differences for PR #64

epiverse-trace · Jun 17, 2024 · 237773c · 237773c
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diff --git a/delays-functions.md b/delays-functions.md
@@ -162,8 +162,8 @@ generate(covid_serialint, times = 10)
 ```
 
 ```{.output}
- [1]  5.534646  9.250007  4.254961  3.436661 13.323202  3.695330  5.519206
- [8]  4.682234  2.675111  2.804316
+ [1]  2.457223  3.312394  3.729976  8.068636  5.572314  2.445653  7.738652
+ [8]  1.729764  3.979938 10.168464
 ```
 
 ::::::::: instructor
@@ -472,10 +472,10 @@ epinow_estimates_cg <- epinow(
 ```
 
 ```{.output}
-WARN [2024-06-17 21:44:52] epinow: There were 5 divergent transitions after warmup. See
+WARN [2024-06-17 21:52:58] 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 [2024-06-17 21:44:52] epinow: Examine the pairs() plot to diagnose sampling problems
+WARN [2024-06-17 21:52:58] epinow: Examine the pairs() plot to diagnose sampling problems
  - 
 ```
 
@@ -601,10 +601,10 @@ epinow_estimates_cgi <- epinow(
 ```
 
 ```{.output}
-WARN [2024-06-17 21:46:37] epinow: There were 10 divergent transitions after warmup. See
+WARN [2024-06-17 21:54:39] epinow: There were 16 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 [2024-06-17 21:46:37] epinow: Examine the pairs() plot to diagnose sampling problems
+WARN [2024-06-17 21:54:39] epinow: Examine the pairs() plot to diagnose sampling problems
  - 
 ```
 
@@ -748,10 +748,10 @@ epinow_estimates_egi <- epinow(
 ```
 
 ```{.output}
-WARN [2024-06-17 21:50:29] epinow: There were 2 divergent transitions after warmup. See
+WARN [2024-06-17 21:58:08] 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 [2024-06-17 21:50:29] epinow: Examine the pairs() plot to diagnose sampling problems
+WARN [2024-06-17 21:58:08] epinow: Examine the pairs() plot to diagnose sampling problems
  - 
 ```
 

diff --git a/fig/delays-functions-rendered-unnamed-chunk-16-1.png b/fig/delays-functions-rendered-unnamed-chunk-16-1.png
diff --git a/fig/delays-functions-rendered-unnamed-chunk-17-1.png b/fig/delays-functions-rendered-unnamed-chunk-17-1.png
diff --git a/fig/delays-functions-rendered-unnamed-chunk-20-1.png b/fig/delays-functions-rendered-unnamed-chunk-20-1.png
diff --git a/fig/delays-functions-rendered-unnamed-chunk-21-1.png b/fig/delays-functions-rendered-unnamed-chunk-21-1.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-17-1.png b/fig/quantify-transmissibility-rendered-unnamed-chunk-17-1.png
diff --git a/fig/quantify-transmissibility-rendered-unnamed-chunk-20-1.png b/fig/quantify-transmissibility-rendered-unnamed-chunk-20-1.png
diff --git a/md5sum.txt b/md5sum.txt
@@ -13,6 +13,6 @@
 "episodes/delays-functions.Rmd" "3b40b34577112812aa7b872f728500f4" "site/built/delays-functions.md" "2024-06-17"
 "instructors/instructor-notes.md" "ca3834a1b0f9e70c4702aa7a367a6bb5" "site/built/instructor-notes.md" "2024-05-21"
 "learners/reference.md" "106717912e909a7c8d9e3e8fea48e17d" "site/built/reference.md" "2024-05-21"
-"learners/setup.md" "4c235f3d33132e2ec79d813610a29bf3" "site/built/setup.md" "2024-06-17"
+"learners/setup.md" "cbdffa25710b2423d1551706af39b13d" "site/built/setup.md" "2024-06-17"
 "profiles/learner-profiles.md" "31b503c4b5bd1f0960ada730eca4a25e" "site/built/learner-profiles.md" "2024-05-21"
 "renv/profiles/lesson-requirements/renv.lock" "201f9680fa680a90ab80d294ff8143d0" "site/built/renv.lock" "2024-05-21"
diff --git a/quantify-transmissibility.md b/quantify-transmissibility.md
@@ -407,12 +407,7 @@ estimates <- epinow(
 ```
 
