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differences for PR #163 
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‎config.yaml

-86
This file was deleted.

‎create-forecast.md

+19-36
Original file line numberDiff line numberDiff line change
@@ -140,6 +140,14 @@ estimates <- EpiNow2::epinow(
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)
141141
```
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143+
``` output
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WARN [2025-04-01 07:26:53] epinow: There were 1 divergent transitions after warmup. See
145+
https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
146+
to find out why this is a problem and how to eliminate them. -
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WARN [2025-04-01 07:26:53] epinow: Examine the pairs() plot to diagnose sampling problems
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-
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```
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143151
::::::::::::::::::::::::::::::::: callout
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### Do not wait for this to complete!
@@ -196,28 +204,18 @@ estimates <- EpiNow2::epinow(
196204
# Add observation model
197205
obs = EpiNow2::obs_opts(scale = obs_scale)
198206
)
199-
```
200207

201-
``` output
202-
WARN [2025-03-28 11:25:34] epinow: There were 3 divergent transitions after warmup. See
203-
https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
204-
to find out why this is a problem and how to eliminate them. -
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WARN [2025-03-28 11:25:34] epinow: Examine the pairs() plot to diagnose sampling problems
206-
-
207-
```
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209-
``` r
210208
base::summary(estimates)
211209
```
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213211
``` output
214212
measure estimate
215213
<char> <char>
216-
1: New infections per day 20377 (13212 -- 31039)
214+
1: New infections per day 20260 (13179 -- 30734)
217215
2: Expected change in reports Stable
218-
3: Effective reproduction no. 0.98 (0.75 -- 1.2)
219-
4: Rate of growth -0.0086 (-0.097 -- 0.07)
220-
5: Doubling/halving time (days) -81 (9.9 -- -7.1)
216+
3: Effective reproduction no. 0.98 (0.76 -- 1.2)
217+
4: Rate of growth -0.009 (-0.093 -- 0.074)
218+
5: Doubling/halving time (days) -77 (9.4 -- -7.5)
221219
```
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223221

@@ -301,15 +299,6 @@ estimate_cases_to_deaths <- EpiNow2::estimate_secondary(
301299
)
302300
```
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304-
``` output
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WARN [2025-03-28 11:25:41] estimate_secondary (chain: 1): Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
306-
Running the chains for more iterations may help. See
307-
https://mc-stan.org/misc/warnings.html#bulk-ess -
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WARN [2025-03-28 11:25:41] estimate_secondary (chain: 1): Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
309-
Running the chains for more iterations may help. See
310-
https://mc-stan.org/misc/warnings.html#tail-ess -
311-
```
312-
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::::::::::::::::::::::::::::::::::::: callout
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@@ -534,17 +523,11 @@ ebola_estimates <- EpiNow2::epinow(
534523
```
535524

536525
``` output
537-
WARN [2025-03-28 11:26:28] epinow: There were 3 divergent transitions after warmup. See
526+
WARN [2025-04-01 07:31:18] epinow: There were 14 divergent transitions after warmup. See
538527
https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
539528
to find out why this is a problem and how to eliminate them. -
540-
WARN [2025-03-28 11:26:28] epinow: Examine the pairs() plot to diagnose sampling problems
529+
WARN [2025-04-01 07:31:18] epinow: Examine the pairs() plot to diagnose sampling problems
541530
-
542-
WARN [2025-03-28 11:26:31] epinow: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
543-
Running the chains for more iterations may help. See
544-
https://mc-stan.org/misc/warnings.html#bulk-ess -
545-
WARN [2025-03-28 11:26:32] epinow: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
546-
Running the chains for more iterations may help. See
547-
https://mc-stan.org/misc/warnings.html#tail-ess -
548531
```
549532

550533
``` r
@@ -554,14 +537,14 @@ summary(ebola_estimates)
554537
``` output
555538
measure estimate
556539
<char> <char>
557-
1: New infections per day 89 (48 -- 199)
540+
1: New infections per day 94 (50 -- 199)
558541
2: Expected change in reports Increasing
559-
3: Effective reproduction no. 1.6 (1.1 -- 2.4)
560-
4: Rate of growth 0.039 (0.0014 -- 0.089)
561-
5: Doubling/halving time (days) 18 (7.8 -- 500)
542+
3: Effective reproduction no. 1.7 (1.2 -- 2.4)
543+
4: Rate of growth 0.042 (0.0057 -- 0.086)
544+
5: Doubling/halving time (days) 16 (8 -- 120)
562545
```
563546

