differences for PR #187

Author: actions-user

config.yaml

@@ -201,13 +201,13 @@ base::summary(estimates)
 ```
 
 ``` output
-                        measure                estimate
-                         <char>                  <char>
-1:       New infections per day  20091 (13574 -- 30897)
-2:   Expected change in reports       Likely decreasing
-3:   Effective reproduction no.      0.97 (0.77 -- 1.2)
-4:               Rate of growth -0.012 (-0.09 -- 0.071)
-5: Doubling/halving time (days)       -58 (9.7 -- -7.7)
+                        measure                  estimate
+                         <char>                    <char>
+1:       New infections per day    20164 (13954 -- 30149)
+2:   Expected change in reports                    Stable
+3:   Effective reproduction no.        0.97 (0.79 -- 1.2)
+4:               Rate of growth -0.0099 (-0.086 -- 0.061)
+5: Doubling/halving time (days)            -70 (11 -- -8)
 ```
 
 
@@ -291,6 +291,12 @@ estimate_cases_to_deaths <- EpiNow2::estimate_secondary(
 )
 ```
 
+``` output
+WARN [2025-09-24 14:04:18] estimate_secondary (chain: 1): Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
+Running the chains for more iterations may help. See
+https://mc-stan.org/misc/warnings.html#tail-ess - 
+```
+
 
 ::::::::::::::::::::::::::::::::::::: callout
 
@@ -515,12 +521,12 @@ ebola_estimates <- EpiNow2::epinow(
 ```
 
 ``` output
-WARN [2025-08-26 01:46:34] epinow: There were 6 divergent transitions after warmup. See
+WARN [2025-09-24 14:05:08] epinow: There were 5 divergent transitions after warmup. See
 https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
 to find out why this is a problem and how to eliminate them. - 
-WARN [2025-08-26 01:46:34] epinow: Examine the pairs() plot to diagnose sampling problems
+WARN [2025-09-24 14:05:08] epinow: Examine the pairs() plot to diagnose sampling problems
  - 
-WARN [2025-08-26 01:46:38] epinow: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
+WARN [2025-09-24 14:05:12] epinow: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
 Running the chains for more iterations may help. See
 https://mc-stan.org/misc/warnings.html#tail-ess - 
 ```
@@ -530,16 +536,16 @@ summary(ebola_estimates)
 ```
 
 ``` output
-                        measure               estimate
-                         <char>                 <char>
-1:       New infections per day         92 (49 -- 185)
-2:   Expected change in reports             Increasing
-3:   Effective reproduction no.       1.6 (1.2 -- 2.4)
-4:               Rate of growth 0.04 (0.0038 -- 0.083)
-5: Doubling/halving time (days)        17 (8.3 -- 180)
+                        measure                estimate
+                         <char>                  <char>
+1:       New infections per day          92 (47 -- 186)
+2:   Expected change in reports              Increasing
+3:   Effective reproduction no.        1.6 (1.1 -- 2.4)
+4:               Rate of growth 0.041 (0.0019 -- 0.086)
+5: Doubling/halving time (days)           17 (8 -- 360)
 ```
 
-The effective reproduction number $R_t$ estimate (on the last date of the data) is 1.6 (1.2 -- 2.4). The exponential growth rate of case numbers is 0.04 (0.0038 -- 0.083).
+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 0.041 (0.0019 -- 0.086).
 
 Visualize the estimates:
 

create-forecast.md

@@ -161,8 +161,8 @@ generate(covid_serialint, times = 10)
 ```
 
 ``` output
- [1]  3.133504  6.369584  2.651628 10.017361  1.305227  2.536725  2.996175
- [8]  7.880128  6.562764  5.961404
+ [1] 6.5005838 3.2863986 9.4190041 9.6313865 3.9843247 5.4318498 4.7479639
+ [8] 0.9639247 1.8253098 8.0700738
 ```
 
 ::::::::: instructor
@@ -588,12 +588,10 @@ epinow_estimates_cgi <- epinow(
 ```
 
 ``` output
-WARN [2025-08-26 01:35:59] epinow: There were 1 divergent transitions after warmup. See
+WARN [2025-09-24 13:54:40] epinow: There were 1 divergent transitions after warmup. See
 https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
 to find out why this is a problem and how to eliminate them. - 
-WARN [2025-08-26 01:35:59] epinow: There were 375 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 12. See
-https://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded - 
-WARN [2025-08-26 01:35:59] epinow: Examine the pairs() plot to diagnose sampling problems
+WARN [2025-09-24 13:54:40] epinow: Examine the pairs() plot to diagnose sampling problems
  - 
 ```
 
@@ -740,7 +738,17 @@ epinow_estimates_egi <- epinow(
   generation_time = generation_time_opts(serial_interval_ebola),
   delays = delay_opts(incubation_period_ebola)
 )
+```
+
+``` output
+WARN [2025-09-24 13:55:32] epinow: There were 1 divergent transitions after warmup. See
+https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
+to find out why this is a problem and how to eliminate them. - 
+WARN [2025-09-24 13:55:32] epinow: Examine the pairs() plot to diagnose sampling problems
+ - 
+```
 
+``` r
 plot(epinow_estimates_egi)
 ```