build based on 275159f

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-08-31T02:36:21","documenter_version":"1.6.0"}}
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-08-31T05:06:02","documenter_version":"1.6.0"}}

dev/checklist/index.html

@@ -10,7 +10,7 @@
 
 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/aa0df564563107a8ded5ce90a5e0f003b303c076/src/checklist.jl#L1-L37">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><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></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/275159f671d921d5d355c6983ed6e6761d360a35/src/checklist.jl#L1-L37">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><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></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. Just make the sure the file path end with <code>.xlsx</code>.</p><pre><code class="language-julia hljs">using PRISMA
 
 clist = checklist(&quot;manuscript.pdf&quot;)
@@ -24,7 +24,7 @@
 df[02, &quot;Yes/No/NA&quot;] = &quot;Yes&quot;
 df[09, &quot;Yes/No/NA&quot;] = &quot;Yes&quot;
 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/aa0df564563107a8ded5ce90a5e0f003b303c076/src/checklist.jl#L179-L253">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_read" href="#PRISMA.checklist_read"><code>PRISMA.checklist_read</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">checklist_read(fn::AbstractString; sheetname::AbstractString=&quot;2020 PRISMA Checklist&quot;, kwargs....)::DataFrame</code></pre><p>reads the template data from a <code>CSV</code>, <code>XLSX</code>, <code>HTML</code>, or <code>JSON</code></p><p><strong>Arguments</strong></p><ul><li><code>fn::AbstractString</code>: the name of the file to read</li><li><code>sheetname::AbstractString=&quot;2020 PRISMA Checklist&quot;</code>: the name of the sheet in the spreadsheet</li><li><code>kwargs...</code>: additional arguments to be passed to the underlying</li></ul><p><code>CSV.read</code>, <code>XLSX.readtable</code>, <code>HTMLTables.read</code>, and <code>JSON3.read</code> functions</p><p><strong>Returns</strong></p><ul><li><code>DataFrame</code>: the template dataframe</li></ul><p><strong>Examples</strong></p><pre><code class="language-julia hljs">using PRISMA: checklist_save, checklist_df, checklist_read
+</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecoeco/PRISMA.jl/blob/275159f671d921d5d355c6983ed6e6761d360a35/src/checklist.jl#L179-L253">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_read" href="#PRISMA.checklist_read"><code>PRISMA.checklist_read</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">checklist_read(fn::AbstractString; sheetname::AbstractString=&quot;2020 PRISMA Checklist&quot;, kwargs....)::DataFrame</code></pre><p>reads the template data from a <code>CSV</code>, <code>XLSX</code>, <code>HTML</code>, or <code>JSON</code></p><p><strong>Arguments</strong></p><ul><li><code>fn::AbstractString</code>: the name of the file to read</li><li><code>sheetname::AbstractString=&quot;2020 PRISMA Checklist&quot;</code>: the name of the sheet in the spreadsheet</li><li><code>kwargs...</code>: additional arguments to be passed to the underlying</li></ul><p><code>CSV.read</code>, <code>XLSX.readtable</code>, <code>HTMLTables.read</code>, and <code>JSON3.read</code> functions</p><p><strong>Returns</strong></p><ul><li><code>DataFrame</code>: the template dataframe</li></ul><p><strong>Examples</strong></p><pre><code class="language-julia hljs">using PRISMA: checklist_save, checklist_df, checklist_read
 
 checklist_save(&quot;checklist.csv&quot;,  checklist_df())
 checklist_save(&quot;checklist.xlsx&quot;, checklist_df())
@@ -34,15 +34,15 @@
 checklist_read(&quot;checklist.csv&quot;)
 checklist_read(&quot;checklist.xlsx&quot;)
 checklist_read(&quot;checklist.json&quot;)
-checklist_read(&quot;checklist.html&quot;)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecoeco/PRISMA.jl/blob/aa0df564563107a8ded5ce90a5e0f003b303c076/src/checklist.jl#L398-L429">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><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></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><p><strong>Examples</strong></p><pre><code class="language-julia hljs">using PRISMA
+checklist_read(&quot;checklist.html&quot;)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecoeco/PRISMA.jl/blob/275159f671d921d5d355c6983ed6e6761d360a35/src/checklist.jl#L398-L429">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><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></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><p><strong>Examples</strong></p><pre><code class="language-julia hljs">using PRISMA
 
 cl::Checklist = checklist(&quot;paper.pdf&quot;)
 
 title = cl.metadata[&quot;title&quot;]
 println(title)
 
 pages = cl.metadata[&quot;pages&quot;]
-println(pages)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecoeco/PRISMA.jl/blob/aa0df564563107a8ded5ce90a5e0f003b303c076/src/checklist.jl#L94-L120">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_save" href="#PRISMA.checklist_save"><code>PRISMA.checklist_save</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">checklist_save(
+println(pages)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecoeco/PRISMA.jl/blob/275159f671d921d5d355c6983ed6e6761d360a35/src/checklist.jl#L94-L120">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_save" href="#PRISMA.checklist_save"><code>PRISMA.checklist_save</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">checklist_save(
     fn::AbstractString, 
     cl::Checklist; 
     sheetname::AbstractString=&quot;2020 PRISMA Checklist&quot;, 
@@ -55,7 +55,7 @@
 checklist_save(&quot;checklist.csv&quot;,  clist)
 checklist_save(&quot;checklist.xlsx&quot;, clist)
 checklist_save(&quot;checklist.json&quot;, clist)
-checklist_save(&quot;checklist.html&quot;, clist)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecoeco/PRISMA.jl/blob/aa0df564563107a8ded5ce90a5e0f003b303c076/src/checklist.jl#L290-L330">source</a></section><section><div><pre><code class="language-julia hljs">checklist_save(
+checklist_save(&quot;checklist.html&quot;, clist)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecoeco/PRISMA.jl/blob/275159f671d921d5d355c6983ed6e6761d360a35/src/checklist.jl#L290-L330">source</a></section><section><div><pre><code class="language-julia hljs">checklist_save(
     fn::AbstractString, 
     cl::Checklist; 
     sheetname::AbstractString=&quot;2020 PRISMA Checklist&quot;, 
@@ -70,4 +70,4 @@
 checklist_save(&quot;checklist.xlsx&quot;, df)
 checklist_save(&quot;checklist.json&quot;, df)
 checklist_save(&quot;checklist.html&quot;, df)
-</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/cecoeco/PRISMA.jl/blob/aa0df564563107a8ded5ce90a5e0f003b303c076/src/checklist.jl#L343-L385">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 1.6.0 on <span class="colophon-date" title="Saturday 31 August 2024 02:36">Saturday 31 August 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/275159f671d921d5d355c6983ed6e6761d360a35/src/checklist.jl#L343-L385">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 1.6.0 on <span class="colophon-date" title="Saturday 31 August 2024 05:06">Saturday 31 August 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>