diff options
| author | Ta180m | 2020-05-02 15:25:32 -0500 |
|---|---|---|
| committer | Ta180m | 2020-05-02 15:25:32 -0500 |
| commit | 2485953be4d3b81ae65244b5b31cb5bf2b5f9524 (patch) | |
| tree | c454615a348819fd98e4f72a5691d111c629e46b | |
| parent | ffc65c7b25d16520301724b441ee2e17a15ce8b7 (diff) | |
Redo tests
| -rw-r--r-- | COVID-19-ESIR.png | bin | 40520 -> 40548 bytes | |||
| -rw-r--r-- | COVID-19-Linear.png | bin | 35357 -> 37147 bytes | |||
| -rw-r--r-- | COVID-19-SIR.png | bin | 40438 -> 40434 bytes | |||
| -rw-r--r-- | README.md | 1 | ||||
| -rw-r--r-- | SARS-ESIR.png | bin | 40906 -> 40882 bytes | |||
| -rw-r--r-- | SARS-Linear.png | bin | 41210 -> 41233 bytes | |||
| -rw-r--r-- | out/COVID-19-ESIR-data.csv | 11 | ||||
| -rw-r--r-- | out/COVID-19-ESIR-prediction.csv | 152 | ||||
| -rw-r--r-- | out/COVID-19-Linear-data.csv | 9 | ||||
| -rw-r--r-- | out/COVID-19-Linear-prediction.csv | 152 | ||||
| -rw-r--r-- | out/COVID-19-SEIR-data.csv | 3 | ||||
| -rw-r--r-- | out/COVID-19-SIR-data.csv | 9 | ||||
| -rw-r--r-- | out/COVID-19-SIR-prediction.csv | 152 | ||||
| -rw-r--r-- | out/SARS-ESIR-data.csv | 11 | ||||
| -rw-r--r-- | out/SARS-ESIR-prediction.csv | 150 | ||||
| -rw-r--r-- | out/SARS-Linear-data.csv | 9 | ||||
| -rw-r--r-- | out/SARS-Linear-prediction.csv | 150 | ||||
| -rw-r--r-- | out/SARS-SEIR-data.csv | 3 | ||||
| -rw-r--r-- | out/SARS-SIR-data.csv | 3 | ||||
| -rw-r--r-- | solver2.py | 8 |
20 files changed, 416 insertions, 407 deletions
diff --git a/COVID-19-ESIR.png b/COVID-19-ESIR.png Binary files differindex 5b2d708..64feceb 100644 --- a/COVID-19-ESIR.png +++ b/COVID-19-ESIR.png diff --git a/COVID-19-Linear.png b/COVID-19-Linear.png Binary files differindex 2e2c2b9..b624344 100644 --- a/COVID-19-Linear.png +++ b/COVID-19-Linear.png diff --git a/COVID-19-SIR.png b/COVID-19-SIR.png Binary files differindex 4497cb1..c309d7e 100644 --- a/COVID-19-SIR.png +++ b/COVID-19-SIR.png @@ -14,6 +14,7 @@ For SARS in Hong Kong use For COVID-19 in the US use `./solver2.py --popcountry=3000000 --initial=100 --mode={SIR,Linear,ESIR,SEIR}` +General usage: ``` usage: solver2.py [-h] [--mode {SIR,Linear,ESIR,SEIR}] [--data [{Actual,S,I,R,E} [{Actual,S,I,R,E} ...]]] diff --git a/SARS-ESIR.png b/SARS-ESIR.png Binary files differindex b334cb1..c623bca 100644 --- a/SARS-ESIR.png +++ b/SARS-ESIR.png diff --git a/SARS-Linear.png b/SARS-Linear.png Binary files differindex 5bbbf4e..23081fd 100644 --- a/SARS-Linear.png +++ b/SARS-Linear.png diff --git a/out/COVID-19-ESIR-data.csv b/out/COVID-19-ESIR-data.csv index 3c6bb37..b929084 100644 --- a/out/COVID-19-ESIR-data.csv +++ b/out/COVID-19-ESIR-data.csv @@ -1,5 +1,6 @@ -Beta: 0.11506079905613333 -Gamma: 0.004485002592721715 -Mu: 1e-08 -R0: 25.654509698111923 -Predicted I: 1266.8145664521824, Actual I: 1320.7366666666667
\ No newline at end of file +Beta: 0.11611254858884054 +Gamma: 0.004524040067261208 +Mu: 0.001 +R0: 21.019497899190398 +Predicted I: 1266.3066498710834 +Actual I: 1320.7366666666667
