[med-svn] [Git][med-team/simrisc][upstream] New upstream version 15.03.00
Frank B. Brokken (@fbb-guest)
gitlab at salsa.debian.org
Sat Jul 1 16:29:53 BST 2023
Frank B. Brokken pushed to branch upstream at Debian Med / simrisc
Commits:
b7db6990 by Frank B. Brokken at 2023-07-01T17:29:10+02:00
New upstream version 15.03.00
- - - - -
27 changed files:
- VERSION
- changelog
- documentation/man/simrisc.yo
- documentation/man/simriscparams.yo
- growth/growth.h
- growth/growth1.cc
- growth/setselfdetect.cc
- growth/writeparameters.cc
- loop/caseinit.cc
- loop/characteristics.cc
- loop/gencases.cc
- loop/postscreen.cc
- options/options1.cc
- probgroup/probgroup.h
- probgroup/probgroup.ih
- probgroup/probindexof.cc
- survival/cptvsdrow.cc
- survival/survival.h
- survival/survival.ih
- tumor/characteristics.cc
- tumor/functionf.cc
- tumor/functionq.cc
- tumor/functionz.cc
- tumor/reset.cc
- tumor/setdeathage.cc
- tumor/tumor.h
- tumor/tumor.ih
Changes:
=====================================
VERSION
=====================================
@@ -1,3 +1,3 @@
#define AUTHOR "Frank B. Brokken (f.b.brokken at rug.nl)";
-#define VERSION "15.02.00"
+#define VERSION "15.03.00"
#define YEARS "2020-2023"
=====================================
changelog
=====================================
@@ -1,3 +1,16 @@
+simrisc (15.03.00)
+
+ * Repaired survival/cptvsdrow: d_vsdRow was set to S3's row instead of
+ S4's element index, which also resulted in errors in computing, e.g., the
+ number of interval cancers. Because of this bug Simrisc before 15.03.00
+ should not anymore be used for lung cancer simulations. Using Simrisc for
+ breast cancer simulations is OK.
+
+ * When using lung cancer simulations the parameters written to file now
+ correctly report the lung cancer parameters.
+
+ -- Frank B. Brokken <f.b.brokken at rug.nl> Sat, 01 Jul 2023 15:34:15 +0200
+
simrisc (15.02.00)
* Costs values are now stored in size_t instead of in uint16_t variables
=====================================
documentation/man/simrisc.yo
=====================================
@@ -84,7 +84,7 @@ filenames) are capitalized, all other single-letter options are lowercase.
Be advised that the default configuration file specifies tt(Screening
Mammo) rounds, which must either be changed to tt(CT) in locally used
- configuration files or in tt(analysis:) sections (see section
+ configuration files or in tt(Analysis:) sections (see section
bf(ANALYSES) below);
it() lsoption(config)(C)(path)nl()
@@ -457,10 +457,14 @@ manpageseealso()
COMMENT(
manpagediagnostics()
- manpagebugs()
- too early for that...
EDN)
+manpagebugs()
+
+Versions before version 15.03.00 should not be used for lung cancer
+simulations. The bug invalidating lung cancer simulations was repaired in
+version 15.03.00.
+
includefile(include/trailer.yo)
=====================================
documentation/man/simriscparams.yo
=====================================
@@ -251,7 +251,7 @@ optional):
sensitivity: 5 - *: 100
# mean stddev dist
- specificity: 99.2 .076 Normal
+ specificity: .992 .076 Normal
)
itt(Mammo:)
@@ -310,9 +310,9 @@ optional):
following specifications:
verb(
costs: 280
- # proportion spread dist
- sensitivity: .94 .005 Normal
- specificity: .95 .005 Normal
+ # proportion
+ sensitivity: .94
+ specificity: .95
)
)
@@ -696,7 +696,7 @@ parameters.
manpagesection(PARAMETER RESPECIFICATION)
Parameters can be respecified by defining a separate parameter configuration
-file or by providing alternate parameter specifications in tt(analysis:)
+file or by providing alternate parameter specifications in tt(Analysis:)
sections of the program's input file, or by providing alternative parameter
specifications as command-line arguments (cf. the bf(simrisc)(1) man-page)
@@ -708,10 +708,10 @@ manpageseealso()
bf(simrisc)(1)
-COMMENT(
- manpagebugs()
+manpagebugs()
- too early for that ...