564-
The effective reproduction number $R_t$ estimate (on the last date of the data) is 1.6 (1.1 -- 2.4). The exponential growth rate of case numbers is 0.039 (0.0014 -- 0.089).
547+
The effective reproduction number $R_t$ estimate (on the last date of the data) is 1.7 (1.2 -- 2.4). The exponential growth rate of case numbers is 0.042 (0.0057 -- 0.086).
565548

566549
Visualize the estimates:
567550

‎delays-functions.md

+12-22
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@@ -161,8 +161,8 @@ generate(covid_serialint, times = 10)
161161
```
162162

163163
``` output
164-
[1] 3.933426 7.847474 7.855466 4.420870 5.829693 9.721162 3.174917 4.002916
165-
[9] 2.159129 8.985319
164+
[1] 2.389521 1.741558 4.221692 5.992384 3.749561 4.400516 2.750818
165+
[8] 1.827925 10.015363 8.185948
166166
```
167167

168168
::::::::: instructor
@@ -585,27 +585,7 @@ epinow_estimates_cgi <- epinow(
585585
generation_time = generation_time_opts(covid_serial_interval),
586586
delays = delay_opts(covid_incubation_time)
587587
)
588-
```
589-
590-
``` output
591-
WARN [2025-03-28 11:17:41] epinow: There were 500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 12. See
592-
https://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded -
593-
WARN [2025-03-28 11:17:41] epinow: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
594-
https://mc-stan.org/misc/warnings.html#bfmi-low -
595-
WARN [2025-03-28 11:17:41] epinow: Examine the pairs() plot to diagnose sampling problems
596-
-
597-
WARN [2025-03-28 11:17:42] epinow: The largest R-hat is NA, indicating chains have not mixed.
598-
Running the chains for more iterations may help. See
599-
https://mc-stan.org/misc/warnings.html#r-hat -
600-
WARN [2025-03-28 11:17:43] epinow: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
601-
Running the chains for more iterations may help. See
602-
https://mc-stan.org/misc/warnings.html#bulk-ess -
603-
WARN [2025-03-28 11:17:44] epinow: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
604-
Running the chains for more iterations may help. See
605-
https://mc-stan.org/misc/warnings.html#tail-ess -
606-
```
607588

