differences for PR #53

epiverse-trace · May 4, 2024 · 0485390 · 0485390
1 parent 1f11815
commit 0485390
Show file tree

Hide file tree

Showing 12 changed files with 241 additions and 127 deletions.
diff --git a/delays-functions.md b/delays-functions.md
@@ -88,6 +88,16 @@ library(tidyverse)
 withr::local_options(list(mc.cores = 4))
 ```
 
+::::::::::::::::::: checklist
+
+### The double-colon
+
+The double-colon `::` in R is used to access functions or objects from a specific package without loading the entire package into the current environment. This allows for a more targeted approach to using package components and helps avoid namespace conflicts.
+
+`::` lets you call a specific function from a package by explicitly mentioning the package name. For example, `dplyr::filter(data, condition)` uses `filter()` from the `{dplyr}` package without loading the entire package.
+
+:::::::::::::::::::
+
 ## Distribution functions
 
 In R, all the statistical distributions have functions to access the following:
@@ -150,8 +160,8 @@ generate(covid_serialint, times = 10)
 ```
 
 ```{.output}
- [1] 2.889660 9.307841 2.218292 3.749691 5.273008 1.416355 2.502361 2.234118
- [9] 2.217577 3.045567
+ [1] 3.7327205 5.9489185 3.9368463 2.3420749 2.1828592 2.1701174 3.8265515
+ [8] 1.8415268 2.4269600 0.8082517
 ```
 
 ::::::::: instructor
@@ -460,10 +470,10 @@ epinow_estimates_cg <- epinow(
 ```
 
 ```{.output}
-WARN [2024-04-29 22:16:50] epinow: There were 5 divergent transitions after warmup. See
+WARN [2024-05-04 04:03:28] epinow: There were 11 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 [2024-04-29 22:16:50] epinow: Examine the pairs() plot to diagnose sampling problems
+WARN [2024-05-04 04:03:28] epinow: Examine the pairs() plot to diagnose sampling problems
  - 
 ```
 
@@ -589,10 +599,10 @@ epinow_estimates_cgi <- epinow(
 ```
 
 ```{.output}
-WARN [2024-04-29 22:18:38] epinow: There were 7 divergent transitions after warmup. See
+WARN [2024-05-04 04:05:16] epinow: There were 8 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 [2024-04-29 22:18:38] epinow: Examine the pairs() plot to diagnose sampling problems
+WARN [2024-05-04 04:05:16] epinow: Examine the pairs() plot to diagnose sampling problems
  - 
 ```
 
@@ -736,10 +746,10 @@ epinow_estimates_egi <- epinow(
 ```
 
 ```{.output}
-WARN [2024-04-29 22:21:52] epinow: There were 3 divergent transitions after warmup. See
+WARN [2024-05-04 04:08:50] 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 [2024-04-29 22:21:52] epinow: Examine the pairs() plot to diagnose sampling problems
+WARN [2024-05-04 04:08:50] epinow: Examine the pairs() plot to diagnose sampling problems
  - 
 ```
 

diff --git a/delays-reuse.md b/delays-reuse.md
@@ -213,6 +213,16 @@ List of <epidist> objects
   Number of offspring distributions: 0
 ```
 
+::::::::::::::::::: checklist
+
+### The double-colon
+
+The double-colon `::` in R is used to access functions or objects from a specific package without loading the entire package into the current environment. This allows for a more targeted approach to using package components and helps avoid namespace conflicts.
+
+`::` lets you call a specific function from a package by explicitly mentioning the package name. For example, `dplyr::filter(data, condition)` uses `filter()` from the `{dplyr}` package without loading the entire package.
+
+:::::::::::::::::::
+
 From the `{epiparameter}` package, we can use the `epidist_db()` function to ask for any `disease` and also for a specific epidemiological distribution (`epi_dist`). 
 
 Let's ask now how many parameters we have in the epidemiological distributions database (`epidist_db`) with the generation time using the string `generation`:

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
@@ -8,11 +8,11 @@
 "episodes/clean-data.Rmd" "5c4185a8ef7befeb1b7c1e3afc0a30dc" "site/built/clean-data.md" "2024-04-29"
 "episodes/describe-cases.Rmd" "5d75abf64023fa00ce11f3b36e3d9a48" "site/built/describe-cases.md" "2024-04-29"
 "episodes/simple-analysis.Rmd" "8b1eacfe982b6c8e13b931f399e94652" "site/built/simple-analysis.md" "2024-04-29"
-"episodes/delays-reuse.Rmd" "99c8549fdb699dea71a19f6022ddbeff" "site/built/delays-reuse.md" "2024-04-29"
-"episodes/quantify-transmissibility.Rmd" "87679a9120c62fde0f6a647d80b72c46" "site/built/quantify-transmissibility.md" "2024-04-29"
-"episodes/delays-functions.Rmd" "53216ab4c9d20d5e157bf4a06429f7a9" "site/built/delays-functions.md" "2024-04-29"
+"episodes/delays-reuse.Rmd" "06905f0486085d5cde368217a42fbbf4" "site/built/delays-reuse.md" "2024-05-04"
+"episodes/quantify-transmissibility.Rmd" "7ecde2de4bca061f1c5434d0ff0ad9fa" "site/built/quantify-transmissibility.md" "2024-05-04"
+"episodes/delays-functions.Rmd" "c95ad968a72ea3738f9b382dffc18a9f" "site/built/delays-functions.md" "2024-05-04"
 "instructors/instructor-notes.md" "ca3834a1b0f9e70c4702aa7a367a6bb5" "site/built/instructor-notes.md" "2024-04-29"
 "learners/reference.md" "106717912e909a7c8d9e3e8fea48e17d" "site/built/reference.md" "2024-04-29"
-"learners/setup.md" "64f432f4e2d4e1986341fd106f85b23d" "site/built/setup.md" "2024-04-29"
+"learners/setup.md" "323d6594b0bdadcaa62b4d03d45467fd" "site/built/setup.md" "2024-05-04"
 "profiles/learner-profiles.md" "31b503c4b5bd1f0960ada730eca4a25e" "site/built/learner-profiles.md" "2024-04-29"
 "renv/profiles/lesson-requirements/renv.lock" "0a590d508237e49dff0968d512a60cd3" "site/built/renv.lock" "2024-04-29"