Adding changes to documentation

Author: SofiaOtero

R/aedseo.R

@@ -36,6 +36,7 @@
 #'   disease threshold?
 #'   - 'seasonal_onset_alarm': Logical. Is there a seasonal onset alarm?
 #'   - 'converged': Logical. Was the IWLS judged to have converged?
+#'   - 'skipped_window': Logical. Was the window skipped?
 #'
 #' @export
 #'

man/aedseo.Rd

@@ -97,4 +97,4 @@ test_that("Test if it works with weeks with NA values", {
   expect_false(all(aedseo_poisson_na$converged))
   # Count if the skipped windows are = ones in output
   expect_equal(skipped_window_count, sum(aedseo_poisson_na$skipped_window))
-})
+})

tests/testthat/test-aedseo.R

@@ -174,7 +174,7 @@ In the following figure, the simulated data (solid circles) is visualized alongs
 plot(tsd_data)
 ```
 
-Next, the time series data object is passed to the `aedseo()` function. Here, a window width of $k=5$ is specified, meaning that a total of 5 weeks is used in the local estimate of the exponential growth rate. Additionally, a 95\% confidence interval is specified. Finally, the exponential growth rate is estimated using quasi-Poisson regression to account for overdispersion in the data.
+Next, the time series data object is passed to the `aedseo()` function. Here, a window width of $k=5$ is specified, meaning that a total of 5 weeks is used in the local estimate of the exponential growth rate. $na_percentage_allowed = 0.4$ defines how many percentage of the observables in the k window that are allowed to be NA, here 0.4*5 = 20%. Additionally, a 95\% confidence interval is specified. Finally, the exponential growth rate is estimated using quasi-Poisson regression to account for overdispersion in the data.
 
 ```{r}
 # Apply the 'aedseo' algorithm
@@ -183,7 +183,8 @@ aedseo_results <- aedseo(
   k = 5,
   level = 0.95,
   disease_threshold = 2000,
-  family = "quasipoisson"
+  family = "quasipoisson",
+  na_percentage_allowed = 0.4
 )
 ```