differences for PR #138

epiverse-trace · May 7, 2024 · 26294df · 26294df
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diff --git a/compare-interventions.md b/compare-interventions.md
@@ -128,11 +128,7 @@ contact_data <- socialmixr::contact_matrix(
 )
 ```
 
-```{.output}
-Using POLYMOD social contact data. To cite this in a publication, use the 'get_citation()' function
-```
-
-```{.output}
+```output
 Removing participants that have contacts without age information. To change this behaviour, set the 'missing.contact.age' option
 ```
 
@@ -171,15 +167,15 @@ uk_population <- population(
 )
 ```
 
-```{.error}
+```error
 Error in population(name = "UK", contact_matrix = contact_matrix, demography_vector = demography_vector, : could not find function "population"
 ```
 
 ```r
 no_vaccination <- no_vaccination(population = uk_population, doses = 2)
 ```
 
-```{.error}
+```error
 Error in no_vaccination(population = uk_population, doses = 2): could not find function "no_vaccination"
 ```
 
@@ -192,7 +188,7 @@ output <- model_vacamole_cpp(
 )
 ```
 
-```{.error}
+```error
 Error in model_vacamole_cpp(population = uk_population, vaccination = no_vaccination, : could not find function "model_vacamole_cpp"
 ```
 
@@ -225,7 +221,7 @@ ggplot(output[output$compartment == "dead", ]) +
   )
 ```
 
-```{.error}
+```error
 Error in ggplot(output[output$compartment == "dead", ]): could not find function "ggplot"
 ```
 

diff --git a/config.yaml b/config.yaml
diff --git a/create-forecast.md b/create-forecast.md
@@ -60,15 +60,12 @@ estimates <- epinow(
 )
 ```
 
-```{.output}
-WARN [2024-03-22 13:04:53] epinow: There were 6 divergent transitions after warmup. See
+```output
+WARN [2024-05-07 02:06:31] epinow: There were 3 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 [2024-03-22 13:04:53] epinow: Examine the pairs() plot to diagnose sampling problems
+WARN [2024-05-07 02:06:31] epinow: Examine the pairs() plot to diagnose sampling problems
  - 
-WARN [2024-03-22 13:04:55] 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 - 
 ```
 
 
@@ -136,26 +133,26 @@ estimates <- epinow(
 )
 ```
 
-```{.output}
-WARN [2024-03-22 13:12:06] epinow: There were 3 divergent transitions after warmup. See
+```output
+WARN [2024-05-07 02:13:27] 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 [2024-03-22 13:12:06] epinow: Examine the pairs() plot to diagnose sampling problems
+WARN [2024-05-07 02:13:27] epinow: Examine the pairs() plot to diagnose sampling problems
  - 
 ```
 
 ```r
 summary(estimates)
 ```
 
-```{.output}
+```output
                                  measure                 estimate
                                   <char>                   <char>
-1: New confirmed cases by infection date    17867 (9893 -- 30108)
+1: New confirmed cases by infection date   17945 (10150 -- 31476)
 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 -- 0.034)
-5:          Doubling/halving time (days)          -44 (20 -- -11)
+3:            Effective reproduction no.       0.89 (0.57 -- 1.3)
+4:                        Rate of growth -0.015 (-0.064 -- 0.039)
+5:          Doubling/halving time (days)          -46 (18 -- -11)
 ```
 
 
@@ -249,10 +246,6 @@ deaths_forecast <- forecast_secondary(
 plot(deaths_forecast)
 ```
 
-```{.warning}
-Warning: Removed 30 rows containing missing values (`position_stack()`).
-```
-
 <img src="fig/create-forecast-rendered-unnamed-chunk-11-1.png" style="display: block; margin: auto;" />
 
 The plot shows the forecast secondary observations (deaths) over the dates which we have recorded cases for. 
@@ -341,38 +334,29 @@ ebola_estimates <- epinow(
 )
 ```
 
