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150  <ul>
151  <li><a href="#r-packages" id="toc-r-packages" class="nav-link active" data-scroll-target="#r-packages">R packages</a></li>
152  <li><a href="#shiny-apps" id="toc-shiny-apps" class="nav-link" data-scroll-target="#shiny-apps">Shiny apps</a></li>
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162<h1 class="title">Software</h1>
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167      <div class="about-contents"><main class="content" id="quarto-document-content">
168
169<p>I’m a long-time R user, and when time permits, I try to contribute to the R community. My book <a href="http://www.modernstatisticswithr.com">Modern Statistics with R</a> is freely available online.</p>
170<section id="r-packages" class="level2">
171<h2 data-anchor-id="r-packages">R packages</h2>
172<table class="table-striped table-hover caption-top table">
173<colgroup>
174<col style="width: 17%">
175<col style="width: 29%">
176<col style="width: 34%">
177<col style="width: 19%">
178</colgroup>
179<thead>
180<tr class="header">
181<th>Package</th>
182<th>Co-authors</th>
183<th>Description</th>
184<th>Links</th>
185</tr>
186</thead>
187<tbody>
188<tr class="odd">
189<td><code>boot.pval</code></td>
190<td></td>
191<td>
191Convenience functions for computing bootstrap p-values, including for various regression models and tests of location</td>
192<td><a href="https://cran.r-project.org/package=boot.pval">CRAN</a> <br> <a href="https://github.com/mthulin/boot.pval">GitHub</a> <br> <a href="https://mthulin.github.io/boot.pval/">Documentation</a></td>
193</tr>
194<tr class="even">
195<td><code>ivo.table</code></td>
196<td>Kajsa Grind<br>Stefan Furne</td>
197<td>Nicely formatted frequency tables and contingency tables.</td>
198<td><a href="https://cran.r-project.org/package=ivo.table">CRAN</a> <br> <a href="https://github.com/mthulin/ivo.table">GitHub</a> <br> <a href="https://mthulin.github.io/ivo.table/">Documentation</a></td>
199</tr>
200<tr class="odd">
201<td><code>nullabor</code></td>
202<td>Di Cook<br>Hadley Wickham<br>Niladri Roy Chowdhury<br>Heike Hofmann</td>
203<td>Visual tools for assessing distributional assumptions and residuals in linear regression models.</td>
204<td><a href="https://cran.r-project.org/package=nullabor">CRAN</a> <br> <a href="https://github.com/dicook/nullabor">GitHub</a> <br> <a href="https://dicook.github.io/nullabor/">Documentation</a></td>
205</tr>
206<tr class="even">
207<td><code>MultSurvTests</code></td>
208<td>Lukas Arnroth</td>
209<td>Multivariate version of the two-sample logrank and Gehan tests.</td>
210<td><a href="https://cran.r-project.org/package=MultSurvTests">CRAN</a> <br> <a href="https://github.com/lukketotte/MultSurvTests">GitHub</a></td>
211</tr>
212<tr class="odd">
213<td><code>pipedreams</code></td>
214<td></td>
215<td>Pipe-friendly wrappers for common R statistical tests and models.</td>
216<td><a href="https://github.com/mthulin/pipedreams">GitHub</a></td>
217</tr>
218</tbody>
219</table>
220<!--
221-   `boot.pval`<br>Convenience functions for computing bootstrap p-values, including for various regression models and tests of location.<br /><a href="https://cran.r-project.org/package=boot.pval">CRAN</a> / <a href="https://github.com/mthulin/boot.pval">GitHub</a> / <a href="https://mthulin.github.io/boot.pval/">Documentation</a>
222-   `ivo.table` *(with Kajsa Grind and Stefan Furne)*<br>Nicely formatted frequency tables and contingency tables.<br /><a href="https://cran.r-project.org/package=ivo.table">CRAN</a> / <a href="https://github.com/mthulin/ivo.table">GitHub</a> / <a href="https://mthulin.github.io/ivo.table/">Documentation</a>
223-   `nullabor` *(with Di Cook, Hadley Wickham, Niladri Roy Chowdhury, and Heike Hofmann)*<br>Visual tools for assessing distributional assumptions and residuals in linear regression models.<br /><a href="https://cran.r-project.org/package=nullabor">CRAN</a> / <a href="https://github.com/dicook/nullabor">GitHub</a> / <a href="https://dicook.github.io/nullabor/">Documentation</a>
224-   `MultSurvTests` *(with Lukas Arnroth)*<br>Multivariate version of the two-sample logrank and Gehan tests.<br /><a href="https://cran.r-project.org/package=MultSurvTests">CRAN</a> / <a href="https://github.com/lukketotte/MultSurvTests">GitHub</a>
225-->
226</section>
227<section id="shiny-apps" class="level2">
228<h2 data-anchor-id="shiny-apps">Shiny apps</h2>
229<p>The <a href="https://www.mansthulin.se/bat">Bioscreen Analysis Tool</a>, developed using R and Shiny, is an online app for analysis of growth curves from Bioscreen C MBR machines. The source code is available on <a href="https://github.com/mthulin/BAT">GitHub</a>.</p>
230
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517        let parent = null;
518        if (lineIds.length > 0) {
519            //compute the position of the single el (top and bottom and make a div)
520            const el = window.document.getElementById(lineIds[0]);
521            top = el.offsetTop;
522            height = el.offsetHeight;
523            parent = el.parentElement.parentElement;
524          if (lineIds.length > 1) {
525            const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
526            const bottom = lastEl.offsetTop + lastEl.offsetHeight;
527            height = bottom - top;
528          }
529          if (top !== null && height !== null && parent !== null) {
530            // cook up a div (if necessary) and position it 
