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| 1 | +# Week 3: Estimate superspreading and simulate transmission chains |
| 2 | + |
| 3 | +<!-- visible for instructors only --> |
| 4 | +<!-- practical-week.md is generated from practical-week.qmd. Please edit that file --> |
| 5 | +<!-- commit .md and .qmd files together --> |
| 6 | + |
| 7 | +Welcome! |
| 8 | + |
| 9 | +A reminder of our Code of Conduct: |
| 10 | +<https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md> |
| 11 | + |
| 12 | +# Practical |
| 13 | + |
| 14 | +<!-- visible for learners and instructors at practical --> |
| 15 | + |
| 16 | +Before your start, as a group: - Create one copy of the Posit Cloud |
| 17 | +project `<paste link>`. - Solve each challenge using the `Code chunk` as |
| 18 | +a guide. - Paste your figure and table outputs. - Write your answer to |
| 19 | +the questions. - Choose one person from your group to share your results |
| 20 | +with everyone. |
| 21 | + |
| 22 | +## Theme |
| 23 | + |
| 24 | +Estimate … using the following available inputs: |
| 25 | + |
| 26 | +- input 1 |
| 27 | +- input 2 |
| 28 | + |
| 29 | +As a group, Write your answer to these questions: |
| 30 | + |
| 31 | +- … phase? |
| 32 | +- … results expected? |
| 33 | +- Interpret: How would you communicate these results to a |
| 34 | + decision-maker? |
| 35 | +- Compare: What differences you identify from other group outputs? (if |
| 36 | + available) |
| 37 | + |
| 38 | +### Inputs |
| 39 | + |
| 40 | +| Group | Incidence | Link | |
| 41 | +|-------|---------------|---------------------------------------------------------------------------| |
| 42 | +| 1 | COVID 30 days | <https://epiverse-trace.github.io/tutorials-middle/data/covid_30days.rds> | |
| 43 | +| 2 | Ebola 35 days | | |
| 44 | +| 3 | Ebola 60 days | | |
| 45 | +| 4 | COVID 60 days | | |
| 46 | + |
| 47 | +| Disease | params | |
| 48 | +|---------|--------| |
| 49 | +| Ebola | … | |
| 50 | +| COVID | … | |
| 51 | + |
| 52 | +### Solution |
| 53 | + |
| 54 | +<!-- visible for instructors and learners after practical (solutions) --> |
| 55 | + |
| 56 | +#### Code |
| 57 | + |
| 58 | +``` r |
| 59 | +# Load packages ----------------------------------------------------------- |
| 60 | +library(epiparameter) |
| 61 | +library(EpiNow2) |
| 62 | +library(tidyverse) |
| 63 | + |
| 64 | +# Read reported cases ----------------------------------------------------- |
| 65 | + |
| 66 | +# runnable howto-like |
| 67 | +``` |
| 68 | + |
| 69 | +#### Outputs |
| 70 | + |
| 71 | +##### Group 4: COVID 60 days |
| 72 | + |
| 73 | +With reporting delay plus Incubation time: |
| 74 | +<img src="https://hackmd.io/_uploads/S1q6ItjvC.png" style="width:50.0%" |
| 75 | +alt="image" /> |
| 76 | + |
| 77 | +With reporting delay plus Incubation time: |
| 78 | + |
| 79 | + > summary(covid60_epinow_delays) |
| 80 | + measure estimate |
| 81 | + <char> <char> |
| 82 | + 1: New infections per day 1987 (760 -- 4566) |
| 83 | + 2: Expected change in daily reports Likely decreasing |
| 84 | + 3: Effective reproduction no. 0.81 (0.43 -- 1.3) |
| 85 | + 4: Rate of growth -0.047 (-0.2 -- 0.092) |
| 86 | + 5: Doubling/halving time (days) -15 (7.5 -- -3.5) |
| 87 | + |
| 88 | +#### Interpretation |
| 89 | + |
| 90 | +Interpretation template: |
| 91 | + |
| 92 | +- From the summary of our analysis we see that the expected change in |
| 93 | + reports is `Likely decreasing` with the estimated new infections, on |
| 94 | + average, of `1987` with 90% credible interval of `760` to `4566`. |
| 95 | + |
| 96 | +- … |
| 97 | + |
| 98 | +Interpretation Helpers: |
| 99 | + |
| 100 | +- About the effective reproduction number: |
| 101 | + - An Rt greater than 1 implies an increase in cases or an epidemic. |
| 102 | + - An Rt less than 1 implies a decrease in cases or extinction. |
| 103 | +- … |
| 104 | + |
| 105 | +# end |
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