoscape-edgehandles-455db19b.js";import{v as un}from"./uuid-a960c1f4.js";import{J as Ct}from"./jszip-133f2485.js";import{s as Dn}from"./cytoscape-svg-5a8e6db6.js";import{F as dt}from"./file-saver-05fab67f.js";import{E as An}from"./jspdf-a7c15206.js";import{U as Fn}from"./svg2pdf.js-d0866cf6.js";import{d as In}from"./cytoscape-dagre-a4f19369.js";import{f as On}from"./cytoscape-fcose-2999cda1.js";import{c as Nn}from"./cytoscape-cola-af60e250.js";import{c as Tn}from"./cytoscape-context-menus-cfc05c35.js";import{i as Pn}from"./@jaames-324f80d4.js";import{p as xn}from"./cytoscape-panzoom-81d89c13.js";import{u as Vn}from"./cytoscape-undo-redo-eac3a982.js";import{a as Rn}from"./cytoscape-automove-085c6bfa.js";import{K as cn}from"./konva-bc9c0e16.js";import{n as zn}from"./cytoscape-node-editing-170df28d.js";import{e as Bn}from"./cytoscape-edge-editing-b8b574b0.js";import{D as St}from"./dexie-d2c71554.js";import"./core-js-bbf708ea.js";import"./lodash-6eb5ace2.js";import"./heap-8ffeb77a.js";import"./functional-red-black-tree-9a31655a.js";import"./lodash.memoize-ae7939c9.js";import"./lodash.throttle-e32db46a.js";import"./dagre-9b2543cb.js";import"./graphlib-a6487d85.js";import"./@babel-75df473a.js";import"./fflate-8981c52c.js";import"./cssesc-5de85916.js";import"./font-family-papandreou-066b018a.js";import"./svgpath-76644159.js";import"./specificity-c7128631.js";import"./cose-base-3e61f9ec.js";import"./layout-base-45dab9bc.js";import"./webcola-fe958753.js";import"./jquery-793df3aa.js";(function(){const e=document.createElement("link").relList;if(e&&e.supports&&e.supports("modulepreload"))return;for(const o of document.querySelectorAll('link[rel="modulepreload"]'))t(o);new MutationObserver(o=>{for(const r of o)if(r.type==="childList")for(const s of r.addedNodes)s.tagName==="LINK"&&s.rel==="modulepreload"&&t(s)}).observe(document,{childList:!0,subtree:!0});function i(o){const r={};return o.integrity&&(r.integrity=o.integrity),o.referrerPolicy&&(r.referrerPolicy=o.referrerPolicy),o.crossOrigin==="use-credentials"?r.credentials="include":o.crossOrigin==="anonymous"?r.credentials="omit":r.credentials="same-origin",r}function t(o){if(o.ep)return;o.ep=!0;const r=i(o);fetch(o.href,r)}})();const Q=Te(null),_t=Te(null),Me=Te(null);let ne=Te({meanStruc:"default",intOvFree:!0,intLvFree:!1,estimator:"default",se:"default",missing:"listwise",n_boot:1e3,fix_first:!0,fix_single:!0,auto_var:!0,auto_cov_lv_x:!0,auto_cov_y:!0,fixed_x:!0,mode:"user model","auto.th":!0,"auto.delta":!0}),ue=Te({gridShow:!1,gridSpace:26,gridColor:"#dedede",gridWidth:1,gridMovePan:!1,gridSnap:!1,gridAlign:!0,gridResize:!1,showLav:!0,showVar:!0,showMean:!0,std:!1,view:"est",ci:.95,number_digits:2}),Fe=Te({lastFitModel:null,lastFitLavFit:null,lastFitData:null}),B=Te({fitting:!1,loadingMode:!1,runCounter:0,modelEmpty:!0,dataAvail:!1,columnNames:null,loadedFileName:null,ids:null,dragged:null,draggedName:null,full:!0,ready:!1,parsedModel:!1,meansModelled:null,buttonDown:!1,showServerErrors:!0,everEdge:!1,drawing:"none",undoEmpty:!0,redoEmpty:!0,server:!1,shinyapps:!1}),mt=Te(0);Cn(B,n=>n.columnNames);const fn=Te({type:"info",message:"",key:0});function ge(n,e){fn.update(i=>({type:n,message:e,key:i.key+1}))}ge("info","Greetings. lavaangui is BETA software. 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o=0;o<t.length;o++)t[o].removeEstimates();if(i.getUserEdges().length==0){i.getLavaanNodes().remove(),i.getLavaanEdges().remove(),Shiny.setInputValue("show_help",Math.random());return}if(!e.dataAvail&&n=="estimate"){ge("danger","Model not send to lavaan because no data available");return}let r=mn(n);Shiny.setInputValue("run-fromJavascript",JSON.stringify(r)),Shiny.setInputValue("runCounter",Math.random()),n==="user model"&&i.getLavaanModifiedEdges().forEach(s=>{s.freePara()})}function Zn(n,e){for(let i=0;i<n.length;i++)if(n[i]===e)return!0;return!1}function nt(n,e){let i;n==null?i="1":i=n.getLabel();let t=!1,o;if(e.isFixed()&&!e.isModifiedLavaan()?(o=e.getValue()+"*"+i,t=!0):e.isForceFree()&&(o="NA*"+i,t=!0),e.hasLabel()){const r=e.getLabel();t?o+=" + "+r+"*"+i:(t=!0,o=r+"*"+i)}else t||(o=i);return o}class Kn{constructor(e,i,t=null,o=null,r=null,s=null){this.mode=e,Object.assign(this,{model:{options:t,syntax:o,R_script:i,ordered_labels:s},forceUpdate:Math.random(),cache:r})}}function 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+`,i.dataAvail?o+=`data <- read.csv("${i.loadedFileName}")
