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Merge pull request #24 from LewisLabUCSD/simulation_growth_rate
Simulation growth rate
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parameters/simulation/simple.yaml → ...inomial_growth/parameters/simple_v01.yaml
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Analysis/simulations/binomial_growth/parameters/sweep_v01.yaml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| # One set of parameters for simulating cells and their lineages | ||
| outdir: 'results' | ||
| prefix: 'sweep_v01' | ||
| data_outdir: 'data/out' | ||
| #num_iterations: 100 | ||
| #num_cells: 10000 | ||
| #num_mt_positions: 10 | ||
| cpus: 36 | ||
|
|
||
| grid: | ||
| cov_constant: [5, 10, 50, 100] | ||
| dominant_clone_sizes: [0.02,0.1,0.2, 0.4] | ||
| dominant_het: [0.02, 0.2, 0.5, 0.8] | ||
| dominant_growth: [0.1, 0.5, 0.8] | ||
| het_err_rate: [0.05, 0.15] |
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Analysis/simulations/binomial_growth/results/0.before_after.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,101 @@ | ||
| Before After A/B | ||
| 0 198 224 1.1313131313131313 | ||
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| 97 223 231 1.0358744394618835 | ||
| 98 205 248 1.2097560975609756 | ||
| 99 202 204 1.00990099009901 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 | ||
| Precision 0.018527408003428943 0.01653002515769531 0.019094637170015902 0.018199307888534185 0.01819155530200554 0.01896134500562538 0.017619657318190676 0.01833408311151479 0.016065456790086752 0.017383118115291585 0.017740581437120186 0.01575176811990491 0.017152158307344394 0.01991669563336525 0.019344142722199933 0.017210686357407155 0.01675838332924371 0.01590293593178758 0.018547567113683886 0.01863077681137966 0.019667387503894768 0.014865563691384514 0.015530686835364295 0.0199376146664293 0.017817567789097797 0.017566989458920653 0.01815847776046762 0.018799478147738524 0.02026701660298504 0.016056764844133903 0.01815963049232899 0.01936317012812521 0.01763691632343531 0.018355328219565387 0.020176071844049445 0.016813063029385105 0.01838511108022077 0.01868121259833419 0.013919738404414838 0.016003963139678775 0.016922721305702108 0.01590303921039196 0.018822739633232125 0.018186482601543215 0.015424558044818897 0.01609654509310918 0.017452447229611673 0.01581834539207803 0.018897408610923754 0.019651591937132968 0.017315123095611208 0.019000968171476396 0.0182669819209044 0.01673144912937058 0.015134136570293378 0.018327516189052803 0.018539889740741663 0.017497016612300624 0.01629801512110323 0.016437460375281793 0.01692916838181492 0.019463395533635627 0.01896195953091781 0.017597624462101148 0.017453218479922275 0.015081590009805412 0.017674531555306447 0.017226870152904108 0.016597753930097933 0.016307203354815697 0.019227273391983907 0.01774068753824219 0.017350803556454776 0.018549398769397426 0.018243901200774893 0.018230618672602263 0.018924456267175843 0.017871817609713424 0.0175774794166614 0.01655006311745274 0.02090277047393086 0.018762823478445476 0.01813744974908946 0.019343858181452143 0.017080949235928986 0.018389396146258976 0.016676360619419316 0.018505332616492443 0.016981855340554585 0.017395435788122523 0.018614734837931544 0.018378768905019088 0.017484793086561992 0.017357097827048147 0.01824964869355767 0.014773224700107088 0.018534683451375104 0.020041297049642488 0.019054085903246393 0.017872730284775793 | ||
