epiverse-trace · avallecam · May 1, 2024 · Mar 18, 2024 · Mar 30, 2024 · Mar 30, 2024
diff --git a/config.yaml b/config.yaml
@@ -14,7 +14,7 @@ carpentry: 'incubator'
 title: 'Real-time analysis and forecasting for outbreak analytics with R'
 
 # Date the lesson was created (YYYY-MM-DD, this is empty by default)
-created:
+created: 
 
 # Comma-separated list of keywords for the lesson
 keywords: 'forecasts, epidemic models, interventions'
@@ -62,21 +62,23 @@ episodes:
 #- quantify-transmissibility.Rmd
 - create-forecast.Rmd
 - severity-static.Rmd
+- superspreading-estimate.Rmd
+- superspreading-simulate.Rmd
 
 # Information for Learners
-learners:
+learners: 
 
 # Information for Instructors
-instructors:
+instructors: 
 
 # Learner Profiles
-profiles:
+profiles: 
 
 # Customisation ---------------------------------------------
 #
 # This space below is where custom yaml items (e.g. pinning
 # sandpaper and varnish versions) should live
 
+
 varnish: epiverse-trace/varnish@epiversetheme
-# this is carpentries/sandpaper#533 in our fork so we can keep it up to date with main
 sandpaper: epiverse-trace/sandpaper@patch-renv-github-bug
diff --git a/episodes/fig/SEE-dist.png b/episodes/fig/SEE-dist.png
diff --git a/episodes/fig/SEE-individual-reproductive-number-fig-b.png b/episodes/fig/SEE-individual-reproductive-number-fig-b.png
diff --git a/episodes/fig/SEE-individual-reproductive-number-fig-c.png b/episodes/fig/SEE-individual-reproductive-number-fig-c.png
diff --git a/episodes/fig/SEE-individual-reproductive-number-fig-d.png b/episodes/fig/SEE-individual-reproductive-number-fig-d.png
diff --git a/episodes/fig/SEE-individual-reproductive-number.png b/episodes/fig/SEE-individual-reproductive-number.png
diff --git a/episodes/fig/SEE-params.png b/episodes/fig/SEE-params.png
diff --git a/episodes/fig/contact-tracing-backward-time.png b/episodes/fig/contact-tracing-backward-time.png
diff --git a/episodes/fig/contact-tracing-serial-interval.png b/episodes/fig/contact-tracing-serial-interval.png
diff --git a/episodes/fig/contact-tracing-strategies.png b/episodes/fig/contact-tracing-strategies.png
diff --git a/episodes/fig/see-intro-secondary-cases-fig-b.png b/episodes/fig/see-intro-secondary-cases-fig-b.png
diff --git a/episodes/fig/see-intro-secondary-cases.png b/episodes/fig/see-intro-secondary-cases.png
diff --git a/episodes/fig/see-intro-superspreading.png b/episodes/fig/see-intro-superspreading.png
diff --git a/episodes/fig/see-nature04153_Fig2-c.jpg b/episodes/fig/see-nature04153_Fig2-c.jpg
diff --git a/episodes/fig/see-nature04153_Fig2.jpg b/episodes/fig/see-nature04153_Fig2.jpg
diff --git a/episodes/superspreading-estimate.Rmd b/episodes/superspreading-estimate.Rmd
diff --git a/episodes/superspreading-simulate.Rmd b/episodes/superspreading-simulate.Rmd
diff --git a/learners/setup.md b/learners/setup.md
@@ -213,7 +213,6 @@ library(EpiNow2)
 library(cfr)
 library(epiparameter)
 library(incidence2)
-library(covidregionaldata)
 library(outbreaks)
 library(tidyverse)
 ```

diff --git a/renv/profiles/lesson-requirements/renv.lock b/renv/profiles/lesson-requirements/renv.lock
@@ -289,6 +289,23 @@
       ],
       "Hash": "40415719b5a479b87949f3aa0aee737c"
     },
+    "bpmodels": {
+      "Package": "bpmodels",
+      "Version": "0.3.1",
+      "Source": "GitHub",
+      "RemoteType": "github",
+      "RemoteHost": "api.github.com",
+      "RemoteRepo": "bpmodels",
+      "RemoteUsername": "epiverse-trace",
+      "RemotePkgRef": "epiverse-trace/bpmodels",
+      "RemoteRef": "HEAD",
+      "RemoteSha": "07c054090f2b07367855b73a0cc2c43e24bc32d3",
+      "Requirements": [
+        "R",
+        "checkmate"
+      ],
+      "Hash": "4374941c8a9cf7a8991072466918c3b2"
+    },
     "broom": {
       "Package": "broom",
       "Version": "1.0.5",
@@ -513,6 +530,19 @@
       ],
       "Hash": "e8a1e41acf02548751f45c718d55aa6a"
     },
+    "crosstalk": {
+      "Package": "crosstalk",
+      "Version": "1.2.1",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R6",
+        "htmltools",
+        "jsonlite",
+        "lazyeval"
+      ],
+      "Hash": "ab12c7b080a57475248a30f4db6298c0"
+    },
     "curl": {
       "Package": "curl",
       "Version": "5.2.0",
@@ -676,6 +706,42 @@
       ],
       "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077"
     },
+    "epichains": {
+      "Package": "epichains",
+      "Version": "0.0.0.9999",
+      "Source": "GitHub",
+      "RemoteType": "github",
+      "RemoteHost": "api.github.com",
+      "RemoteRepo": "epichains",
+      "RemoteUsername": "epiverse-trace",
+      "RemotePkgRef": "epiverse-trace/epichains",
+      "RemoteRef": "HEAD",
+      "RemoteSha": "7b5b80b7b8531fba18e827636a45b0d064e73c76",
+      "Requirements": [
+        "R",
+        "checkmate",
+        "stats",
+        "utils"
+      ],
+      "Hash": "e4d58df3ff7111aa1c89356cad126c3b"
