/dports/biology/gemma/GEMMA-0.98.3/src/ |
H A D | param.cpp | 476 ni_test = 0; in ReadFiles() 1033 ni_test = 0; in CheckData() 1038 ni_test++; in CheckData() 1428 double d, tr, r = (double)ni_test / (double)(ni_test - 1); in compKtoV() 1436 gsl_matrix_const_submatrix(G, 0, i * ni_test, ni_test, ni_test); in compKtoV() 1439 gsl_matrix_const_submatrix(G, 0, j * ni_test, ni_test, ni_test); in compKtoV() 1441 gsl_matrix_submatrix(KiKj, 0, t * ni_test, ni_test, ni_test); in compKtoV() 1792 gsl_matrix_submatrix(K, 0, i * ni_test, ni_test, ni_test); in CalcS() 1798 gsl_matrix_submatrix(A, 0, i * ni_test, ni_test, ni_test); in CalcS() 2028 ni_test = 0; in ProcessCvtPhen() [all …]
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H A D | lmm.cpp | 74 ni_test = cPar.ni_test; in CopyFromParam() 481 size_t ni_test = p->ni_test; in LogL_f() local 516 0.5 * (double)ni_test * (safe_log((double)ni_test) - safe_log(2 * M_PI) - 1.0); in LogL_f() 539 size_t ni_test = p->ni_test; in LogL_dev1() local 637 size_t ni_test = p->ni_test; in LogL_dev2() local 714 size_t ni_test = p->ni_test; in LogL_dev12() local 794 size_t ni_test = p->ni_test; in LogRL_f() local 859 size_t ni_test = p->ni_test; in LogRL_dev1() local 938 size_t ni_test = p->ni_test; in LogRL_dev2() local 1028 size_t ni_test = p->ni_test; in LogRL_dev12() local [all …]
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H A D | bslmm.cpp | 93 ni_test = cPar.ni_test; in CopyFromParam() 460 for (size_t i = 0; i < ni_test; ++i) { in CalcPosterior() 495 cHyp.pve = d / (double)ni_test; in CalcPosterior() 542 for (size_t i = 0; i < ni_test; ++i) { in CalcPosterior() 611 cHyp.pge = d / (double)ni_test; in CalcPosterior() 650 cHyp.pve = d / (double)ni_test; in CalcCC_PVEnZ() 668 cHyp.pge = d / (double)ni_test; in CalcCC_PVEnZ() 671 cHyp.pve = cHyp.pge + d / (double)ni_test; in CalcCC_PVEnZ() 905 gsl_vector *z = gsl_vector_alloc(ni_test); in MCMC() 1528 cHyp.pve = d / (double)ni_test; in CalcPosterior() [all …]
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H A D | gemma_io.cpp | 687 int ni_test = 0; in ReadFile_geno() local 689 ni_test += indicator_idv[i]; in ReadFile_geno() 895 size_t ni_test = 0; in ReadFile_bed() local 897 ni_test += indicator_idv[i]; in ReadFile_bed() 1749 int ni_test = UtX->size1; in ReadFile_geno() local 1954 size_t ni_test = UtX->size1; in ReadFile_bed() local 2827 geno_var /= (double)ni_test; in BimbamKinUncentered() 2876 matrix_kin, 0, ni_test * i_vc, ni_test, ni_test); in BimbamKinUncentered() 2892 gsl_matrix_submatrix(matrix_kin, 0, ni_test * i_vc, ni_test, ni_test); in BimbamKinUncentered() 3102 matrix_kin, 0, ni_test * i_vc, ni_test, ni_test); in PlinkKin() [all …]
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H A D | varcov.cpp | 261 size_t ni_test = 0; in AnalyzeBimbam() local 263 ni_test += indicator_idv[i]; in AnalyzeBimbam() 266 gsl_vector *geno = gsl_vector_alloc(ni_test); in AnalyzeBimbam() 272 for (size_t i = 0; i < ni_test; i++) { in AnalyzeBimbam() 361 size_t ni_test = 0; in AnalyzePlink() local 363 ni_test += indicator_idv[i]; in AnalyzePlink() 366 gsl_vector *geno = gsl_vector_alloc(ni_test); in AnalyzePlink() 372 for (size_t i = 0; i < ni_test; i++) { in AnalyzePlink()
