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‎docs/03-writing_code.md

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## collate en_US.UTF-8
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## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
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‎docs/03-writing_code_activity.md

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‎docs/04-refactoring.md

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The `outer()` function performs the same calculation as the nested loop in the original code, but more efficiently. It returns a matrix of all possible combinations of x and y values, with each element of the matrix being the product of the corresponding x and y values. The `rowSums()` function is then used to sum the elements of each row of the matrix, which is equivalent to summing the products of x and y for each index `i` in the original loop. This method avoids the need for the nested loop, resulting in a faster and more efficient computation.
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One optimized way to perform the same calculation is by using the `%*%` operator to perform matrix multiplication. This can be done by converting x and y to matrices and transposing one of them so that their dimensions align for matrix multiplication. This code should be much faster than the original implementation because it takes advantage of highly optimized matrix multiplication algorithms in R.

‎docs/05-annotation.md

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‎docs/05-annotation_activity.md

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‎docs/404.html

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‎docs/About.md

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‎docs/about-the-authors.html

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‎docs/ai-for-bioinformatics-hands-on-exercise.html

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‎docs/ai-for-bioinformatics.html

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‎docs/annotating-your-code.html

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‎docs/annotation-hands-on-exercise.html

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‎docs/ethics-of-using-ai.html

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<p>Overall, we hope that these guidelines and tips will help us all to use AI tools more responsibly for writing code. We recognize however, that as this is emerging technology and more ethical issues will emerge as we continue to use these tools in new ways. AI tools can even help us to use them more responsibly when we ask the right additional questions when writing code, but remember that human review is always necessary. Staying up-to-date on the current ethical considerations will also help us all continue to use AI responsibly.</p>
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‎docs/index.html

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<h1 class="title">AI for Efficient Programming</h1>
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‎docs/index.md

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‎docs/introduction.html

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<p>We used AI bots (including ChatGPT, Bard, Sage, and Claude) as part of the process of creating this book. The words are all original content, but we used AI bots to edit for grammar and tone. We firmly believe this new technology can be used in ethical ways and we put into practice all the rules and suggestions offered over the following modules while we created this book.</p>
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‎docs/languages-and-cloud-computing.html

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‎docs/refactoring-code-hands-on-exercise.html

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‎docs/refactoring-code.html

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<p>The <code>outer()</code> function performs the same calculation as the nested loop in the original code, but more efficiently. It returns a matrix of all possible combinations of x and y values, with each element of the matrix being the product of the corresponding x and y values. The <code>rowSums()</code> function is then used to sum the elements of each row of the matrix, which is equivalent to summing the products of x and y for each index <code>i</code> in the original loop. This method avoids the need for the nested loop, resulting in a faster and more efficient computation.</p>
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<p>So much faster! We can look at another option by regenerating the response:</p>
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<p>One optimized way to perform the same calculation is by using the <code>%*%</code> operator to perform matrix multiplication. This can be done by converting x and y to matrices and transposing one of them so that their dimensions align for matrix multiplication. This code should be much faster than the original implementation because it takes advantage of highly optimized matrix multiplication algorithms in R.</p>
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<p>While this second suggestion is faster, you will need to consider what aspects of the codebase are most important in each instance. For example, this code runs more quickly, but <a href="https://stat.ethz.ch/R-manual/R-patched/library/base/html/matmult.html">the <code>%*%</code> operator</a> might be unfamiliar to some R programmers. In cases where efficiency is less important, or the data are not large, you might consider maximizing readability.</p>
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