-```{.output}
-WARN [2024-03-22 13:13:55] epinow: There were 442 divergent transitions after warmup. See
+```output
+WARN [2024-05-07 02:15:30] epinow: There were 22 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 [2024-03-22 13:13:55] epinow: Examine the pairs() plot to diagnose sampling problems
+WARN [2024-05-07 02:15:30] epinow: Examine the pairs() plot to diagnose sampling problems
  - 
-WARN [2024-03-22 13:13:57] 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 [2024-03-22 13:13:59] 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 [2024-03-22 13:14:00] 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}
+```output
                                  measure               estimate
                                   <char>                 <char>
-1: New confirmed cases by infection date        123 (49 -- 429)
+1: New confirmed cases by infection date        101 (47 -- 274)
 2:        Expected change in daily cases             Increasing
-3:            Effective reproduction no.       1.9 (1.1 -- 4.3)
-4:                        Rate of growth 0.052 (0.0086 -- 0.13)
-5:          Doubling/halving time (days)         13 (5.3 -- 81)
+3:            Effective reproduction no.         1.7 (1 -- 3.1)
+4:                        Rate of growth 0.043 (0.003 -- 0.096)
+5:          Doubling/halving time (days)        16 (7.2 -- 230)
 ```
 
-The effective reproduction number $R_t$ estimate (on the last date of the data) is 1.9 (1.1 -- 4.3). The exponential growth rate of case numbers is 0.052 (0.0086 -- 0.13).
+The effective reproduction number $R_t$ estimate (on the last date of the data) is 1.7 (1 -- 3.1). The exponential growth rate of case numbers is 0.043 (0.003 -- 0.096).
 
 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/introduction-rendered-unnamed-chunk-5-1.png b/fig/introduction-rendered-unnamed-chunk-5-1.png
diff --git a/fig/model-choices-rendered-unnamed-chunk-3-1.png b/fig/model-choices-rendered-unnamed-chunk-3-1.png
diff --git a/fig/model-choices-rendered-unnamed-chunk-4-1.png b/fig/model-choices-rendered-unnamed-chunk-4-1.png
diff --git a/fig/modelling-interventions-rendered-baseline-1.png b/fig/modelling-interventions-rendered-baseline-1.png
diff --git a/fig/modelling-interventions-rendered-plot_masks-1.png b/fig/modelling-interventions-rendered-plot_masks-1.png
diff --git a/fig/modelling-interventions-rendered-plot_vaccinate-1.png b/fig/modelling-interventions-rendered-plot_vaccinate-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/simulating-transmission-rendered-plot-1.png b/fig/simulating-transmission-rendered-plot-1.png
diff --git a/fig/simulating-transmission-rendered-traj-1.png b/fig/simulating-transmission-rendered-traj-1.png
diff --git a/fig/simulating-transmission-rendered-visualise-1.png b/fig/simulating-transmission-rendered-visualise-1.png
diff --git a/introduction.md b/introduction.md
@@ -81,7 +81,7 @@ Case incidence data must be stored in a data frame with the observed number of c
 example_confirmed
 ```
 
