<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>GNU GENERAL PUBLIC LICENSE • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="bootstrap-toc.css"><scriptsrc="bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="pkgdown.css"rel="stylesheet"><scriptsrc="pkgdown.js"></script><metaproperty="og:title"content="GNU GENERAL PUBLIC LICENSE"><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<p>The GNU General Public License is a free, copyleft license for software and other kinds of works.</p>
<p>The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program–to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too.</p>
<p>When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things.</p>
<p>To protect your rights, we need to prevent others from denying you these rights or asking you to surrender the rights. Therefore, you have certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect the freedom of others.</p>
<p>For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass on to the recipients the same freedoms that you received. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights.</p>
<p>Developers that use the GNU GPL protect your rights with two steps:</p>
<p>(1) assert copyright on the software, and (2) offer you this License giving you legal permission to copy, distribute and/or modify it.</p>
<p>Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License giving you legal permission to copy, distribute and/or modify it.</p>
<p>For the developers’ and authors’ protection, the GPL clearly explains that there is no warranty for this free software. For both users’ and authors’ sake, the GPL requires that modified versions be marked as changed, so that their problems will not be attributed erroneously to authors of previous versions.</p>
<p>Some devices are designed to deny users access to install or run modified versions of the software inside them, although the manufacturer can do so. This is fundamentally incompatible with the aim of protecting users’ freedom to change the software. The systematic pattern of such abuse occurs in the area of products for individuals to use, which is precisely where it is most unacceptable. Therefore, we have designed this version of the GPL to prohibit the practice for those products. If such problems arise substantially in other domains, we stand ready to extend this provision to those domains in future versions of the GPL, as needed to protect the freedom of users.</p>
<p>Finally, every program is threatened constantly by software patents. States should not allow patents to restrict development and use of software on general-purpose computers, but in those that do, we wish to avoid the special danger that patents applied to a free program could make it effectively proprietary. To prevent this, the GPL assures that patents cannot be used to render the program non-free.</p>
<p>The precise terms and conditions for copying, distribution and modification follow.</p>
<p><em>“This License”</em> refers to version 3 of the GNU General Public License.</p>
<p><em>“Copyright”</em> also means copyright-like laws that apply to other kinds of works, such as semiconductor masks.</p>
<p><em>“The Program”</em> refers to any copyrightable work licensed under this License. Each licensee is addressed as <em>“you”</em>. <em>“Licensees”</em> and “recipients” may be individuals or organizations.</p>
@ -155,9 +83,8 @@ Everyone is permitted to copy and distribute verbatim copies of this license doc
<p>To <em>“convey”</em> a work means any kind of propagation that enables other parties to make or receive copies. Mere interaction with a user through a computer network, with no transfer of a copy, is not conveying.</p>
<p>An interactive user interface displays “Appropriate Legal Notices” to the extent that it includes a convenient and prominently visible feature that (1) displays an appropriate copyright notice, and (2) tells the user that there is no warranty for the work (except to the extent that warranties are provided), that licensees may convey the work under this License, and how to view a copy of this License. If the interface presents a list of user commands or options, such as a menu, a prominent item in the list meets this criterion.</p>
<p>The <em>“source code”</em> for a work means the preferred form of the work for making modifications to it. <em>“Object code”</em> means any non-source form of a work.</p>
<p>A <em>“Standard Interface”</em> means an interface that either is an official standard defined by a recognized standards body, or, in the case of interfaces specified for a particular programming language, one that is widely used among developers working in that language.</p>
<p>The <em>“System Libraries”</em> of an executable work include anything, other than the work as a whole, that (a) is included in the normal form of packaging a Major Component, but which is not part of that Major Component, and (b) serves only to enable use of the work with that Major Component, or to implement a Standard Interface for which an implementation is available to the public in source code form. A “Major Component”, in this context, means a major essential component (kernel, window system, and so on) of the specific operating system (if any) on which the executable work runs, or a compiler used to produce the work, or an object code interpreter used to run it.</p>
@ -165,95 +92,90 @@ Everyone is permitted to copy and distribute verbatim copies of this license doc
<p>The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding Source.</p>
<p>The Corresponding Source for a work in source code form is that same work.</p>
<p>All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided the stated conditions are met. This License explicitly affirms your unlimited permission to run the unmodified Program. The output from running a covered work is covered by this License only if the output, given its content, constitutes a covered work. This License acknowledges your rights of fair use or other equivalent, as provided by copyright law.</p>
<p>You may make, run and propagate covered works that you do not convey, without conditions so long as your license otherwise remains in force. You may convey covered works to others for the sole purpose of having them make modifications exclusively for you, or provide you with facilities for running those works, provided that you comply with the terms of this License in conveying all material for which you do not control copyright. Those thus making or running the covered works for you must do so exclusively on your behalf, under your direction and control, on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you.</p>
<p>Conveying under any other circumstances is permitted solely under the conditions stated below. Sublicensing is not allowed; section 10 makes it unnecessary.</p>
<ahref="#protecting-users-legal-rights-from-anti-circumvention-law-"class="anchor"></a>3. Protecting Users’ Legal Rights From Anti-Circumvention Law.</h2>
<divclass="section level2">
<h2id="id_3-protecting-users-legal-rights-from-anti-circumvention-law">3. Protecting Users’ Legal Rights From Anti-Circumvention Law.<aclass="anchor"aria-label="anchor"href="#id_3-protecting-users-legal-rights-from-anti-circumvention-law"></a></h2>
<p>No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention of such measures.</p>
<p>When you convey a covered work, you waive any legal power to forbid circumvention of technological measures to the extent such circumvention is effected by exercising rights under this License with respect to the covered work, and you disclaim any intention to limit operation or modification of the work as a means of enforcing, against the work’s users, your or third parties’ legal rights to forbid circumvention of technological measures.</p>
<p>You may convey verbatim copies of the Program’s source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating that this License and any non-permissive terms added in accord with section 7 apply to the code; keep intact all notices of the absence of any warranty; and give all recipients a copy of this License along with the Program.</p>
<p>You may charge any price or no price for each copy that you convey, and you may offer support or warranty protection for a fee.</p>
<p>You may convey a work based on the Program, or the modifications to produce it from the Program, in the form of source code under the terms of section 4, provided that you also meet all of these conditions:</p>
<divclass="sourceCode"id="cb1"><preclass="sourceCode R"><codeclass="sourceCode r"><aclass="sourceLine"id="cb1-1"data-line-number="1">a<spanclass="er">)</span> The work must carry prominent notices stating that you modified</a>
<aclass="sourceLine"id="cb1-2"data-line-number="2">it, and giving a relevant date.</a>
<aclass="sourceLine"id="cb1-4"data-line-number="4">b<spanclass="er">)</span> The work must carry prominent notices stating that it is</a>
<aclass="sourceLine"id="cb1-5"data-line-number="5">released under this License and any conditions added under section</a>
<aclass="sourceLine"id="cb1-6"data-line-number="6"><spanclass="fl">7.</span> This requirement modifies the requirement <spanclass="cf">in</span> section <spanclass="dv">4</span> to</a>
<aclass="sourceLine"id="cb1-7"data-line-number="7"><spanclass="st">"keep intact all notices"</span>.</a>
<aclass="sourceLine"id="cb1-17"data-line-number="17">d<spanclass="er">)</span> If the work has interactive user interfaces, each must display</a>
<aclass="sourceLine"id="cb1-18"data-line-number="18">Appropriate Legal Notices; however, <spanclass="cf">if</span> the Program has interactive</a>
<aclass="sourceLine"id="cb1-19"data-line-number="19">interfaces that do not display Appropriate Legal Notices, your</a>
<aclass="sourceLine"id="cb1-20"data-line-number="20">work need not make them do so.</a></code></pre></div>
<divclass="sourceCode"id="cb1"><preclass="sourceCode R"><codeclass="sourceCode r"><spanid="cb1-1"><ahref="#cb1-1"aria-hidden="true"tabindex="-1"></a>a<spanclass="er">)</span> The work must carry prominent notices stating that you modified</span>
<spanid="cb1-2"><ahref="#cb1-2"aria-hidden="true"tabindex="-1"></a>it, and giving a relevant date.</span>
<spanid="cb1-4"><ahref="#cb1-4"aria-hidden="true"tabindex="-1"></a>b<spanclass="er">)</span> The work must carry prominent notices stating that it is</span>
<spanid="cb1-5"><ahref="#cb1-5"aria-hidden="true"tabindex="-1"></a>released under this License and any conditions added under section</span>
