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fix room for all pending scripts
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‎instructors/03-practical-tutors.qmd‎

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Original file line numberDiff line numberDiff line change
@@ -57,7 +57,7 @@ Estimate extent of individual-level variation (i.e. the dispersion parameter) of
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- Line list of cases
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- Contact tracing data
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As a group, Write your answers to these questions:
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Within your room, Write your answers to these questions:
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- From descriptive and estimation steps:
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- What set has more infections related to fewer clusters in the contact network?
@@ -67,11 +67,11 @@ As a group, Write your answers to these questions:
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- What is the proportion of new cases originating from a cluster of at least 10 cases?
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- Would you recommend a backward tracing strategy?
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- Interpret: How would you communicate these results to a decision-maker?
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- Compare: What differences do you identify from other group outputs? (if available)
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- Compare: What differences do you identify from other room outputs? (if available)
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### Inputs
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| Group | Data |
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| Room | Data |
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|---|---|
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| 1 | <https://epiverse-trace.github.io/tutorials-middle/data/set-01-contacts.rds>, <https://epiverse-trace.github.io/tutorials-middle/data/set-01-linelist.rds> |
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| 2 | <https://epiverse-trace.github.io/tutorials-middle/data/set-02-contacts.rds>, <https://epiverse-trace.github.io/tutorials-middle/data/set-02-linelist.rds> |
@@ -90,7 +90,7 @@ Use the file `03-practical-activity-1.R`
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### Your Answers
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Group 1
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Room 1
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| output | paste here |
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|---|---|
@@ -114,7 +114,7 @@ Write your answers to the questions above:
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------------------------
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Group 2
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Room 2
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| output | paste here |
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|---|---|
@@ -139,7 +139,7 @@ Write your answers to the questions above:
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------------------------
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Group 3
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Room 3
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| output | paste here |
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|---|---|
@@ -164,7 +164,7 @@ Write your answers to the questions above:
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------------------------
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Group 4
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Room 4
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| output | paste here |
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|---|---|
@@ -189,7 +189,7 @@ Write your answers to the questions above:
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------------------------
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Group 5
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Room 5
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| output | paste here |
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|---|---|
@@ -214,7 +214,7 @@ Write your answers to the questions above:
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------------------------
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Group 6
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Room 6
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| output | paste here |
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|---|---|
@@ -253,26 +253,26 @@ Write your answers to the questions above:
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#### Outputs
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Group 1
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Room 1
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| contact network | histogram of secondary cases |
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| -------- | -------- |
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| ![Untitled-1](https://hackmd.io/_uploads/H1DVLbsTyx.png) | ![Untitled](https://hackmd.io/_uploads/BkW48Wo6yg.png) |
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Group 2
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Room 2
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| contact network | histogram of secondary cases |
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| -------- | -------- |
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| ![Untitled](https://hackmd.io/_uploads/Hkhg8WspJg.png) | ![Untitled-1](https://hackmd.io/_uploads/HyIlUWopJx.png) |
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Group 3
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Room 3
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| contact network | histogram of secondary cases |
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| -------- | -------- |
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| ![Untitled](https://hackmd.io/_uploads/HkzkUZjpyx.png) | ![Untitled-1](https://hackmd.io/_uploads/SkjCBZjpJe.png) |
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```r
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#> R k prop_5 prop_10 prop_25
@@ -311,7 +311,7 @@ Estimate the potential for large outbreaks that could occur based on 1000 simula
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- Basic reproduction number
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- Dispersion parameter
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As a group, Write your answers to these questions:
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Within your room, Write your answers to these questions:
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- You have been assigned to explore `Chain ID`. From the output data frame, describe:
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- How many generations there are.
@@ -321,11 +321,11 @@ As a group, Write your answers to these questions:
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- What is the maximum size of chain? (The cumulative number of case)
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- What is the maximum length of chain? (The number of days until the chain stops)
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- Interpret: How would you communicate these results to a decision-maker?
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- Compare: What differences do you identify from other group outputs? (if available)
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- Compare: What differences do you identify from other room outputs? (if available)
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### Inputs
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| Group | Parameters | Chain ID |
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| Room | Parameters | Chain ID |
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|---|---|---|
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| 1 | R = 0.8, k = 0.01 | 957 |
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| 2 | R = 0.8, k = 0.1 | 281 |
@@ -343,7 +343,7 @@ Use the file `03-practical-activity-2.R`
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### Your Answers
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Group 1
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Room 1
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| output | paste here |
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|---|---|
@@ -365,7 +365,7 @@ Write your answers to the questions above:
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------------------------
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Group 2
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Room 2
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| output | paste here |
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|---|---|
@@ -387,7 +387,7 @@ Write your answers to the questions above:
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------------------------
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Group 3
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Room 3
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| output | paste here |
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|---|---|
@@ -409,7 +409,7 @@ Write your answers to the questions above:
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------------------------
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Group 4
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Room 4
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| output | paste here |
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|---|---|
@@ -431,7 +431,7 @@ Write your answers to the questions above:
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------------------------
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Group 5
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Room 5
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| output | paste here |
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|---|---|
@@ -453,7 +453,7 @@ Write your answers to the questions above:
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------------------------
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Group 6
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Room 6
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| output | paste here |
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|---|---|
@@ -489,20 +489,20 @@ Write your answers to the questions above:
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#### Outputs
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Group 1
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Room 1
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| contact network | secondary cases | simulated chains |
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| -------- | -------- | -------- |
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| ![Untitled-1](https://hackmd.io/_uploads/H1DVLbsTyx.png) | ![Untitled](https://hackmd.io/_uploads/BkW48Wo6yg.png) | ![image](https://hackmd.io/_uploads/Sy3x3MNAJe.png) |
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Group 2
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Room 2
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| contact network | secondary cases | simulated chains |
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| -------- | -------- | -------- |
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| ![Untitled](https://hackmd.io/_uploads/Hkhg8WspJg.png) | ![Untitled-1](https://hackmd.io/_uploads/HyIlUWopJx.png) | ![image](https://hackmd.io/_uploads/rkw-hGN0kl.png) |
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Room 3
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| contact network | secondary cases | simulated chains |
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| -------- | -------- | -------- |
@@ -546,7 +546,7 @@ Interpretation Helpers:
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From the plot of cumulative cases by day for each simulated chain:
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| Group | Parameters | Number of Chains Above 100 | Max Chain Size | Max Chain Length |
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| Room | Parameters | Number of Chains Above 100 | Max Chain Size | Max Chain Length |
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|-------|--------------------|-----------------------------|----------------|------------------|
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| 1 | R = 0.8, k = 0.01 | 10 | ~200 | ~20 days |
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| 2 | R = 0.8, k = 0.1 | 8 | ~420 | ~60 days |

