Let's discuss this transmissibility output [internal test]

[avallecam]

Goal 1.1: Intepret the outputs. Discuss as a group.

We estimated $R_{t}$, new infections, new reports, growth rate, and doubling/halving time using the following inputs:

• reported cases
• generation time
• reporting delay
• incubation period (with and without)

As a group, write:

• An interpretation of the effective reproduction number. Use the visual and numeric estimates (with their uncertainty) to justify your conclusion.
• What changes do you identify in the estimates and forecast when more delays are included? How would you explain this changes?

[avallecam]

Group 1: COVID 30 days

G1	Without Incubation time	With Incubation time
->

Without incubation time:

> summary(covid30_epinow)
                            measure              estimate
                             <char>                <char>
1:           New infections per day  7722 (5556 -- 10954)
2: Expected change in daily reports            Increasing
3:       Effective reproduction no.      1.5 (1.2 -- 1.9)
4:                   Rate of growth 0.095 (0.027 -- 0.17)
5:     Doubling/halving time (days)       7.3 (4.2 -- 25)

With incubation time:

> summary(covid30_epinow_delay)
                            measure               estimate
                             <char>                 <char>
1:           New infections per day  13193 (5129 -- 33668)
2: Expected change in daily reports      Likely increasing
3:       Effective reproduction no.      1.5 (0.92 -- 2.5)
4:                   Rate of growth 0.099 (-0.049 -- 0.26)
5:     Doubling/halving time (days)         7 (2.7 -- -14)

Reply your Interpretation and Discussion:

[avallecam]

Hi, first entry here!

[avallecam]

Group 2: Ebola 35 days

G2	Without Incubation time	With Incubation time
->

Without incubation time:

> summary(ebola35_epinow)
                            measure                estimate
                             <char>                  <char>
1:           New infections per day             8 (3 -- 18)
2: Expected change in daily reports                  Stable
3:       Effective reproduction no.       1.1 (0.49 -- 2.2)
4:                   Rate of growth -0.016 (-0.14 -- 0.096)
5:     Doubling/halving time (days)       -43 (7.2 -- -4.8)

With incubation time:

> summary(ebola35_epinow_delays)
                            measure               estimate
                             <char>                 <char>
1:           New infections per day            5 (0 -- 26)
2: Expected change in daily reports      Likely decreasing
3:       Effective reproduction no.     0.66 (0.13 -- 2.2)
4:                   Rate of growth -0.039 (-0.18 -- 0.12)
5:     Doubling/halving time (days)      -18 (5.5 -- -3.9)

Reply with your Interpretation and Discussion:

[avallecam]

new reply!

[avallecam]

Goal 1.2: Reproduce the output. Collaborative writing.

Instructions, as a group:

• Access the Posit Cloud project <paste link>
• Access the required Input Parameters
• Add the required delays for an appropriate estimate of the effective reproduction number
• REPORT: Reply pasting the code ready to run as a comment.

Input Data

1 COVID 30 dias

2 Ebola 35 dias

3 Ebola 60 dias

4 COVID 60 dias

Input Parameters

• Non-explicit input parameters could be accessed from historical outbreaks.

• Ebola:

  • The time difference between symptom onset and case report follows a Lognormal distribution with uncertainty. The mean follows a Normal distribution with mean = 4 and sd = 0.5. The standard deviation follows a Normal distribution with mean = 1 and sd = 0.5. Bound the distribution with max = 5.

• COVID

  • The time difference between symptom onset and case report follows a Gamma distribution with uncertainty. The mean follows a Normal distribution with mean = 2 and sd = 0.5. The standard deviation follows a Normal distribution with mean = 1 and sd = 0.5. Bound the distribution with a max = 5.