transmission-heterogeneity-results

This repository holds the results for the branching process model with imported cases. This includes generating serial interval for COVID-19, parsing data from raw COVID-19 cases data and reproducing figures from the paper. To reproduce the results, the branchpro package, which is provided in the link above, is required. The jupyter library is also required.

More details can be found in the paper:

• R. Creswell,^† D. Augustin,^† I. Bouros,^† H. J. Farm,^† S. Miao,^† A. Ahern,^† M. Robinson, A. Lemenuel-Diot, D. J. Gavaghan, B. C. Lambert and R. N. Thompson: “Heterogeneity in the onwards transmission risk between local and imported cases affects practical estimates of the time-dependent reproduction number,” Phil. Trans. R. Soc. A. 380: 20210308 (2022). ^†Joint first authors.

Reproduce all results (serial interval, parsed data for COVID-19 cases, figures)

To reproduce all results, including intermediate files:

make

To delete all files created:

make clean

Serial interval

To generate serial interval for COVID-19:

make serial_interval

To delete file of serial interval for COVID-19:

make clean_serial_interval

COVID-19 cases

To parse all data from raw COVID-19 cases:

make data

To parse specific data:

make X_data

where X is the name of region. A list of commands to parse the data are given below.

To delete files of parsed data:

make clean_data

List of commands to parse data

1. australia_data - to parse Australia's data
2. hainan_data - to parse Hainan's data
3. hawaii_data - to parse Hawaii's data
4. hong_kong_data - to parse Hong Kong's data
5. new_zealand_data - to parse New Zealand's data
6. ontario_data - to parse Ontario's data

For example, to parse Australia's data:

make australia_data

Calculate epsilon

The value of epsilon (relative transmissibility of imported cases) has been approximated for several territories where appropriate data is available. These calculations can be performed using

make calculate_epsilon

Figures

To reproduce all figures:

make figures

The appropriate COVID-19 data and serial intervals generated as described above are required to reproduce the figures.

To reproduce specfic figure(s):

make figX

where X is the figure number. A list of commands to reproduce the figures are given below.

To delete all figures, except the schematic figure (Figure_1_schematic.pdf):

make clean_figures

List of commands to reproduce figures

1. fig2_fig3 - to reproduce Figure 2 and Figure 3
2. fig4 - to reproduce Figure 4
3. figS1_figS2 - to reproduce Figure S1 and Figure S2
4. figS3 - to reproduce Figure S3
5. figS4 - to reproduce Figure S4
6. figS5_figS6 - to reproduce Figure S5 and Figure S6
7. figS7 - to reproduce Figure S7
8. figS8 - to reproduce Figure S8

Figure_1_schematic.pdf is not reproducible as it is a schematic figure, not created from data.

For example, to reproduce Figure 2 and Figure 3:

make fig2_fig3