\ No newline at end of file diff --git a/out/COVID-19-ESIR-prediction.csv b/out/COVID-19-ESIR-prediction.csv index 15ad69e..f11dbc1 100644 --- a/out/COVID-19-ESIR-prediction.csv +++ b/out/COVID-19-ESIR-prediction.csv @@ -1,78 +1,78 @@ ,Actual,S,I,R 1/22/20,0.0033333333333333335,9999.666666666666,0.33333333333333337,0.0 -1/23/20,0.0033333333333333335,9999.626113386881,0.37230581397620527,0.0015807991430292917 -1/24/20,0.006666666666666667,9999.58081926442,0.4158343279178975,0.0033464076627307353 -1/25/20,0.006666666666666667,9999.530230241262,0.46445133279667583,0.005318425940276048 -1/26/20,0.016666666666666666,9999.47370935019,0.5187689595900552,0.007521690219182955 -1/27/20,0.016666666666666666,9999.410195932789,0.5798064388452426,0.009997628365004882 -1/28/20,0.016666666666666666,9999.339138100348,0.6480941545637604,0.012767745089180731 -1/29/20,0.016666666666666666,9999.260059689912,0.7240897547339856,0.01585055535425662 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+4/7/20,1320.7366666666667,8678.486594408621,1266.3066498710834,55.206755720292904 diff --git a/out/COVID-19-Linear-data.csv b/out/COVID-19-Linear-data.csv index d0469e1..a4fada7 100644 --- a/out/COVID-19-Linear-data.csv +++ b/out/COVID-19-Linear-data.csv @@ -1,4 +1,5 @@ -Beta: 0.0005306298181865554 -Gamma: 0.00121221978960238 -R0: 0.4377340006638624 -Predicted I: 377.76904311879434, Actual I: 1320.7366666666667
\ No newline at end of file +Beta: 0.001 +Gamma: 0.001264208619688091 +R0: 0.7910086867203316 +Predicted I: 697.635036958848 +Actual I: 1320.7366666666667
\ No newline at end of file diff --git a/out/COVID-19-Linear-prediction.csv b/out/COVID-19-Linear-prediction.csv index 656dbe1..f0c09aa 100644 --- a/out/COVID-19-Linear-prediction.csv +++ b/out/COVID-19-Linear-prediction.csv @@ -1,78 +1,78 @@ ,Actual,S,I,R 1/22/20,0.0033333333333333335,9999.666666666666,0.33333333333333337,0.0 -1/23/20,0.0033333333333333335,9994.361952905527,5.6344290411453315,0.003618053328386932 -1/24/20,0.006666666666666667,9989.060053236995,10.926290161791322,0.013656601213288695 -1/25/20,0.006666666666666667,9983.760966168222,16.208929375068454,0.03010445670892412 -1/26/20,0.016666666666666666,9978.46469020716,21.4823593440476,0.052950448791872544 -1/27/20,0.016666666666666666,9973.171223862553,26.746592715725946,0.08218342172213045 -1/28/20,0.016666666666666666,9967.880565643929,32.00164212109187,0.11779223497955642 -1/29/20,0.016666666666666666,9962.592714061611,37.24752017512499,0.15976576326387115 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b/out/COVID-19-SEIR-data.csv index 4b2d494..81ae1a4 100644 --- a/out/COVID-19-SEIR-data.csv +++ b/out/COVID-19-SEIR-data.csv @@ -3,4 +3,5 @@ Gamma: 0.001 Mu: 0.0009999999999999992 Sigma: 0.005265008086429555 R0: 46.4494661074415 -Predicted I: 1267.3615656181303, Actual I: 1320.7366666666667
\ No newline at end of file +Predicted I: 1267.3615656181303 +Actual I: 1320.7366666666667
\ No newline at end of file diff --git a/out/COVID-19-SIR-data.csv b/out/COVID-19-SIR-data.csv index a0805e1..a3e4ce6 100644 --- a/out/COVID-19-SIR-data.csv +++ b/out/COVID-19-SIR-data.csv @@ -1,4 +1,5 @@ -Beta: 0.11506051868918243 -Gamma: 0.004484787817138545 -R0: 25.65573297570077 -Predicted I: 1266.8105911330124, Actual I: 1320.7366666666667
\ No newline at end of file +Beta: 0.11506078739615723 +Gamma: 0.004484934156558218 +R0: 25.654955765160217 +Predicted I: 1266.8203435457365 +Actual I: 1320.7366666666667
