[med-svn] [Git][med-team/simrisc][master] 3 commits: Ready for simrisc 14.05.00-1
Frank B. Brokken (@fbb-guest)
gitlab at salsa.debian.org
Sun May 23 09:17:26 BST 2021
Frank B. Brokken pushed to branch master at Debian Med / simrisc
Commits:
0dc8e0fe by Frank B. Brokken at 2021-05-23T10:17:01+02:00
Ready for simrisc 14.05.00-1
- - - - -
db3173d8 by Frank B. Brokken at 2021-05-23T10:17:08+02:00
New upstream version 14.05.00
- - - - -
ec447e05 by Frank B. Brokken at 2021-05-23T10:17:10+02:00
Update upstream source from tag 'upstream/14.05.00'
Update to upstream version '14.05.00'
with Debian dir 4128bcbae93aa8c8add9f778e54f996a847f9beb
- - - - -
16 changed files:
- VERSION
- build
- changelog
- debian/changelog
- debian/control
- documentation/man/simrisc.yo
- main.cc
- screening/beir7err.cc → screening/beir7err1.cc
- + screening/beir7err2.cc
- + screening/errrisk1404.cc
- + screening/errrisk1405.cc
- screening/radiationrisk.cc
- screening/screening.h
- screening/screening.ih
- screening/screening1.cc
- usage.cc
Changes:
=====================================
VERSION
=====================================
@@ -1,3 +1,3 @@
#define AUTHOR "Frank B. Brokken (f.b.brokken at rug.nl)";
-#define VERSION "14.04.00"
+#define VERSION "14.05.00"
#define YEARS "2020-2021"
=====================================
build
=====================================
@@ -1,4 +1,4 @@
-#!/usr/bin/icmake -qt.
+#!/usr/bin/icmake -t.
#define LOGENV "SIMRISC"
=====================================
changelog
=====================================
@@ -1,3 +1,11 @@
+simrisc (14.05.00)
+
+ * Added option --err (-e) to select the previously used but inorrect
+ algorithm for computing the Beir7 risk vector, instead of using the
+ (now default) correct algorithm for computing the risk vector.
+
+ -- Frank B. Brokken <f.b.brokken at rug.nl> Sat, 22 May 2021 22:09:08 +0200
+
simrisc (14.04.00)
* Modalities support spread-variation. See the simriscparams(7) man-page for
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+simrisc (14.05.00-1) unstable; urgency=medium
+
+ * Upstream added option --err (-e) to select the previously used but
+ inorrect algorithm for computing the Beir7 risk vector, instead of using
+ the (now default) correct algorithm for computing the risk vector.
+
+ -- Frank B. Brokken <f.b.brokken at rug.nl> Sat, 22 May 2021 22:10:34 +0200
+
simrisc (14.04.00-1) unstable; urgency=medium
* New upstream version 14.04.00 supports varying parameter values when
@@ -12,7 +20,7 @@ simrisc (14.04.00-1) unstable; urgency=medium
documentation/manual/simrisc.yo, automatically updated upstream at new
releases.
* Nilesh's addition of the FORTIFIY_SOURCE parameter to gcc's preprocessing
- run is not required as it doesn't invlolve compilation: the patch was
+ run is not required as it doesn't involve compilation: the patch was
removed.
-- Frank B. Brokken <f.b.brokken at rug.nl> Sun, 11 Apr 2021 12:09:35 +0200
=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Uploaders: tony mancill <tmancill at debian.org>,
Build-Depends: debhelper-compat (= 13),
ghostscript,
icmake (>= 9.03.01),
- libbobcat-dev (>= 5.07.00),
+ libbobcat-dev (>= 5.08.01),
texlive-fonts-recommended,
texlive-latex-base,
texlive-latex-extra,
@@ -23,7 +23,7 @@ Rules-Requires-Root: no
Package: simrisc
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: simulation model for breast cancer risk
+Description: simulation model for breast cancer risk.
SiMRiSC is simulation model for breast cancer screening.