<spanid="cb1-6"><ahref="#cb1-6"aria-hidden="true"tabindex="-1"></a><spanclass="fl">7.</span> This requirement modifies the requirement <spanclass="cf">in</span> section <spanclass="dv">4</span> to</span>
<spanid="cb1-7"><ahref="#cb1-7"aria-hidden="true"tabindex="-1"></a><spanclass="st">"keep intact all notices"</span>.</span>
<spanid="cb1-9"><ahref="#cb1-9"aria-hidden="true"tabindex="-1"></a>c<spanclass="er">)</span> You must license the entire work, as a whole, under this</span>
<spanid="cb1-10"><ahref="#cb1-10"aria-hidden="true"tabindex="-1"></a>License to anyone who comes into possession of a copy. This</span>
<spanid="cb1-11"><ahref="#cb1-11"aria-hidden="true"tabindex="-1"></a>License will therefore apply, along with any applicable section <spanclass="dv">7</span></span>
<spanid="cb1-12"><ahref="#cb1-12"aria-hidden="true"tabindex="-1"></a>additional terms, to the whole of the work, and all its parts,</span>
<spanid="cb1-13"><ahref="#cb1-13"aria-hidden="true"tabindex="-1"></a>regardless of how they are packaged. This License gives no</span>
<spanid="cb1-14"><ahref="#cb1-14"aria-hidden="true"tabindex="-1"></a>permission to license the work <spanclass="cf">in</span> any other way, but it does not</span>
<spanid="cb1-15"><ahref="#cb1-15"aria-hidden="true"tabindex="-1"></a>invalidate such permission <spanclass="cf">if</span> you have separately received it.</span>
<spanid="cb1-17"><ahref="#cb1-17"aria-hidden="true"tabindex="-1"></a>d<spanclass="er">)</span> If the work has interactive user interfaces, each must display</span>
<spanid="cb1-18"><ahref="#cb1-18"aria-hidden="true"tabindex="-1"></a>Appropriate Legal Notices; however, <spanclass="cf">if</span> the Program has interactive</span>
<spanid="cb1-19"><ahref="#cb1-19"aria-hidden="true"tabindex="-1"></a>interfaces that do not display Appropriate Legal Notices, your</span>
<spanid="cb1-20"><ahref="#cb1-20"aria-hidden="true"tabindex="-1"></a>work need not make them do so.</span></code></pre></div>
<p>A compilation of a covered work with other separate and independent works, which are not by their nature extensions of the covered work, and which are not combined with it such as to form a larger program, in or on a volume of a storage or distribution medium, is called an “aggregate” if the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation’s users beyond what the individual works permit. Inclusion of a covered work in an aggregate does not cause this License to apply to the other parts of the aggregate.</p>
<p>You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey the machine-readable Corresponding Source under the terms of this License, in one of these ways:</p>
<divclass="sourceCode"id="cb2"><preclass="sourceCode R"><codeclass="sourceCode r"><aclass="sourceLine"id="cb2-1"data-line-number="1">a<spanclass="er">)</span> Convey the object code <spanclass="cf">in</span>, or embodied <spanclass="cf">in</span>, a physical product</a>
<aclass="sourceLine"id="cb2-2"data-line-number="2">(including a physical distribution medium), accompanied by the</a>
<aclass="sourceLine"id="cb2-3"data-line-number="3">Corresponding Source fixed on a durable physical medium</a>
<aclass="sourceLine"id="cb2-4"data-line-number="4">customarily used <spanclass="cf">for</span> software interchange.</a>
<aclass="sourceLine"id="cb2-6"data-line-number="6">b<spanclass="er">)</span> Convey the object code <spanclass="cf">in</span>, or embodied <spanclass="cf">in</span>, a physical product</a>
<aclass="sourceLine"id="cb2-7"data-line-number="7">(including a physical distribution medium), accompanied by a</a>
<aclass="sourceLine"id="cb2-8"data-line-number="8">written offer, valid <spanclass="cf">for</span> at least three years and valid <spanclass="cf">for</span> as</a>
<aclass="sourceLine"id="cb2-9"data-line-number="9">long as you offer spare parts or customer support <spanclass="cf">for</span> that product</a>
<aclass="sourceLine"id="cb2-10"data-line-number="10">model, to give anyone who possesses the object code <spanclass="kw">either</span> (<spanclass="dv">1</span>) a</a>
<aclass="sourceLine"id="cb2-11"data-line-number="11">copy of the Corresponding Source <spanclass="cf">for</span> all the software <spanclass="cf">in</span> the</a>
<aclass="sourceLine"id="cb2-12"data-line-number="12">product that is covered by this License, on a durable physical</a>
<aclass="sourceLine"id="cb2-13"data-line-number="13">medium customarily used <spanclass="cf">for</span> software interchange, <spanclass="cf">for</span> a price no</a>
<aclass="sourceLine"id="cb2-14"data-line-number="14">more than your reasonable cost of physically performing this</a>
<aclass="sourceLine"id="cb2-15"data-line-number="15">conveying of source, <spanclass="kw">or</span> (<spanclass="dv">2</span>) access to copy the</a>
<aclass="sourceLine"id="cb2-16"data-line-number="16">Corresponding Source from a network server at no charge.</a>
<aclass="sourceLine"id="cb2-18"data-line-number="18">c<spanclass="er">)</span> Convey individual copies of the object code with a copy of the</a>
<aclass="sourceLine"id="cb2-19"data-line-number="19">written offer to provide the Corresponding Source. This</a>
<aclass="sourceLine"id="cb2-20"data-line-number="20">alternative is allowed only occasionally and noncommercially, and</a>
<aclass="sourceLine"id="cb2-21"data-line-number="21">only <spanclass="cf">if</span> you received the object code with such an offer, <spanclass="cf">in</span> accord</a>
<aclass="sourceLine"id="cb2-24"data-line-number="24">d<spanclass="er">)</span> Convey the object code by offering access from a designated</a>
<aclass="sourceLine"id="cb2-25"data-line-number="25"><spanclass="kw">place</span> (gratis or <spanclass="cf">for</span> a charge), and offer equivalent access to the</a>
<aclass="sourceLine"id="cb2-26"data-line-number="26">Corresponding Source <spanclass="cf">in</span> the same way through the same place at no</a>
<aclass="sourceLine"id="cb2-27"data-line-number="27">further charge. You need not require recipients to copy the</a>
<aclass="sourceLine"id="cb2-28"data-line-number="28">Corresponding Source along with the object code. If the place to</a>
<aclass="sourceLine"id="cb2-29"data-line-number="29">copy the object code is a network server, the Corresponding Source</a>
<aclass="sourceLine"id="cb2-30"data-line-number="30">may be on a different <spanclass="kw">server</span> (operated by you or a third party)</a>
<aclass="sourceLine"id="cb2-31"data-line-number="31">that supports equivalent copying facilities, provided you maintain</a>
<aclass="sourceLine"id="cb2-32"data-line-number="32">clear directions <spanclass="cf">next</span> to the object code saying where to find the</a>
<aclass="sourceLine"id="cb2-33"data-line-number="33">Corresponding Source. Regardless of what server hosts the</a>
<aclass="sourceLine"id="cb2-34"data-line-number="34">Corresponding Source, you remain obligated to ensure that it is</a>
<aclass="sourceLine"id="cb2-35"data-line-number="35">available <spanclass="cf">for</span> as long as needed to satisfy these requirements.</a>
<aclass="sourceLine"id="cb2-37"data-line-number="37">e<spanclass="er">)</span> Convey the object code using peer<spanclass="op">-</span>to<spanclass="op">-</span>peer transmission, provided</a>
<aclass="sourceLine"id="cb2-38"data-line-number="38">you inform other peers where the object code and Corresponding</a>
<aclass="sourceLine"id="cb2-39"data-line-number="39">Source of the work are being offered to the general public at no</a>
<aclass="sourceLine"id="cb2-40"data-line-number="40">charge under subsection 6d.</a></code></pre></div>
<divclass="sourceCode"id="cb2"><preclass="sourceCode R"><codeclass="sourceCode r"><spanid="cb2-1"><ahref="#cb2-1"aria-hidden="true"tabindex="-1"></a>a<spanclass="er">)</span> Convey the object code <spanclass="cf">in</span>, or embodied <spanclass="cf">in</span>, a physical product</span>
<spanid="cb2-2"><ahref="#cb2-2"aria-hidden="true"tabindex="-1"></a>(including a physical distribution medium), accompanied by the</span>
<spanid="cb2-3"><ahref="#cb2-3"aria-hidden="true"tabindex="-1"></a>Corresponding Source fixed on a durable physical medium</span>
<spanid="cb2-4"><ahref="#cb2-4"aria-hidden="true"tabindex="-1"></a>customarily used <spanclass="cf">for</span> software interchange.</span>
<spanid="cb2-6"><ahref="#cb2-6"aria-hidden="true"tabindex="-1"></a>b<spanclass="er">)</span> Convey the object code <spanclass="cf">in</span>, or embodied <spanclass="cf">in</span>, a physical product</span>
<spanid="cb2-7"><ahref="#cb2-7"aria-hidden="true"tabindex="-1"></a>(including a physical distribution medium), accompanied by a</span>
<spanid="cb2-8"><ahref="#cb2-8"aria-hidden="true"tabindex="-1"></a>written offer, valid <spanclass="cf">for</span> at least three years and valid <spanclass="cf">for</span> as</span>
<spanid="cb2-9"><ahref="#cb2-9"aria-hidden="true"tabindex="-1"></a>long as you offer spare parts or customer support <spanclass="cf">for</span> that product</span>
<spanid="cb2-10"><ahref="#cb2-10"aria-hidden="true"tabindex="-1"></a>model, to give anyone who possesses the object code <spanclass="fu">either</span> (<spanclass="dv">1</span>) a</span>
<spanid="cb2-11"><ahref="#cb2-11"aria-hidden="true"tabindex="-1"></a>copy of the Corresponding Source <spanclass="cf">for</span> all the software <spanclass="cf">in</span> the</span>
<spanid="cb2-12"><ahref="#cb2-12"aria-hidden="true"tabindex="-1"></a>product that is covered by this License, on a durable physical</span>
<spanid="cb2-13"><ahref="#cb2-13"aria-hidden="true"tabindex="-1"></a>medium customarily used <spanclass="cf">for</span> software interchange, <spanclass="cf">for</span> a price no</span>
<spanid="cb2-14"><ahref="#cb2-14"aria-hidden="true"tabindex="-1"></a>more than your reasonable cost of physically performing this</span>
<spanid="cb2-15"><ahref="#cb2-15"aria-hidden="true"tabindex="-1"></a>conveying of source, <spanclass="fu">or</span> (<spanclass="dv">2</span>) access to copy the</span>
<spanid="cb2-16"><ahref="#cb2-16"aria-hidden="true"tabindex="-1"></a>Corresponding Source from a network server at no charge.</span>
<spanid="cb2-18"><ahref="#cb2-18"aria-hidden="true"tabindex="-1"></a>c<spanclass="er">)</span> Convey individual copies of the object code with a copy of the</span>
<spanid="cb2-19"><ahref="#cb2-19"aria-hidden="true"tabindex="-1"></a>written offer to provide the Corresponding Source. This</span>
<spanid="cb2-20"><ahref="#cb2-20"aria-hidden="true"tabindex="-1"></a>alternative is allowed only occasionally and noncommercially, and</span>
