check vignettes

epinowcast · Nov 15, 2024 · d13f0ed · d13f0ed
1 parent db2acdd
commit d13f0ed
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Showing 4 changed files with 15 additions and 14 deletions.
diff --git a/vignettes/approx-inference.Rmd b/vignettes/approx-inference.Rmd
@@ -133,10 +133,11 @@ We now prepare the data for fitting with the latent individual model, and perfor
 linelist <- as_epidist_linelist(
   obs_cens_trunc_samp$ptime_lwr,
   obs_cens_trunc_samp$ptime_upr,
-  obs_cens_trunc_samp$sdate_lwr,
-  obs_cens_trunc_samp$sdate_upr,
+  obs_cens_trunc_samp$stime_lwr,
+  obs_cens_trunc_samp$stime_upr,
   obs_time = obs_cens_trunc_samp$obs_time
 )
+
 data <- as_latent_individual(linelist)
 
 t <- proc.time()

diff --git a/vignettes/ebola.Rmd b/vignettes/ebola.Rmd
@@ -219,10 +219,11 @@ To prepare the data for use with the latent individual model, we set `obs_cens`
 linelist <- as_epidist_linelist(
   obs_cens$ptime_lwr,
   obs_cens$ptime_upr,
-  obs_cens$sdate_lwr,
-  obs_cens$sdate_upr,
+  obs_cens$stime_lwr,
+  obs_cens$stime_upr,
   obs_time = obs_cens$obs_time
 )
+
 obs_prep <- as_latent_individual(linelist)
 head(obs_prep)
 ```

diff --git a/vignettes/epidist.Rmd b/vignettes/epidist.Rmd
@@ -250,8 +250,8 @@ To do so, we first prepare the `data` using `as_latent_individual()`:
 linelist <- as_epidist_linelist(
   obs_cens_trunc_samp$ptime_lwr,
   obs_cens_trunc_samp$ptime_upr,
-  obs_cens_trunc_samp$sdate_lwr,
-  obs_cens_trunc_samp$sdate_upr,
+  obs_cens_trunc_samp$stime_lwr,
+  obs_cens_trunc_samp$stime_upr,
   obs_time = obs_cens_trunc_samp$obs_time
 )
 

diff --git a/vignettes/faq.Rmd b/vignettes/faq.Rmd
@@ -47,14 +47,13 @@ obs_cens_trunc_samp <- simulate_gillespie(seed = 101) |>
   filter(.data$stime_upr <= obs_time) |>
   slice_sample(n = sample_size, replace = FALSE)
 
-# Note: this functionality will be integrated into the package shortly
-as_epidist_linelist_time <- function(data) {
-  class(data) <- c("epidist_linelist", class(data))
-  epidist_validate_data(data)
-  return(data)
-}
-
-linelist <- as_epidist_linelist_time(obs_cens_trunc_samp)
+linelist <- as_epidist_linelist(
+  obs_cens_trunc_samp$ptime_lwr,
+  obs_cens_trunc_samp$ptime_upr,
+  obs_cens_trunc_samp$stime_lwr,
+  obs_cens_trunc_samp$stime_upr,
+  obs_time = obs_cens_trunc_samp$obs_time
+)
 data <- as_latent_individual(linelist)
 
 fit <- epidist(