| Dropout 0.01265 0.01195 0.0134 0.0137 0.0143 0.0127 0.0127 0.01275 0.011 0.01205 0.01305 0.0115 0.01245 0.0142 0.0136 0.0117 0.0126 0.0117 0.01365 0.01405 0.01405 0.0111 0.0124 0.0138 0.0133 0.0136 0.013 0.0134 0.01315 0.01215 0.01375 0.0137 0.0124 0.01365 0.0151 0.01335 0.0125 0.01315 0.0107 0.0116 0.0111 0.01085 0.0134 0.0125 0.0107 0.01175 0.0132 0.01215 0.0135 0.01415 0.01385 0.0143 0.013 0.0122 0.01155 0.0131 0.0126 0.013 0.01225 0.01215 0.0131 0.0137 0.01295 0.01275 0.0117 0.01105 0.0121 0.01235 0.0123 0.01135 0.0141 0.0135 0.01205 0.01275 0.01315 0.0125 0.01325 0.0128 0.01135 0.01225 0.0143 0.01305 0.01285 0.01365 0.01165 0.0132 0.0115 0.01405 0.0115 0.0129 0.01415 0.01305 0.01345 0.0128 0.0124 0.0112 0.01315 0.01385 0.01335 0.01285 |
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101
Analysis/simulations/binomial_growth/results/1.before_after.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,101 @@ | ||
| Before After A/B | ||
| 0 232 242 1.043103448275862 | ||
| 1 200 171 0.855 | ||
| 2 213 221 1.0375586854460095 | ||
| 3 231 259 1.121212121212121 | ||
| 4 179 194 1.0837988826815643 | ||
| 5 193 183 0.9481865284974094 | ||
| 6 208 232 1.1153846153846154 | ||
| 7 191 225 1.1780104712041886 | ||
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| 12 213 237 1.1126760563380282 | ||
| 13 190 205 1.0789473684210527 | ||
| 14 215 216 1.0046511627906978 | ||
| 15 203 203 1.0 | ||
| 16 208 234 1.125 | ||
| 17 192 219 1.140625 | ||
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| 25 195 193 0.9897435897435898 | ||
| 26 225 248 1.1022222222222222 | ||
| 27 211 211 1.0 | ||
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| 40 192 192 1.0 | ||
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| 62 200 195 0.975 | ||
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| 86 197 213 1.0812182741116751 | ||
| 87 202 217 1.0742574257425743 | ||
| 88 183 184 1.005464480874317 | ||
| 89 214 229 1.0700934579439252 | ||
| 90 217 231 1.064516129032258 | ||
| 91 209 214 1.0239234449760766 | ||
| 92 231 236 1.0216450216450217 | ||
| 93 205 222 1.0829268292682928 | ||
| 94 199 240 1.2060301507537687 | ||
| 95 198 217 1.095959595959596 | ||
| 96 186 204 1.096774193548387 | ||
| 97 173 190 1.0982658959537572 | ||
| 98 181 169 0.9337016574585635 | ||
| 99 193 217 1.1243523316062176 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 | ||
| Precision 0.017774874620052016 0.014439277044265243 0.016285105329129374 0.018680593315441734 0.014181174601065728 0.014784356044203808 0.016713407620360846 0.01559607945672057 0.01785893123423735 0.016574756116380075 0.01611045181131616 0.015893128501414392 0.01696836864712912 0.014923884035382654 0.01659015452750959 0.015857547883730328 0.01651226672756088 0.015450618518383035 0.015296715468619888 0.0152906919664126 0.014700156805128197 0.014287955149275184 0.016855043238467166 0.014150818467953295 0.018040592168374926 0.01527547609796931 0.017936600986377324 0.01651443110040077 0.01550654999253032 0.015068878121633546 0.016229833154320368 0.015226415874142406 0.015596920303654147 0.014108307181461895 0.01533133605547797 0.014519466428029686 0.014299643880858885 0.015838565505176018 0.014786491581095323 0.01737477899024523 0.014598639073107931 0.01680893340883484 0.016504240128026374 0.017098408633767107 0.015269016212994455 0.015775259355462954 0.015225917276400802 0.01459684302972116 0.016565912259415328 0.015682885781993908 0.014040387946516263 0.015078410440493751 0.015640583835454625 0.013716253123715938 0.016319669224815037 0.015338449556692045 0.01552473593614538 0.014206018633619215 0.014119466599599619 0.015576418710519815 0.016727837160835823 0.01562586022399158 0.015091982585416847 0.01650047312660928 0.017181383350535023 0.015570837077891603 0.016922926958053263 0.014725893370847773 0.017291555381095322 0.013920673860825366 0.016502560607219142 0.015498987445507834 0.016292641152336307 0.01430755888115873 0.015652411086658116 0.014864879533943078 0.014818405412214393 0.0160012408968202 0.017750197888304644 0.0165390759336691 0.013932760911971983 0.015711596104657742 0.015882759115245126 0.016136468941288448 0.015404134686083242 0.015711948119778767 0.015613680984043199 0.016075778282823142 0.013973919545389882 0.01675430288904257 0.017355365018125755 0.01639933685957738 0.017812960358240457 0.016022784595095256 0.01615371491919955 0.015323579539813677 0.014911194161899495 0.013584797163414986 0.013587829534714027 0.015469922752721074 | ||
