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| 1 | +# Week 2: Name |
| 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 | +<!-- does not work for instructors text messages --> |
| 7 | +<!-- works for text on PDF and MD only --> |
| 8 | + |
| 9 | +This practical is based in the following tutorial episodes: |
| 10 | + |
| 11 | +- <link/episode> |
| 12 | +- <link/episode> |
| 13 | + |
| 14 | +Welcome! |
| 15 | + |
| 16 | +- A reminder of our Code of Conduct: |
| 17 | +- <https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md> |
| 18 | +- If you experience or witness unacceptable behaviour, or have any other |
| 19 | + concerns, please report by email or online form available at the “How |
| 20 | + to report a violation” section. |
| 21 | +- To report an issue involving one of the organisers, please use the |
| 22 | + LSHTM’s Report and Support tool, where your concern will be triaged by |
| 23 | + a member of LSHTM’s Equity and Diversity Team. |
| 24 | +- <https://reportandsupport.lshtm.ac.uk/> |
| 25 | + |
| 26 | +Roll call: |
| 27 | + |
| 28 | +- Group 1: …, … |
| 29 | +- Group 2: …, … |
| 30 | +- Group 3: …, … |
| 31 | +- Group 4: …, … |
| 32 | +- Group 5: …, … |
| 33 | +- Group 6: …, … |
| 34 | + |
| 35 | +# Practical |
| 36 | + |
| 37 | +<!-- visible for learners and instructors at practical --> |
| 38 | + |
| 39 | +This practical has two activities. |
| 40 | + |
| 41 | +Before your start, as a group: |
| 42 | + |
| 43 | +- Create one copy of the Posit Cloud project `<paste link>`. |
| 44 | +- Solve each challenge using the `Code chunk` as a guide. |
| 45 | +- Paste your figure and table outputs. |
| 46 | +- Write your answer to the questions. |
| 47 | +- Choose one person from your group to share your results with everyone. |
| 48 | + |
| 49 | +During the practical, instead of copy-paste, we encourage learners to |
| 50 | +increase their fluency writing R by using: |
| 51 | + |
| 52 | +- Tab key <kbd>↹</kbd> for [code completion |
| 53 | + feature](https://support.posit.co/hc/en-us/articles/205273297-Code-Completion-in-the-RStudio-IDE) |
| 54 | + and [possible arguments |
| 55 | + displayed](https://docs.posit.co/ide/user/ide/guide/code/console.html). |
| 56 | +- The double-colon `package::function()` notation. This helps us |
| 57 | + remember package functions and avoid namespace conflicts. |
| 58 | +- [R |
| 59 | + shortcuts](https://positron.posit.co/keyboard-shortcuts.html#r-shortcuts): |
| 60 | + - `Cmd/Ctrl`+`Shift`+`M` to Insert the pipe operator (`|>` or `%>%`) |
| 61 | + - `Alt`+`-` to Insert the assignment operator (`<-`) |
| 62 | +- The `help()` function or `?` operator to access function reference |
| 63 | + manual. |
| 64 | + |
| 65 | +# Paste your !Error messages here |
| 66 | + |
| 67 | + |
| 68 | + |
| 69 | + |
| 70 | + |
| 71 | + |
| 72 | +## Activity 1: Theme |
| 73 | + |
| 74 | +Estimate … using the following available inputs: |
| 75 | + |
| 76 | +- input 1 |
| 77 | +- input 2 |
| 78 | + |
| 79 | +As a group, Write your answer to these questions: |
| 80 | + |
| 81 | +- … phase? |
| 82 | +- … results expected? |
| 83 | +- Interpret: How would you communicate these results to a |
| 84 | + decision-maker? |
| 85 | +- Compare: What differences you identify from other group outputs? (if |
| 86 | + available) |
| 87 | + |
| 88 | +### Inputs |
| 89 | + |
| 90 | +| Group | Incidence | Link | |
| 91 | +|-------|---------------|---------------------------------------------------------------------------| |
| 92 | +| 1 | COVID 30 days | <https://epiverse-trace.github.io/tutorials-middle/data/covid_30days.rds> | |
| 93 | +| 2 | Ebola 35 days | | |
| 94 | +| 3 | Ebola 60 days | | |
| 95 | +| 4 | COVID 60 days | | |
| 96 | + |
| 97 | +| Disease | params | |
| 98 | +|---------|--------| |
| 99 | +| Ebola | … | |
| 100 | +| COVID | … | |
| 101 | + |
| 102 | +### Solution |
| 103 | + |
| 104 | +<!-- visible for instructors and learners after practical (solutions) --> |
| 105 | + |
| 106 | +#### Code |
| 107 | + |
| 108 | +``` r |
| 109 | +# Load packages ----------------------------------------------------------- |
| 110 | +library(epiparameter) |
| 111 | +library(EpiNow2) |
| 112 | +library(tidyverse) |
| 113 | + |
| 114 | +# Read reported cases ----------------------------------------------------- |
| 115 | + |
| 116 | +# runnable howto-like |
| 117 | +``` |
| 118 | + |
| 119 | +#### Outputs |
| 120 | + |
| 121 | +##### Group 4: COVID 60 days |
| 122 | + |
| 123 | +With reporting delay plus Incubation time: |
| 124 | +<img src="https://hackmd.io/_uploads/S1q6ItjvC.png" style="width:50.0%" |
| 125 | +alt="image" /> |
| 126 | + |
| 127 | +With reporting delay plus Incubation time: |
| 128 | + |
| 129 | + > summary(covid60_epinow_delays) |
| 130 | + measure estimate |
| 131 | + <char> <char> |
| 132 | + 1: New infections per day 1987 (760 -- 4566) |
| 133 | + 2: Expected change in daily reports Likely decreasing |
| 134 | + 3: Effective reproduction no. 0.81 (0.43 -- 1.3) |
| 135 | + 4: Rate of growth -0.047 (-0.2 -- 0.092) |
| 136 | + 5: Doubling/halving time (days) -15 (7.5 -- -3.5) |
| 137 | + |
| 138 | +#### Interpretation |
| 139 | + |
| 140 | +Interpretation template: |
| 141 | + |
| 142 | +- From the summary of our analysis we see that the expected change in |
| 143 | + reports is `Likely decreasing` with the estimated new infections, on |
| 144 | + average, of `1987` with 90% credible interval of `760` to `4566`. |
| 145 | + |
| 146 | +- … |
| 147 | + |
| 148 | +Interpretation Helpers: |
| 149 | + |
| 150 | +- About the effective reproduction number: |
| 151 | + - An Rt greater than 1 implies an increase in cases or an epidemic. |
| 152 | + - An Rt less than 1 implies a decrease in cases or extinction. |
| 153 | +- … |
| 154 | + |
| 155 | +# Continue your learning path |
| 156 | + |
| 157 | +<!-- Suggest learners to Epiverse-TRACE documentation or external resources ---> |
| 158 | + |
| 159 | +Where |
| 160 | + |
| 161 | +- <link> |
| 162 | + |
| 163 | +# end |
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