add steps to cfr activity

Author: avallecam

instructors/data/02-practical-activity-2.R

@@ -3,6 +3,7 @@
 # Practical 2
 # Activity 2
 
+# step: fill in your room number
 room_number <- #<COMPLETE> replace with 1/2/3/4
 
 # Load packages -----------------------------------------------------------
@@ -12,6 +13,7 @@ library(tidyverse)
 
 
 # Read reported cases -----------------------------------------------------
+# step: Paste the URL links as a string to read input data.
 disease_dat <- readr::read_rds(
   #<COMPLETE>
 )
@@ -20,6 +22,7 @@ disease_dat
 
 
 # Create incidence object ------------------------------------------------
+# step: Fill in the argument to plot an incidence curve.
 disease_incidence <- disease_dat %>%
   incidence2::incidence(
     #<COMPLETE>
@@ -30,10 +33,17 @@ plot(disease_incidence)
 
 # Confirm {cfr} data input format ----------------------------------------
 
-# Is the input data already adapted to {cfr} input? 
+# step: Check if the column names in incidence data
+# match the {cfr} requirement of column names:
+# date, cases, deaths
+
+disease_dat
+
+# Is the input data already adapted to {cfr} input?
+# If yes, use:
 disease_adapted <- disease_dat
 # OR
-# Does the input data need to be adapted to {cfr}? 
+# If not, use cfr::prepare_data() to adapted it:
 disease_adapted <- disease_incidence %>%
   cfr::prepare_data(
     #<COMPLETE>
@@ -42,12 +52,14 @@ disease_adapted <- disease_incidence %>%
 disease_adapted
 
 # Access delay distribution -----------------------------------------------
+# step: Access to the probability distribution for the delay from case onset to death.
 
-# What delay you need to use to adjust the CFR?
+# What delay you need to use to adjust the CFR? (based on the disease)
 disease_delay <- epiparameter::#<COMPLETE>
 
 
 # Estimate naive and adjusted CFR ----------------------------------------
+# step: Estimate the naive and delay-adjusted CFR.
 
 # Estimate static CFR
 disease_adapted %>%
@@ -59,4 +71,6 @@ disease_adapted %>%
     delay_density = #<COMPLETE>
   )
 
+# step: Paste both outputs. Reply to questions.
+
 # nolint end