+`:o+=`#make sure your data is loaded into the 'data' variable
+`;let r=e.getLatentNodes();r=r.nodes(function($){const y=$.connectedEdges(function(w){return w.isDirected()&&w.source().id()==$.id()});return y.length>0&&y.every(w=>w.target().isLatent())});let s=e.getLatentNodes();s=s.nodes(function($){const y=$.connectedEdges(function(T){return T.isDirected()&&T.target().id()==$.id()}),w=$.connectedEdges(function(T){return T.isDirected()});return w.length>0&&y.length==w.length});let l=e.getLatentNodes(),d=!1;for(let $=0;$<l.length;$++){const y=l[$],w=y.connectedEdges(function(T){return T.isDirected()&&T.source().id()==y.id()&&(T.target().isObserved()||r.some(C=>C.id()===y.id()))});w.length>0&&(d||(t+=`# measurement model
+`,d=!0),t+=" "+y.getLabel()+" =~ "+Mt(w,"target")+`
+`)}function u($){return $.isDirected()&&!$.source().isConstant()&&!($.source().isLatent()&&$.target().isObserved())&&!($.source().isLatent()&&r.some(w=>w.id()===$.source().id())&&$.target().isLatent())&&($.isUserAdded()||$.isModifiedLavaan())&&!s.some(w=>w.id()===$.target().id())}let a=e.edges(u),m=[];for(let $=0;$<a.length;$++)Zn(m,a[$].target())||m.push(a[$].target());if(m.length>0){t+=`
+# regressions`;for(let $=0;$<m.length;$++){const y=m[$],w=y.connectedEdges(T=>u(T)&&T.target().same(y));if(w.length>0){let T="";for(var g=0;g<w.length;g++){var c=w[g].source();g>0&&(T+=" + "),T+=nt(c,w[g])}t+=`
+ `+y.getLabel()+" ~ "+T}}}let f=e.edges(function($){return($.isUndirected()||$.myIsLoop())&&($.isUserAdded()||$.isModifiedLavaan())});if(f.length>0){t+=`
+
+# (residual) (co)variances`;for(let $=0;$<f.length;$++){let y=f[$].source().data("label");t+=`
+ `+y+" ~~ "+nt(f[$].target(),f[$])}}const b=e.nodes(function($){return $.isConstant()});for(let $=0;$<b.length;$++){const w=b[$].connectedEdges(function(T){return T.isUserAdded()});if(w.length>0){t+=`
+# intercepts
+`;for(var g=0;g<w.length;g++){var c=w[g].target();t+=c.getLabel()+" ~ "+nt(void 0,w[g])+`
+`}}}d=!1;for(let $=0;$<s.length;$++){const y=s[$],w=y.connectedEdges(function(T){return T.isDirected()&&T.target().id()==y.id()});w.length>0&&(d||(t+=`
+
+ #  formative factors
+`,d=!0),t+=" "+y.getLabel()+" <~ "+Mt(w,"source")+`
+`)}t=`'
+`+t+`'
+
+`;function h($,y=60){return $.split(`
+`).map(w=>{if(w.includes("+")&&w.length>y){const T=w.split(" + ");let C=[],p=T[0];const P=w.match(/^\s*/)[0],A=p.indexOf("~")+1;for(let J=1;J<T.length;J++)p.length+T[J].length+3>y?(C.push(p+" + "),p=P+" ".repeat(A)+T[J]):p+=" + "+T[J];return C.push(p),C.join(`
+`)}return w}).join(`
+`)}t=h(t);const L=e.nodes(function($){return $.isOrdered()}).map($=>$.getLabel()),v=Qn(L);return o+="model <-"+t,o+="result <- lavaan(model, data, "+v,new Kn(n,o,v,t=t,W(Fe),L)}function Qn(n){const e=W(ne),i=ke(e.meanStruc),t=ke(e.intOvFree),o=ke(e.intLvFree);let r=`meanstructure = ${i},
+		 int.ov.free = ${t}, int.lv.free = ${o},
+		 estimator = ${ct(e.estimator)}, se = ${ct(e.se)},
+		 missing = ${ct(e.missing)}, auto.fix.first = ${ke(e.fix_first)},
+		 auto.fix.single = ${ke(e.fix_single)}, auto.var = ${ke(e.auto_var)},
+		 auto.cov.lv.x = ${ke(e.auto_cov_lv_x)}, auto.cov.y = ${ke(e.auto_cov_y)},
+  		 fixed.x = ${ke(e.fixed_x)}, auto.th = ${ke(e["auto.th"])}, 
+  		 auto.delta = ${ke(e["auto.delta"])}`;if(e.se=="boot"){const s=`, bootstrap = ${e.n_boot})`;r=r+s}else r=r+")";return n.length>0&&(r=`ordered = ${'c("'+n.join('", "')+'")'}, 
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diff --git a/inst/www/index.html b/inst/www/index.html
index 4fd31ee..e618072 100644
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