Merge pull request #380 from epiforecasts/fixes

fix errors introduced in #378
epiforecasts · Apr 27, 2023 · c38963d · c38963d
2 parents 304043e + 35fd1d7
commit c38963d
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Showing 4 changed files with 10 additions and 6 deletions.
diff --git 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),

diff --git 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
diff --git 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)