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More MSCombo tweaks #23

Merged
merged 13 commits into from
Nov 2, 2023
+14 −19
Merged

More MSCombo tweaks #23

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81e9123
finished BMD calcs
cwsimmon Jun 29, 2023
1c3cd08
1st stage of mscombo development
cwsimmon Jul 13, 2023
e3e68ff
intermediate commit for mscombo
cwsimmon Jul 17, 2023
fe11330
added handling of removed datasets
cwsimmon Aug 1, 2023
e896366
debug attempt
cwsimmon Aug 10, 2023
286e8c7
added combo loglike calc
cwsimmon Aug 29, 2023
8fe1602
updated bmdl & bmdu methods
cwsimmon Sep 13, 2023
ba4136d
Added slopeFactor
cwsimmon Oct 27, 2023
aeb0921
Merge branch 'main' into mscombo
cwsimmon Oct 27, 2023
356063e
bug fix for windows compilation
cwsimmon Nov 1, 2023
3915c6f
removed unused prG and prB in struct.
cwsimmon Nov 2, 2023
0af5189
Merge branch 'main' into mscombo
cwsimmon Nov 2, 2023
36f3b4f
bug fix for previous commit
cwsimmon Nov 2, 2023
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10 changes: 7 additions & 3 deletions src/code_base/bmds_helper.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -542,12 +542,14 @@ double getclmt(python_multitumor_analysis *pyAnal, python_multitumor_result *pyR

lb[0] = lminbmd; //BMD lower limit
for (int i=1; i<x.size(); i++){
lb[i] = pyAnal->prB[3]; //beta min value
//lb[i] = pyAnal->prB[3]; //beta min value
lb[i] = 0.0; //beta min value
}

ub[0] = log(maxDose);
for (int i=1; i<x.size(); i++){
ub[i] = pyAnal->prB[4]; //beta max value
//ub[i] = pyAnal->prB[4]; //beta max value
ub[i] = 1e4; //beta max value
}

local_opt.set_lower_bounds(lb);
Expand Down Expand Up @@ -4010,7 +4012,9 @@ void BMDS_ENTRY_API __stdcall runMultitumorModel(struct python_multitumor_analys
for (int j=0; j<pyAnal->nmodels[i]; j++){
double bmr = pyAnal->models[i][j].BMR;
double bmdl = pyRes->models[i][j].bmdsRes.BMDL;
pyRes->models[i][j].bmdsRes.slopeFactor = bmr/bmdl;
if (bmdl > 0.0){
pyRes->models[i][j].bmdsRes.slopeFactor = bmr/bmdl;
}
}
}

Expand Down
4 changes: 1 addition & 3 deletions src/code_base/bmds_helper.h
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Expand Up @@ -281,8 +281,6 @@ struct python_multitumor_analysis{
double alpha; // alpha of the analysis
int prior_cols; // colunns in the prior
std::vector<int> degree; // degree of selected polynomial used for each ind multistage (size ndatasets)
std::vector<double> prG; //background prior
std::vector<double> prB; //beta prior
};

struct python_multitumor_result{
Expand Down Expand Up @@ -407,7 +405,7 @@ void convertFromPythonDichoRes(struct dichotomous_model_result *res, struct pyth

void selectMultitumorModel();

void runMultitumorModel(struct python_multitumor_analysis *pyAnal, struct python_multitumor_result *pyRes);
void BMDS_ENTRY_API __stdcall runMultitumorModel(struct python_multitumor_analysis *pyAnal, struct python_multitumor_result *pyRes);

double DLgamma(double x);
double LogLik_Constant(std::vector<double> Y, std::vector<double> n_group);
Expand Down
5 changes: 1 addition & 4 deletions src/pybmdscpp/main.cpp
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Expand Up @@ -292,10 +292,7 @@ PYBIND11_MODULE(bmdscore, m) {
.def_readwrite("BMR", &python_multitumor_analysis::BMR)
.def_readwrite("alpha", &python_multitumor_analysis::alpha)
.def_readwrite("prior_cols", &python_multitumor_analysis::prior_cols)
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@cwsimmon can we delete prior_cols too - is that no longer needed as well?

.def_readwrite("degree", &python_multitumor_analysis::degree)
.def_readwrite("prG", &python_multitumor_analysis::prG)
.def_readwrite("prB", &python_multitumor_analysis::prB);
// .def_readwrite("prior", &python_multitumor_analysis::prior);
.def_readwrite("degree", &python_multitumor_analysis::degree);
py::class_<python_multitumor_result>(m, "python_multitumor_result")
.def(py::init<>())
.def_readwrite("ndatasets", &python_multitumor_result::ndatasets)
Expand Down
14 changes: 5 additions & 9 deletions src/tests/src/test_cpp.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4252,9 +4252,6 @@ void runMultitumorModel(){
anal.alpha = alpha;
anal.prior_cols = prCols;

anal.prG.insert(anal.prG.begin(), prRFreqMultistageCancerG, prRFreqMultistageCancerG + anal.prior_cols);
anal.prB.insert(anal.prB.begin(), prRFreqMultistageCancerB, prRFreqMultistageCancerB + anal.prior_cols);

struct python_multitumor_result res;
res.ndatasets = numDatasets;

Expand Down Expand Up @@ -4293,7 +4290,6 @@ void runMultitumorModel(){
modAnal.doses = doses[dataset];
modAnal.n = numDataRows;

std::cout<<"b4 if"<<std::endl;
//needs to be changed based on model degree
if (degree[dataset] == 0){
//handle autoselect degree
Expand All @@ -4316,7 +4312,6 @@ void runMultitumorModel(){
count = 1;
}

std::cout<<"after if"<<std::endl;
anal.nmodels.push_back(count);
anal.models.push_back(modGroup);
res.nmodels.push_back(count);
Expand All @@ -4328,10 +4323,11 @@ void runMultitumorModel(){
res.selectedModelIndex.push_back(0);
res.selectedModelIndex.push_back(0);
std::cout<<"Selected model Indexes: ";
for (auto elem : res.selectedModelIndex) {
std::cout << elem << ", ";
}
std::cout<<std::endl;
//for (auto elem : res.selectedModelIndex) {
// std::cout << elem << ", ";
//}
//std::cout<<std::endl;

res.validResult.push_back(true);
res.validResult.push_back(true);
res.validResult.push_back(true);
Expand Down