 ```{.output}
-WARN [2024-06-17 20:58:18] epinow: There were 9 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 [2024-06-17 20:58:18] epinow: Examine the pairs() plot to diagnose sampling problems
- - 
-WARN [2024-06-17 20:58:19] epinow: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
+WARN [2024-06-17 21:05:15] 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 - 
 ```
@@ -458,22 +453,22 @@ summary(estimates)
 ```{.output}
                                  measure                 estimate
                                   <char>                   <char>
-1: New confirmed cases by infection date     7301 (4102 -- 12577)
+1: New confirmed cases by infection date     7234 (3944 -- 12739)
 2:        Expected change in daily cases        Likely decreasing
-3:            Effective reproduction no.        0.9 (0.57 -- 1.3)
-4:                        Rate of growth -0.013 (-0.064 -- 0.035)
-5:          Doubling/halving time (days)          -52 (20 -- -11)
+3:            Effective reproduction no.        0.9 (0.56 -- 1.3)
+4:                        Rate of growth -0.014 (-0.066 -- 0.038)
+5:          Doubling/halving time (days)          -51 (18 -- -11)
 ```
 
 As these estimates are based on partial data, they have a wide uncertainty interval.
 
-+ From the summary of our analysis we see that the expected change in daily cases is Likely decreasing with the estimated new confirmed cases 7301 (4102 -- 12577).
++ From the summary of our analysis we see that the expected change in daily cases is Likely decreasing with the estimated new confirmed cases 7234 (3944 -- 12739).
 
-+ The effective reproduction number $R_t$ estimate (on the last date of the data) is 0.9 (0.57 -- 1.3). 
++ The effective reproduction number $R_t$ estimate (on the last date of the data) is 0.9 (0.56 -- 1.3). 
 
-+ The exponential growth rate of case numbers is -0.013 (-0.064 -- 0.035).
++ The exponential growth rate of case numbers is -0.014 (-0.066 -- 0.038).
 
-+ The doubling time (the time taken for case numbers to double) is -52 (20 -- -11).
++ The doubling time (the time taken for case numbers to double) is -51 (18 -- -11).
 
 ::::::::::::::::::::::::::::::::::::: callout
 ### `Expected change in daily cases` 
@@ -542,17 +537,17 @@ estimates_regional <- regional_epinow(
 ```
 
 ```{.output}
-INFO [2024-06-17 20:58:21] Producing following optional outputs: regions, summary, samples, plots, latest
-INFO [2024-06-17 20:58:22] Reporting estimates using data up to: 2020-04-28
-INFO [2024-06-17 20:58:22] No target directory specified so returning output
-INFO [2024-06-17 20:58:22] Producing estimates for: East Midlands, East of England, England, London, North East, North West, Northern Ireland, Scotland, South East, South West, Wales, West Midlands, Yorkshire and The Humber
-INFO [2024-06-17 20:58:22] Regions excluded: none
-INFO [2024-06-17 21:43:06] Completed regional estimates
-INFO [2024-06-17 21:43:06] Regions with estimates: 13
-INFO [2024-06-17 21:43:06] Regions with runtime errors: 0
-INFO [2024-06-17 21:43:06] Producing summary
-INFO [2024-06-17 21:43:06] No summary directory specified so returning summary output
-INFO [2024-06-17 21:43:07] No target directory specified so returning timings
+INFO [2024-06-17 21:05:18] Producing following optional outputs: regions, summary, samples, plots, latest
+INFO [2024-06-17 21:05:18] Reporting estimates using data up to: 2020-04-28
+INFO [2024-06-17 21:05:18] No target directory specified so returning output
+INFO [2024-06-17 21:05:18] Producing estimates for: East Midlands, East of England, England, London, North East, North West, Northern Ireland, Scotland, South East, South West, Wales, West Midlands, Yorkshire and The Humber
+INFO [2024-06-17 21:05:18] Regions excluded: none
+INFO [2024-06-17 21:51:03] Completed regional estimates
+INFO [2024-06-17 21:51:03] Regions with estimates: 13
+INFO [2024-06-17 21:51:03] Regions with runtime errors: 0
+INFO [2024-06-17 21:51:03] Producing summary
+INFO [2024-06-17 21:51:03] No summary directory specified so returning summary output
+INFO [2024-06-17 21:51:03] No target directory specified so returning timings
 ```
 
 ```r
@@ -562,49 +557,49 @@ estimates_regional$summary$summarised_results$table
 ```{.output}
                       Region New confirmed cases by infection date
                       <char>                                <char>
- 1:            East Midlands                      344 (212 -- 553)
- 2:          East of England                      542 (327 -- 833)
- 3:                  England                   3548 (2229 -- 5440)
- 4:                   London                      294 (189 -- 457)
- 5:               North East                      253 (144 -- 427)
- 6:               North West                      555 (331 -- 861)