531            let div = window.document.getElementById("code-annotation-line-highlight");
532            if (div === null) {
533              div = window.document.createElement("div");
534              div.setAttribute("id", "code-annotation-line-highlight");
535              div.style.position = 'absolute';
536              parent.appendChild(div);
537            }
538            div.style.top = top - 2 + "px";
539            div.style.height = height + 4 + "px";
540            div.style.left = 0;
541            let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
542            if (gutterDiv === null) {
543              gutterDiv = window.document.createElement("div");
544              gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
545              gutterDiv.style.position = 'absolute';
546              const codeCell = window.document.getElementById(targetCell);
547              const gutter = codeCell.querySelector('.code-annotation-gutter');
548              gutter.appendChild(gutterDiv);
549            }
550            gutterDiv.style.top = top - 2 + "px";
551            gutterDiv.style.height = height + 4 + "px";
552          }
553          selectedAnnoteEl = annoteEl;
554        }
555      };
556      const unselectCodeLines = () => {
557        const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
558        elementsIds.forEach((elId) => {
559          const div = window.document.getElementById(elId);
560          if (div) {
561            div.remove();
562          }
563        });
564        selectedAnnoteEl = undefined;
565      };
566        // Handle positioning of the toggle
567    window.addEventListener(
568      "resize",
569      throttle(() => {
570        elRect = undefined;
571        if (selectedAnnoteEl) {
572          selectCodeLines(selectedAnnoteEl);
573        }
574      }, 10)
575    );
576    function throttle(fn, ms) {
577    let throttle = false;
578    let timer;
579      return (...args) => {
580        if(!throttle) { // first call gets through
581            fn.apply(this, args);
582            throttle = true;
583        } else { // all the others get throttled
584            if(timer) clearTimeout(timer); // cancel #2
585            timer = setTimeout(() => {
586              fn.apply(this, args);
587              timer = throttle = false;
588            }, ms);
589        }
590      };
591    }
592      // Attach click handler to the DT
593      const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
594      for (const annoteDlNode of annoteDls) {
595        annoteDlNode.addEventListener('click', (event) => {
596          const clickedEl = event.target;
597          if (clickedEl !== selectedAnnoteEl) {
598            unselectCodeLines();
599            const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
600            if (activeEl) {
601              activeEl.classList.remove('code-annotation-active');
602            }
603            selectCodeLines(clickedEl);
604            clickedEl.classList.add('code-annotation-active');
605          } else {
606            // Unselect the line
607            unselectCodeLines();
608            clickedEl.classList.remove('code-annotation-active');
609          }
610        });
611      }
612  const findCites = (el) => {
613    const parentEl = el.parentElement;
614    if (parentEl) {
615      const cites = parentEl.dataset.cites;
616      if (cites) {
617        return {
618          el,
619          cites: cites.split(' ')
620        };
621      } else {
622        return findCites(el.parentElement)
623      }
624    } else {
625      return undefined;
626    }
627  };
628  var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
629  for (var i=0; i<bibliorefs.length; i++) {
630    const ref = bibliorefs[i];
631    const citeInfo = findCites(ref);
632    if (citeInfo) {
633      tippyHover(citeInfo.el, function() {
634        var popup = window.document.createElement('div');
635        citeInfo.cites.forEach(function(cite) {
636          var citeDiv = window.document.createElement('div');
637          citeDiv.classList.add('hanging-indent');
638          citeDiv.classList.add('csl-entry');
639          var biblioDiv = window.document.getElementById('ref-' + cite);
640          if (biblioDiv) {
641            citeDiv.innerHTML = biblioDiv.innerHTML;
642          }
643          popup.appendChild(citeDiv);
644        });
645        return popup.innerHTML;
646      });
647    }
648  }
649});
650</script>
650
651</div> <!-- /content -->
652<footer class="footer">
653  <div class="nav-footer">
654    <div class="nav-footer-left">
655<p><span>© 2025 Måns Thulin</span></p>
656</div>   
657    <div class="nav-footer-center">
658<p><span>E-mail: <a href="mailto:[email protected]">[email protected]</a></span></p>
659</div>
660    <div class="nav-footer-right">
661<p><span>Made with <a href="http://www.r-project.org"><iconify-icon role="img" inline="" icon="fa-brands:r-project" aria-label="Icon r-project from fa-brands Iconify.design set." title="Icon r-project from fa-brands Iconify.design set."></iconify-icon></a> and <a href="https://quarto.org/"><iconify-icon role="img" inline="" icon="simple-icons:quarto" aria-label="Icon quarto from simple-icons Iconify.design set." title="Icon quarto from simple-icons Iconify.design set."></iconify-icon></a></span></p>
662</div>
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664</footer>
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