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<h3>
Frank B. Brokken pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/simrisc">Debian Med / simrisc</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/simrisc/-/commit/db3173d816e28070d65b35b99712d597e5e1b83e">db3173d8</a></strong>
<div>
<span>by Frank B. Brokken</span>
<i>at 2021-05-23T10:17:08+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 14.05.00</pre>
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<h4>14 changed files:</h4>
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<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
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<li class="file-stats">
<a href="#80754af91bfb6d1073585b046fe0a474ce868509">
build
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<a href="#46e2bfdf35ce8caa4b542110e7ed030b6b9fb042">
changelog
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<a href="#409e27072aac598482c19c4aceae11d9e758b31d">
documentation/man/simrisc.yo
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<a href="#a2eba7fc67affd0911b220b6e7fc3c6267af676d">
main.cc
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<a href="#99f91f94af8b6e2bc1f365b71c98030217fcb80b">
screening/beir7err.cc
→
screening/beir7err1.cc
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<li class="file-stats">
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+
screening/beir7err2.cc
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+
screening/errrisk1404.cc
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screening/errrisk1405.cc
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<li class="file-stats">
<a href="#0ee8d6943df361f841d29037583bc2faf7e01482">
screening/radiationrisk.cc
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<a href="#383269c2f39780236041650a7a3d721ff6c3c780">
screening/screening.h
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<a href="#1e7c84daa94b8fed45f9302ea5d11cd4df67deac">
screening/screening.ih
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<a href="#55dd6865e7572a97c02399ab22622028d5a3e441">
screening/screening1.cc
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<a href="#db137b6df838a1e6a0a54283d0c276635038303c">
usage.cc
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<h4>Changes:</h4>
<li id="b33892fbddeffc3368077b4904ad0b3d562a7312">
<a href="https://salsa.debian.org/med-team/simrisc/-/commit/db3173d816e28070d65b35b99712d597e5e1b83e#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#define AUTHOR "Frank B. Brokken (f.b.brokken@rug.nl)";</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">#define VERSION "14.0<span class="idiff left right">4</span>.00"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">#define VERSION "14.0<span class="idiff left right">5</span>.00"</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">#define YEARS "2020-2021"</span></pre>
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<li id="80754af91bfb6d1073585b046fe0a474ce868509">
<a href="https://salsa.debian.org/med-team/simrisc/-/commit/db3173d816e28070d65b35b99712d597e5e1b83e#80754af91bfb6d1073585b046fe0a474ce868509"><strong>build</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/icmake -<span class="idiff left right">q</span>t.</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/icmake -t.</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#define LOGENV "SIMRISC"</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<li id="46e2bfdf35ce8caa4b542110e7ed030b6b9fb042">
<a href="https://salsa.debian.org/med-team/simrisc/-/commit/db3173d816e28070d65b35b99712d597e5e1b83e#46e2bfdf35ce8caa4b542110e7ed030b6b9fb042"><strong>changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">simrisc (14.05.00)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Added option --err (-e) to select the previously used but inorrect</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> algorithm for computing the Beir7 risk vector, instead of using the</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> (now default) correct algorithm for computing the risk vector.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Frank B. Brokken <f.b.brokken@rug.nl> Sat, 22 May 2021 22:09:08 +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">simrisc (14.04.00)</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Modalities support spread-variation. See the simriscparams(7) man-page for</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,6 +91,14 @@ filenames) are capitalized, all other single-letter options are lowercase.</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"> also requires the specification of tt(tumor-age), and is mutually</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"> exclusive with the tt(case) option;</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> it() loption(err) (soption(e))nl()</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> before version 14.05.00 the Beir7 risk vector was computed using an</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> incorrect algorithm. The error was fixed in simrisc 14.05.00. When it</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> is required to use the erroneous algorithm, e.g., to compare the</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> results of simulations with previously obtained results, option tt(-e)</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> must be specified. However, option tt(-e) should not be used for real</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> simulations;</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"> it() loption(help) (soption(h))nl()</span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"> shows help information and terminates;</span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,6 +9,7 @@ Arg::LongOption g_longOpts[] =</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"> <span class="n" style="color: #333;">Arg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LongOption</span><span class="p">{</span><span class="s" style="color: #d14;">"config"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'C'</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"> <span class="n" style="color: #333;">Arg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LongOption</span><span class="p">{</span><span class="s" style="color: #d14;">"data"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'D'</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"> <span class="n" style="color: #333;">Arg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LongOption</span><span class="p">{</span><span class="s" style="color: #d14;">"death-age"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'a'</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"> <span class="n" style="color: #333;">Arg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LongOption</span><span class="p">{</span><span class="s" style="color: #d14;">"err"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'e'</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"> <span