<spanid="cb2-21"><ahref="#cb2-21"aria-hidden="true"tabindex="-1"></a>only <spanclass="cf">if</span> you received the object code with such an offer, <spanclass="cf">in</span> accord</span>
<spanid="cb2-24"><ahref="#cb2-24"aria-hidden="true"tabindex="-1"></a>d<spanclass="er">)</span> Convey the object code by offering access from a designated</span>
<spanid="cb2-25"><ahref="#cb2-25"aria-hidden="true"tabindex="-1"></a><spanclass="fu">place</span> (gratis or <spanclass="cf">for</span> a charge), and offer equivalent access to the</span>
<spanid="cb2-26"><ahref="#cb2-26"aria-hidden="true"tabindex="-1"></a>Corresponding Source <spanclass="cf">in</span> the same way through the same place at no</span>
<spanid="cb2-27"><ahref="#cb2-27"aria-hidden="true"tabindex="-1"></a>further charge. You need not require recipients to copy the</span>
<spanid="cb2-28"><ahref="#cb2-28"aria-hidden="true"tabindex="-1"></a>Corresponding Source along with the object code. If the place to</span>
<spanid="cb2-29"><ahref="#cb2-29"aria-hidden="true"tabindex="-1"></a>copy the object code is a network server, the Corresponding Source</span>
<spanid="cb2-30"><ahref="#cb2-30"aria-hidden="true"tabindex="-1"></a>may be on a different <spanclass="fu">server</span> (operated by you or a third party)</span>
<spanid="cb2-31"><ahref="#cb2-31"aria-hidden="true"tabindex="-1"></a>that supports equivalent copying facilities, provided you maintain</span>
<spanid="cb2-32"><ahref="#cb2-32"aria-hidden="true"tabindex="-1"></a>clear directions <spanclass="cf">next</span> to the object code saying where to find the</span>
<spanid="cb2-33"><ahref="#cb2-33"aria-hidden="true"tabindex="-1"></a>Corresponding Source. Regardless of what server hosts the</span>
<spanid="cb2-34"><ahref="#cb2-34"aria-hidden="true"tabindex="-1"></a>Corresponding Source, you remain obligated to ensure that it is</span>
<spanid="cb2-35"><ahref="#cb2-35"aria-hidden="true"tabindex="-1"></a>available <spanclass="cf">for</span> as long as needed to satisfy these requirements.</span>
<spanid="cb2-37"><ahref="#cb2-37"aria-hidden="true"tabindex="-1"></a>e<spanclass="er">)</span> Convey the object code using peer<spanclass="sc">-</span>to<spanclass="sc">-</span>peer transmission, provided</span>
<spanid="cb2-38"><ahref="#cb2-38"aria-hidden="true"tabindex="-1"></a>you inform other peers where the object code and Corresponding</span>
<spanid="cb2-39"><ahref="#cb2-39"aria-hidden="true"tabindex="-1"></a>Source of the work are being offered to the general public at no</span>
<spanid="cb2-40"><ahref="#cb2-40"aria-hidden="true"tabindex="-1"></a>charge under subsection 6d.</span></code></pre></div>
<p>A separable portion of the object code, whose source code is excluded from the Corresponding Source as a System Library, need not be included in conveying the object code work.</p>
<p>A <em>“User Product”</em> is either (1) a <em>“consumer product”</em>, which means any tangible personal property which is normally used for personal, family, or household purposes, or (2) anything designed or sold for incorporation into a dwelling. In determining whether a product is a consumer product, doubtful cases shall be resolved in favor of coverage. For a particular product received by a particular user, “normally used” refers to a typical or common use of that class of product, regardless of the status of the particular user or of the way in which the particular user actually uses, or expects or is expected to use, the product. A product is a consumer product regardless of whether the product has substantial commercial, industrial or non-consumer uses, unless such uses represent the only significant mode of use of the product.</p>
<p><em>“Installation Information”</em> for a User Product means any methods, procedures, authorization keys, or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source. The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made.</p>
@ -261,61 +183,56 @@ Everyone is permitted to copy and distribute verbatim copies of this license doc
<p>The requirement to provide Installation Information does not include a requirement to continue to provide support service, warranty, or updates for a work that has been modified or installed by the recipient, or for the User Product in which it has been modified or installed. Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network.</p>
<p>Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form), and must require no special password or key for unpacking, reading or copying.</p>
<p><em>“Additional permissions”</em> are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions.</p>
<p>When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission.</p>
<p>Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms:</p>
<divclass="sourceCode"id="cb3"><preclass="sourceCode R"><codeclass="sourceCode r"><aclass="sourceLine"id="cb3-1"data-line-number="1">a<spanclass="er">)</span> Disclaiming warranty or limiting liability differently from the</a>
<aclass="sourceLine"id="cb3-2"data-line-number="2">terms of sections <spanclass="dv">15</span> and <spanclass="dv">16</span> of this License; or</a>
<aclass="sourceLine"id="cb3-4"data-line-number="4">b<spanclass="er">)</span> Requiring preservation of specified reasonable legal notices or</a>
<aclass="sourceLine"id="cb3-5"data-line-number="5">author attributions <spanclass="cf">in</span> that material or <spanclass="cf">in</span> the Appropriate Legal</a>
<aclass="sourceLine"id="cb3-6"data-line-number="6">Notices displayed by works containing it; or</a>
<aclass="sourceLine"id="cb3-12"data-line-number="12">d<spanclass="er">)</span> Limiting the use <spanclass="cf">for</span> publicity purposes of names of licensors or</a>
<aclass="sourceLine"id="cb3-13"data-line-number="13">authors of the material; or</a>
<aclass="sourceLine"id="cb3-15"data-line-number="15">e<spanclass="er">)</span> Declining to grant rights under trademark law <spanclass="cf">for</span> use of some</a>
<aclass="sourceLine"id="cb3-16"data-line-number="16">trade names, trademarks, or service marks; or</a>
<aclass="sourceLine"id="cb3-18"data-line-number="18">f<spanclass="er">)</span> Requiring indemnification of licensors and authors of that</a>
<aclass="sourceLine"id="cb3-19"data-line-number="19">material by anyone who conveys the <spanclass="kw">material</span> (or modified versions of</a>
<aclass="sourceLine"id="cb3-20"data-line-number="20">it) with contractual assumptions of liability to the recipient, <spanclass="cf">for</span></a>
<aclass="sourceLine"id="cb3-21"data-line-number="21">any liability that these contractual assumptions directly impose on</a>
<aclass="sourceLine"id="cb3-22"data-line-number="22">those licensors and authors.</a></code></pre></div>
<divclass="sourceCode"id="cb3"><preclass="sourceCode R"><codeclass="sourceCode r"><spanid="cb3-1"><ahref="#cb3-1"aria-hidden="true"tabindex="-1"></a>a<spanclass="er">)</span> Disclaiming warranty or limiting liability differently from the</span>
<spanid="cb3-2"><ahref="#cb3-2"aria-hidden="true"tabindex="-1"></a>terms of sections <spanclass="dv">15</span> and <spanclass="dv">16</span> of this License; or</span>
<spanid="cb3-4"><ahref="#cb3-4"aria-hidden="true"tabindex="-1"></a>b<spanclass="er">)</span> Requiring preservation of specified reasonable legal notices or</span>
<spanid="cb3-5"><ahref="#cb3-5"aria-hidden="true"tabindex="-1"></a>author attributions <spanclass="cf">in</span> that material or <spanclass="cf">in</span> the Appropriate Legal</span>
<spanid="cb3-6"><ahref="#cb3-6"aria-hidden="true"tabindex="-1"></a>Notices displayed by works containing it; or</span>
<spanid="cb3-8"><ahref="#cb3-8"aria-hidden="true"tabindex="-1"></a>c<spanclass="er">)</span> Prohibiting misrepresentation of the origin of that material, or</span>
<spanid="cb3-9"><ahref="#cb3-9"aria-hidden="true"tabindex="-1"></a>requiring that modified versions of such material be marked <spanclass="cf">in</span></span>
<spanid="cb3-10"><ahref="#cb3-10"aria-hidden="true"tabindex="-1"></a>reasonable ways as different from the original version; or</span>
<spanid="cb3-12"><ahref="#cb3-12"aria-hidden="true"tabindex="-1"></a>d<spanclass="er">)</span> Limiting the use <spanclass="cf">for</span> publicity purposes of names of licensors or</span>
<spanid="cb3-13"><ahref="#cb3-13"aria-hidden="true"tabindex="-1"></a>authors of the material; or</span>
<spanid="cb3-15"><ahref="#cb3-15"aria-hidden="true"tabindex="-1"></a>e<spanclass="er">)</span> Declining to grant rights under trademark law <spanclass="cf">for</span> use of some</span>
<spanid="cb3-16"><ahref="#cb3-16"aria-hidden="true"tabindex="-1"></a>trade names, trademarks, or service marks; or</span>
<spanid="cb3-18"><ahref="#cb3-18"aria-hidden="true"tabindex="-1"></a>f<spanclass="er">)</span> Requiring indemnification of licensors and authors of that</span>
<spanid="cb3-19"><ahref="#cb3-19"aria-hidden="true"tabindex="-1"></a>material by anyone who conveys the <spanclass="fu">material</span> (or modified versions of</span>
<spanid="cb3-20"><ahref="#cb3-20"aria-hidden="true"tabindex="-1"></a>it) with contractual assumptions of liability to the recipient, <spanclass="cf">for</span></span>
<spanid="cb3-21"><ahref="#cb3-21"aria-hidden="true"tabindex="-1"></a>any liability that these contractual assumptions directly impose on</span>
<spanid="cb3-22"><ahref="#cb3-22"aria-hidden="true"tabindex="-1"></a>those licensors and authors.</span></code></pre></div>
<p>All other non-permissive additional terms are considered “further restrictions” within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying.</p>
<p>If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement of the additional terms that apply to those files, or a notice indicating where to find the applicable terms.</p>
<p>Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way.</p>
<p>You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11).</p>
<p>However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation.</p>
<p>Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice.</p>
<p>Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10.</p>
<ahref="#acceptance-not-required-for-having-copies-"class="anchor"></a>9. Acceptance Not Required for Having Copies.</h2>
<divclass="section level2">
<h2id="id_9-acceptance-not-required-for-having-copies">9. Acceptance Not Required for Having Copies.<aclass="anchor"aria-label="anchor"href="#id_9-acceptance-not-required-for-having-copies"></a></h2>
<p>You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so.</p>