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H A D | prdt.cpp | 134 size_t ni_test = u_hat->size, ni_total = G->size1; in AddBV() local 136 gsl_matrix *Goo = gsl_matrix_alloc(ni_test, ni_test); in AddBV() 137 gsl_matrix *Gfo = gsl_matrix_alloc(ni_total - ni_test, ni_test); in AddBV() 138 gsl_matrix *U = gsl_matrix_alloc(ni_test, ni_test); in AddBV() 139 gsl_vector *eval = gsl_vector_alloc(ni_test); in AddBV() 140 gsl_vector *Utu = gsl_vector_alloc(ni_test); in AddBV() 142 gsl_permutation *pmt = gsl_permutation_alloc(ni_test); in AddBV()
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H A D | ldr.cpp | 60 ni_test = cPar.ni_test; in CopyFromParam()
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H A D | lm.cpp | 63 ni_test = cPar.ni_test; in CopyFromParam() 197 << ni_test - snpInfo[i].n_miss << "\t" << snpInfo[i].a_minor in WriteFiles() 457 x_mean /= (double)(ni_test - n_miss); in AnalyzeBimbam() 459 for (size_t i = 0; i < ni_test; ++i) { in AnalyzeBimbam() 600 x_mean /= (double)(ni_test - n_miss); in AnalyzePlink() 602 for (size_t i = 0; i < ni_test; ++i) { in AnalyzePlink()
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H A D | bslmmdap.cpp | 83 ni_test = cPar.ni_test; in CopyFromParam() 486 for (size_t i = 0; i < ni_test; ++i) { in CalcMarginal() 497 logm = -0.5 * logdet_H - 0.5 * tau * Hi_yy + 0.5 * log(tau) * (double)ni_test; in CalcMarginal() 522 for (size_t i = 0; i < ni_test; ++i) { in CalcMarginal() 559 0.5 * log(tau) * (double)ni_test; in CalcMarginal() 585 gsl_matrix *Xgamma = gsl_matrix_alloc(ni_test, 1); in DAP_CalcBF() 590 tau = (double)ni_test / tau; in DAP_CalcBF()
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H A D | lmm.h | 39 size_t ni_test; variable 71 size_t ni_total, ni_test; // Number of individuals. variable
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H A D | vc.cpp | 2237 size_t ni_test = XWz->size1; in BimbamXwz() local 2283 geno_var /= (double)ni_test; in BimbamXwz() 2286 for (size_t i = 0; i < ni_test; ++i) { in BimbamXwz() 2331 size_t ni_test = XWz->size1; in PlinkXwz() local 2410 geno_var /= (double)ni_test; in PlinkXwz() 2413 for (size_t i = 0; i < ni_test; ++i) { in PlinkXwz() 2493 size_t ni_test = XWz->size1; in BimbamXtXwz() local 2536 geno_var /= (double)ni_test; in BimbamXtXwz() 2584 size_t ni_test = XWz->size1; in PlinkXtXwz() local 2660 geno_var /= (double)ni_test; in PlinkXtXwz() [all …]
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H A D | gemma.cpp | 1956 gsl_matrix *K = gsl_matrix_safe_alloc(cPar.ni_test, cPar.n_vc * cPar.ni_test); in BatchRun() 1957 gsl_matrix *A = gsl_matrix_safe_alloc(cPar.ni_test, cPar.n_vc * cPar.ni_test); in BatchRun() 1961 gsl_vector *y = gsl_vector_safe_alloc(cPar.ni_test); in BatchRun() 1980 gsl_vector_set(ns, cPar.n_vc, cPar.ni_test); in BatchRun() 2119 gsl_matrix *K = gsl_matrix_safe_alloc(cPar.ni_test, cPar.n_vc * cPar.ni_test); in BatchRun() 2120 gsl_matrix *A = gsl_matrix_safe_alloc(cPar.ni_test, cPar.n_vc * cPar.ni_test); in BatchRun() 2122 gsl_vector *y = gsl_vector_safe_alloc(cPar.ni_test); in BatchRun() 2210 gsl_vector_set(s, cPar.n_vc, cPar.ni_test); in BatchRun() 2856 gsl_vector *y = gsl_vector_safe_alloc(cPar.ni_test); in BatchRun() 2966 gsl_vector *y = gsl_vector_safe_alloc(cPar.ni_test); in BatchRun() [all …]