class="n" style="color: #333;">Arg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LongOption</span><span class="p">{</span><span class="s" style="color: #d14;">"help"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"> <span class="n" style="color: #333;">Arg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LongOption</span><span class="p">{</span><span class="s" style="color: #d14;">"last-case"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'l'</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"> <span class="n" style="color: #333;">Arg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LongOption</span><span class="p">{</span><span class="s" style="color: #d14;">"one-analysis"</span><span class="p">,</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">},</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,7 +28,7 @@ auto const *g_longEnd = g_longOpts + size(g_longOpts);</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">try</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">Arg</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Arg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">initialize</span><span class="p">(</span><span class="s" style="color: #d14;">"a:B:l:C:D:hoP:R:S:s:t:vV"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">Arg</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Arg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">initialize</span><span class="p">(</span><span class="s" style="color: #d14;">"a:B:<span class="idiff left right">e</span>l:C:D:hoP:R:S:s:t:vV"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">g_longOpts</span><span class="p">,</span> <span class="n" style="color: #333;">g_longEnd</span><span class="p">,</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">versionHelp</span><span class="p">(</span><span class="n" style="color: #333;">usage</span><span class="p">,</span> <span class="n" style="color: #333;">Icmake</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="sc" style="color: #d14;">'o'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#define XERR</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "screening.ih"</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// static</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Screening</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">beir7Err</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">age</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"> <span class="n" style="color: #333;">Round</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">round</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">biradIdx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">eta</span><span class="p">,</span> <span class="n" style="color: #333;">Modalities</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modalities</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">risk</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">factor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beta</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">60.0</span><span class="p">,</span> <span class="n" style="color: #333;">eta</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1000</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">ModBase</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">modBase</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">modalities</span><span class="p">.</span><span class="n" style="color: #333;">use</span><span class="p">(</span><span class="n" style="color: #333;">round</span><span class="p">.</span><span class="n" style="color: #333;">modalityIndices</span><span class="p">()))</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"> <span class="n" style="color: #333;">risk</span> <span class="o" style="font-weight: 600;">*=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">factor</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">modBase</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dose</span><span class="p">(</span><span class="n" style="color: #333;">biradIdx</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">risk</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#define XERR</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "screening.ih"</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// static</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Screening</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">errRisk1404</span><span class="p">(</span><span class="n" style="color: #333;">DoubleVect</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">vect</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"> <span class="n" style="color: #333;">Modalities</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modalities</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"> <span class="n" style="color: #333;">Round</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">round</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">biRadIdx</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">eta</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// compute beir7Err once, </span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">error</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beir7Err</span><span class="p">(</span><span class="n" style="color: #333;">round</span><span class="p">,</span> <span class="n" style="color: #333;">biRadIdx</span><span class="p">,</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="n" style="color: #333;">eta</span><span class="p">,</span> <span class="n" style="color: #333;">modalities</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// then visit all subsequent ages</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">round</span><span class="p">.</span><span class="n" style="color: #333;">rndAge</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">END_AGE</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">age</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"> <span class="n" style="color: #333;">vect</span><span class="p">[</span><span class="n" style="color: #333;">age</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">error</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#define XERR</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "screening.ih"</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// static</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Screening</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">errRisk1405</span><span class="p">(</span><span class="n" style="color: #333;">DoubleVect</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">vect</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"> <span class="n" style="color: #333;">Modalities</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modalities</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"> <span class="n" style="color: #333;">Round</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">round</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">biRadIdx</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">eta</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// visit all subsequent ages, and compute</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// beir7Err separately for each age </span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">round</span><span class="p">.