It was originally designed by Marcel Greuter around 2010,
and then updated by Chris de Jonge in 2015. This current
=====================================
documentation/man/simrisc.yo
=====================================
@@ -91,6 +91,14 @@ filenames) are capitalized, all other single-letter options are lowercase.
also requires the specification of tt(tumor-age), and is mutually
exclusive with the tt(case) option;
+ it() loption(err) (soption(e))nl()
+ before version 14.05.00 the Beir7 risk vector was computed using an
+ incorrect algorithm. The error was fixed in simrisc 14.05.00. When it
+ is required to use the erroneous algorithm, e.g., to compare the
+ results of simulations with previously obtained results, option tt(-e)
+ must be specified. However, option tt(-e) should not be used for real
+ simulations;
+
it() loption(help) (soption(h))nl()
shows help information and terminates;
=====================================
main.cc
=====================================
@@ -9,6 +9,7 @@ Arg::LongOption g_longOpts[] =
Arg::LongOption{"config", 'C'},
Arg::LongOption{"data", 'D'},
Arg::LongOption{"death-age", 'a'},
+ Arg::LongOption{"err", 'e'},
Arg::LongOption{"help", 'h'},
Arg::LongOption{"last-case", 'l'},
Arg::LongOption{"one-analysis", 'o'},
@@ -27,7 +28,7 @@ auto const *g_longEnd = g_longOpts + size(g_longOpts);
int main(int argc, char **argv)
try
{
- Arg const &arg = Arg::initialize("a:B:l:C:D:hoP:R:S:s:t:vV",
+ Arg const &arg = Arg::initialize("a:B:el:C:D:hoP:R:S:s:t:vV",
g_longOpts, g_longEnd, argc, argv);
arg.versionHelp(usage, Icmake::version, arg.option('o') ? 0 : 1);
=====================================
screening/beir7err.cc → screening/beir7err1.cc
=====================================
=====================================
screening/beir7err2.cc
=====================================
@@ -0,0 +1,18 @@
+//#define XERR
+#include "screening.ih"
+
+// static
+double Screening::beir7Err(uint16_t age,
+ Round const &round, uint16_t biradIdx, double beta,
+ double eta, Modalities const &modalities)
+{
+ double risk = 1;
+
+ double factor = beta * pow(age / 60.0, eta) / 1000;
+
+ for (ModBase const *modBase: modalities.use(round.modalityIndices()))
+ risk *= (1 + factor * modBase->dose(biradIdx));
+
+ return risk;
+}
+
=====================================
screening/errrisk1404.cc
=====================================
@@ -0,0 +1,17 @@
+//#define XERR
+#include "screening.ih"
+
+// static
+void Screening::errRisk1404(DoubleVect &vect,
+ Modalities const &modalities,
+ Round const &round,
+ uint16_t biRadIdx,
+ double beta, double eta)
+{
+ // compute beir7Err once,
+ double error = beir7Err(round, biRadIdx, beta, eta, modalities);
+
+ // then visit all subsequent ages
+ for (uint16_t age = round.rndAge() + 1; age != END_AGE; ++age)
+ vect[age] *= error;
+}
=====================================
screening/errrisk1405.cc
=====================================
@@ -0,0 +1,14 @@
+//#define XERR
+#include "screening.ih"
+
+// static
+void Screening::errRisk1405(DoubleVect &vect,
+ Modalities const &modalities,
+ Round const &round, uint16_t biRadIdx,
+ double beta, double eta)
+{
+ // visit all subsequent ages, and compute
+ // beir7Err separately for each age
+ for (uint16_t age = round.rndAge() + 1; age != END_AGE; ++age)
+ vect[age] *= beir7Err(age, round, biRadIdx, beta, eta, modalities);
+}
=====================================
screening/radiationrisk.cc
=====================================
@@ -8,26 +8,20 @@ DoubleVect Screening::radiationRisk(
Uint16Vect const &biRadIndices,
double beta, double eta) // beir7 values
{