-END)
+Versions before version 15.03.00 should not be used for lung cancer
+simulations. The bug invalidating lung cancer simulations was repaired in
+version 15.03.00.
includefile(include/trailer.yo)
=====================================
growth/growth.h
=====================================
@@ -27,11 +27,11 @@ class Growth
{
StringVect d_base;
- bool d_bc; // --cancer: breast was specified
+ bool d_bc; // not --cancer: breast was specified
double d_start;
- double d_selfSD;
- VSD d_selfMean;
+ double d_selfSD; // SD of d_selfMean's mean value
+ VSD d_selfMean; // mean and SD/Distr. used when 'vary'is set
AgeGroupVSDvect d_doublingTime;
AgeGroupVSD const &(Growth::*d_ageGroupVSD)(uint16_t idx) const;
@@ -39,13 +39,13 @@ class Growth
public:
Growth();
- AgeGroupVSD const &ageGroupVSD(uint16_t idx) const;
+ AgeGroupVSD const &ageGroupVSD(uint16_t idx) const; // .f
void vary(std::ostream &out);
- double start() const;
- VSD const &selfMu() const;
- double selfSigma() const;
+ double start() const; // .f
+ VSD const &selfMu() const; // .f
+ double selfSigma() const; // .f
void writeParameters(std::ostream &out) const;
=====================================
growth/growth1.cc
=====================================
@@ -4,6 +4,7 @@
Growth::Growth()
:
d_base{ "Tumor:", "Growth:", "" },
+ d_bc{ Globals::isBreast() },
d_selfMean(VARY_NONNEG)
{
setStart();
=====================================
growth/setselfdetect.cc
=====================================
@@ -1,4 +1,4 @@
-//#define XERR
+#define XERR
#include "growth.ih"
void Growth::setSelfDetect()
=====================================
growth/writeparameters.cc
=====================================
@@ -7,14 +7,28 @@ void Growth::writeParameters(ostream &out) const
out << " Growth:\n"
" diameters:\n" <<
- setw(6) << ' ' << "start: " <<
+ setw(8) << ' ' << "start: " <<
setw(4) << d_start << '\n' <<
- setw(6) << ' ' << "self-detect std.dev.: " <<
+ setw(8) << ' ' << "self-detect std.dev.: " <<
setw(4) << d_selfSD << '\n' <<
- setw(6) << ' ' << "self-detect mean: " <<
- d_selfMean << '\n';
+ setw(8) << ' ' << "self-detect mean: " <<
+ d_selfMean << '\n' <<
+ setw(6) << ' ' << "DoublingTime:\n";
- AgeGroupVSD::fmt(8, 1, 2, 0, 2);
- out << setw(6) << ' ' << "DoublingTime:\n" <<
- d_doublingTime << '\n';
+ if (d_bc)
+ {
+ AgeGroupVSD::fmt(8, 1, 2, 0, 2);
+ out << d_doublingTime << '\n';
+ }
+ else
+ {
+ auto const &first = d_doublingTime.front();
+ double sd = first.stdDev();
+
+ out << setw(8) << ' ' << "value: " << first.value() << '\n';
+ if (sd >= 0)
+ out << setw(8) << ' ' << "std.dev: " << sd << '\n';
+
+ out.put('\n');
+ }
}
=====================================
loop/caseinit.cc
=====================================
@@ -1,6 +1,8 @@
#define XERR
#include "loop.ih"
+extern size_t g_caseIdx;
+
void Loop::caseInit()
{
g_log << "\nLoop::caseInit\n";
=====================================
loop/characteristics.cc
=====================================
@@ -1,28 +1,14 @@
-//#define XERR
+#define XERR
#include "loop.ih"
// treatmentDeath(): characteristics(LEFT_POST, TUMOR_POST);
-extern size_t g_caseIdx;
-extern size_t g_err;
-
void Loop::characteristics(Status natural, Status tumor)
{
-// auto hit =
-// [&]()
-// {
-// return natural == LEFT_POST and tumor == TUMOR_POST and
-// g_caseIdx >= g_err;
-// };
-
-
-//if (hit())xerr("tumor.charact. " << g_caseIdx);
// the tumor was self-detected: determine
d_tumor.characteristics(); // its characteristics
-//if (hit()) xerr("treatmentCosts " << g_caseIdx);
-
d_selfDetected = true;
