differences for PR #11

epiverse-trace · Mar 28, 2024 · f867043 · f867043
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diff --git a/config.yaml b/config.yaml
diff --git a/create-forecast.md b/create-forecast.md
@@ -61,10 +61,10 @@ estimates <- epinow(
 ```
 
 ```{.output}
-WARN [2024-03-25 20:01:41] epinow: There were 1 divergent transitions after warmup. See
+WARN [2024-03-28 21:06:56] 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 [2024-03-25 20:01:41] epinow: Examine the pairs() plot to diagnose sampling problems
+WARN [2024-03-28 21:06:56] epinow: Examine the pairs() plot to diagnose sampling problems
  - 
 ```
 
@@ -131,28 +131,17 @@ estimates <- epinow(
   rt = rt_opts(prior = list(mean = rt_log_mean, sd = rt_log_sd)),
   obs = obs_opts(scale = obs_scale)
 )
-```
-
-```{.output}
-WARN [2024-03-25 20:08:12] 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 [2024-03-25 20:08:12] epinow: Examine the pairs() plot to diagnose sampling problems
- - 
-```
-
-```r
 summary(estimates)
 ```
 
 ```{.output}
                                  measure                 estimate
                                   <char>                   <char>
-1: New confirmed cases by infection date   17836 (10068 -- 30847)
+1: New confirmed cases by infection date   18064 (10003 -- 30881)
 2:        Expected change in daily cases        Likely decreasing
-3:            Effective reproduction no.       0.88 (0.56 -- 1.3)
-4:                        Rate of growth -0.016 (-0.065 -- 0.037)
-5:          Doubling/halving time (days)          -43 (19 -- -11)
+3:            Effective reproduction no.       0.89 (0.56 -- 1.3)
+4:                        Rate of growth -0.014 (-0.066 -- 0.035)
+5:          Doubling/halving time (days)          -48 (20 -- -11)
 ```
 
 
@@ -339,10 +328,10 @@ ebola_estimates <- epinow(
 ```
 
 ```{.output}
-WARN [2024-03-25 20:10:14] epinow: There were 17 divergent transitions after warmup. See
+WARN [2024-03-28 21:16:07] epinow: There were 19 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 [2024-03-25 20:10:14] epinow: Examine the pairs() plot to diagnose sampling problems
+WARN [2024-03-28 21:16:07] epinow: Examine the pairs() plot to diagnose sampling problems
  - 
 ```
 
@@ -353,14 +342,14 @@ summary(ebola_estimates)
 ```{.output}
                                  measure                estimate
                                   <char>                  <char>
-1: New confirmed cases by infection date         103 (46 -- 258)
+1: New confirmed cases by infection date         101 (46 -- 262)
 2:        Expected change in daily cases              Increasing
-3:            Effective reproduction no.          1.7 (1 -- 2.9)
-4:                        Rate of growth 0.043 (0.0024 -- 0.092)
-5:          Doubling/halving time (days)         16 (7.6 -- 290)
+3:            Effective reproduction no.            1.7 (1 -- 3)
+4:                        Rate of growth 0.042 (0.0026 -- 0.093)
+5:          Doubling/halving time (days)         17 (7.5 -- 260)
 ```
 
-The effective reproduction number $R_t$ estimate (on the last date of the data) is 1.7 (1 -- 2.9). The exponential growth rate of case numbers is 0.043 (0.0024 -- 0.092).
+The effective reproduction number $R_t$ estimate (on the last date of the data) is 1.7 (1 -- 3). The exponential growth rate of case numbers is 0.042 (0.0026 -- 0.093).
 
 Visualize the estimates:
 

diff --git a/fig/create-forecast-rendered-unnamed-chunk-11-1.png b/fig/create-forecast-rendered-unnamed-chunk-11-1.png
diff --git a/fig/create-forecast-rendered-unnamed-chunk-3-1.png b/fig/create-forecast-rendered-unnamed-chunk-3-1.png
diff --git a/fig/create-forecast-rendered-unnamed-chunk-9-1.png b/fig/create-forecast-rendered-unnamed-chunk-9-1.png
diff --git a/fig/quantify-transmissibility-rendered-unnamed-chunk-15-1.png b/fig/quantify-transmissibility-rendered-unnamed-chunk-15-1.png
diff --git a/fig/quantify-transmissibility-rendered-unnamed-chunk-16-1.png b/fig/quantify-transmissibility-rendered-unnamed-chunk-16-1.png
diff --git a/fig/quantify-transmissibility-rendered-unnamed-chunk-19-1.png b/fig/quantify-transmissibility-rendered-unnamed-chunk-19-1.png
diff --git a/fig/severity-static-rendered-unnamed-chunk-13-1.png b/fig/severity-static-rendered-unnamed-chunk-13-1.png
diff --git a/fig/severity-static-rendered-unnamed-chunk-7-1.png b/fig/severity-static-rendered-unnamed-chunk-7-1.png
diff --git a/md5sum.txt b/md5sum.txt
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