| Dropout 0.0141 0.0121 0.013 0.0145 0.01115 0.0122 0.0135 0.0127 0.01435 0.01315 0.01315 0.0125 0.0135 0.01185 0.0135 0.01275 0.013 0.0124 0.01245 0.0125 0.01185 0.01165 0.01375 0.01165 0.01435 0.0129 0.01475 0.0138 0.01225 0.0115 0.01275 0.0122 0.01295 0.0111 0.0129 0.0123 0.01195 0.0134 0.0125 0.0147 0.01165 0.01355 0.013 0.01375 0.0122 0.01285 0.0124 0.0117 0.01335 0.01285 0.0116 0.01255 0.01215 0.0111 0.0134 0.01135 0.0125 0.0115 0.0119 0.0126 0.01325 0.0124 0.0127 0.0137 0.0141 0.0127 0.01335 0.01165 0.01455 0.01115 0.01325 0.0125 0.0132 0.0115 0.0124 0.01255 0.01125 0.0131 0.0149 0.0137 0.01185 0.0125 0.01245 0.0134 0.01275 0.0127 0.01275 0.0131 0.0114 0.01335 0.0145 0.01355 0.0144 0.0128 0.0128 0.0117 0.01235 0.01085 0.0113 0.0124 |
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101
Analysis/simulations/binomial_growth/results/100.before_after.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,101 @@ | ||
| Before After A/B | ||
| 0 232 242 1.043103448275862 | ||
| 1 200 171 0.855 | ||
| 2 213 221 1.0375586854460095 | ||
| 3 231 259 1.121212121212121 | ||
| 4 179 194 1.0837988826815643 | ||
| 5 193 183 0.9481865284974094 | ||
| 6 208 232 1.1153846153846154 | ||
| 7 191 225 1.1780104712041886 | ||
| 8 229 242 1.056768558951965 | ||
| 9 221 220 0.995475113122172 | ||
| 10 215 208 0.9674418604651163 | ||
| 11 204 212 1.0392156862745099 | ||
| 12 213 237 1.1126760563380282 | ||
| 13 190 205 1.0789473684210527 | ||
| 14 215 216 1.0046511627906978 | ||
| 15 203 203 1.0 | ||
| 16 208 234 1.125 | ||
| 17 192 219 1.140625 | ||
| 18 187 220 1.1764705882352942 | ||
| 19 201 203 1.0099502487562189 | ||
| 20 184 202 1.0978260869565217 | ||
| 21 196 170 0.8673469387755102 | ||
| 22 217 224 1.032258064516129 | ||
| 23 181 191 1.0552486187845305 | ||
| 24 229 254 1.1091703056768558 | ||
| 25 195 193 0.9897435897435898 | ||
| 26 225 248 1.1022222222222222 | ||
| 27 211 211 1.0 | ||
| 28 188 228 1.2127659574468086 | ||
| 29 196 203 1.0357142857142858 | ||
| 30 210 214 1.019047619047619 | ||
| 31 201 196 0.9751243781094527 | ||
| 32 198 209 1.0555555555555556 | ||
| 33 174 202 1.160919540229885 | ||
| 34 194 200 1.0309278350515463 | ||
| 35 189 183 0.9682539682539683 | ||
| 36 182 193 1.0604395604395604 | ||
| 37 197 206 1.0456852791878173 | ||
| 38 190 182 0.9578947368421052 | ||
| 39 221 231 1.0452488687782806 | ||
| 40 192 192 1.0 | ||
| 41 214 231 1.0794392523364487 | ||
| 42 207 229 1.106280193236715 | ||
| 43 220 230 1.0454545454545454 | ||
| 44 197 202 1.0253807106598984 | ||
| 45 200 218 1.09 | ||
| 46 197 207 1.0507614213197969 | ||
| 47 188 205 1.0904255319148937 | ||
| 48 213 225 1.056338028169014 | ||
| 49 197 219 1.1116751269035532 | ||
| 50 179 182 1.0167597765363128 | ||
| 51 199 192 0.964824120603015 | ||
| 52 188 230 1.2234042553191489 | ||
| 53 174 192 1.103448275862069 | ||
| 54 212 210 0.9905660377358491 | ||
| 55 197 218 1.1065989847715736 | ||
| 56 196 216 1.1020408163265305 | ||
| 57 177 196 1.1073446327683616 | ||
| 58 176 179 1.0170454545454546 | ||
| 59 195 222 1.1384615384615384 | ||
| 60 214 220 1.02803738317757 | ||
| 61 198 218 1.101010101010101 | ||
| 62 200 195 0.975 | ||
