differences for PR #187

Author: actions-user

config.yaml

@@ -140,6 +140,14 @@ estimates <- EpiNow2::epinow(
 )
 ```
 
+``` output
+WARN [2025-09-16 12:37:04] epinow: There were 2 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 [2025-09-16 12:37:04] epinow: Examine the pairs() plot to diagnose sampling problems
+ - 
+```
+
 ::::::::::::::::::::::::::::::::: callout
 
 ### Do not wait for this to complete!
@@ -196,18 +204,36 @@ estimates <- EpiNow2::epinow(
   # Add observation model
   obs = EpiNow2::obs_opts(scale = obs_scale)
 )
+```
+
+``` output
+WARN [2025-09-16 12:42:08] 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 [2025-09-16 12:42:08] epinow: There were 500 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 [2025-09-16 12:42:08] epinow: Examine the pairs() plot to diagnose sampling problems
+ - 
+WARN [2025-09-16 12:42:09] epinow: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
+Running the chains for more iterations may help. See
+https://mc-stan.org/misc/warnings.html#bulk-ess - 
+WARN [2025-09-16 12:42:10] 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 - 
+```
 
+``` r
 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   20148 (13173 -- 30177)
+2:   Expected change in reports                   Stable
+3:   Effective reproduction no.       0.97 (0.77 -- 1.2)
+4:               Rate of growth -0.0099 (-0.09 -- 0.067)
+5: Doubling/halving time (days)         -70 (10 -- -7.7)
 ```
 
 
@@ -512,34 +538,21 @@ ebola_estimates <- EpiNow2::epinow(
   # horizon needs to be 14 days to create two week forecast (default is 7 days)
   forecast = EpiNow2::forecast_opts(horizon = 14)
 )
-```
 
-``` output
-WARN [2025-08-26 01:46:34] epinow: There were 6 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 [2025-08-26 01:46:38] 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 - 
-```
-
-``` r
 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          91 (48 -- 189)
+2:   Expected change in reports              Increasing
+3:   Effective reproduction no.        1.6 (1.2 -- 2.4)
+4:               Rate of growth 0.041 (0.0036 -- 0.087)
+5: Doubling/halving time (days)           17 (8 -- 190)
 ```
 
-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 (1.2 -- 2.4). The exponential growth rate of case numbers is 0.041 (0.0036 -- 0.087).
 
 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] 3.492157 2.822130 5.519427 3.704806 2.092871 1.705613 4.284163 3.869586
+ [9] 3.035544 2.764683
 ```
 
 ::::::::: 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 [2025-09-16 12:31:55] 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 [2025-09-16 12:31:55] epinow: Examine the pairs() plot to diagnose sampling problems
  - 
 ```