-```{.output}
+```output
            date confirm
          <Date>   <num>
   1: 2020-02-22      14
@@ -134,6 +134,12 @@ epinow_estimates <- epinow(
 )
 ```
 
+```output
+WARN [2024-05-07 01:08:57] 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 - 
+```
+
 As an output, we get the time-varying (or [effective](../learners/reference.md#effectiverepro)) reproduction number, as well as the cases by date of report and date of infection:
 
 

diff --git a/md5sum.txt b/md5sum.txt
@@ -1,19 +1,19 @@
 "file" "checksum" "built" "date"
-"CODE_OF_CONDUCT.md" "549f00b0992a7743c2bc16ea6ce3db57" "site/built/CODE_OF_CONDUCT.md" "2024-03-22"
-"LICENSE.md" "14377518ee654005a18cf28549eb30e3" "site/built/LICENSE.md" "2024-03-22"
-"config.yaml" "d11647b34aa74192704ce8944e83b0d8" "site/built/config.yaml" "2024-03-22"
-"index.md" "adfca1a79e0106ee8b3f7731d0678b59" "site/built/index.md" "2024-03-22"
-"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-03-22"
-"episodes/introduction.Rmd" "1861ec911e99b7feab3b65e0dbd91d41" "site/built/introduction.md" "2024-03-22"
-"episodes/read-delays.Rmd" "2c7422e552f8e16c28449877182c0704" "site/built/read-delays.md" "2024-03-22"
-"episodes/quantify-transmissibility.Rmd" "f507b32d4af315d95acc3f3f5a60c202" "site/built/quantify-transmissibility.md" "2024-03-22"
-"episodes/create-forecast.Rmd" "3fdb0f4223f220d061431f18846bf1f4" "site/built/create-forecast.md" "2024-03-22"
-"episodes/simulating-transmission.Rmd" "3f006aa142099aaeaa4688c064bd5d4a" "site/built/simulating-transmission.md" "2024-03-22"
-"episodes/model-choices.Rmd" "775bfba024103820482bc56907d86f14" "site/built/model-choices.md" "2024-03-22"
-"episodes/modelling-interventions.Rmd" "4955dd207b237ad495b601315bb3e8df" "site/built/modelling-interventions.md" "2024-03-22"
-"episodes/compare-interventions.Rmd" "1f04f6fa8980d60273755c7faf20e70c" "site/built/compare-interventions.md" "2024-03-22"
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-"renv/profiles/lesson-requirements/renv.lock" "dda4545bb8627af07463d0f71122ebe5" "site/built/renv.lock" "2024-03-22"
+"CODE_OF_CONDUCT.md" "549f00b0992a7743c2bc16ea6ce3db57" "site/built/CODE_OF_CONDUCT.md" "2024-05-07"
+"LICENSE.md" "14377518ee654005a18cf28549eb30e3" "site/built/LICENSE.md" "2024-05-07"
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+"episodes/quantify-transmissibility.Rmd" "f507b32d4af315d95acc3f3f5a60c202" "site/built/quantify-transmissibility.md" "2024-05-07"
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diff --git a/model-choices.md b/model-choices.md
@@ -267,7 +267,13 @@ output <- model_ebola_r(
   funeral_risk = 0.5,
   time_end = 100
 )
+```
+
+```error
+Error in model_ebola_r(population = guinea_population, transmissibility = 1.1/12, : could not find function "model_ebola_r"
+```
 
+```r
 ggplot(output[output$compartment == "infectious", ]) +
   geom_line(
     aes(time, value),
@@ -285,7 +291,9 @@ ggplot(output[output$compartment == "infectious", ]) +
   )
 ```
 
-<img src="fig/model-choices-rendered-unnamed-chunk-3-1.png" style="display: block; margin: auto;" />
+```error
+Error in eval(expr, envir, enclos): object 'output' not found
+```
 
 2. Run model 100 times and plot the mean, upper and lower 95% quantiles of the number of infectious individuals through time
 
@@ -311,9 +319,21 @@ output_samples <- Map(
     output
   }
 )
+```
+
+```error
+Error in model_ebola_r(population = guinea_population, transmissibility = 1.1/12, : could not find function "model_ebola_r"
+```
 
+```r
 output_samples <- bind_rows(output_samples) # requires the dplyr package
+```
 
+```error
+Error in eval(expr, envir, enclos): object 'output_samples' not found
+```
+
+```r
 ggplot(
   output_samples[output_samples$compartment == "infectious", ],
   aes(time, value)
@@ -338,7 +358,9 @@ ggplot(
   )
 ```
 
-<img src="fig/model-choices-rendered-unnamed-chunk-4-1.png" style="display: block; margin: auto;" />
+```error
+Error in eval(expr, envir, enclos): object 'output_samples' not found
+```
 
 :::::::::::::::::::::::::::