differences for PR #217

Author: actions-user

config.yaml

@@ -199,38 +199,25 @@ estimates <- EpiNow2::epinow(
 ```
 
 ``` output
-WARN [2025-10-17 16:09:53] epinow: There were 15 divergent transitions after warmup. See
+WARN [2025-11-04 02:14:03] epinow: There were 4 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 [2025-10-17 16:09:53] epinow: There were 496 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 [2025-10-17 16:09:53] epinow: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
-https://mc-stan.org/misc/warnings.html#bfmi-low - 
-WARN [2025-10-17 16:09:53] epinow: Examine the pairs() plot to diagnose sampling problems
+WARN [2025-11-04 02:14:03] epinow: Examine the pairs() plot to diagnose sampling problems
  - 
-WARN [2025-10-17 16:09:54] epinow: The largest R-hat is NA, indicating chains have not mixed.
-Running the chains for more iterations may help. See
-https://mc-stan.org/misc/warnings.html#r-hat - 
-WARN [2025-10-17 16:09:55] 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 [2025-10-17 16:09:57] 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      18224 (0 -- 28832)
-2:   Expected change in reports       Likely decreasing
-3:   Effective reproduction no.     0.92 (0.046 -- 1.2)
-4:               Rate of growth -0.029 (-0.35 -- 0.054)
-5: Doubling/halving time (days)          -24 (13 -- -2)
+                        measure                 estimate
+                         <char>                   <char>
+1:       New infections per day   20235 (13425 -- 29972)
+2:   Expected change in reports                   Stable
+3:   Effective reproduction no.       0.97 (0.77 -- 1.2)
+4:               Rate of growth -0.011 (-0.092 -- 0.068)
+5: Doubling/halving time (days)         -65 (10 -- -7.5)
 ```
 
 
@@ -315,10 +302,7 @@ estimate_cases_to_deaths <- EpiNow2::estimate_secondary(
 ```
 
 ``` output
-WARN [2025-10-17 16:10:02] estimate_secondary (chain: 1): 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 [2025-10-17 16:10:02] estimate_secondary (chain: 1): Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
+WARN [2025-11-04 02:14:10] 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 - 
 ```
@@ -553,31 +537,21 @@ 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 [2025-10-17 16:10:58] epinow: There were 23 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 [2025-10-17 16:10:58] epinow: Examine the pairs() plot to diagnose sampling problems
- - 
-```
-
-``` r
 summary(ebola_estimates)
 ```
 
 ``` output
                         measure                estimate
                          <char>                  <char>
-1:       New infections per day          93 (49 -- 199)
+1:       New infections per day          92 (48 -- 193)
 2:   Expected change in reports              Increasing
-3:   Effective reproduction no.        1.7 (1.2 -- 2.4)
-4:               Rate of growth 0.042 (0.0033 -- 0.086)
-5: Doubling/halving time (days)           16 (8 -- 210)
+3:   Effective reproduction no.        1.6 (1.2 -- 2.4)
+4:               Rate of growth 0.041 (0.0025 -- 0.088)
+5: Doubling/halving time (days)         17 (7.9 -- 270)
 ```
 
-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 (0.0033 -- 0.086).
+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 (0.0025 -- 0.088).
 
 Visualize the estimates:
 

create-forecast.md

@@ -167,8 +167,8 @@ epiparameter::generate(covid_serialint, times = 10)
 ```
 
 ``` output
- [1] 5.611452 5.189468 7.284840 4.451059 9.886059 5.290563 1.762559 1.771989
- [9] 5.081965 7.320946
+ [1]  2.768040  7.552861 10.198738  4.275607  5.760451  4.899755  3.444418
+ [8]  2.738078  4.003060  5.263222
 ```
 
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