<ahref="#automatic-licensing-of-downstream-recipients-"class="anchor"></a>10. Automatic Licensing of Downstream Recipients.</h2>
<divclass="section level2">
<h2id="id_10-automatic-licensing-of-downstream-recipients">10. Automatic Licensing of Downstream Recipients.<aclass="anchor"aria-label="anchor"href="#id_10-automatic-licensing-of-downstream-recipients"></a></h2>
<p>Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License.</p>
<p>An <em>“entity transaction”</em> is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party’s predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts.</p>
<p>You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it.</p>
<p>A <em>“contributor”</em> is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor’s “contributor version”.</p>
<p>A contributor’s <em>“essential patent claims”</em> are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, “control” includes the right to grant patent sublicenses in a manner consistent with the requirements of this License.</p>
<p>Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor’s essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version.</p>
@ -325,104 +242,92 @@ Everyone is permitted to copy and distribute verbatim copies of this license doc
<p>A patent license is “discriminatory” if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007.</p>
<p>Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.</p>
<ahref="#no-surrender-of-others-freedom-"class="anchor"></a>12. No Surrender of Others’ Freedom.</h2>
<divclass="section level2">
<h2id="id_12-no-surrender-of-others-freedom">12. No Surrender of Others’ Freedom.<aclass="anchor"aria-label="anchor"href="#id_12-no-surrender-of-others-freedom"></a></h2>
<p>If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.</p>
<ahref="#use-with-the-gnu-affero-general-public-license-"class="anchor"></a>13. Use with the GNU Affero General Public License.</h2>
<divclass="section level2">
<h2id="id_13-use-with-the-gnu-affero-general-public-license">13. Use with the GNU Affero General Public License.<aclass="anchor"aria-label="anchor"href="#id_13-use-with-the-gnu-affero-general-public-license"></a></h2>
<p>Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such.</p>
<ahref="#revised-versions-of-this-license-"class="anchor"></a>14. Revised Versions of this License.</h2>
<divclass="section level2">
<h2id="id_14-revised-versions-of-this-license">14. Revised Versions of this License.<aclass="anchor"aria-label="anchor"href="#id_14-revised-versions-of-this-license"></a></h2>
<p>The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.</p>
<p>Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License “or any later version” applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation.</p>
<p>If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy’s public statement of acceptance of a version permanently authorizes you to choose that version for the Program.</p>
<p>Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version.</p>
<ahref="#disclaimer-of-warranty-"class="anchor"></a>15. Disclaimer of Warranty.</h2>
<divclass="section level2">
<h2id="id_15-disclaimer-of-warranty">15. Disclaimer of Warranty.<aclass="anchor"aria-label="anchor"href="#id_15-disclaimer-of-warranty"></a></h2>
<p>THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.</p>
<ahref="#limitation-of-liability-"class="anchor"></a>16. Limitation of Liability.</h2>
<divclass="section level2">
<h2id="id_16-limitation-of-liability">16. Limitation of Liability.<aclass="anchor"aria-label="anchor"href="#id_16-limitation-of-liability"></a></h2>
<p>IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.</p>
<ahref="#interpretation-of-sections-15-and-16-"class="anchor"></a>17. Interpretation of Sections 15 and 16.</h2>
<divclass="section level2">
<h2id="id_17-interpretation-of-sections-15-and-16">17. Interpretation of Sections 15 and 16.<aclass="anchor"aria-label="anchor"href="#id_17-interpretation-of-sections-15-and-16"></a></h2>
<p>If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.</p>
<ahref="#end-of-terms-and-conditions"class="anchor"></a># END OF TERMS AND CONDITIONS</h2>
<divclass="section level2">
<h2id="id_-end-of-terms-and-conditions"># END OF TERMS AND CONDITIONS<aclass="anchor"aria-label="anchor"href="#id_-end-of-terms-and-conditions"></a></h2>
<ahref="#how-to-apply-these-terms-to-your-new-programs"class="anchor"></a>How to Apply These Terms to Your New Programs</h1>
<divclass="section level1">
<h1id="how-to-apply-these-terms-to-your-new-programs">How to Apply These Terms to Your New Programs<aclass="anchor"aria-label="anchor"href="#how-to-apply-these-terms-to-your-new-programs"></a></h1>
<p>If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.</p>
<p>To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.</p>
<divclass="sourceCode"id="cb4"><preclass="sourceCode R"><codeclass="sourceCode r"><aclass="sourceLine"id="cb4-1"data-line-number="1"><spanclass="op"><</span>one line to give the program<spanclass="st">'s name and a brief idea of what it does.></span></a>
<aclass="sourceLine"id="cb4-2"data-line-number="2"><spanclass="st">Copyright (C) <year><name of author></span></a>
<aclass="sourceLine"id="cb4-14"data-line-number="14"><spanclass="st">You should have received a copy of the GNU General Public License</span></a>
<aclass="sourceLine"id="cb4-15"data-line-number="15"><spanclass="st">along with this program. If not, see <http://www.gnu.org/licenses/>.</span></a></code></pre></div>
<divclass="sourceCode"id="cb4"><preclass="sourceCode R"><codeclass="sourceCode r"><spanid="cb4-1"><ahref="#cb4-1"aria-hidden="true"tabindex="-1"></a><spanclass="sc"><</span>one line to give the program<spanclass="st">'s name and a brief idea of what it does.></span></span>
<spanid="cb4-2"><ahref="#cb4-2"aria-hidden="true"tabindex="-1"></a><spanclass="st">Copyright (C) <year><name of author></span></span>
<spanid="cb4-4"><ahref="#cb4-4"aria-hidden="true"tabindex="-1"></a><spanclass="st">This program is free software: you can redistribute it and/or modify</span></span>
<spanid="cb4-5"><ahref="#cb4-5"aria-hidden="true"tabindex="-1"></a><spanclass="st">it under the terms of the GNU General Public License as published by</span></span>
<spanid="cb4-6"><ahref="#cb4-6"aria-hidden="true"tabindex="-1"></a><spanclass="st">the Free Software Foundation, either version 3 of the License, or</span></span>
<spanid="cb4-7"><ahref="#cb4-7"aria-hidden="true"tabindex="-1"></a><spanclass="st">(at your option) any later version.</span></span>
<spanid="cb4-9"><ahref="#cb4-9"aria-hidden="true"tabindex="-1"></a><spanclass="st">This program is distributed in the hope that it will be useful,</span></span>
<spanid="cb4-10"><ahref="#cb4-10"aria-hidden="true"tabindex="-1"></a><spanclass="st">but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
<spanid="cb4-11"><ahref="#cb4-11"aria-hidden="true"tabindex="-1"></a><spanclass="st">MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
<spanid="cb4-12"><ahref="#cb4-12"aria-hidden="true"tabindex="-1"></a><spanclass="st">GNU General Public License for more details.</span></span>
<spanid="cb4-14"><ahref="#cb4-14"aria-hidden="true"tabindex="-1"></a><spanclass="st">You should have received a copy of the GNU General Public License</span></span>
<spanid="cb4-15"><ahref="#cb4-15"aria-hidden="true"tabindex="-1"></a><spanclass="st">along with this program. If not, see <http://www.gnu.org/licenses/>.</span></span></code></pre></div>
<p>Also add information on how to contact you by electronic and paper mail.</p>
<p>If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:</p>
<divclass="sourceCode"id="cb5"><preclass="sourceCode R"><codeclass="sourceCode r"><aclass="sourceLine"id="cb5-1"data-line-number="1"><spanclass="op"><</span>program<spanclass="op">></span><spanclass="st"></span><spanclass="kw">Copyright</span> (C) <spanclass="op"><</span>year<spanclass="op">></span><spanclass="st"></span><spanclass="er"><</span>name of author<spanclass="op">></span></a>
<aclass="sourceLine"id="cb5-2"data-line-number="2">This program comes with ABSOLUTELY NO WARRANTY; <spanclass="cf">for</span> details type <spanclass="st">'show w'</span>.</a>
<aclass="sourceLine"id="cb5-3"data-line-number="3">This is free software, and you are welcome to redistribute it</a>
<aclass="sourceLine"id="cb5-4"data-line-number="4">under certain conditions; type <spanclass="st">'show c'</span><spanclass="cf">for</span> details.</a></code></pre></div>
<divclass="sourceCode"id="cb5"><preclass="sourceCode R"><codeclass="sourceCode r"><spanid="cb5-1"><ahref="#cb5-1"aria-hidden="true"tabindex="-1"></a><spanclass="sc"><</span>program<spanclass="sc">></span><spanclass="fu">Copyright</span> (C) <spanclass="sc"><</span>year<spanclass="sc">></span><spanclass="er"><</span>name of author<spanclass="sc">></span></span>
<spanid="cb5-2"><ahref="#cb5-2"aria-hidden="true"tabindex="-1"></a>This program comes with ABSOLUTELY NO WARRANTY; <spanclass="cf">for</span> details type <spanclass="st">'show w'</span>.</span>
<spanid="cb5-3"><ahref="#cb5-3"aria-hidden="true"tabindex="-1"></a>This is free software, and you are welcome to redistribute it</span>
<spanid="cb5-4"><ahref="#cb5-4"aria-hidden="true"tabindex="-1"></a>under certain conditions; type <spanclass="st">'show c'</span><spanclass="cf">for</span> details.</span></code></pre></div>
<p>The hypothetical commands <em>‘show w’</em> and <em>‘show c’</em> should show the appropriate parts of the General Public License. Of course, your program’s commands might be different; for a GUI interface, you would use an “about box”.</p>
<p>You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <ahref="http://www.gnu.org/licenses/"class="uri">http://www.gnu.org/licenses/</a>.</p>
<p>The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <ahref="http://www.gnu.org/philosophy/why-not-lgpl.html"class="uri">http://www.gnu.org/philosophy/why-not-lgpl.html</a>.</p>
<p>You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <ahref="http://www.gnu.org/licenses/"class="external-link uri">http://www.gnu.org/licenses/</a>.</p>
<p>The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <ahref="http://www.gnu.org/philosophy/why-not-lgpl.html"class="external-link uri">http://www.gnu.org/philosophy/why-not-lgpl.html</a>.</p>
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<em>simplerspec: Soil and plant spectroscopic model building and prediction</em>.
R package version 0.1.0.9001, <ahref="https://github.com/philipp-baumann/simplerspec"class="external-link">https://github.com/philipp-baumann/simplerspec</a>.
