fix examples

R/create.R

@@ -569,7 +569,7 @@ create_initial_conditions <- function(data) {
       ))
     }
     if (data$week_effect > 0) {
-      out$day_of_week_simplex = rep(1 / data$week_effect, data$week_effect)
+      out$day_of_week_simplex = array(rep(1 / data$week_effect, data$week_effect))
     }
     return(out)
   }

R/report.R

@@ -28,7 +28,7 @@
 #'
 #' # run model
 #' out <- estimate_infections(cases,
-#'   samples = 100,
+#'   stan = stan_opts(samples = 100),
 #'   generation_time = generation_time,
 #'   delays = delay_opts(incubation_period, reporting_delay),
 #'   rt = NULL
@@ -55,13 +55,13 @@ report_cases <- function(case_estimates,
 
   # define delay distributions
   delay_defs <- purrr::map(
-    delays,
+    seq_along(delays$delays),
     ~ EpiNow2::lognorm_dist_def(
-      mean = .$mean,
-      mean_sd = .$mean_sd,
-      sd = .$sd,
-      sd_sd = .$sd_sd,
-      max_value = .$max,
+      mean = delays$delay_mean_mean[.x],
+      mean_sd = delays$delay_mean_sd[.x],
+      sd = delays$delay_sd_mean[.x],
+      sd_sd = delays$delay_sd_sd[.x],
+      max_value = delays$delay_max[.x],
       samples = samples
     )
   )
@@ -248,7 +248,7 @@ report_summary <- function(summarised_estimates,
 #'
 #' # run model
 #' out <- estimate_infections(cases,
-#'   samples = 100,
+#'   stan = stan_opts(samples = 100),
 #'   generation_time = generation_time,
 #'   delays = delay_opts(incubation_period, reporting_delay),
 #'   rt = NULL

R/simulate_infections.R

@@ -60,7 +60,7 @@
 #' )
 #'
 #' # update Rt trajectory and simulate new infections using it
-#' R <- c(rep(NA_real_, 40), rep(0.5, 10), rep(0.8, 7))
+#' R <- c(rep(NA_real_, 26), rep(0.5, 10), rep(0.8, 7))
 #' sims <- simulate_infections(est, R)
 #' plot(sims)
 #'

R/summarise.R

@@ -471,7 +471,7 @@ summarise_key_measures <- function(regional_results = NULL,
 #' # example delays
 #' generation_time <- get_generation_time(disease = "SARS-CoV-2", source = "ganyani")
 #' incubation_period <- get_incubation_period(disease = "SARS-CoV-2", source = "lauer")
-#' reporting_delay <- example_delay(rlnorm(100, log(6), 1), max_value = 15)
+#' reporting_delay <- estimate_delay(rlnorm(100, log(6), 1), max_value = 15)
 #'
 #' cases <- example_confirmed[1:30]
 #' cases <- data.table::rbindlist(list(
@@ -484,7 +484,7 @@ summarise_key_measures <- function(regional_results = NULL,
 #'   reported_cases = cases,
 #'   generation_time = generation_time,
 #'   delays = delay_opts(incubation_period, reporting_delay),
-#'   samples = 100, stan_args = list(warmup = 100),
+#'   stan = stan_opts(samples = 100, warmup = 100),
 #'   output = c("region", "timing")
 #' )
 #'