From 52899a047dd31fb1cb740a20fd92cab992a70198 Mon Sep 17 00:00:00 2001
From: Andree Valle Campos <avallecam@gmail.com>
Date: Thu, 21 Mar 2024 21:16:45 +0000
Subject: [PATCH] add epiparameter get_parameters for epinow2 (#4)

---
 episodes/delays-functions.Rmd | 48 +++++++++++++++++++++++------------
 1 file changed, 32 insertions(+), 16 deletions(-)

diff --git a/episodes/delays-functions.Rmd b/episodes/delays-functions.Rmd
index 16d18d83..94e2219f 100644
--- a/episodes/delays-functions.Rmd
+++ b/episodes/delays-functions.Rmd
@@ -40,16 +40,6 @@ This episode requires you to be familiar with:
 
 <!-- to activate for EpiNow2@dist-interfase
 
-But still, we need to extract them as usable numbers. We use `epiparameter::get_parameters()` for this:
-
-```{r}
-covid_serialint_parameters <- epiparameter::get_parameters(covid_serialint)
-
-covid_serialint_parameters
-```
-
-This gets a vector of class `<numeric>` useful as input for any other package! 
-
 :::::::::::::::::: callout
 
 If we write the `[]` next to the last object create like in `covid_serialint_parameters[]`, within `[]` we can use the 
@@ -342,6 +332,26 @@ quantile(covid_serialint_discrete, p = 0.999) %>%
 
 :::::::::::::::::::::::::::::::::::::::::::
 
+:::::::::::::::::::::::::::::: callout
+
+### Log normal distributions
+
+If you need the log normal **distribution parameters** instead of the summary statistics, we can use `epiparameter::get_parameters()`:
+
+```{r}
+covid_serialint_parameters <- 
+  epiparameter::get_parameters(covid_serialint)
+
+covid_serialint_parameters
+```
+
+This gets a vector of class `<numeric>` ready to use as input for any other package!
+
+**BONUS TIP:** If we write the `[]` next to the last object create like in `covid_serialint_parameters[]`, within `[]` we can use the 
+Tab key <kbd>↹</kbd> 
+to use the [code completion feature](https://support.posit.co/hc/en-us/articles/205273297-Code-Completion-in-the-RStudio-IDE) and have a quick access to `covid_serialint_parameters["meanlog"]` and `covid_serialint_parameters["sdlog"]`. We invite you to try this out in code chunks and the R console!
+
+::::::::::::::::::::::::::::::
 
 ## Plug-in `{epiparameter}` to `{EpiNow2}`
 
@@ -354,8 +364,8 @@ Now we can plug everything into the `EpiNow2::dist_spec()` function!
 ```{r}
 serial_interval_covid <-
   dist_spec(
-    mean = covid_serialint$summary_stats$mean,
-    sd = covid_serialint$summary_stats$sd,
+    mean = covid_serialint_parameters["meanlog"],
+    sd = covid_serialint_parameters["sdlog"],
     max = covid_serialint_discrete_max,
     distribution = "lognormal"
   )
@@ -521,10 +531,13 @@ covid_serialint_discrete_max <-
   discretise() %>%
   quantile(p = 0.999)
 
+covid_serialint_parameters <- 
+  epiparameter::get_parameters(covid_serialint)
+
 covid_serial_interval <-
   dist_spec(
-    mean = covid_serialint$summary_stats$mean,
-    sd = covid_serialint$summary_stats$sd,
+    mean = covid_serialint_parameters["meanlog"],
+    sd = covid_serialint_parameters["sdlog"],
     max = covid_serialint_discrete_max,
     distribution = "lognormal"
   )
@@ -543,10 +556,13 @@ covid_incubation_discrete_max <-
   discretise() %>%
   quantile(p = 0.999)
 
+covid_incubation_parameters <- 
+  epiparameter::get_parameters(covid_incubation)
+
 covid_incubation_time <-
   dist_spec(
-    mean = covid_incubation$summary_stats$mean,
-    sd = covid_incubation$summary_stats$sd,
+    mean = covid_incubation_parameters["meanlog"],
+    sd = covid_incubation_parameters["sdlog"],
     max = covid_incubation_discrete_max,
     distribution = "lognormal" # do not forget this!
   )