- DoubleVect radiationRiskVect = DoubleVect(END_AGE, 1);
+ DoubleVect vect = DoubleVect(END_AGE, 1);
for (size_t rndIdx = 0, end = d_roundVect.size(); rndIdx != end; ++rndIdx)
{
- auto const &round = d_roundVect[rndIdx]; // use round[rndIdx]
-
- // use the bi-rad index
- // of the round's age
- uint16_t biRadIdx = biRadIndices[rndIdx]; // categroy
-
- if (Random::instance().uniform() > d_rate)
- continue;
-
- double error = beir7Err(round, biRadIdx, beta, eta, modalities);
-
- for (uint16_t age = round.rndAge() + 1; age != END_AGE; ++age)
- radiationRiskVect[age] *= error;
+ if (Random::instance().uniform() <= d_rate)
+ (*d_errRiskVector)
+ (
+ vect, modalities,
+ d_roundVect[rndIdx], biRadIndices[rndIdx],
+ beta, eta
+ );
}
- return radiationRiskVect;
+ return vect;
}
=====================================
screening/screening.h
=====================================
@@ -42,6 +42,10 @@ class Screening
double d_rate;
+ // points to static members: // errRisk1404 or
+ void (*d_errRiskVector)(DoubleVect &, // errRiskA1405
+ Modalities const &,
+ Round const &, uint16_t, double, double);
public:
Screening(Modalities const &modalities);
@@ -71,9 +75,25 @@ class Screening
bool increasingAge(Round const &round) const;
+ static void errRisk1404(DoubleVect &riskVect,
+ Modalities const &modalities,
+ Round const &round, uint16_t biRadIdx,
+ double beta, double eta);
+
+ static void errRisk1405(DoubleVect &riskVect,
+ Modalities const &modalities,
+ Round const &round, uint16_t biRadIdx,
+ double beta, double eta);
+
+ // called by errRiskRelative
static double beir7Err(Round const &round, uint16_t idx, double beta,
double eta, Modalities const &modalities);
+ // called by earRisk
+ static double beir7Err(uint16_t age, Round const &round,
+ uint16_t idx, double beta, double eta,
+ Modalities const &modalities);
+
};
inline double Screening::rate() const
=====================================
screening/screening.ih
=====================================
@@ -1,13 +1,7 @@
#include "screening.h"
#include "../xerr/xerr.ih"
-//#include <cmath>
-//#include <sstream>
-
-//#include <bobcat/mstream>
-
-// #include "../enums/enums.h"
-// #include "../error/error.h"
+#include <bobcat/arg>
#include "../random/random.h"
#include "../modbase/modbase.h"
=====================================
screening/screening1.cc
=====================================
@@ -4,7 +4,8 @@
Screening::Screening(Modalities const &modalities)
:
d_modalities(modalities),
- d_base{ "Screening:", "" }
+ d_base{ "Screening:", "" },
+ d_errRiskVector(Arg::instance().option('e') ? errRisk1404 : errRisk1405)
{
setAttendanceRate();
setRounds();
=====================================
usage.cc
=====================================
@@ -25,8 +25,11 @@ Where:
'<base>/data-$.txt', use ! to suppress)
--death-age (-a) age - run one simulation using a specific natural
death-age (also requires --tumor-age)
+ --err (-e) - use the previously used Beir7 ERR function
+ (excess relative risk) instead of the
+ excess absolute risk function, using the
+ cases' subsequent simulated ages;
--help (-h) - provide this help
-
--last-case (-l) nCases - perform simulations until 'nCases' have been
analyzed and only write the data for the
final case to the data file;
View it on GitLab: https://salsa.debian.org/med-team/simrisc/-/compare/3e419abb75173965ed9f5598e14c3d349f3a22aa...ec447e0537d4fa58f68d2f127715a7a65115557c
--
View it on GitLab: https://salsa.debian.org/med-team/simrisc/-/compare/3e419abb75173965ed9f5598e14c3d349f3a22aa...ec447e0537d4fa58f68d2f127715a7a65115557c
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