rename and update functionality for linelist handling

NAMESPACE

@@ -3,14 +3,14 @@
 S3method(add_mean_sd,default)
 S3method(add_mean_sd,gamma_samples)
 S3method(add_mean_sd,lognormal_samples)
-S3method(as_direct_model,epidist_linelist)
-S3method(as_epidist_linelist,data.frame)
-S3method(as_epidist_linelist,default)
-S3method(as_latent_individual,epidist_linelist)
+S3method(as_direct_model,epidist_linelist_data)
+S3method(as_epidist_linelist_data,data.frame)
+S3method(as_epidist_linelist_data,default)
+S3method(as_latent_individual,epidist_linelist_data)
 S3method(assert_epidist,default)
 S3method(assert_epidist,epidist_direct_model)
 S3method(assert_epidist,epidist_latent_individual)
-S3method(assert_epidist,epidist_linelist)
+S3method(assert_epidist,epidist_linelist_data)
 S3method(epidist,default)
 S3method(epidist_family_model,default)
 S3method(epidist_family_model,epidist_latent_individual)
@@ -25,7 +25,7 @@ S3method(epidist_stancode,default)
 S3method(epidist_stancode,epidist_latent_individual)
 export(add_mean_sd)
 export(as_direct_model)
-export(as_epidist_linelist)
+export(as_epidist_linelist_data)
 export(as_latent_individual)
 export(assert_epidist)
 export(epidist)
@@ -40,11 +40,11 @@ export(epidist_model_prior)
 export(epidist_prior)
 export(epidist_stancode)
 export(is_direct_model)
-export(is_epidist_linelist)
+export(is_epidist_linelist_data)
 export(is_latent_individual)
 export(new_epidist_direct_model)
 export(new_epidist_latent_individual)
-export(new_epidist_linelist)
+export(new_epidist_linelist_data)
 export(observe_process)
 export(predict_delay_parameters)
 export(predict_dpar)
@@ -57,18 +57,21 @@ importFrom(brms,bf)
 importFrom(brms,prior)
 importFrom(checkmate,assert_class)
 importFrom(checkmate,assert_data_frame)
+importFrom(checkmate,assert_date)
 importFrom(checkmate,assert_factor)
 importFrom(checkmate,assert_integer)
 importFrom(checkmate,assert_names)
 importFrom(checkmate,assert_numeric)
 importFrom(checkmate,assert_true)
 importFrom(cli,cli_abort)
+importFrom(cli,cli_alert_info)
 importFrom(cli,cli_inform)
 importFrom(cli,cli_warn)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,filter)
 importFrom(dplyr,mutate)
 importFrom(dplyr,select)
+importFrom(lubridate,days)
 importFrom(stats,as.formula)
 importFrom(stats,setNames)
 importFrom(tibble,tibble)

R/direct_model.R

@@ -7,14 +7,14 @@ as_direct_model <- function(data) {
   UseMethod("as_direct_model")
 }
 
-#' The direct model method for `epidist_linelist` objects
+#' The direct model method for `epidist_linelist_data` objects
 #'
-#' @param data An `epidist_linelist` object
-#' @method as_direct_model epidist_linelist
+#' @param data An `epidist_linelist_data` object
+#' @method as_direct_model epidist_linelist_data
 #' @family direct_model
 #' @autoglobal
 #' @export
-as_direct_model.epidist_linelist <- function(data) {
+as_direct_model.epidist_linelist_data <- function(data) {
   assert_epidist(data)
 
   data <- data |>

R/latent_individual.R

@@ -7,11 +7,11 @@ as_latent_individual <- function(data) {
   UseMethod("as_latent_individual")
 }
 
-#' @method as_latent_individual epidist_linelist
+#' @method as_latent_individual epidist_linelist_data
 #' @family latent_individual
 #' @autoglobal
 #' @export
-as_latent_individual.epidist_linelist <- function(data) {
+as_latent_individual.epidist_linelist_data <- function(data) {
   assert_epidist(data)
   data <- data |>
     mutate(