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