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R analysis code; paper; README Mar 9, 2020
beast update xml Mar 17, 2020
paper update paper Mar 17, 2020
README.md Update README.md Mar 10, 2020

README.md

Code to reproduce analyses in "Genomic epidemiology of a densely sampled COVID19 outbreak in China"

Important files:

  • beast/seir.xml: Main results using PhyDyn package and SEIJR model
    • Sequence data can not be included in the xml but can be retrieved from GISAID
  • R/eda1.R: Exploratory data analysis and outlier detection using treedater
  • Other scripts in R/ will reproduce tables, figures, RTT

Sequences:

                Sequence ID      GISAID ID
1                 WFCDC0001 EPI_ISL_413691
2                 WFCDC0002 EPI_ISL_413692
3                 WFCDC0003 EPI_ISL_413693
4                 WFCDC0004 EPI_ISL_413694
5                 WFCDC0012 EPI_ISL_413697
6                 WFCDC0014 EPI_ISL_413711
7                 WFCDC0015 EPI_ISL_413729
8                 WFCDC0016 EPI_ISL_413746
9                 WFCDC0018 EPI_ISL_413748
10                WFCDC0019 EPI_ISL_413749
11                WFCDC0020 EPI_ISL_413750
12                WFCDC0021 EPI_ISL_413751
13                WFCDC0024 EPI_ISL_413753
14                WFCDC0026 EPI_ISL_413761
15                WFCDC0028 EPI_ISL_413791
16                WFCDC0029 EPI_ISL_413809
17                WFCDC0006 EPI_ISL_413695
18                WFCDC0009 EPI_ISL_413696
19                WFCDC0017 EPI_ISL_413747
20                WFCDC0023 EPI_ISL_413752
21     Australia/VIC01/2020 EPI_ISL_406844
22           Finland/1/2020 EPI_ISL_407079
23      Foshan/20SF207/2020 EPI_ISL_406534
24      Foshan/20SF210/2020 EPI_ISL_406535
25      France/IDF0373/2020 EPI_ISL_406597
26     Germany/BavPat1/2020 EPI_ISL_406862
27   Guangdong/20SF012/2020 EPI_ISL_403932
28   Guangdong/20SF014/2020 EPI_ISL_403934
29   Guangdong/20SF040/2020 EPI_ISL_403937
30   Guangdong/20SF201/2020 EPI_ISL_406538
31   Guangzhou/20SF206/2020 EPI_ISL_406533
32      Japan/AI/I-004/2020 EPI_ISL_407084
33       Nonthaburi/61/2020 EPI_ISL_403962
34       Nonthaburi/74/2020 EPI_ISL_403963
35   Shenzhen/SZTH-003/2020 EPI_ISL_406594
36         Singapore/1/2020 EPI_ISL_406973
37            Taiwan/2/2020 EPI_ISL_406031
38             USA-WA1/2020 EPI_ISL_404895
39             USA/AZ1/2020 EPI_ISL_406223
40             USA/CA1/2020 EPI_ISL_406034
41             USA/CA2/2020 EPI_ISL_406036
42             USA/IL1/2020 EPI_ISL_404253
43          Wuhan-Hu-1/2019 EPI_ISL_402125
44   Wuhan/HBCDC-HB-01/2019 EPI_ISL_402132
45 Wuhan/IPBCAMS-WH-01/2019 EPI_ISL_402123
46 Wuhan/IPBCAMS-WH-02/2019 EPI_ISL_403931
47 Wuhan/IPBCAMS-WH-03/2019 EPI_ISL_403930
48 Wuhan/IPBCAMS-WH-04/2019 EPI_ISL_403929
49    Wuhan/IVDC-HB-01/2019 EPI_ISL_402119
50    Wuhan/IVDC-HB-05/2019 EPI_ISL_402121
51          Wuhan/WH01/2019 EPI_ISL_406798
52          Wuhan/WH04/2020 EPI_ISL_406801
53    Wuhan/IVDC-HB-04/2020 EPI_ISL_402120

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