</p>
<pre>@Manual{,
title = {simplerspec: Soil and plant spectroscopic model building and prediction},
<p>The simplerspec package aims to facilitate spectra and additional data handling and model development for spectroscopy applications such as infrared soil spectroscopy. Different helper functions are designed to create a data and modeling workflow. Data inputs and outputs are stored in common S3 <code>R</code> objects (<code>lists</code> and <code>data frames</code>), using in addition <ahref="https://rdatatable.gitlab.io/data.table/"><code>data.table</code></a> and <ahref="https://tibble.tidyverse.org/index.html"><code>tibble</code></a> extensions. The functions are built to work in a pipeline and cover commonly used procedures for spectral model development and application.</p>
<p>The simplerspec package aims to facilitate spectral and additional data handling and model development for spectroscopy applications such as infrared soil spectroscopy. Different helper functions are designed to create a data and modeling workflow. Data inputs and outputs are stored in common S3 <code>R</code> objects (<code>lists</code> and <code>data frames</code>), using in addition <ahref="https://rdatatable.gitlab.io/data.table/"class="external-link"><code>data.table</code></a> and <ahref="https://tibble.tidyverse.org/index.html"class="external-link"><code>tibble</code></a> extensions. The functions are built to work in a pipeline and cover commonly used procedures for spectral model development and application.</p>
<p>The newest version of the package is available on this GitHub repository. Note that the package is still under development. If you find bugs you are highly welcome to report issues (write me an <ahref="mailto:philipp.baumann@usys.ethz.ch">email</a> or create an <ahref="https://github.com/philipp-baumann/simplerspec/issues">issue</a>). You can install <code>simplerspec</code> using the remotes package.</p>
<p>The newest version of the package is available on this GitHub repository. If you find bugs you are highly welcome to report issues (write me an <ahref="mailto:info@spectral-cockpit.space">email</a> or create an <ahref="https://github.com/philipp-baumann/simplerspec/issues"class="external-link">issue</a>). You can install {simplerspec} from GitHub or directly from the r-universe.</p>
<p>The current version of the package features among others the following functions:</p>
<ol>
<olstyle="list-style-type: decimal">
<li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/read-opus-universal.R"><code><ahref="reference/read_opus_univ.html">read_opus_univ()</a></code></a>: Read spectra and metadata from Bruker OPUS binary files into R list</li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/read-opus-universal.R"class="external-link"><code>read_opus_univ()</code></a>: Read spectra and metadata from Bruker OPUS binary files into R list</li>
<li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/gather-spc.R"><code><ahref="reference/gather_spc.html">gather_spc()</a></code></a>: Gather spectra and metadata from list into a tibble object (list-columns)</li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/gather-spc.R"class="external-link"><code>gather_spc()</code></a>: Gather spectra and metadata from list into a tibble object (list-columns)</li>
<li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/resample-spc.R"><code><ahref="reference/resample_spc.html">resample_spc()</a></code></a>: Resample spectra to new wavenumber intervals</li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/resample-spc.R"class="external-link"><code>resample_spc()</code></a>: Resample spectra to new wavenumber intervals</li>
<li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/average-spc.R"><code><ahref="reference/average_spc.html">average_spc()</a></code></a>: Average spectra for replicate scans</li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/average-spc.R"class="external-link"><code>average_spc()</code></a>: Average spectra for replicate scans</li>
<li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/preprocess-spc.R"><code><ahref="reference/preprocess_spc.html">preprocess_spc()</a></code></a>: Perform pre-processing of spectra</li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/preprocess-spc.R"class="external-link"><code>preprocess_spc()</code></a>: Perform pre-processing of spectra</li>
<li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/select-spc.R"><code><ahref="reference/select_spc_vars.html">select_spc_vars()</a></code></a>: Select every <code>n</code>-th spectral variable and corresponding X-unit values.</li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/select-spc.R"class="external-link"><code>select_spc_vars()</code></a>: Select every <code>n</code>-th spectral variable and corresponding X-unit values.</li>
<li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/join-chem-spectra.R"><code><ahref="reference/join_spc_chem.html">join_spc_chem()</a></code></a>: Join chemical and spectral data sets by <code>sample_id</code>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/join-chem-spectra.R"class="external-link"><code>join_spc_chem()</code></a>: Join chemical and spectral data sets by <code>sample_id</code>
</li>
<li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/plot-spc-extended.R"><code><ahref="reference/plot_spc_ext.html">plot_spc_ext()</a></code></a>: Extended spectral plotting; e.g. group spectra using different panels or color spectra based on chemical reference values to explore trends.</li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/plot-spc-extended.R"class="external-link"><code>plot_spc_ext()</code></a>: Extended spectral plotting; e.g. group spectra using different panels or color spectra based on chemical reference values to explore trends.</li>
<li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/pls-modeling.R"><code><ahref="reference/fit_pls.html">fit_pls()</a></code></a>: Perform model tuning and evaluation based on Partial Least Squares (PLS) regression</li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/pls-modeling.R"class="external-link"><code>fit_pls()</code></a>: Perform model tuning and evaluation based on Partial Least Squares (PLS) regression</li>
<li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/select-ref-spectra.R"><code><ahref="reference/select_ref_spc.html">select_ref_spc()</a></code></a>: Select a set of reference samples to measured by traditional analysis methods when no a priori sample data except spectra are available (based on Kennard-Stones sampling)</li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/select-ref-spectra.R"class="external-link"><code>select_ref_spc()</code></a>: Select a set of reference samples to measured by traditional analysis methods when no a priori sample data except spectra are available (based on Kennard-Stones sampling)</li>
<li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/predict-spc.R"><code><ahref="reference/predict_from_spc.html">predict_from_spc()</a></code></a>: Predict multiple chemical properties from a list of calibrated models and new soil spectra</li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/predict-spc.R"class="external-link"><code>predict_from_spc()</code></a>: Predict multiple chemical properties from a list of calibrated models and new soil spectra</li>
<li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/utils-stats.R"><code><ahref="reference/assess_multimodels.html">assess_multimodels()</a></code></a>: Assess model performance given multiple pairs of predicted and measured variables.</li>
<ahref="https://github.com/philipp-baumann/simplerspec/blob/master/R/utils-stats.R"class="external-link"><code>assess_multimodels()</code></a>: Assess model performance given multiple pairs of predicted and measured variables.</li>
<ahref="#motivation-and-key-concepts"class="anchor"></a>Motivation and key concepts</h2>
<divclass="section level2">
<h2id="motivation-and-key-concepts">Motivation and key concepts<aclass="anchor"aria-label="anchor"href="#motivation-and-key-concepts"></a>
</h2>
<p>Many R packages are available to do tasks in spectral modeling such as pre-processing of spectral data. The motivation to create this package was:</p>
<ol>
<olstyle="list-style-type: decimal">
<li>Avoid repetition of code in model development (common source of errors).</li>
<li>Provide a reproducible data analysis workflow for FT-IR spectroscopy.</li>
<li>R packages are an ideal way to organize and share R code.</li>
@ -142,144 +142,151 @@
<p>This package builds mainly upon functions from the following R packages:</p>
<ul>
<li>
<ahref="https://cran.r-project.org/web/packages/prospectr/index.html"><code>prospectr</code></a>: Various utilities for pre-processing and sample selection based on spectroscopic data. An introduction to the package with examples can be found <ahref="http://antoinestevens.github.io/prospectr/">here</a>.</li>
<ahref="https://cran.r-project.org/web/packages/prospectr/index.html"class="external-link"><code>prospectr</code></a>: Various utilities for pre-processing and sample selection based on spectroscopic data. An introduction to the package with examples can be found <ahref="https://l-ramirez-lopez.r-universe.dev/articles/prospectr/prospectr.html"class="external-link">here</a>.</li>
<li>
<code>plyr</code> and <ahref="https://dplyr.tidyverse.org/"><code>dplyr</code></a>: Fast data manipulation tools with an unified interface. See <ahref="https://github.com/hadley/dplyr">here</a> for details.</li>
<code>plyr</code> and <ahref="https://dplyr.tidyverse.org"class="external-link"><code>dplyr</code></a>: Fast data manipulation tools with an unified interface.</li>
<li>
<code>ggplot2</code>: Alternative plotting system for R, based on the grammar of graphics. See <ahref="http://ggplot2.org/">here</a>.</li>
<code>ggplot2</code>: Alternative plotting system for R, based on the grammar of graphics. See <ahref="https://ggplot2.tidyverse.org"class="external-link">here</a>.</li>
<li>
<code>caret</code>: Classification and regression training. A set of functions that attempt to streamline the process for creating predictive models. See <ahref="http://topepo.github.io/caret/index.html">here</a> for details.</li>
<code>caret</code>: Classification and regression training. A set of functions that attempt to streamline the process for creating predictive models. See <ahref="https://topepo.github.io/caret/"class="external-link">here</a> for details.</li>
</ul>
<p>Consistent and reproducible data and metadata management is an important prerequisite for spectral model development. Therefore, simplerspec functions are based on storing spectral data and related data in R data structures which keep related data in rows. Every row representing an observation contains data related to a single spectral measurement. Simplerspec functions uses tibble data frames as principal data structures because they allow to store lists within the well-known data frame structures. Lists are flexible data structures and can e.g. contain other lists, vectors, data.frames, or matrices.</p>
<p>List-columns features provided within the tibble framework are an excellent base to work with functional programming tools in R, which allows to efficiently write code. Simplerspec internally uses popular functional programming extension tools provided by the <ahref="https://purrr.tidyverse.org/"><code>purrr</code></a> package for processing and transforming spectra. For learning more, I would recommend <ahref="https://jennybc.github.io/purrr-tutorial/ls13_list-columns.html">this nice purrr list-column tutorial</a> provided by Jenny Brian. Further, simplerspec well integrates with the data processing API provided by the dplyr package, which makes spectroscopic analysis tidy and easy to understand.</p>
<p>List-columns features provided within the tibble framework are an excellent base to work with functional programming tools in R, which allows to efficiently write code. Simplerspec internally uses popular functional programming extension tools provided by the <ahref="https://purrr.tidyverse.org/"class="external-link"><code>purrr</code></a> package for processing and transforming spectra. For learning more, I would recommend <ahref="https://github.com/jennybc/purrr-tutorial/tree/gh-pages"class="external-link">this nice purrr list-column tutorial</a> provided by Jenny Brian. Further, simplerspec well integrates with the data processing API provided by the dplyr package, which makes spectroscopic analysis tidy and easy to understand.</p>
<p>Bruker FTIR spectrometers produce binary files in the OPUS format that can contain different types of spectra and many parameters such as instrument type and settings that were used at the time of data acquisition and internal processing (e.g. Fourier transform operations). Basically, the entire set of setup measurement parameters, selected spectra, supplementary metadata such as the time of measurement are written into OPUS binary files. In contrast to simple text files that contain only plain text with a defined character encoding, binary files can contain any type of data represented as sequences of bytes (a single byte is sequence of 8 bits and 1 bit either represents 0 or 1).</p>
<p>Simplerspec comes with reader function <code><ahref="reference/read_opus_univ.html">read_opus_univ()</a></code> that is intended to be a universal Bruker OPUS file reader that extracts spectra and key metadata from files. Usually, one is mostly interested to extract the final absorbance spectra (shown as <em>AB</em> in the OPUS viewer software).</p>