\ No newline at end of file diff --git a/out/COVID-19-SIR-prediction.csv b/out/COVID-19-SIR-prediction.csv index dda0000..b6a6306 100644 --- a/out/COVID-19-SIR-prediction.csv +++ b/out/COVID-19-SIR-prediction.csv @@ -1,78 +1,78 @@ ,Actual,S,I,R 1/22/20,0.0033333333333333335,9999.666666666666,0.33333333333333337,0.0 -1/23/20,0.0033333333333333335,9999.626113483311,0.3723057932824626,0.0015807234055033998 -1/24/20,0.006666666666666667,9999.580819471055,0.4158342816934694,0.003346247251000438 -1/25/20,0.006666666666666667,9999.530230573782,0.46445125535619813,0.00531817086165759 -1/26/20,0.016666666666666666,9999.473709826556,0.5187688441820978,0.007521329263086074 -1/27/20,0.016666666666666666,9999.410196574465,0.5798062772339272,0.009997148300881093 -1/28/20,0.016666666666666666,9999.339138930427,0.6480939379280791,0.012767131645821241 -1/29/20,0.016666666666666666,9999.260060733477,0.7240894731817856,0.01584979334159779 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+4/7/20,1320.7366666666667,8677.945415242773,1266.8203435457365,55.234241211489994 diff --git a/out/SARS-ESIR-data.csv b/out/SARS-ESIR-data.csv index 21d4469..7fa0191 100644 --- a/out/SARS-ESIR-data.csv +++ b/out/SARS-ESIR-data.csv @@ -1,5 +1,6 @@ -Beta: 0.2367418297398915 -Gamma: 0.08679182290949222 -Mu: 0.10967338538708958 -R0: 1.205006381498899 -Predicted I: 934.6265172952101, Actual I: 877.5
\ No newline at end of file +Beta: 0.2367380660038712 +Gamma: 0.08679089871294347 +Mu: 0.10967080829342284 +R0: 1.2050086992077278 +Predicted I: 934.6300578153925 +Actual I: 877.5
\ No newline at end of file diff --git a/out/SARS-ESIR-prediction.csv b/out/SARS-ESIR-prediction.csv index 53f7c9b..37ecdf5 100644 --- a/out/SARS-ESIR-prediction.csv +++ b/out/SARS-ESIR-prediction.csv @@ -1,77 +1,77 @@ ,Actual,S,I,R 4/10/03,499.0,9500.0,500.0,0.0 -4/11/03,529.5,9444.227075391838,514.0807218021808,41.692202805979804 -4/12/03,554.0,9391.905808241256,527.8835492084675,80.21064255027629 -4/14/03,595.0,9342.737831622848,541.4072053704581,115.85496300669492 -4/15/03,616.0,9296.461524712588,554.6500653009963,148.88840998641558 -4/16/03,634.0,9252.833038871782,567.6114509240942,179.55551020412332 -4/17/03,648.5,9211.626297647057,580.2916310749339,208.0820712780086 -4/18/03,679.0,9172.632996770366,592.6918214998664,234.67518172976713 -4/19/03,679.0,9135.662331729156,604.8142120510969,259.52345621974825 -4/21/03,701.0,9100.538906279773,616.661803432948,282.7992902872789 -4/22/03,717.0,9067.13469857277,628.2339699615961,304.63133146563365 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b/out/SARS-Linear-data.csv index a322350..f41c322 100644 --- a/out/SARS-Linear-data.csv +++ b/out/SARS-Linear-data.csv @@ -1,4 +1,5 @@ -Beta: 0.00225573366659839 -Gamma: 0.01741524200420521 -R0: 0.12952640371312119 -Predicted I: 946.0965063014658, Actual I: 877.5
\ No newline at end of file +Beta: 0.002255721398145891 +Gamma: 0.017414910100826592 +R0: 0.12952816782205634 +Predicted I: 946.1041288549815 +Actual I: 877.5
\ No newline at end of file diff --git a/out/SARS-Linear-prediction.csv b/out/SARS-Linear-prediction.csv index d5f8509..0b3866e 100644 --- a/out/SARS-Linear-prediction.csv +++ b/out/SARS-Linear-prediction.csv @@ -1,77 +1,77 @@ ,Actual,S,I,R 4/10/03,499.0,9500.0,500.0,0.0 -4/11/03,529.5,9478.594681592454,512.5877002660018,8.817618141544223 -4/12/03,554.0,9457.237593461185,524.9102776965382,17.852128842276684 -4/14/03,595.0,9435.928626930277,536.9724293164429,27.098943753279666 -4/15/03,616.0,9414.667673579052,548.7787404283372,36.55358599260962 -4/16/03,634.0,9393.45462522877,560.3337228510325,46.21165192019811 -4/17/03,648.5,9372.289373942072,571.6418164995505,56.06880955837544 -4/18/03,679.0,9351.171812023005,582.7073893851227,66.12079859187072 -4/19/03,679.0,9330.101832016997,593.5347376151906,76.36343036781183 -4/21/03,701.0,9309.07932671087,604.1280853934052,86.79258789572535 -4/22/03,717.0,9288.104189132835,614.4915850196279,97.40422584753672 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b/out/SARS-SEIR-data.csv index 36fe951..6170d61 100644 --- a/out/SARS-SEIR-data.csv +++ b/out/SARS-SEIR-data.csv @@ -3,4 +3,5 @@ Gamma: 0.001 Mu: 0.001 Sigma: 0.5156784257190153 R0: 12.83932927130887 -Predicted I: 1009.5304659757634, Actual I: 877.5
