| /dports/biology/gemma/GEMMA-0.98.3/src/ |
| H A D | lmm.cpp | 76 n_cvt = cPar.n_cvt; in CopyFromParam()
480 size_t n_cvt = p->n_cvt; in LogL_f() local
518 index_yy = GetabIndex(n_cvt + 2, n_cvt + 2, n_cvt); in LogL_f()
538 size_t n_cvt = p->n_cvt; in LogL_dev1() local
618 index_yy = GetabIndex(n_cvt + 2, n_cvt + 2, n_cvt); in LogL_dev1()
636 size_t n_cvt = p->n_cvt; in LogL_dev2() local
688 index_yy = GetabIndex(n_cvt + 2, n_cvt + 2, n_cvt); in LogL_dev2()
713 size_t n_cvt = p->n_cvt; in LogL_dev12() local
766 index_yy = GetabIndex(n_cvt + 2, n_cvt + 2, n_cvt); in LogL_dev12()
843 index_ww = GetabIndex(n_cvt + 2, n_cvt + 2, n_cvt); in LogRL_f()
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| H A D | ldr.cpp | 62 n_cvt = cPar.n_cvt; in CopyFromParam()
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| H A D | param.cpp | 228 n_cvt = 1; in ReadFiles()
231 n_cvt = 1; in ReadFiles()
1367 assert(ni_test - n_cvt != 0); in compAKtoS()
1399 auto cols = n_cvt + 2; in GetabIndex()
1702 if (n_cvt == 1) { in JackknifeAKtoS()
1948 for (size_t j = 0; j < n_cvt; ++j) { in CheckCvt()
1969 if (n_cvt == set_remove.size()) { in CheckCvt()
1971 n_cvt = 1; in CheckCvt()
1981 n_cvt++; in CheckCvt()
2105 for (size_t j = 0; j < n_cvt; ++j) { in CopyCvt()
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| H A D | lmm.h | 40 size_t n_cvt; variable
74 size_t n_cvt; variable
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| H A D | ldr.h | 46 size_t n_cvt; // Number of covariates. variable
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| H A D | lm.h | 48 size_t n_cvt; variable
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| H A D | param.h | 245 size_t n_cvt; // Number of covariates. variable
372 size_t GetabIndex(const size_t a, const size_t b, const size_t n_cvt);
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| H A D | gemma_io.h | 51 vector<vector<double>> &cvt, size_t &n_cvt);
185 vector<vector<double>> &cvt, size_t &n_cvt);
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| H A D | mvlmm.h | 60 size_t n_cvt; variable
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| H A D | gemma.cpp | 1732 gsl_matrix *W = gsl_matrix_safe_alloc(Y->size1, cPar.n_cvt); in BatchRun()
2060 gsl_matrix *W = gsl_matrix_safe_alloc(Y->size1, cPar.n_cvt); in BatchRun()
2319 gsl_matrix *W = gsl_matrix_safe_alloc(Y->size1, cPar.n_cvt); in BatchRun()
2557 gsl_matrix *W = gsl_matrix_safe_alloc(Y->size1, cPar.n_cvt); in BatchRun()
2857 gsl_matrix *W = gsl_matrix_safe_alloc(y->size, cPar.n_cvt); in BatchRun()
2967 gsl_matrix *W = gsl_matrix_safe_alloc(y->size, cPar.n_cvt); in BatchRun()
3300 outfile << "## number of covariates = " << cPar.n_cvt << endl; in WriteLog()
3488 for (size_t j = 0; j < cPar.n_cvt; j++) { in WriteLog()
3489 c = i * cPar.n_cvt + j; in WriteLog()
3496 for (size_t j = 0; j < cPar.n_cvt; j++) { in WriteLog()
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| H A D | bslmm.h | 72 size_t n_cvt; // Number of covariates. variable
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| H A D | lm.cpp | 65 n_cvt = cPar.n_cvt; in CopyFromParam()
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| H A D | vc.cpp | 169 size_t n1 = (p->K)->size1, n_vc = log_sigma2->size - 1, n_cvt = (p->W)->size2; in UpdateParam() local
172 gsl_matrix *HiW = gsl_matrix_alloc(n1, n_cvt); in UpdateParam()
173 gsl_matrix *WtHiW = gsl_matrix_alloc(n_cvt, n_cvt); in UpdateParam()
174 gsl_matrix *WtHiWi = gsl_matrix_alloc(n_cvt, n_cvt); in UpdateParam()
175 gsl_matrix *WtHiWiWtHi = gsl_matrix_alloc(n_cvt, n1); in UpdateParam()
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| H A D | gemma_io.cpp | 443 vector<vector<double>> &cvt, size_t &n_cvt) { in ReadFile_cvt() argument
483 n_cvt = 0; in ReadFile_cvt()
493 n_cvt = cvt[i].size(); in ReadFile_cvt()
495 if (flag_na != 0 && n_cvt != cvt[i].size()) { in ReadFile_cvt()
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| H A D | bslmm.cpp | 95 n_cvt = cPar.n_cvt; in CopyFromParam()
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| H A D | mvlmm.cpp | 82 n_cvt = cPar.n_cvt; in CopyFromParam()
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