- 7:         Northern Ireland                         43 (22 -- 82)
- 8:                 Scotland                      290 (167 -- 526)
- 9:               South East                      593 (348 -- 987)
-10:               South West                      418 (302 -- 611)
-11:                    Wales                        95 (63 -- 141)
-12:            West Midlands                      269 (150 -- 490)
-13: Yorkshire and The Humber                      477 (290 -- 778)
+ 1:            East Midlands                      350 (215 -- 560)
+ 2:          East of England                      533 (339 -- 846)
+ 3:                  England                   3576 (2184 -- 5585)
+ 4:                   London                      296 (189 -- 465)
+ 5:               North East                      254 (150 -- 434)
+ 6:               North West                      558 (325 -- 881)
+ 7:         Northern Ireland                         44 (23 -- 86)
+ 8:                 Scotland                      292 (154 -- 536)
+ 9:               South East                      591 (359 -- 986)
+10:               South West                      419 (288 -- 597)
+11:                    Wales                        95 (65 -- 141)
+12:            West Midlands                      275 (149 -- 487)
+13: Yorkshire and The Humber                      479 (285 -- 773)
     Expected change in daily cases Effective reproduction no.
                             <fctr>                     <char>
- 1:              Likely increasing          1.2 (0.85 -- 1.6)
- 2:              Likely increasing          1.2 (0.83 -- 1.6)
- 3:              Likely decreasing         0.91 (0.64 -- 1.2)
- 4:              Likely decreasing         0.79 (0.56 -- 1.1)
- 5:              Likely decreasing         0.91 (0.59 -- 1.3)
- 6:              Likely decreasing         0.86 (0.58 -- 1.2)
- 7:              Likely decreasing           0.64 (0.38 -- 1)
- 8:              Likely decreasing         0.92 (0.62 -- 1.4)
+ 1:              Likely increasing          1.2 (0.86 -- 1.6)
+ 2:              Likely increasing          1.2 (0.84 -- 1.6)
+ 3:              Likely decreasing         0.92 (0.63 -- 1.3)
+ 4:              Likely decreasing         0.79 (0.55 -- 1.1)
+ 5:              Likely decreasing         0.91 (0.62 -- 1.3)
+ 6:              Likely decreasing         0.87 (0.57 -- 1.2)
+ 7:              Likely decreasing         0.65 (0.39 -- 1.1)
+ 8:              Likely decreasing         0.92 (0.57 -- 1.4)
  9:                         Stable         0.99 (0.67 -- 1.4)
 10:                     Increasing           1.4 (1.1 -- 1.8)
-11:                     Decreasing        0.57 (0.41 -- 0.78)
-12:              Likely decreasing          0.7 (0.44 -- 1.1)
-13:                         Stable            1 (0.71 -- 1.4)
-                Rate of growth Doubling/halving time (days)
-                        <char>                       <char>
- 1:    0.024 (-0.021 -- 0.069)               29 (10 -- -33)
- 2:    0.022 (-0.023 -- 0.066)               31 (10 -- -30)
- 3:   -0.012 (-0.052 -- 0.029)              -59 (24 -- -13)
- 4:   -0.029 (-0.066 -- 0.011)              -24 (62 -- -10)
- 5:    -0.012 (-0.06 -- 0.036)              -58 (19 -- -12)
- 6:   -0.018 (-0.063 -- 0.021)              -38 (32 -- -11)
- 7:    -0.053 (-0.1 -- 0.0044)            -13 (160 -- -6.8)
- 8:   -0.011 (-0.056 -- 0.043)              -64 (16 -- -12)
- 9: -0.00099 (-0.048 -- 0.048)             -700 (14 -- -14)
-10:     0.047 (0.015 -- 0.085)               15 (8.1 -- 46)
-11:  -0.065 (-0.094 -- -0.031)            -11 (-22 -- -7.4)
-12:   -0.042 (-0.088 -- 0.011)             -16 (61 -- -7.8)
-13:   0.0026 (-0.041 -- 0.051)              260 (14 -- -17)
+11:                     Decreasing        0.57 (0.42 -- 0.77)
+12:              Likely decreasing         0.71 (0.44 -- 1.1)
+13:                         Stable             1 (0.7 -- 1.4)
+               Rate of growth Doubling/halving time (days)
+                       <char>                       <char>
+ 1:   0.025 (-0.018 -- 0.071)              28 (9.8 -- -38)
+ 2:   0.021 (-0.022 -- 0.066)               33 (11 -- -32)
+ 3:  -0.011 (-0.054 -- 0.033)              -63 (21 -- -13)
+ 4:  -0.029 (-0.067 -- 0.012)              -24 (58 -- -10)
+ 5:  -0.012 (-0.056 -- 0.039)              -56 (18 -- -12)
+ 6:  -0.018 (-0.064 -- 0.022)              -38 (32 -- -11)
+ 7:   -0.051 (-0.1 -- 0.0082)             -13 (85 -- -6.9)
+ 8:   -0.01 (-0.064 -- 0.048)              -67 (14 -- -11)
+ 9: -0.0013 (-0.048 -- 0.049)             -530 (14 -- -15)
+10:    0.047 (0.011 -- 0.083)               15 (8.3 -- 64)
+11: -0.064 (-0.092 -- -0.032)            -11 (-21 -- -7.5)
+12:  -0.041 (-0.089 -- 0.012)             -17 (58 -- -7.8)
+13:  0.0027 (-0.043 -- 0.049)              260 (14 -- -16)
 ```
 