<divclass="sourceCode"id="cb2"><preclass="r"><spanclass="co"># Load simplerspec package for spectral model development wrapper functions</span>
<spanclass="co">#> Extracted spectra data from file: <BF_lo_01_soil_cal.0></span>
<spanclass="co">#> Extracted spectra data from file: <BF_lo_01_soil_cal.1></span>
<spanclass="co">#> Extracted spectra data from file: <BF_lo_01_soil_cal.2></span>
<spanclass="co">#> Extracted spectra data from file: <BF_lo_02_soil_cal.0></span>
<spanclass="co">#> ...</span></pre></div>
<p>Pipes can make R code more readable and allows step-wise data processing when developing spectral models. The pipe operator (<code><ahref="reference/pipe.html">%>%</a></code>, called “then”) is a new operator in R that was introduced with the magrittr package. It facilitates readability of code and avoids to type intermediate objects. The basic behavior of the pipe operator is that the object on the left hand side is passed as the first argument to the function on the right hand side. When loading the tidyverse packages, the pipe operator is attached to the current R session. More details can be found <ahref="https://github.com/smbache/magrittr">here</a>.</p>
<p>Pipes can make R code more readable and allows step-wise data processing when developing spectral models. The pipe operator (<code>%>%</code>, called “then”) is a new operator in R that was introduced with the magrittr package. It facilitates readability of code and avoids to type intermediate objects. The basic behavior of the pipe operator is that the object on the left hand side is passed as the first argument to the function on the right hand side. When loading the tidyverse packages, the pipe operator is attached to the current R session. More details can be found <ahref="https://magrittr.tidyverse.org"class="external-link">here</a>.</p>
<p>The model development process can be quickly coded as the example below illustrates:</p>
<divclass="sourceCode"id="cb3"><preclass="r"><spanclass="co">## Spectral data processing pipe ===============================================</span>
<spanclass="kw">pls_ncomp_max</span><spanclass="kw">=</span><spanclass="fl">7</span><spanclass="co"># maximum number of PLS components tested during tuning</span>
<span> pls_ncomp_max <spanclass="op">=</span><spanclass="fl">7</span><spanclass="co"># maximum number of PLS components tested during tuning</span></span>
<ahref="#projects-using-simplerspec"class="anchor"></a>Projects using simplerspec</h2>
<divclass="section level2">
<h2id="projects-using-simplerspec">Projects using simplerspec<aclass="anchor"aria-label="anchor"href="#projects-using-simplerspec"></a>
</h2>
<ul>
<li><ahref="https://sae-interactive-data.ethz.ch/simplerspec.drc/">Spectral platform for soil samples of the Democratic Republic of Congo</a></li>
<li><ahref="https://sae-interactive-data.ethz.ch/simplerspec.drc/"class="external-link">Spectral platform for soil samples of the Democratic Republic of Congo</a></li>
<p><ahref="https://www.buymeacoffee.com/specphil"class="external-link"><imgsrc="https://www.buymeacoffee.com/assets/img/custom_images/orange_img.png"alt="“Buy Me A Coffee”"></a></p>
<p>I would like to thank the following people for the inspiration by concepts, code and packages:</p>
<ul>
<li>Antoine Stevens and Leonardo Ramirez-Lopez for their contributions to the <ahref="https://cran.r-project.org/web/packages/prospectr/index.html">prospectr package</a> and the <em>Guide to Diffuse Reflectance Spectroscopy & Multivariate Calibration</em>
<li>Antoine Stevens and Leonardo Ramirez-Lopez for their contributions to the <ahref="https://l-ramirez-lopez.r-universe.dev/prospectr"class="external-link">prospectr package</a> and the <em>Guide to Diffuse Reflectance Spectroscopy & Multivariate Calibration</em>
</li>
<li>Andrew Sila, Tomislav Hengl, and Thomas Terhoeven-Urselmans for the <ahref="https://github.com/cran/soil.spec/blob/master/R/read.opus.R"><code>read.opus()</code></a> function from the <ahref="https://cran.r-project.org/web/packages/soil.spec/index.html">soil.spec</a> package developed at ICRAF.</li>
<li>Andrew Sila, Tomislav Hengl, and Thomas Terhoeven-Urselmans for the <ahref="https://github.com/cran/soil.spec/blob/master/R/read.opus.R"class="external-link"><code>read.opus()</code></a> function from the <ahref="https://cran.r-project.org/src/contrib/Archive/soil.spec/"class="external-link">soil.spec</a> package developed at ICRAF.</li>
<li>
<ahref="http://hadley.nz/">Hadley Wickham</a> for his work and concepts on data science within R</li>
<ahref="https://hadley.nz"class="external-link">Hadley Wickham</a> for his work and concepts on data science within R</li>
<li>
<ahref="https://github.com/topepo">Max Kuhn</a> for the creation of the caret package and for his excellent teaching materials on <ahref="http://appliedpredictivemodeling.com/blog/">applied predictive modeling</a>
<ahref="https://github.com/topepo"class="external-link">Max Kuhn</a> for the creation of the caret package and for his excellent teaching materials on <ahref="https://link.springer.com/book/10.1007/978-1-4614-6849-3"class="external-link">applied predictive modeling</a>
<code><ahref="../reference/resample_spc.html">resample_spc()</a></code> now supports flexible spectra and x-axis types as inputs. Its interface has been carefully augmented without breaking previous functionality (<ahref="https://github.com/philipp-baumann/simplerspec/issues/9"><ahref='https://github.com/philipp-baumann/simplerspec/issues/9'>#9</a></a>
<ul>
<li>New argument <code>column_in</code> specifies the string or name (unquoting support) of the input column that contains the list of spectra. The following spectrum types, which are automatically matched against the list-column that contains the corresponding x-unit value vectors, are currently supported: <code>spc</code> (raw or unprocessed spectra), <code>spc_rs</code> (resampled spectra), <code>spc_mean</code> (mean spectra), <code>spc_nocomp</code> (spectra prior atmospheric compensation), <code>sc_sm</code> (single channel sample spectra), <code>sc_rf</code> (single channel reference spectra), <code>spc_pre</code> (preprocessed spectra).</li>
<code><ahref="../reference/resample_spc.html">resample_spc()</a></code> now supports flexible spectra and x-axis types as inputs. Its interface has been carefully augmented without breaking previous functionality (<ahref="https://github.com/philipp-baumann/simplerspec/issues/9"class="external-link">#9</a>
<ul><li>New argument <code>column_in</code> specifies the string or name (unquoting support) of the input column that contains the list of spectra. The following spectrum types, which are automatically matched against the list-column that contains the corresponding x-unit value vectors, are currently supported: <code>spc</code> (raw or unprocessed spectra), <code>spc_rs</code> (resampled spectra), <code>spc_mean</code> (mean spectra), <code>spc_nocomp</code> (spectra prior atmospheric compensation), <code>sc_sm</code> (single channel sample spectra), <code>sc_rf</code> (single channel reference spectra), <code>spc_pre</code> (preprocessed spectra).</li>
<li>New argument <code>interpol_method</code> specifying the interpolation method is introduced. Default is <code>"linear"</code> to achieve identical results with both prospectr v0.1.0 and v0.2.0. The current CRAN prospectr v0.2.0 has changed the default of <code>interpol</code> to <code>"spline"</code>. The previous <code><ahref="../reference/resample_spc.html">resample_spc()</a></code> unfortunatelty did not explicitly state the method internally, and relied on the default instead. The measures taken ensure downward compatibility of <code><ahref="../reference/resample_spc.html">resample_spc()</a></code> with previous versions of prospectr and simplerspec.</li>
<li>The arguments gain more defensive checks inside the function (supplied types and presence of objects in spectra).</li>
<li>The function components and the help are updated accordingly. Clearer vocabulary to describe the functionality and more consistent terminology for physical quantities and R objects are used.</li>
</ul>
</li>
</ul></li>
<li>Add UTF-8 support to DESCRIPTION because roxygen2 version 7.1.0 requires it.</li>
<ul><li>Start using Kirill’s <ahref="https://fledge.cynkra.com/"class="external-link">fledge</a> for tracking and communicating the simplerspec development process in <code>NEWS</code>.</li>
<code><ahref="../reference/read_opus_bin_univ.html">read_opus_bin_univ()</a></code>: Add support for Bruker files that have undefined <code>PLF</code> value (<code>:= NULL</code>)</li>
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Assess multiple pairs of measured and predicted values — assess_multimodels • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Assess multiple pairs of measured and predicted values — assess_multimodels"><metaproperty="og:description"content="Returnperformancemetricsfortestsetpredictionsand
measured values, e.g. for different model outcome variables."><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Average spectra in list-column by entries in grouping column — average_spc • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Average spectra in list-column by entries in grouping column — average_spc"><metaproperty="og:description"content="Averagespectrainlist-columnofspectratibble(spc_tbl)by
groups given in group column."><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<p>For memory efficiency and subsequent modeling, consider slicing the
extra row copies of <code>spc_mean</code> resulting from <code>average_spc()</code> for example by</p><ul>
<li><p><code>split(x = spc_tbl, f = spc_tbl$<by>) %>% lapply(., function(x) x x[1, ]) %>% do.call(., rbind)</code></p></li>
extra row copies of <code>spc_mean</code> resulting from <code>average_spc()</code> for example by</p><ul><li><p><code>split(x = spc_tbl, f = spc_tbl$<by>) %>% lapply(., function(x) x x[1, ]) %>% do.call(., rbind)</code></p></li>
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Bind list-columns within a tibble into a list of data.tables — bind_lcols_dts • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Bind list-columns within a tibble into a list of data.tables — bind_lcols_dts"><metaproperty="og:description"content="Bindonetomanylist-columnsinspectraltibbleintoalist
of data.tables."><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Create a data frame containing start and end positions (wavenumbers)
where variable importance in projection (VIP) is > 1 — create_vip_rects • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Createadataframecontainingstartandendpositions(wavenumbers)
where variable importance in projection (VIP) is > 1 — create_vip_rects"><metaproperty="og:description"content="GivenadataframewithVIPoutputs(wavenumberandvip
columns), start and end values denoting spectral regions where VIP &gt; 1
are returned as data frame. The functions can be used as helper
function for plotting VIP."><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Calculate model evaluation metrics — evaluate_model • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Calculate model evaluation metrics — evaluate_model"><metaproperty="og:description"content="Calculatesummarystatisticsofobservedvaluesandmodel
evaluation statistics for assessing agreement between observed (obs) and
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Extract multiple tibble list-columns and return data as list of
into single data tables and return a list of data.tables."><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<title>Extract VIPs (variable importance in the projection) for a PLS
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Extract VIPs (variable importance in the projection) for a PLS
regression model output returned from model fitting with
derived number of PLS components in the finalModel are computed."><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<p>VIPs are extracted based on the <code>finalModel</code> sublist
in the <code><ahref='https://rdrr.io/pkg/caret/man/train.html'>caret::train</a></code> output contained in the <code>model</code> element
of the <code><ahref='fit_pls.html'>simplerspec::fit_pls()</a></code> model output list. The VIPs for
in the <code><ahref="https://rdrr.io/pkg/caret/man/train.html"class="external-link">caret::train</a></code> output contained in the <code>model</code> element
of the <code><ahref="fit_pls.html">simplerspec::fit_pls()</a></code> model output list. The VIPs for
derived number of PLS components in the <code>finalModel</code> are computed.</p>
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Calibration sampling, model tuning, and PLS regression — fit_pls • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Calibration sampling, model tuning, and PLS regression — fit_pls"><metaproperty="og:description"content="Performcalibrationsamplinganduseselected
calibration set for model tuning"><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<code>"loocv"</code> (performs leave-one-out cross-validation), and <code>"none"</code>
(if <code>resampling_method = "none"</code>) are supported.</p></td>
</tr>
<tr>
<th>cv</th>
<td><p>Depreciated. Use <code>resampling_method</code> instead.</p></td>
</tr>
<tr>
<th>resampling_seed</th>
<td><p>Random seed (integer) that will be used for generating
resampling indices, which will be supplied to <code><ahref='https://rdrr.io/pkg/caret/man/trainControl.html'>caret::trainControl</a></code>.