@@ -31,12 +17,8 @@ void Loop::characteristics(Status natural, Status tumor)
// diameterCheck()
d_caseCost += treatmentCosts(d_tumor.selfDetectAge());
-//if (hit()) xerr("setDeathAge " << g_caseIdx);
-
d_tumor.setDeathAge();
-//if (hit()) xerr("setStatus " << g_caseIdx);
-
if (d_naturalDeathAge < d_tumor.deathAge()) // naturally caused death
setStatus(natural, d_naturalDeathAge);
else // or tumor caused death
=====================================
loop/gencases.cc
=====================================
@@ -4,7 +4,7 @@
// -> ORG/womanloop.cpp
size_t g_caseIdx; // -> loop.ih if (caseIdx > 24842)
-size_t g_err = 4726;
+size_t g_err = 2262;
void Loop::genCases(size_t iter, size_t nCases)
{
@@ -29,7 +29,6 @@ void Loop::genCases(size_t iter, size_t nCases)
d_sumDeathAge += d_deathAge;
d_totalCost += d_caseCost;
-//xerr("write data");
if (dataTable.stream() and (showAll or caseIdx + 1 == nCases))
writeData(dataTable, caseIdx);
}
=====================================
loop/postscreen.cc
=====================================
@@ -1,4 +1,4 @@
-//#define XERR
+#define XERR
#include "loop.ih"
extern size_t g_caseIdx;
=====================================
options/options1.cc
=====================================
@@ -44,5 +44,5 @@ Options::Options()
if (d_arg.option(&value, "log"))
logOption(value);
- setSimulationType();
+ setSimulationType(); // 'c'
}
=====================================
probgroup/probgroup.h
=====================================
@@ -35,8 +35,8 @@ class ProbGroup
{
N_PROBCATS = 4, // # of probability categories
};
-
- Group d_group;
+ // cf Group::extract(). begin()
+ Group d_group; // not used, end() is inclusive
std::vector<double> d_prob;
std::vector<double> d_cumProbs;
=====================================
probgroup/probgroup.ih
=====================================
@@ -9,6 +9,9 @@
#include "../globals/globals.h"
-//#include "../options/options.h"
-
using namespace std;
+
+extern size_t g_caseIdx;
+extern size_t g_err;
+
+
=====================================
probgroup/probindexof.cc
=====================================
@@ -3,9 +3,6 @@
// see README.probgroup
-extern size_t g_caseIdx;
-extern size_t g_err;
-
// with Survival::cptVSDrow 'value' is the tumor diameter
// then, the group is determined from the diameter, and in the selected
// group the column index of that row of S3 is omputed as 'idx'
@@ -14,13 +11,6 @@ extern size_t g_err;
RowCol ProbGroup::probIndexOf(Vector const &vect,
double value, double prob)
{
-//if (g_caseIdx >= g_err){
-//xerr("PROB INDEX FOR " << prob << " value " << value);
-//for (ProbGroup const &group: vect)
-//cerr << group.begin() << '-' << group.end() << "; ";
-//cerr<<'\n';
-//}
-
size_t rowIdx = 0;
for (ProbGroup const &group: vect)
@@ -29,16 +19,10 @@ RowCol ProbGroup::probIndexOf(Vector const &vect,
{
uint16_t idx = group.indexOf(prob);
-// if (g_caseIdx >= g_err) xerr("INDEX " << idx);
-
-// xerr("Case " << g_caseIdx << ", row: " << rowIdx <<
-// ", col: " << idx);
-
return RowCol{ rowIdx, idx };
}
++rowIdx;
}
-//if (g_caseIdx >= g_err) xerr("NO INDEX FOUND ");
return RowCol{ static_cast<uint16_t>(string::npos), 0 };
}
=====================================
survival/cptvsdrow.cc
=====================================
@@ -1,13 +1,10 @@
-//#define XERR
+#define XERR
#include "survival.ih"
-extern size_t g_caseIdx;
-extern size_t g_err;
-
- // determine the row of d_vsdMatrix to use by finding the rowindex in s3
- // containing 'diameter' and then computing the lowest column index
- // in that row exceeding a random proportion value. That index becomes
- // d_vsdRow.
