From 20ed5d233d16f966937c634f09d54b605e29f247 Mon Sep 17 00:00:00 2001
From: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date: Thu, 27 Apr 2023 22:49:30 +0100
Subject: [PATCH 1/2] default to neg bin obs model

---
 R/create.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/create.R b/R/create.R
index 7f5e8789f..6ef9ce2fc 100644
--- a/R/create.R
+++ b/R/create.R
@@ -396,7 +396,7 @@ create_gp_data <- function(gp = gp_opts(), data) {
 #' create_obs_model(obs_opts(week_length = 3), dates = dates)
 create_obs_model <- function(obs = obs_opts(), dates) {
   data <- list(
-    model_type = as.numeric(obs$family %in% "poisson"),
+    model_type = as.numeric(obs$family %in% "negbin"),
     phi_mean = obs$phi[1],
     phi_sd = obs$phi[2],
     week_effect = ifelse(obs$week_effect, obs$week_length, 1),

From 35fd1d77caf955bcdf46323fa0790644875aec47 Mon Sep 17 00:00:00 2001
From: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date: Thu, 27 Apr 2023 22:49:57 +0100
Subject: [PATCH 2/2] forecast correct part of cases in test/example

---
 R/estimate_secondary.R                   | 6 ++++--
 man/estimate_secondary.Rd                | 6 ++++--
 tests/testthat/test-estimate_secondary.R | 2 +-
 3 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/R/estimate_secondary.R b/R/estimate_secondary.R
index 1e9a6a59d..451bd8400 100644
--- a/R/estimate_secondary.R
+++ b/R/estimate_secondary.R
@@ -88,7 +88,9 @@
 #' plot(inc, primary = TRUE)
 #'
 #' # forecast future secondary cases from primary
-#' inc_preds <- forecast_secondary(inc, cases[seq_len(.N)][, value := primary])
+#' inc_preds <- forecast_secondary(
+#'   inc, cases[seq(61, .N)][, value := primary]
+#' )
 #' plot(inc_preds, new_obs = cases, from = "2020-05-01")
 #'
 #' #### Prevalence data example ####
@@ -116,7 +118,7 @@
 #'
 #' # forecast future secondary cases from primary
 #' prev_preds <- forecast_secondary(
-#'  prev, cases[10seq_len(.N)][, value := primary]
+#'  prev, cases[seq(101, .N)][, value := primary]
 #' )
 #' plot(prev_preds, new_obs = cases, from = "2020-06-01")
 #'
diff --git a/man/estimate_secondary.Rd b/man/estimate_secondary.Rd
index 4ba8aa211..720262ed4 100644
--- a/man/estimate_secondary.Rd
+++ b/man/estimate_secondary.Rd
@@ -112,7 +112,9 @@ inc <- estimate_secondary(cases[1:60],
 plot(inc, primary = TRUE)
 
 # forecast future secondary cases from primary
-inc_preds <- forecast_secondary(inc, cases[seq_len(.N)][, value := primary])
+inc_preds <- forecast_secondary(
+  inc, cases[seq(61, .N)][, value := primary]
+)
 plot(inc_preds, new_obs = cases, from = "2020-05-01")
 
 #### Prevalence data example ####
@@ -140,7 +142,7 @@ plot(prev, primary = TRUE)
 
 # forecast future secondary cases from primary
 prev_preds <- forecast_secondary(
- prev, cases[10seq_len(.N)][, value := primary]
+ prev, cases[seq(101, .N)][, value := primary]
 )
 plot(prev_preds, new_obs = cases, from = "2020-06-01")
 
diff --git a/tests/testthat/test-estimate_secondary.R b/tests/testthat/test-estimate_secondary.R
index 909aa5479..e155a913b 100644
--- a/tests/testthat/test-estimate_secondary.R
+++ b/tests/testthat/test-estimate_secondary.R
@@ -97,7 +97,7 @@ test_that("estimate_secondary can recover simulated parameters", {
 
 test_that("forecast_secondary can return values from simulated data and plot
            them", {
-  inc_preds <- forecast_secondary(inc, cases[seq_len(.N)][, value := primary])
+  inc_preds <- forecast_secondary(inc, cases[seq(61, .N)][, value := primary])
   expect_equal(names(inc_preds), c("samples", "forecast", "predictions"))
   # validation plot of observations vs estimates
   expect_error(plot(inc_preds, new_obs = cases, from = "2020-05-01"), NA)