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H A D | ldr.h | 44 size_t ni_test, ns_test; // Number of individuals & SNPs used variable
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H A D | lm.h | 45 size_t ni_total, ni_test; // Number of individuals. variable
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H A D | param.h | 233 size_t ni_total, ni_test, ni_cvt, ni_study, ni_ref; variable 363 const size_t ni_test, const gsl_vector *ns,
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H A D | gemma_io.h | 106 const bool calc_K, const size_t ni_test, 110 gsl_matrix *K, const bool calc_K, const size_t ni_test,
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H A D | mvlmm.h | 58 size_t ni_total, ni_test; // Number of individuals. variable
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H A D | bslmmdap.h | 54 size_t ni_test, ns_test; // Number of individuals and SNPs variable
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H A D | bslmm.h | 71 size_t ni_test, ns_test; // Num. individuals & SNPs used in analysis. variable
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H A D | mvlmm.cpp | 80 ni_test = cPar.ni_test; in CopyFromParam() 3245 x_mean /= (double)(ni_test - n_miss); in AnalyzeBimbam() 3247 for (size_t i = 0; i < ni_test; ++i) { in AnalyzeBimbam() 3720 x_mean /= (double)(ni_test - n_miss); in AnalyzePlink() 3722 for (size_t i = 0; i < ni_test; ++i) { in AnalyzePlink() 4231 x_mean /= (double)(ni_test - n_miss); in AnalyzeBimbamGXE() 4233 for (size_t i = 0; i < ni_test; ++i) { in AnalyzeBimbamGXE() 4706 x_mean /= (double)(ni_test - n_miss); in AnalyzePlinkGXE() 4708 for (size_t i = 0; i < ni_test; ++i) { in AnalyzePlinkGXE()
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/dports/graphics/blender/blender-2.91.0/extern/quadriflow/3rd/lemon-1.3.1/test/ |
H A D | nagamochi_ibaraki_test.cc | 70 NagamochiIbaraki<Graph, CapMap> ni_test(g, cap); in checkNagamochiIbarakiCompile() local 71 const NagamochiIbaraki<Graph, CapMap>& const_ni_test = ni_test; in checkNagamochiIbarakiCompile() 73 ni_test.init(); in checkNagamochiIbarakiCompile() 74 ni_test.start(); in checkNagamochiIbarakiCompile() 75 b = ni_test.processNextPhase(); in checkNagamochiIbarakiCompile() 76 ni_test.run(); in checkNagamochiIbarakiCompile()
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/dports/math/lemon/lemon-1.3.1/test/ |
H A D | nagamochi_ibaraki_test.cc | 70 NagamochiIbaraki<Graph, CapMap> ni_test(g, cap); in checkNagamochiIbarakiCompile() local 71 const NagamochiIbaraki<Graph, CapMap>& const_ni_test = ni_test; in checkNagamochiIbarakiCompile() 73 ni_test.init(); in checkNagamochiIbarakiCompile() 74 ni_test.start(); in checkNagamochiIbarakiCompile() 75 b = ni_test.processNextPhase(); in checkNagamochiIbarakiCompile() 76 ni_test.run(); in checkNagamochiIbarakiCompile()
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