 ```r

diff --git a/setup.md b/setup.md
@@ -33,17 +33,18 @@ Also check out the [glossary](../reference.md) for any terms you may be unfamili
 
 ### Epiverse-TRACE R packages
 
-Our strategy is to gradually incorporate specialised **R packages** into our traditional analysis pipeline. These packages should fill the gaps in these epidemiology-specific tasks in response to outbreaks.
+Our strategy is to gradually incorporate specialised **R packages** into traditional analysis pipeline. These packages should fill the gaps in these epidemiology-specific tasks in response to outbreaks.
 
-![In **R**, the fundamental unit of shareable code is the **package**. A package bundles together code, data, documentation, and tests and is easy to share with others ([Wickham and Bryan, 2023](https://r-pkgs.org/introduction.html))](episodes/fig/pkgs-hexlogos-2.png)
+![In **R**, the fundamental unit of shareable code is the **package**. A package bundles together code, data, documentation, and tests and is easy to share with others ([Wickham and Bryan, 2023](https://r-pkgs.org/introduction.html))](episodes/fig/pkgs-hexlogos-2.png).
 
 :::::::::::::::::::::::::::: prereq
 
 This course assumes intermediate R knowledge. This workshop is for you if:
 
-- You can use the magrittr pipe `%>%` and/or native pipe `|>`
-- You are familiar with functions from `{dplyr}`, `{tidyr}`, and `{ggplot2}`
 - You can read data into R, transform and reshape data, and make a wide variety of graphs
+- You are familiar with functions from `{dplyr}`, `{tidyr}`, and `{ggplot2}`
+- You can use the magrittr pipe `%>%` and/or native pipe `|>`.
+
 
 We expect participants to have some exposure to basic Statistical, Mathematical and Epidemic theory concepts, but NOT intermediate or expert familiarity with modeling.
 
@@ -74,7 +75,7 @@ This tutorial requires **R version 4.0.0 or later**.
 
 To check if your R version is up to date:
 
-- In RStudio your R version will be printed in [the console window](https://docs.posit.co/ide/user/ide/guide/code/console.html). Or run `sessionInfo()` there.
+- In RStudio your R version will be printed in [the console window](https://docs.posit.co/ide/user/ide/guide/code/console.html). Or run `sessionInfo()`.
 
 - **To update R**, download and install the latest version from the [R project website](https://cran.rstudio.com/) for your operating system.
 

diff --git a/simple-analysis.md b/simple-analysis.md
@@ -155,9 +155,9 @@ base::print(peaks_nb)
 # A data frame: 3 × 6
   sex     observed_peak observed_count lower_ci   median     upper_ci  
 * <chr>   <date>                 <int> <date>     <date>     <date>    
-1 female  2020-03-26              1314 2020-03-18 2020-03-23 2020-03-31
-2 male    2020-03-27              1299 2020-03-19 2020-03-26 2020-03-30
-3 unknown 2020-04-10                32 2020-03-24 2020-04-07 2020-04-20
+1 female  2020-03-26              1314 2020-03-18 2020-03-25 2020-03-29
+2 male    2020-03-27              1299 2020-03-18 2020-03-24 2020-03-31
+3 unknown 2020-04-10                32 2020-03-24 2020-04-07 2020-04-11
 ```