‎instructors/04-practical-tutors.qmd‎

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Original file line numberDiff line numberDiff line change
@@ -59,17 +59,17 @@ Generate disease trajectories of infectious subjects and new infections using th
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- Age group of the infectious population
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- Disease parameters (basic reproduction number, pre infectious period, infectious period)
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As a group, Write your answers to these questions:
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Within your room, Write your answers to these questions:
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- What is the location (time) and size of epidemic peak for infectious subjects in each age group?
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- What is the number of new infections at the epidemic peak?
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- Change the basic reproduction number to 1.1 and 3. Are the changes in location (time) and size of the peak of new infections as expected? (based on the concept definition of reproduction number)
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- Interpret: How would you communicate these results to a decision-maker?
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- Compare: What differences do you identify from other group outputs? (if available)
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- Compare: What differences do you identify from other room outputs? (if available)
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### Inputs
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| Group | Country | Survey Link |
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| Room | Country | Survey Link |
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|---|---|---|
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| 1 | Italy | <https://doi.org/10.5281/zenodo.3874557> |
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| 2 | Vietnam | <https://doi.org/10.5281/zenodo.3874802> |
@@ -95,7 +95,7 @@ Use the file `04-practical-activity-1.R`
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### Your Answers
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Group 1
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Room 1
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| output | paste here |
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|---|---|
@@ -117,7 +117,7 @@ Write your answers to the questions above:
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------------------------
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Group 2
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Room 2
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| output | paste here |
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|---|---|
@@ -139,7 +139,7 @@ Write your answers to the questions above:
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------------------------
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Group 3
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Room 3
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| output | paste here |
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|---|---|
@@ -220,16 +220,16 @@ Compare the disease trajectories of new infections against an intervention using
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- Type of intervention (on contacts, on transmission, or vaccination)
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- Reduction effect or rate of vaccination
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As a group, write your answers to these questions:
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Within your room, write your answers to these questions:
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- How does the time to start of the intervention (early/late) impact the timing and size of the peak of new infectious individuals?
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- Is the observed impact of the intervention in these results expected?
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- Interpret: How would you communicate these results to a decision-maker?
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- Compare: What differences do you identify from other group outputs? (if available)
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- Compare: What differences do you identify from other room outputs? (if available)
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### Inputs
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| Group | Intervention | Early Start | Late Start | Duration (days) | Effect (Reduction or Rate) |
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| Room | Intervention | Early Start | Late Start | Duration (days) | Effect (Reduction or Rate) |
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|---|---|---|---|---|---|
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| 1 | School | 100 | 200 | 100 | Age 0–19: 0.5; Age 20+: 0.01 |
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| 2 | Mask | 100 | 200 | 200 | All ages: 0.163 |
@@ -244,7 +244,7 @@ Use the file `04-practical-activity-2.R`
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### Your Answers
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Group 1
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Room 1
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| output | paste here |
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|---|---|
@@ -266,7 +266,7 @@ Write your answers to the questions above:
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------------------------
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Group 2
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Room 2
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| output | paste here |
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|---|---|
@@ -288,7 +288,7 @@ Write your answers to the questions above:
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------------------------
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Group 3
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| output | paste here |
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|---|---|
@@ -342,14 +342,14 @@ Interpretation Helpers:
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Combine two intervention in the same simulation and compare the disease trajectories of new infections against the baseline or only one intervention. Use the intervention parameters above.
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As a group, Write your answers to these questions:
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Within your room, Write your answers to these questions:
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- Interpret: How would you communicate these results to a decision-maker?
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- Compare: What differences do you identify from other group outputs? (if available)
348+
- Compare: What differences do you identify from other room outputs? (if available)
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### Inputs
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| Group | Combine interventions | Compare against |
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| Room | Combine interventions | Compare against |
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|---|---|---|
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| 1 | School closure AND Vaccine | School closure |
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| 2 | Mask mandate AND School contact | Mask mandate |
@@ -366,7 +366,7 @@ Use the file `04-practical-activity-3.R`
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### Your Answers
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Group 1
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Room 1
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| output | paste here |
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|---|---|
@@ -388,7 +388,7 @@ Write your answers to the questions above:
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------------------------
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Group 2
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Room 2
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| output | paste here |
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|---|---|
@@ -410,7 +410,7 @@ Write your answers to the questions above:
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------------------------
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Group 3
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Room 3
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| output | paste here |
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|---|---|

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