(if <code>resampling_method = "none"</code>) are supported.</p></dd>
<dt>cv</dt>
<dd><p>Depreciated. Use <code>resampling_method</code> instead.</p></dd>
<dt>resampling_seed</dt>
<dd><p>Random seed (integer) that will be used for generating
resampling indices, which will be supplied to <code><ahref="https://rdrr.io/pkg/caret/man/trainControl.html"class="external-link">caret::trainControl</a></code>.
This makes sure that modeling results are constant when re-fitting.
Default is <code>resampling_seed = 123</code>.</p></td>
</tr>
<tr>
<th>pls_ncomp_max</th>
<td><p>Maximum number of PLS components that are evaluated
Default is <code>resampling_seed = 123</code>.</p></dd>
<dt>pls_ncomp_max</dt>
<dd><p>Maximum number of PLS components that are evaluated
by caret::train. Caret will aggregate a performance profile using resampling
for an integer sequence from 1 to <code>pls_ncomp_max</code></p></td>
</tr>
<tr>
<th>ncomp_fixed</th>
<td><p>Integer of fixed number of PLS components. Will only be
for an integer sequence from 1 to <code>pls_ncomp_max</code></p></dd>
<dt>ncomp_fixed</dt>
<dd><p>Integer of fixed number of PLS components. Will only be
used when <code>tuning_method = "none"</code> and <code>resampling_method = "none"</code>
are used.</p></td>
</tr>
<tr>
<th>print</th>
<td><p>Logical expression whether model evaluation graphs shall be
printed</p></td>
</tr>
<tr>
<th>env</th>
<td><p>Environment where function is evaluated. Default is
<code>parent.frame</code>.</p></td>
</tr>
</table>
are used.</p></dd>
<dt>print</dt>
<dd><p>Logical expression whether model evaluation graphs shall be
printed</p></dd>
<dt>env</dt>
<dd><p>Environment where function is evaluated. Default is
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Calibration sampling, and random forest model tuning and evaluation — fit_rf • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Calibration sampling, and random forest model tuning and evaluation — fit_rf"><metaproperty="og:description"content="Performcalibrationsamplinganduseselected
calibration set for model tuning"><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
affects how caret selects a final tuning value set from a list of candidate
values. Possible values are <code>"resampling"</code>, which will use a
specified resampling method such as repeated k-fold cross-validation (see
@ -203,63 +148,58 @@ that lead to optimal model performance. The value <code>"none"</code> will force
caret to compute a final model for a predefined canditate PLS tuning
parameter number of PLS components. In this case, the value
supplied by <code>ncomp_fixed</code>` is used to set model complexity at
a fixed number of components.</p></td>
</tr>
<tr>
<th>resampling_seed</th>
<td><p>Random seed (integer) that will be used for generating
resampling indices, which will be supplied to <code><ahref='https://rdrr.io/pkg/caret/man/trainControl.html'>caret::trainControl</a></code>.
a fixed number of components.</p></dd>
<dt>resampling_seed</dt>
<dd><p>Random seed (integer) that will be used for generating
resampling indices, which will be supplied to <code><ahref="https://rdrr.io/pkg/caret/man/trainControl.html"class="external-link">caret::trainControl</a></code>.
This makes sure that modeling results are constant when re-fitting.
Default is <code>resampling_seed = 123</code>.</p></td>
</tr>
<tr>
<th>cv</th>
<td><p>Depreciated. Use <code>resampling_method</code> instead.</p></td>
</tr>
<tr>
<th>ntree_max</th>
<td><p>Maximum random forest trees
Default is <code>resampling_seed = 123</code>.</p></dd>
<dt>cv</dt>
<dd><p>Depreciated. Use <code>resampling_method</code> instead.</p></dd>
<dt>ntree_max</dt>
<dd><p>Maximum random forest trees
by caret::train. Caret will aggregate a performance profile using resampling
for an integer sequence from 1 to <code>ntree_max</code> trees.</p></td>
</tr>
<tr>
<th>print</th>
<td><p>Logical expression whether model evaluation graphs shall be
printed</p></td>
</tr>
<tr>
<th>env</th>
<td><p>Environment where function is evaluated. Default is
<code>parent.frame</code>.</p></td>
</tr>
</table>
for an integer sequence from 1 to <code>ntree_max</code> trees.</p></dd>
<dt>print</dt>
<dd><p>Logical expression whether model evaluation graphs shall be
printed</p></dd>
<dt>env</dt>
<dd><p>Environment where function is evaluated. Default is
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Gather measurements of different spectra types, corresponding
x-axis values and metadata from nested list. — gather_spc • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Gathermeasurementsofdifferentspectratypes,corresponding
x-axis values and metadata from nested list. — gather_spc"><metaproperty="og:description"content='Gatherspectra,correspondingx-axisvalues,anddeviceand
measurement metadata from a nested list into a spectra tibble, so that one
row represents one spectral measurement. Spectra, x-axis values and metadata
are mapped from the individual list elements (named after file name including
@ -50,32 +9,18 @@ the extension) and transformed into (list-)columns of a spectra tibble,
which is an extended data frame. For each measurement, spectral data and
metadata are combined into one row of the tidy data frame. In addition, the ID
columns unique_id, file_id, and sample_id are extracted from
"metadata" (data frame) list entries and returned as identifier columns of
"metadata" (data frame) list entries and returned as identifier columns of
the spectra tibble. List-columns facilitate keeping related data together in
a rectangular data structure. They can be manipulated easily during
subsequent transformations, for example using the standardized functions of
the simplerspec data processing pipeline.'><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<p>Spectra tibble (<code>spc_tbl</code> with classes <code>"tbl_df"</code>, <code>"tbl"</code>, and
<code>"data.frame"</code>) with the following (list-)columns:</p><ul>
<li><p><code>"unique_id"</code>: Character vector with unique measurement identifier, likely
<p>Spectra tibble (<code>spc_tbl</code> with classes <code>"tbl_df"</code>, <code>"tbl"</code>, and
<code>"data.frame"</code>) with the following (list-)columns:</p><ul><li><p><code>"unique_id"</code>: Character vector with unique measurement identifier, likely
a string with file names in combination with date and time (extracted from
each <code>"metadata"</code> data frame column).</p></li>
<li><p><code>"file_id"</code> : Character vector with file name including the extension
@ -204,15 +135,13 @@ List(s) of data.table's containing spectra type(s).</p></li>
<code>"wavenumbers_sc_rf"</code>, <code>"wavelengths_sc_rf"</code>, or <code>"x_values_sc_rf"</code>:
List(s) of numeric vectors with matched x-axis values (see <em>"Details on
spectra data checks and matching"</em> below).</p></li>
</ul>
<h2class="hasAnchor"id="details-on-spectra-data-checks-and-matching"><aclass="anchor"href="#details-on-spectra-data-checks-and-matching"></a>Details on spectra data checks and matching</h2>
<h2>Details on spectra data checks and matching</h2>
<p><code>gather_spc()</code> checks whether these conditions are met for each measurement
in the list <code>data</code>:</p><ol>
<li><p>Make sure that the first level <code>data</code> elements are named (assumed to be
in the list <code>data</code>:</p><ol><li><p>Make sure that the first level <code>data</code> elements are named (assumed to be
the file name the data originate from), and remove missing measurements with
an informative message.</p></li>
<li><p>Remove any duplicated file names and raise a message if there are
@ -223,8 +152,7 @@ all data elements for incomplete spectral measurements.</p></li>
<li><p>Match spectra types and possible corresponding x-axis types from
a lookup list. For each selected spectrum type (left), at least one of
the element names of the x-axis type (right) needs to be present for each
measurement in the list <code>data</code>:</p><ul>
<li><p><code>"spc"</code> : <code>"wavenumbers"</code>, <code>"wavelengths"</code>, or <code>"x_values"</code></p></li>
measurement in the list <code>data</code>:</p><ul><li><p><code>"spc"</code> : <code>"wavenumbers"</code>, <code>"wavelengths"</code>, or <code>"x_values"</code></p></li>
<li><p><code>"spc_nocomp"</code> : <code>"wavenumbers"</code>, <code>"wavelengths"</code>, or <code>"x_values"</code></p></li>
<li><p><code>"sc_sm"</code> : <code>"wavenumbers_sc_sm"</code>, <code>"wavelengths_sc_sm"</code>, or
<code>"x_values_sc_sm"</code></p></li>
@ -234,34 +162,29 @@ measurement in the list <code>data</code>:</p><ul>
<li><p>Check if <code>"metadata"</code> elements are present and remove data elements for
measurements with missing or incorrectly named metadata elements
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Join chemical and spectral data frames — join_chem_spec • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Join chemical and spectral data frames — join_chem_spec"><metaproperty="og:description"content="Combinesspectraldata(data.frame)andchemical
data (data.frame)."><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<divclass="sourceCode"><preclass="sourceCode r"><code><span><spanclass="fu">join_chem_spec</span><spanclass="op">(</span><spanclass="va">dat_chem</span>, <spanclass="va">dat_spec</span>, by <spanclass="op">=</span><spanclass="st">"sample_ID"</span><spanclass="op">)</span></span></code></pre></div>
</div>
<divid="arguments">
<h2>Arguments</h2>
<dl><dt>dat_chem</dt>
<dd><p>data.frame that contains chemical values of
the sample</p></dd>
<dt>dat_spec</dt>
<dd><p>List that contains spectral data</p></dd>
<dt>by</dt>
<dd><p>character of column name that defines sample_ID</p></dd>
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Join spectra data and chemical data tibbles — join_spc_chem • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Join spectra data and chemical data tibbles — join_spc_chem"><metaproperty="og:description"content="Combinesspectraldata(tibbleclass)andchemical
data (tibble class)."><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<divclass="sourceCode"><preclass="sourceCode r"><code><span><spanclass="fu">join_spc_chem</span><spanclass="op">(</span><spanclass="va">spc_tbl</span>, <spanclass="va">chem_tbl</span>, by <spanclass="op">=</span><spanclass="st">"sample_id"</span><spanclass="op">)</span></span></code></pre></div>
</div>
<divid="arguments">
<h2>Arguments</h2>