| 63 211 217 1.028436018957346 | ||
| 64 212 239 1.1273584905660377 | ||
| 65 197 205 1.0406091370558375 | ||
| 66 208 243 1.1682692307692308 | ||
| 67 186 203 1.0913978494623655 | ||
| 68 210 231 1.1 | ||
| 69 179 188 1.0502793296089385 | ||
| 70 213 220 1.0328638497652582 | ||
| 71 194 214 1.1030927835051547 | ||
| 72 209 221 1.0574162679425838 | ||
| 73 187 194 1.0374331550802138 | ||
| 74 193 230 1.1917098445595855 | ||
| 75 187 202 1.0802139037433156 | ||
| 76 186 210 1.1290322580645162 | ||
| 77 200 215 1.075 | ||
| 78 223 235 1.053811659192825 | ||
| 79 212 218 1.028301886792453 | ||
| 80 184 176 0.9565217391304348 | ||
| 81 200 211 1.055 | ||
| 82 195 228 1.1692307692307693 | ||
| 83 200 215 1.075 | ||
| 84 191 211 1.1047120418848169 | ||
| 85 204 217 1.0637254901960784 | ||
| 86 197 213 1.0812182741116751 | ||
| 87 202 217 1.0742574257425743 | ||
| 88 183 184 1.005464480874317 | ||
| 89 214 229 1.0700934579439252 | ||
| 90 217 231 1.064516129032258 | ||
| 91 209 214 1.0239234449760766 | ||
| 92 231 236 1.0216450216450217 | ||
| 93 205 222 1.0829268292682928 | ||
| 94 199 240 1.2060301507537687 | ||
| 95 198 217 1.095959595959596 | ||
| 96 186 204 1.096774193548387 | ||
| 97 173 190 1.0982658959537572 | ||
| 98 181 169 0.9337016574585635 | ||
| 99 193 217 1.1243523316062176 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 | ||
| Precision 0.9053343152768173 0.9058330461878304 0.9232589573551012 0.916482412352132 0.8971464745345369 0.8699916326185805 0.9132069362411877 0.9001989732490203 0.8904501689529695 0.8812029948889961 0.9234369683470863 0.9160964691820674 0.9122718701132659 0.9102441613783896 0.8835110175309542 0.8831280527149521 0.8866577383231028 0.891969255307803 0.8877470598442474 0.8990381930359846 0.8933192389598298 0.8768552533772952 0.9066505181918149 0.8854333213015398 0.9318776312586093 0.874846955609239 0.9227351883130221 0.9024621355233058 0.9080307926274411 0.9207186975839388 0.903539853184143 0.9096547777616428 0.8625850018400312 0.9211102564717877 0.9369588117364431 0.9127973246989262 0.8718353230699721 0.8963523962920568 0.9274497967752864 0.8971131064258279 0.8874078897633767 0.9221893913077865 0.89038083308393 0.9196363201183576 0.8990139984444427 0.8925961839258993 0.8924299531450274 0.8988605344662638 0.9105766187448416 0.9107945910458832 0.9010096345773427 0.9012813866460151 0.9201340789163046 0.8888592390672232 0.9047398844789604 0.9168057064175388 0.9221005357113179 0.9151911958765684 0.8988058898486487 0.8930237042496367 0.8912124008038032 0.9066449140308311 0.8741331201918078 0.8746660118459745 0.9215318136425799 0.9197635523892517 0.9553123158138869 0.911785881033049 0.8970396394503338 0.9170653893736757 0.8946395989820531 0.9177375414554036 0.9027090581406318 0.9057789168045044 0.9045839399799852 0.8895726158777356 0.928415227013113 0.9267345262030126 0.9291908063931112 0.9094367867188001 0.8552762800101579 0.9306725156004713 0.9150032186894909 0.8780914315198273 0.8957532140783929 0.9127513046117037 0.9191691128298592 0.8957086746955916 0.9282106647790493 0.9161330660678371 0.9010035670959031 0.8752031800859229 0.9162085415310172 0.9007077347972232 0.9150838743097466 0.9168824549047767 0.9035673797735703 0.9004088940866354 0.9072233382075773 0.8925732018237296 | ||
| Dropout 5e-05 0.0 0.0 0.0 0.0 0.0001 0.0 0.0 0.0 0.0 0.0 5e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0001 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0001 0.0 0.0 5e-05 0.0 0.0 0.0 0.0 0.0 0.0 5e-05 5e-05 0.0 0.0 0.0 0.0 0.0 5e-05 0.0001 0.0 0.0 0.0 0.0 0.0 5e-05 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 5e-05 0.0 0.0 0.0 0.0001 0.0 0.0 0.0 0.0 0.0 0.0 0.0 |
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