build based on 5aeed02

Author: Documenter.jl

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-30T07:02:54","documenter_version":"1.5.0"}}
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-30T11:47:17","documenter_version":"1.5.0"}}

dev/checklist/index.html

@@ -11,7 +11,7 @@
 
 df = checklist_df()
 df[3, "Location where item is reported"] = "Sysemtatic review is in the title."
-df[3, &quot;Location where item is reported&quot;] = &quot;The completed abastract is located on page one.&quot;</code></pre><p>Additionally, the <code>checklist()</code> function uses <code>checklist_df()</code> as a template  but takes a paper in PDF format, parses it using natural language processing  via <a href="https://github.com/FluxML/Flux.jl"><code>Flux.jl</code></a> and  <a href="https://github.com/chengchingwen/Transformers.jl"><code>Transformers.jl</code></a>, and returns a  completed checklist along with the paper&#39;s metadata, represented by the type <code>Checklist</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecoeco/PRISMA.jl/blob/c5ca6e86af12b8d4e9b6117bb6b02cf4a93f01e4/src/checklist.jl#L1-L34">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="PRISMA.checklist" href="#PRISMA.checklist"><code>PRISMA.checklist</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">PRISMA.checklist(paper::AbstractString)::Checklist
+df[3, &quot;Location where item is reported&quot;] = &quot;The completed abastract is located on page one.&quot;</code></pre><p>Additionally, the <code>checklist()</code> function uses <code>checklist_df()</code> as a template  but takes a paper in PDF format, parses it using natural language processing  via <a href="https://github.com/FluxML/Flux.jl"><code>Flux.jl</code></a> and  <a href="https://github.com/chengchingwen/Transformers.jl"><code>Transformers.jl</code></a>, and returns a  completed checklist along with the paper&#39;s metadata, represented by the type <code>Checklist</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecoeco/PRISMA.jl/blob/5aeed02209d22344866037e281c98f29176a4e9c/src/checklist.jl#L1-L34">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="PRISMA.checklist" href="#PRISMA.checklist"><code>PRISMA.checklist</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">PRISMA.checklist(paper::AbstractString)::Checklist
 PRISMA.checklist(bytes::Vector{UInt8})::Checklist</code></pre><p>Returns a completed PRISMA checklist as the type <code>Checklist</code>. The <code>Checklist</code> type includes a completed checklist as a <code>DataFrame</code> and the metadata of the paper as a <code>LittleDict</code>. The <code>paper</code> argument can be a path to a pdf file or an array of bytes. This function uses the C++ library <code>Poppler</code> via <code>Poppler_jll</code> to parse the pdf and the natural language processing functionality in Julia via <a href="https://github.com/FluxML/Flux.jl"><code>Flux.jl</code></a> and <a href="https://github.com/chengchingwen/Transformers.jl"><code>Transformers.jl</code></a> to  find items from the checklist in the paper and populate the  <code>Comments or location in manuscript</code> and <code>Yes/No/NA</code> columns in the <code>DataFrame</code>  from <code>checklist_df()</code>.</p><p>The following metadata is parsed from the pdf file and stored in the <code>LittleDict</code> as:</p><ul><li><code>&quot;title&quot;</code>: the title of the paper</li><li><code>&quot;subject&quot;</code>: the subject of the paper</li><li><code>&quot;author&quot;</code>: the author of the paper</li><li><code>&quot;creator&quot;</code>: the creator of the paper</li><li><code>&quot;producer&quot;</code>: the producer of the paper</li><li><code>&quot;creation date&quot;</code>: the date the paper was created</li><li><code>&quot;modification date&quot;</code>: the date the paper was last modified</li><li><code>&quot;pages&quot;</code>: the number of pages in the paper</li><li><code>&quot;paper size&quot;</code>: the size of the paper</li><li><code>&quot;paper rotation&quot;</code>: the rotation of the paper</li><li><code>&quot;file size&quot;</code>: the size of the pdf file</li><li><code>&quot;optimized&quot;</code>: whether the pdf was optimized</li><li><code>&quot;pdf version&quot;</code>: the version of the pdf</li></ul><p>All keys and values in the dictionary ar eof type <code>String</code>. If the parsing fails the value will be an empty string.</p><p><strong>Arguments</strong></p><ul><li><code>paper::AbstractString</code>: a path to a pdf file as a string</li><li><code>bytes::Vector{UInt8}</code>: the pdf data as an array of bytes</li></ul><p><strong>Returns</strong></p><ul><li><code>Checklist</code>: a completed checklist with paper metadata</li></ul><p><strong>Examples</strong></p><p>Export a completed checklist to an Microsoft® Excel spreadsheet using the <code>XLSX</code> package.</p><pre><code class="language-julia hljs">using PRISMA, XLSX
 
 clist = checklist(&quot;manuscript.pdf&quot;)
@@ -29,4 +29,4 @@
 clist.df[02, &quot;Yes/No/NA&quot;] = &quot;Yes&quot;
 clist.df[09, &quot;Yes/No/NA&quot;] = &quot;Yes&quot;
 clist.df[10, &quot;Yes/No/NA&quot;] = &quot;Yes&quot;
-</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecoeco/PRISMA.jl/blob/c5ca6e86af12b8d4e9b6117bb6b02cf4a93f01e4/src/checklist.jl#L162-L245">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="PRISMA.Checklist" href="#PRISMA.Checklist"><code>PRISMA.Checklist</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">PRISMA.Checklist</code></pre><p>This types represents a PRISMA checklist in the form of a <code>DataFrame</code> and the metadata of the paper that was used to generate it as a <code>LittleDict</code> or an small ordered dictionary withs keys and values.</p><p><strong>Keyword Arguments</strong></p><ul><li><code>df::DataFrame</code>: the checklist as a <code>DataFrame</code></li><li><code>metadata::LittleDict</code>: the metadata of the paper</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecoeco/PRISMA.jl/blob/c5ca6e86af12b8d4e9b6117bb6b02cf4a93f01e4/src/checklist.jl#L91-L103">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../flow_diagram/">Flow Diagram »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Tuesday 30 July 2024 07:02">Tuesday 30 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecoeco/PRISMA.jl/blob/5aeed02209d22344866037e281c98f29176a4e9c/src/checklist.jl#L162-L245">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="PRISMA.Checklist" href="#PRISMA.Checklist"><code>PRISMA.Checklist</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">PRISMA.Checklist</code></pre><p>This types represents a PRISMA checklist in the form of a <code>DataFrame</code> and the metadata of the paper that was used to generate it as a <code>LittleDict</code> or an small ordered dictionary withs keys and values.</p><p><strong>Keyword Arguments</strong></p><ul><li><code>df::DataFrame</code>: the checklist as a <code>DataFrame</code></li><li><code>metadata::LittleDict</code>: the metadata of the paper</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecoeco/PRISMA.jl/blob/5aeed02209d22344866037e281c98f29176a4e9c/src/checklist.jl#L91-L103">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../flow_diagram/">Flow Diagram »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Tuesday 30 July 2024 11:47">Tuesday 30 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>