A tool to estimate Instantaneous Reproduction Number(Rt) for the pandemic
Project description
A tool to estimate Instantaneous Reproduction Number(Rt)
cal_r() provide real-time estimation of time-varying distribution of Rt and infected numbers from a range of epidemic observations (e.g., Onset or report cases).
It provides:
A wide range of observations;
R_t estimation taking into account the accuracy of time alignment and abrupt change;
A smooth R_t curve together with its posterior distribution.
Usage
dart = DARtTool.DARt(filename='input.csv')
dart.cal_r()
dart.plot()
Examples of input file
Input file should contain date and corresponding observations, the date should be sorted from the oldest to the latest. See 'Example_input.csv':
::
date newCasesByPublishDate
2021/1/1 53285
2021/1/2 57725
2021/1/3 54990
2021/1/4 58784
2021/1/5 60916
2021/1/6 62322
2021/1/7 52618
2021/1/8 68053
2021/1/9 59937
2021/1/10 54940
2021/1/11 46169
2021/1/12 45533
2021/1/13 47525
2021/1/14 48682
2021/1/15 55761
2021/1/16 41346
2021/1/17 38598
2021/1/18 37535
2021/1/19 33355
2021/1/20 38905
2021/1/21 37892
2021/1/22 40261
2021/1/23 33552
2021/1/24 30004
2021/1/25 22195
2021/1/26 20089
2021/1/27 25308
2021/1/28 28680
2021/1/29 29079
2021/1/30 23275
2021/1/31 21088
2021/2/1 18607
2021/2/2 16840
2021/2/3 19202
2021/2/4 20634
2021/2/5 19114
2021/2/6 18262
2021/2/7 15845
2021/2/8 14104
2021/2/9 12364
2021/2/10 13013
2021/2/11 13494
2021/2/12 15144
2021/2/13 13308
2021/2/14 10972
2021/2/15 9765
2021/2/16 10625
2021/2/17 12718
2021/2/18 12057
2021/2/19 12027
2021/2/20 10406
2021/2/21 9834
2021/2/22 10641
2021/2/23 8489
2021/2/24 9938
2021/2/25 9985
2021/2/26 8523
2021/2/27 7434
2021/2/28 6035
2021/3/1 5455
2021/3/2 6391
2021/3/3 6385
2021/3/4 6573
2021/3/5 5947
2021/3/6 6040
2021/3/7 5177
2021/3/8 4712
2021/3/9 5766
2021/3/10 5926
2021/3/11 6753
2021/3/12 6609
2021/3/13 5534
2021/3/14 4618
2021/3/15 5089
2021/3/16 5294
2021/3/17 5758
2021/3/18 6303
2021/3/19 4802
2021/3/20 5587
2021/3/21 5312
2021/3/22 5342
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