+ // determine the row of d_vsdMatrix to use by locating the row in s3
+ // containing 'diameter' in its ProbGrooup.end() value. Then compute
+ // the lowest column index in that row exceeding a random proportion
+ // value. That index becomes d_vsdRow.
RowCol Survival::cptVSDrow(double diameter)
{
// if diameter > 100 the last line in S3 must be used. probIndexOf uses
@@ -23,13 +20,9 @@ RowCol Survival::cptVSDrow(double diameter)
Random::instance().uniformVSD()
);
- d_vsdRow = rowCol.first;
+ d_vsdRow = rowCol.second;
g_log << " Survival::cptVSDRow: S3 row = " << d_vsdRow <<
" for diameter " << diameter << '\n';
-
return rowCol;
}
-
-// Random::instance().uniform()
-// Random::instance().uniformCase()
=====================================
survival/survival.h
=====================================
@@ -61,7 +61,10 @@ class Survival
// computes d_vsdRow using S3, S4 and the tumor diameter (calls
// cptVSDrow()).
- VSDmatrix d_vsdMatrix;
+ // 1st idx: BC: always 0
+ // LC: 0..3 for lung0..lung4
+ // 2nd idx: elements contain the BC/LC
+ VSDmatrix d_vsdMatrix; // a..d VSD params (0: a, thru 3: d)
ProbGroup::Vector d_s3; // contains the lines of S3
Uint16Vect d_bc; // contains the BC: specifications
=====================================
survival/survival.ih
=====================================
@@ -10,4 +10,7 @@
#include "../parser/parser.h"
#include "../log/log.h"
+extern size_t g_caseIdx;
+extern size_t g_err;
+
using namespace std;
=====================================
tumor/characteristics.cc
=====================================
@@ -1,15 +1,9 @@
-//#define XERR
+#define XERR
#include "tumor.ih"
-extern size_t g_caseIdx;
-extern size_t g_err;
-
// (ORG: calculateSize)
void Tumor::characteristics(double age)
{
- //if (g_caseIdx >= g_err) xerr("AGE: " << age << ",
- // detectable age: " << d_detectableAge);
-
check("size");
if ((d_present = (d_detectableAge <= age))) // there is a tumor
@@ -32,7 +26,4 @@ void Tumor::characteristics(double age)
}
d_rowCol = d_survival.setVSD(d_diameter);
-
-//if (g_caseIdx >= g_err) xerr(" diameter = " << d_diameter);
-
}
=====================================
tumor/functionf.cc
=====================================
@@ -1,4 +1,4 @@
-//#define XERR
+#define XERR
#include "tumor.ih"
extern size_t g_caseIdx;
@@ -6,28 +6,6 @@ extern size_t g_err;
double Tumor::functionF(double years) const
{
-///xerr(1 << ' ' << reinterpret_cast<void *>(d_functionQ) << \ <-*****
-/// ' ' << reinterpret_cast<void *>(d_functionZ) << '\n');
-
-//xerr("a..d: " << d_survival[0].value() << ' ' << \ .
-// d_survival[1].value() << ' ' << \ .
-// d_survival[2].value() << ' ' << \ .
-// d_survival[3].value());
-
-// auto hit =
-// [&]()
-// {
-// return
-// g_caseIdx >= g_err;
-// };
-
-//if (hit())
-//{
-//xerr(years << ", diameter: " << d_diameter);
-//functionQ(years);
-//functionZ(years);
-//}
-
return years <= 0 ?
