differences for PR #151

config.yaml

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+#------------------------------------------------------------
+# Values for this lesson.
+#------------------------------------------------------------
+
+# Which carpentry is this (swc, dc, lc, or cp)?
+# swc: Software Carpentry
+# dc: Data Carpentry
+# lc: Library Carpentry
+# cp: Carpentries (to use for instructor training for instance)
+# incubator: The Carpentries Incubator
+carpentry: 'epiverse-trace'
+
+# Overall title for pages.
+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:
+
+# Comma-separated list of keywords for the lesson
+keywords: 'forecasts, epidemic models, interventions'
+
+# Life cycle stage of the lesson
+# possible values: pre-alpha, alpha, beta, stable
+life_cycle: 'pre-alpha'
+
+# License of the lesson materials (recommended CC-BY 4.0)
+license: 'CC-BY 4.0'
+
+# Link to the source repository for this lesson
+source: 'https://github.com/epiverse-trace/tutorials-middle'
+
+# Default branch of your lesson
+branch: 'main'
+
+# Who to contact if there are any issues
+contact: '[email protected]'
+
+# Navigation ------------------------------------------------
+#
+# Use the following menu items to specify the order of
+# individual pages in each dropdown section. Leave blank to
+# include all pages in the folder.
+#
+# Example -------------
+#
+# episodes:
+# - introduction.md
+# - first-steps.md
+#
+# learners:
+# - setup.md
+#
+# instructors:
+# - instructor-notes.md
+#
+# profiles:
+# - one-learner.md
+# - another-learner.md
+
+# Order of episodes in your lesson
+episodes:
+- delays-access.Rmd
+- quantify-transmissibility.Rmd
+- delays-functions.Rmd
+- create-forecast.Rmd
+- severity-static.Rmd
+- superspreading-estimate.Rmd
+- superspreading-simulate.Rmd
+
+# Information for Learners
+learners:
+
+# Information for Instructors
+instructors:
+
+# Learner 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
+sandpaper: epiverse-trace/sandpaper@patch-renv-github-bug

data-covid-filter.R

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+
+library(tidyverse)
+library(incidence2)
+
+# read data ---------------------------------------------------------------
+
+incidence_class <- incidence2::covidregionaldataUK %>%
+  as_tibble() %>%
+  filter(region == "London") %>%
+  # preprocess missing values
+  tidyr::replace_na(
+    list(
+      deaths_new = 0,
+      cases_new = 0
+    )
+  ) %>%
+  # compute the daily incidence
+  incidence2::incidence(
+    date_index = "date",
+    counts = c("cases_new","deaths_new"),
+    date_names_to = "date",
+    complete_dates = TRUE
+  ) %>%
+  identity()
+
+
+incidence_class %>%
+  # filter(date < ymd(20200415)) %>%
+  # filter(date < ymd(20200701)) %>%
+  plot()
+
+covid_incidence2 <- incidence_class %>%
+  cfr::prepare_data(
+    cases_variable = "cases_new",
+    deaths_variable = "deaths_new") %>%
+  as_tibble()
+
+covid_incidence2
+
+covid_incidence2 %>%
+  write_rds(file.path("episodes", "data", "covid_490days.rds"))
+
+covid_incidence2 %>%
+  filter(date < ymd(20200415)) %>%
+  write_rds(file.path("episodes", "data", "covid_150days.rds"))
+
+covid_incidence2 %>%
+  filter(date < ymd(20200701)) %>%
+  write_rds(file.path("episodes", "data", "covid_300days.rds"))