608-
``` r
609589
base::plot(epinow_estimates_cgi)
610590
```
611591

@@ -748,7 +728,17 @@ epinow_estimates_egi <- epinow(
748728
generation_time = generation_time_opts(serial_interval_ebola),
749729
delays = delay_opts(incubation_period_ebola)
750730
)
731+
```
732+
733+
``` output
734+
WARN [2025-04-01 07:23:18] epinow: There were 2 divergent transitions after warmup. See
735+
https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
736+
to find out why this is a problem and how to eliminate them. -
737+
WARN [2025-04-01 07:23:18] epinow: Examine the pairs() plot to diagnose sampling problems
738+
-
739+
```
751740

741+
``` r
752742
plot(epinow_estimates_egi)
753743
```
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‎fig/create-forecast-rendered-unnamed-chunk-10-1.png

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‎fig/delays-functions-rendered-unnamed-chunk-16-1.png

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‎md5sum.txt

+17-17
Original file line numberDiff line numberDiff line change
@@ -1,18 +1,18 @@
11
"file" "checksum" "built" "date"
2-
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3-
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4-
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5-
"index.md" "32bc80d6f4816435cc0e01540cb2a513" "site/built/index.md" "2025-03-28"
6-
"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2025-03-28"
7-
"episodes/delays-access.Rmd" "d3c66680f2ac0cf0158a7ac0412c86a3" "site/built/delays-access.md" "2025-03-28"
8-
"episodes/quantify-transmissibility.Rmd" "0d6c92bd94a969f8661d0c26fdfdec52" "site/built/quantify-transmissibility.md" "2025-03-28"
9-
"episodes/delays-functions.Rmd" "0c5c40267d32e39a63d7f75aee9143e4" "site/built/delays-functions.md" "2025-03-28"
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12-
"episodes/superspreading-estimate.Rmd" "cd00e83816dc1bf867a8173f326358b5" "site/built/superspreading-estimate.md" "2025-03-28"
13-
"episodes/superspreading-simulate.Rmd" "8c0d9627c6ea746a6ddff139926c8664" "site/built/superspreading-simulate.md" "2025-03-28"
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"renv/profiles/lesson-requirements/renv.lock" "2b96d44749f98edb3029c09b87aad501" "site/built/renv.lock" "2025-03-28"
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"episodes/delays-access.Rmd" "d3c66680f2ac0cf0158a7ac0412c86a3" "site/built/delays-access.md" "2025-04-01"
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"episodes/quantify-transmissibility.Rmd" "0d6c92bd94a969f8661d0c26fdfdec52" "site/built/quantify-transmissibility.md" "2025-04-01"
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"episodes/delays-functions.Rmd" "0c5c40267d32e39a63d7f75aee9143e4" "site/built/delays-functions.md" "2025-04-01"
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‎network.html

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‎quantify-transmissibility.md

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@@ -470,6 +470,14 @@ estimates <- EpiNow2::epinow(
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)
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```
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473+
``` output
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WARN [2025-04-01 07:20:45] epinow: There were 1 divergent transitions after warmup. See
475+
https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
476+
to find out why this is a problem and how to eliminate them. -
477+
WARN [2025-04-01 07:20:45] epinow: Examine the pairs() plot to diagnose sampling problems
478+
-
479+
```
480+
473481
<!-- ```{r, message = FALSE,warning=FALSE, eval = TRUE, echo=FALSE} -->
474482
<!-- estimates <- EpiNow2::epinow( -->
475483
<!-- # reported cases -->
@@ -533,24 +541,24 @@ summary(estimates)
533541
```
534542

535543
``` output
536-
measure estimate
537-
<char> <char>
538-
1: New infections per day 7858 (4640 -- 13390)
539-
2: Expected change in reports Stable
540-
3: Effective reproduction no. 0.97 (0.73 -- 1.3)
541-
4: Rate of growth -0.012 (-0.11 -- 0.08)
542-
5: Doubling/halving time (days) -56 (8.7 -- -6.4)
544+
measure estimate
545+
<char> <char>
546+
1: New infections per day 7927 (4642 -- 12995)
547+
2: Expected change in reports Likely decreasing
548+
3: Effective reproduction no. 0.96 (0.72 -- 1.2)
549+
4: Rate of growth -0.012 (-0.11 -- 0.078)
550+
5: Doubling/halving time (days) -58 (8.9 -- -6.3)
543551
```
544552

545553
As these estimates are based on partial data, they have a wide uncertainty interval.
546554

547-
+ From the summary of our analysis we see that the expected change in reports is Stable with the estimated new infections 7858 (4640 -- 13390).
555+
+ From the summary of our analysis we see that the expected change in reports is Likely decreasing with the estimated new infections 7927 (4642 -- 12995).
548556

549-
+ The effective reproduction number $R_t$ estimate (on the last date of the data) is 0.97 (0.73 -- 1.3).
557+
+ The effective reproduction number $R_t$ estimate (on the last date of the data) is 0.96 (0.72 -- 1.2).
550558

551-
+ The exponential growth rate of case numbers is -0.012 (-0.11 -- 0.08).
559+
+ The exponential growth rate of case numbers is -0.012 (-0.11 -- 0.078).
552560

553-
+ The doubling time (the time taken for case numbers to double) is -56 (8.7 -- -6.4).
561+
+ The doubling time (the time taken for case numbers to double) is -58 (8.9 -- -6.3).
554562

555563
::::::::::::::::::::::::::::::::::::: callout
556564
### `Expected change in reports`

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