\ No newline at end of file +Predicted I: 1009.5304659757634 +Actual I: 877.5
\ No newline at end of file diff --git a/out/SARS-SIR-data.csv b/out/SARS-SIR-data.csv index d6e9dfa..de7798e 100644 --- a/out/SARS-SIR-data.csv +++ b/out/SARS-SIR-data.csv @@ -1,4 +1,5 @@ Beta: 0.031663066064741584 Gamma: 0.018520041050816886 R0: 1.7096650044058612 -Predicted I: 1006.3748700651734, Actual I: 877.5
\ No newline at end of file +Predicted I: 1006.3748700651734 +Actual I: 877.5
\ No newline at end of file @@ -148,7 +148,7 @@ class Learner(object): df = compose_df(prediction, extended_actual, correction_factor, new_index) with open(f'out/{args.disease}-{args.mode}-data.csv', 'w+') as file: file.write(f'Beta: {beta}\nGamma: {gamma}\nR0: {beta/gamma}\n') - file.write(f'Predicted I: {prediction.y[1][-1] * int(args.popmodel)}, Actual I: {extended_actual[-1] * correction_factor}') + file.write(f'Predicted I: {prediction.y[1][-1] * int(args.popmodel)}\nActual I: {extended_actual[-1] * correction_factor}') elif args.mode == 'SIR': optimal = minimize( loss_sir, @@ -164,7 +164,7 @@ class Learner(object): df = compose_df(prediction, extended_actual, correction_factor, new_index) with open(f'out/{args.disease}-{args.mode}-data.csv', 'w+') as file: file.write(f'Beta: {beta}\nGamma: {gamma}\nR0: {beta/gamma}\n') - file.write(f'Predicted I: {prediction.y[1][-1] * int(args.popmodel)}, Actual I: {extended_actual[-1] * correction_factor}') + file.write(f'Predicted I: {prediction.y[1][-1] * int(args.popmodel)}\nActual I: {extended_actual[-1] * correction_factor}') elif args.mode == 'ESIR': optimal = minimize( loss_esir, @@ -180,7 +180,7 @@ class Learner(object): df = compose_df(prediction, extended_actual, correction_factor, new_index) with open(f'out/{args.disease}-{args.mode}-data.csv', 'w+') as file: file.write(f'Beta: {beta}\nGamma: {gamma}\nMu: {mu}\nR0: {beta/(gamma + mu)}\n') - file.write(f'Predicted I: {prediction.y[1][-1] * int(args.popmodel)}, Actual I: {extended_actual[-1] * correction_factor}') + file.write(f'Predicted I: {prediction.y[1][-1] * int(args.popmodel)}\nActual I: {extended_actual[-1] * correction_factor}') elif args.mode == 'SEIR': # exposed_data = self.load_exposed(self.country) @@ -198,7 +198,7 @@ class Learner(object): df = compose_df(prediction, extended_actual, correction_factor, new_index) with open(f'out/{args.disease}-{args.mode}-data.csv', 'w+') as file: file.write(f'Beta: {beta}\nGamma: {gamma}\nMu: {mu}\nSigma: {sigma}\nR0: {(beta * sigma)/((mu + gamma) * (mu + sigma))}\n') - file.write(f'Predicted I: {prediction.y[1][-1] * int(args.popmodel)}, Actual I: {extended_actual[-1] * correction_factor}') + file.write(f'Predicted I: {prediction.y[1][-1] * int(args.popmodel)}\nActual I: {extended_actual[-1] * correction_factor}') fig, ax = plt.subplots(figsize=(15, 10)) ax.set_title(f'{args.disease} cases over time ({args.mode} Model)') df.plot(ax=ax) |