1
:
=====================================
tumor/functionq.cc
=====================================
@@ -1,4 +1,4 @@
-//#define XERR
+#define XERR
#include "tumor.ih"
// For the std. simulations survival[0] and survival[1] are returning the
@@ -13,18 +13,5 @@ extern size_t g_err;
double Tumor::functionQ(double years) const
{
-// auto hit = // tumorinfo.survival?
-// [&]()
-// {
-// return
-// g_caseIdx >= g_err;
-// };
-
-//if (hit())
-//{
-//xerr("d_survival[1] " << &d_survival[1] << ' ' << d_survival[1].value());
-//xerr("d_survival[0] " << &d_survival[0]);
-//}
-
return d_survival[0].value() * pow(years, d_survival[1].value());
}
=====================================
tumor/functionz.cc
=====================================
@@ -3,7 +3,5 @@
double Tumor::functionZ(double years) const
{
-xerr("");
- return d_survival[2].value() * log(years)
- + d_survival[3].value();
+ return d_survival[2].value() * log(years) + d_survival[3].value();
}
=====================================
tumor/reset.cc
=====================================
@@ -37,7 +37,6 @@ void Tumor::reset()
d_doublingDays = random.logNormal(group.value(), group.stdDev());
-
d_doublingYears = d_doublingDays / N_YEARDAYS;
double selfDetectDiam = random.logNormal(d_growth.selfMu().value(),
@@ -58,12 +57,4 @@ void Tumor::reset()
" p(survival) = " << d_pSurvival << "\n"
" preperiod = " << d_prePeriod << "\n"
" detectableAge = " << d_detectableAge << '\n';
-
}
-
-//xerr("idx: " << idx << ", value: " << group.value() << ", stdev = " <<
-//group.stdDev());
-
-//xerr("doublingdays: " << d_doublingDays);
-
-// xerr("LEAVING " << d_prePeriod << ' ' << d_detectableAge);
=====================================
tumor/setdeathage.cc
=====================================
@@ -12,14 +12,6 @@ extern size_t g_err;
void Tumor::setDeathAge(double detectionAge)
{
-// auto hit =
-// [&]()
-// {
-// return g_caseIdx >= g_err;
-// };
-
-//if (hit()) xerr(g_caseIdx << " self detect: " << d_selfDetectAge << ' ' << detectionAge);
-
check("death age");
// interval halving: search between 0 and 100
@@ -31,9 +23,6 @@ void Tumor::setDeathAge(double detectionAge)
{
mid = (low + high) / 2;
-//if (hit()) xerr("iter: " << iter << " mid: " << mid);
-
-
switch (weakCompare(functionF(mid), d_pSurvival))
{
case -1: // use the lhs half: low..mid
@@ -55,7 +44,4 @@ void Tumor::setDeathAge(double detectionAge)
g_log << " Tumor::setDeathAge(" << detectionAge << ") = " <<
d_deathAge << '\n';
-
-//if (hit()) xerr("death age: " << d_deathAge);
-
}
=====================================
tumor/tumor.h
=====================================
@@ -81,7 +81,7 @@ class Tumor: public Globals
double detectableAge() const; // .f
double volume() const;
- double diameter() const;
+ double diameter() const; // .f
bool metastasis() const; // only with lung cancer .f
@@ -102,8 +102,6 @@ class Tumor: public Globals
RowCol const &rowCol() const; // .f
-// void s4ColIdx(); // cpt Survival S4 column index
-
private:
std::ostream &insert(std::ostream &out) const;
=====================================
tumor/tumor.ih
=====================================
@@ -36,3 +36,6 @@ inline double Tumor::diameter(double volume)
{
return pow(6 / M_PI * volume, 1 / 3.);
}
+
+extern size_t g_caseIdx;
+extern size_t g_err;
View it on GitLab: https://salsa.debian.org/med-team/simrisc/-/commit/b7db6990b1347e3126f3869fc4a10c4fbbae4401
--
View it on GitLab: https://salsa.debian.org/med-team/simrisc/-/commit/b7db6990b1347e3126f3869fc4a10c4fbbae4401
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