<dl><dt>spc_tbl</dt>
<dd><p>Tibble that contains spectral data</p></dd>
<dt>chem_tbl</dt>
<dd><p>Tibble that contains chemical reference values of
the samples</p></dd>
<dt>by</dt>
<dd><p>character of column name that defines sample_ID</p></dd>
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Merge list-columns of spectra, x-axis values, metadata and additional
measured variables into a single long form data.table — merge_dts • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Mergelist-columnsofspectra,x-axisvalues,metadataandadditional
measured variables into a single long form data.table — merge_dts"><metaproperty="og:description"content="Helperfunctionthatmergesallspectraandrelateddatainto
a single long form data.table than can subsequently be used for plotting."><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Wrapper function around merge_dts() for list of tibbles to
aggregate data for plotting. — merge_dts_l • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Wrapperfunctionaroundmerge_dts()forlistoftibblesto
aggregate data for plotting. — merge_dts_l"><metaproperty="og:description"content="Insteadofasinglespectraltibble(dataframe)multiple
spectral tibbles can be merged into a long-form data.table for plotting
<title>Plot stacked ggplot2 graphs with the Variable Importance for the
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Plot stacked ggplot2 graphs with the Variable Importance for the
Projection (VIP) scores, mean replicate spectra (absorbance) per sample_id,
and the preprocessed spectra. — plot_pls_vip • simplerspec</title>
<code><ahref="fit_pls.html">simplerspec::fit_pls()</a></code>. This object contains a nested list with
the <code><ahref="https://rdrr.io/pkg/caret/man/train.html"class="external-link">caret::train()</a></code> object (class <code>train</code>), based on which
VIPs at finally selected number of PLS components are computed.</p></dd>
<dt>y1</dt>
<dd><p>Character vector of list-column name in
<code>mout$data$calibration</code>, where spectra for bottom graph are extracted.
Default is <code>"spc_mean"</code>, which plots the mean calibration spectra after
resampling.</p></td>
</tr>
<tr>
<th>y2</th>
<td><p>Character string of list-column name in
resampling.</p></dd>
<dt>y2</dt>
<dd><p>Character string of list-column name in
<code>mout$data$calibration</code>, where spectra for bottom graph are extracted.
Default is <code>"spc_pre"</code>, which plots the preprocessed calibration
spectra after resampling.</p></td>
</tr>
<tr>
<th>by</th>
<td><p>Character string that is used to assign spectra to the same group
spectra after resampling.</p></dd>
<dt>by</dt>
<dd><p>Character string that is used to assign spectra to the same group
and therefore ensures that all spectra are plotted with the same colour.
Default is <code>"sample_id"</code></p></td>
</tr>
<tr>
<th>xlab</th>
<td><p>Character string of X axis title for shared x axis of stacked
graphs. Default is <code><ahref='https://rdrr.io/r/base/expression.html'>expression(paste("Wavenumber [", cm^-1, "]"))</a></code></p></td>
</tr>
<tr>
<th>ylab1</th>
<td><p>Y axis title of bottom spectrum. Default is <code>"Absorbance"</code>.</p></td>
</tr>
<tr>
<th>ylab2</th>
<td><p>Y axis title of bottom spectrum. Default is
<code>"Preprocessed Abs."</code>.</p></td>
</tr>
<tr>
<th>alpha</th>
<td><p>Double between 0 and 1 that defines transparency of spectra
lines in returned graph (ggplot plot object).</p></td>
</tr>
</table>
Default is <code>"sample_id"</code></p></dd>
<dt>xlab</dt>
<dd><p>Character string of X axis title for shared x axis of stacked
graphs. Default is <code>expression(paste("Wavenumber [", cm^-1, "]"))</code></p></dd>
<dt>ylab1</dt>
<dd><p>Y axis title of bottom spectrum. Default is <code>"Absorbance"</code>.</p></dd>
<dt>ylab2</dt>
<dd><p>Y axis title of bottom spectrum. Default is
<code>"Preprocessed Abs."</code>.</p></dd>
<dt>alpha</dt>
<dd><p>Double between 0 and 1 that defines transparency of spectra
lines in returned graph (ggplot plot object).</p></dd>
additional measure variable, e.g. determined by chemical reference analysis.'><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
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of calibration models and a tibble containing preprocessed spectra as
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Read ASD fieldspec spectrometer data export into into simplerspec
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Read ASD binary files and gather spectra and metadata in tibble data
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Read a Bruker OPUS spectrum binary file — read_opus_bin_univ • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Read a Bruker OPUS spectrum binary file — read_opus_bin_univ"><metaproperty="og:description"content="Readsinglebinaryfileacquiredwithan
Bruker Vertex FTIR Instrument"><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
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containing spectra are in OPUS binary format.
read_opus_univ is a wrapper for read_opus_bin_univ())" />
read_opus_univ is a wrapper for read_opus_bin_univ())"><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Remove outlier spectra — remove_outliers • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Remove outlier spectra — remove_outliers"><metaproperty="og:description"content="Removeoutlierspectrabasedonthe
pcout() function of the mvoutlier package."><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Resample spectra in list-column to new x-axis interval — resample_spc • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Resample spectra in list-column to new x-axis interval — resample_spc"><metaproperty="og:description"content="Resamples(interpolates)differentspectratypeswith
corresponding x-axis values that are both stored in list-columns of a spectra
tibble. A spectra tibble hosts spectra, x-axis vectors, metadata, and
further linked data with standardized naming conventions. Data input for
resampling can for example be generated with simplerspec::gather_spc().
Resampling is a key harmonizing step to process and later model spectra
measured at different resolutions and spectral ranges (i.e., different
<p>A spectra tibble (<code>spc_tbl</code>) containing two added list-columns:</p><ul>
<li><p><code>spc_rs:</code> Resampled spectra as list of <code>data.table</code>s</p></li>
<p>A spectra tibble (<code>spc_tbl</code>) containing two added list-columns:</p><ul><li><p><code>spc_rs:</code> Resampled spectra as list of <code>data.table</code>s</p></li>
<li><p><code>wavenumbers_rs</code> or <code>wavelengths_rs</code>: Resampled x-axis values as list of
numeric vectors</p></li>
</ul>
<h2class="hasAnchor"id="matching-spectrum-type-and-corresponding-x-axis-type"><aclass="anchor"href="#matching-spectrum-type-and-corresponding-x-axis-type"></a>Matching spectrum type and corresponding x-axis type</h2>
<h2>Matching spectrum type and corresponding x-axis type</h2>
<p>The combinations of input spectrum types (<code>column_in</code>) and
corresponding x-axis types are generated from a simple lookup list. The
following key-value(s) pairs can be matched at given key, which is the column
name from <code>column_in</code> containing the spectra.</p><ul>
<li><p><code>"spc"</code> : <code>"wavenumbers"</code> or <code>"wavelengths"</code> (raw spectra)</p></li>
name from <code>column_in</code> containing the spectra.</p><ul><li><p><code>"spc"</code> : <code>"wavenumbers"</code> or <code>"wavelengths"</code> (raw spectra)</p></li>
<li><p><code>"spc_rs"</code> : <code>"wavenumbers_rs"</code> or <code>"wavelengths_rs"</code>) (resampled spectra)</p></li>
<li><p><code>"spc_mean"</code> : <code>"wavenumbers_rs"</code> or <code>"wavelengths_rs"</code> (mean spectra)</p></li>
<li><p><code>"spc_nocomp"</code><code>"wavenumbers"</code> or <code>"wavelengths"</code> (spectra prior
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Samples in this list will be analyzed using laboratory reference methods."><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
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<!-- Generated by pkgdown: do not edit by hand --><htmllang="en"><head><metahttp-equiv="Content-Type"content="text/html; charset=UTF-8"><metacharset="utf-8"><metahttp-equiv="X-UA-Compatible"content="IE=edge"><metaname="viewport"content="width=device-width, initial-scale=1.0"><title>Slice spectra into defined x-axis ranges — slice_xvalues • simplerspec</title><!-- jquery --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js"integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo="crossorigin="anonymous"></script><!-- Bootstrap --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css"integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE="crossorigin="anonymous"><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js"integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4="crossorigin="anonymous"></script><!-- bootstrap-toc --><linkrel="stylesheet"href="../bootstrap-toc.css"><scriptsrc="../bootstrap-toc.js"></script><!-- Font Awesome icons --><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css"integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk="crossorigin="anonymous"><linkrel="stylesheet"href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css"integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw="crossorigin="anonymous"><!-- clipboard.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js"integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI="crossorigin="anonymous"></script><!-- headroom.js --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js"integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js"integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4="crossorigin="anonymous"></script><!-- pkgdown --><linkhref="../pkgdown.css"rel="stylesheet"><scriptsrc="../pkgdown.js"></script><metaproperty="og:title"content="Slice spectra into defined x-axis ranges — slice_xvalues"><metaproperty="og:description"content="Slicespectracontainedinlist-columnofspectraltibble
(data frame). A list of x-axis value ranges can be specified. Spectra are
cut based on these ranges."><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
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grouping column within tibble."><metaname="robots"content="noindex"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
Philipp Baumann
8 months ago