From 5a53e3a4addec72f81f556adc6a6cc411cfef8c2 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: Thu, 22 Feb 2024 15:14:00 +0100
Subject: [PATCH 1/2] Get EpiEstim chunk to work with SI passed as epidist

---
 .../skeleton/rmdchunks/EpiEstim.Rmd                 | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiEstim.Rmd b/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiEstim.Rmd
index 65551c2f..ba8855b2 100644
--- a/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiEstim.Rmd
+++ b/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/EpiEstim.Rmd
@@ -16,13 +16,12 @@ library(EpiEstim)
 # Function to process a distrcrete object and output `si_discr` argument for
 # EpiEstim::make_config
 
-wrap_si <- function(x) {
-  stopifnot(inherits(x, "distcrete"))
-  max_x <- x$q(0.999)
-  x <- si$d(seq_len(max_x))
-  x[1] <- 0
-  x <- x / sum(x)
-  x
+wrap_si <- function(si) {
+  domain <- seq(1L, to = si$prob_dist$qf(0.999), by = 1L)
+  pmf <- si$prob_dist$d(domain)
+  pmf[1] <- 0
+  pmf <- pmf / sum(pmf)
+  pmf
 }
 
 

From 90bf4bff433a6ba95c45b018a417dce6d3e24223 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: Thu, 22 Feb 2024 15:14:15 +0100
Subject: [PATCH 2/2] Get i2extras to work with SI passed as epidist

---
 .../templates/transmissibility/skeleton/rmdchunks/i2extras.Rmd  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/i2extras.Rmd b/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/i2extras.Rmd
index 44cd846e..b03fdc07 100644
--- a/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/i2extras.Rmd
+++ b/inst/rmarkdown/templates/transmissibility/skeleton/rmdchunks/i2extras.Rmd
@@ -141,7 +141,7 @@ This section contains:
 
 ```{r }
 res_R_wl <- last_trends %>%
-  mutate(R = map(model, epitrix::lm2R0_sample, w = si, 500)) %>%
+  mutate(R = map(model, epitrix::lm2R0_sample, w = si$prob_dist$d(si_x))) %>%
   dplyr::select({{ group_var }}, R) %>%
   unnest(R)