</span><span class="n" style="color: #333;">rndAge</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">END_AGE</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">age</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"> <span class="n" style="color: #333;">vect</span><span class="p">[</span><span class="n" style="color: #333;">age</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">beir7Err</span><span class="p">(</span><span class="n" style="color: #333;">age</span><span class="p">,</span> <span class="n" style="color: #333;">round</span><span class="p">,</span> <span class="n" style="color: #333;">biRadIdx</span><span class="p">,</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="n" style="color: #333;">eta</span><span class="p">,</span> <span class="n" style="color: #333;">modalities</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,26 +8,20 @@ DoubleVect Screening::radiationRisk(</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"> <span class="n" style="color: #333;">Uint16Vect</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">biRadIndices</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">eta</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// beir7 values</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"> <span class="n" style="color: #333;">DoubleVect</span> <span class="n" style="color: #333;"><span class="idiff left right">radiationRiskV</span>ect</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DoubleVect</span><span class="p">(</span><span class="n" style="color: #333;">END_AGE</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"> <span class="n" style="color: #333;">DoubleVect</span> <span class="n" style="color: #333;"><span class="idiff left right">v</span>ect</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DoubleVect</span><span class="p">(</span><span class="n" style="color: #333;">END_AGE</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">rndIdx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d_roundVect</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">rndIdx</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">end</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">rndIdx</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">round</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d_roundVect</span><span class="p">[</span><span class="n" style="color: #333;">rndIdx</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// use round[rndIdx]</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// use the bi-rad index</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// of the round's age</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">biRadIdx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">biRadIndices</span><span class="p">[</span><span class="n" style="color: #333;">rndIdx</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// categroy</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Random</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">instance</span><span class="p">().</span><span class="n" style="color: #333;">uniform</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">d_rate</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">error</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">beir7Err</span><span class="p">(</span><span class="n" style="color: #333;">round</span><span class="p">,</span> <span class="n" style="color: #333;">biRadIdx</span><span class="p">,</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="n" style="color: #333;">eta</span><span class="p">,</span> <span class="n" style="color: #333;">modalities</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">round</span><span class="p">.</span><span class="n" style="color: #333;">rndAge</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">age</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">END_AGE</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">age</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"> <span class="n" style="color: #333;">radiationRiskVect</span><span class="p">[</span><span class="n" style="color: #333;">age</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">error</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">Random</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">instance</span><span class="p">().</span><span class="n" style="color: #333;">uniform</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">d_rate</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d_errRiskVector</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"> <span class="n" style="color: #333;">vect</span><span class="p">,</span> <span class="n" style="color: #333;">modalities</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"> <span class="n" style="color: #333;">d_roundVect</span><span class="p">[</span><span class="n" style="color: #333;">rndIdx</span><span class="p">],</span> <span class="n" style="color: #333;">biRadIndices</span><span class="p">[</span><span class="n" style="color: #333;">rndIdx</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="n" style="color: #333;">eta</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"> <span class="p">);</span> </span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">radiationRiskV</span>ect</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">v</span>ect</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,6 +42,10 @@ class Screening</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">d_rate</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// points to static members: // errRisk1404 or </span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d_errRiskVector</span><span class="p">)(</span><span class="n" style="color: #333;">DoubleVect</span> <span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// errRiskA1405</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">Modalities</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">Round</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"> <span class="nl">public:</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> <span class="n" style="color: #333;">Screening</span><span class="p">(</span><span class="n" style="color: #333;">Modalities</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modalities</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,9 +75,25 @@ class Screening</td>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">increasingAge</span><span class="p">(</span><span class="n" style="color: #333;">Round</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">round</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">errRisk1404</span><span class="p">(</span><span class="n" style="color: #333;">DoubleVect</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">riskVect</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">Modalities</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modalities</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">Round</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">round</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">biRadIdx</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">eta</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">errRisk1405</span><span class="p">(</span><span class="n" style="color: #333;">DoubleVect</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">riskVect</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">Modalities</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modalities</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">Round</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">round</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">biRadIdx</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">eta</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// called by errRiskRelative </span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">beir7Err</span><span class="p">(</span><span class="n" style="color: #333;">Round</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">round</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">eta</span><span class="p">,</span> <span class="n" style="color: #333;">Modalities</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modalities</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// called by earRisk</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">beir7Err</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">age</span><span class="p">,</span> <span class="n" style="color: #333;">Round</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">round</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">idx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">beta</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">eta</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">Modalities</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modalities</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">Screening</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">rate</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span></span>
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<a href="https://salsa.debian.org/med-team/simrisc/-/commit/db3173d816e28070d65b35b99712d597e5e1b83e#1e7c84daa94b8fed45f9302ea5d11cd4df67deac"><strong>screening/screening.ih</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#include "screening.h"</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">#include "../xerr/xerr.ih"</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">//#include <cmath></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">//#include <sstream></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">//#include <bobcat/mstream></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">// #include "../enums/enums.h"</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">// #include "../error/error.h"</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">#include <bobcat/arg></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">#include "../random/random.h"</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">#include "../modbase/modbase.h"</span>
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<a href="https://salsa.debian.org/med-team/simrisc/-/commit/db3173d816e28070d65b35b99712d597e5e1b83e#55dd6865e7572a97c02399ab22622028d5a3e441"><strong>screening/screening1.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,8 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="n" style="color: #333;">Screening</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Screening</span><span class="p">(</span><span class="n" style="color: #333;">Modalities</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">modalities</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"> <span class="n" style="color: #333;">d_modalities</span><span class="p">(</span><span class="n" style="color: #333;">modalities</span><span class="p">),</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"> <span class="n" style="color: #333;">d_base</span><span class="p">{</span> <span class="s" style="color: #d14;">"Screening:"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"> <span class="n" style="color: #333;">d_base</span><span class="p">{</span> <span class="s" style="color: #d14;">"Screening:"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span> <span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"> <span class="n" style="color: #333;">d_errRiskVector</span><span class="p">(</span><span class="n" style="color: #333;">Arg</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">instance</span><span class="p">().</span><span class="n" style="color: #333;">option</span><span class="p">(</span><span class="sc" style="color: #d14;">'e'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">errRisk1404</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">errRisk1405</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"> <span class="n" style="color: #333;">setAttendanceRate</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"> <span class="n" style="color: #333;">setRounds</span><span class="p">();</span></span>
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<a href="https://salsa.debian.org/med-team/simrisc/-/commit/db3173d816e28070d65b35b99712d597e5e1b83e#db137b6df838a1e6a0a54283d0c276635038303c"><strong>usage.cc</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,8 +25,11 @@ Where:</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="s" style="color: #d14;"> '<base>/data-$.txt', use ! to suppress)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="s" style="color: #d14;"> --death-age (-a) age - run one simulation using a specific natural</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="s" style="color: #d14;"> death-age (also requires --tumor-age)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="s" style="color: #d14;"> --err (-e) - use the previously used Beir7 ERR function</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="s" style="color: #d14;"> (excess relative risk) instead of the</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="s" style="color: #d14;"> excess absolute risk function, using the</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"><span class="s" style="color: #d14;"> cases' subsequent simulated ages;</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="s" style="color: #d14;"> --help (-h) - provide this help</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="s" style="color: #d14;"> --last-case (-l) nCases - perform simulations until 'nCases' have been</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="s" style="color: #d14;"> analyzed and only write the data for the </span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="s" style="color: #d14;"> final case to the data file; </span></span>
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