+    },
+    "epicontacts": {
+      "Package": "epicontacts",
+      "Version": "1.1.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "colorspace",
+        "dplyr",
+        "grDevices",
+        "igraph",
+        "methods",
+        "threejs",
+        "visNetwork"
+      ],
+      "Hash": "ce65f8ac65b26b2a6c17497a4cd5d3a0"
+    },
     "epiparameter": {
       "Package": "epiparameter",
       "Version": "0.0.0.9000",
@@ -747,6 +813,21 @@
       ],
       "Hash": "66fa5a16464666772f4929f8f5b2fc71"
     },
+    "fitdistrplus": {
+      "Package": "fitdistrplus",
+      "Version": "1.1-11",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "MASS",
+        "R",
+        "grDevices",
+        "methods",
+        "stats",
+        "survival"
+      ],
+      "Hash": "f40ef9686e85681a1ccbf33d9236aeb9"
+    },
     "fontawesome": {
       "Package": "fontawesome",
       "Version": "0.5.2",
@@ -1080,6 +1161,21 @@
       ],
       "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f"
     },
+    "htmlwidgets": {
+      "Package": "htmlwidgets",
+      "Version": "1.6.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "grDevices",
+        "htmltools",
+        "jsonlite",
+        "knitr",
+        "rmarkdown",
+        "yaml"
+      ],
+      "Hash": "04291cc45198225444a397606810ac37"
+    },
     "httr": {
       "Package": "httr",
       "Version": "1.4.7",
@@ -1106,6 +1202,29 @@
       ],
       "Hash": "99df65cfef20e525ed38c3d2577f7190"
     },
+    "igraph": {
+      "Package": "igraph",
+      "Version": "2.0.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "Matrix",
+        "R",
+        "cli",
+        "cpp11",
+        "grDevices",
+        "graphics",
+        "lifecycle",
+        "magrittr",
+        "methods",
+        "pkgconfig",
+        "rlang",
+        "stats",
+        "utils",
+        "vctrs"
+      ],
+      "Hash": "c3b7d801d722e26e4cd888e042bf9af5"
+    },
     "incidence2": {
       "Package": "incidence2",
       "Version": "2.2.3",
@@ -1215,6 +1334,16 @@
       ],
       "Hash": "7c5e89f04e72d6611c77451f6331a091"
     },
+    "lazyeval": {
+      "Package": "lazyeval",
+      "Version": "0.2.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "d908914ae53b04d4c0c0fd72ecc35370"
+    },
     "lifecycle": {
       "Package": "lifecycle",
       "Version": "1.0.4",
@@ -1902,6 +2031,42 @@
       ],
       "Hash": "960e2ae9e09656611e0b8214ad543207"
     },
+    "superspreading": {
+      "Package": "superspreading",
+      "Version": "0.2.0.9000",
+      "Source": "GitHub",
+      "Remotes": "epiverse-trace/epiparameter, epiverse-trace/bpmodels",
+      "RemoteType": "github",
+      "RemoteHost": "api.github.com",
+      "RemoteRepo": "superspreading",
+      "RemoteUsername": "epiverse-trace",
+      "RemotePkgRef": "epiverse-trace/superspreading",
+      "RemoteRef": "HEAD",
+      "RemoteSha": "4549ff929acb90aee04dc3b66a7fb30503affbc5",
+      "Requirements": [
+        "bpmodels",
+        "checkmate",
+        "rlang",
+        "stats"
+      ],
+      "Hash": "b6902d57c67ae90e59f588c01319aea7"
+    },
+    "survival": {
+      "Package": "survival",
+      "Version": "3.5-7",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "Matrix",
+        "R",
+        "graphics",
+        "methods",
+        "splines",
+        "stats",
+        "utils"
+      ],
+      "Hash": "b8e943d262c3da0b0febd3e04517c197"
+    },
     "sys": {
       "Package": "sys",
       "Version": "3.4.2",
@@ -1932,6 +2097,22 @@
       ],
       "Hash": "997aac9ad649e0ef3b97f96cddd5622b"
     },
+    "threejs": {
+      "Package": "threejs",
+      "Version": "0.3.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "base64enc",
+        "crosstalk",
+        "htmlwidgets",
+        "igraph",
+        "methods",
+        "stats"
+      ],
+      "Hash": "2ad32c3a8745e827977f394bc387e3b0"
+    },
     "tibble": {
       "Package": "tibble",
       "Version": "3.2.1",
@@ -2116,6 +2297,24 @@
       ],
       "Hash": "c826c7c4241b6fc89ff55aaea3fa7491"
     },
+    "visNetwork": {
+      "Package": "visNetwork",
+      "Version": "2.1.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "grDevices",
+        "htmltools",
+        "htmlwidgets",
+        "jsonlite",
+        "magrittr",
+        "methods",
+        "stats",
+        "utils"
+      ],
+      "Hash": "3e48b097e8d9a91ecced2ed4817a678d"
+    },
     "vroom": {
       "Package": "vroom",
       "Version": "1.6.5",
@@ -2142,6 +2341,19 @@
       ],
       "Hash": "390f9315bc0025be03012054103d227c"
     },
+    "webshot": {
+      "Package": "webshot",
+      "Version": "0.5.5",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "callr",
+        "jsonlite",
+        "magrittr"
+      ],
+      "Hash": "16858ee1aba97f902d24049d4a44ef16"
+    },
     "withr": {
       "Package": "withr",
       "Version": "3.0.0",