diff --git a/R/diagnostics.R b/R/diagnostics.R index 828c9959c..19d26d848 100644 --- a/R/diagnostics.R +++ b/R/diagnostics.R @@ -28,7 +28,7 @@ #' sdate_lwr = "date_of_sample_tested" #' ) |> #' as_epidist_aggregate_data() |> -#' as_epidist_naive_model() |> +#' as_epidist_marginal_model() |> #' epidist(chains = 2, cores = 2, refresh = ifelse(interactive(), 250, 0)) #' epidist_diagnostics(fit) epidist_diagnostics <- function(fit) { diff --git a/R/epidist.R b/R/epidist.R index 10386f78d..e510291ff 100644 --- a/R/epidist.R +++ b/R/epidist.R @@ -43,7 +43,7 @@ #' sdate_lwr = "date_of_sample_tested" #' ) |> #' as_epidist_aggregate_data() |> -#' as_epidist_naive_model() |> +#' as_epidist_marginal_model() |> #' epidist(chains = 2, cores = 2, refresh = ifelse(interactive(), 250, 0)) #' #' summary(fit) diff --git a/R/marginal_model.R b/R/marginal_model.R index 562b20f31..cbc796170 100644 --- a/R/marginal_model.R +++ b/R/marginal_model.R @@ -222,8 +222,7 @@ epidist_formula_model.epidist_marginal_model <- function( #' #' This method transforms data into the format required by the marginal model #' by: -#' 1. Identifying required columns for the marginal model using -#' [.marginal_required_cols()] +#' 1. Identifying required columns for the marginal model #' 2. Summarising the data by counting unique combinations of these columns and #' any variables in the model formula using [.summarise_n_by_formula()] #' 3. Converting the summarised data to a marginal model object using diff --git a/R/naive_model.R b/R/naive_model.R index c02524f88..3ebba5229 100644 --- a/R/naive_model.R +++ b/R/naive_model.R @@ -143,8 +143,7 @@ epidist_formula_model.epidist_naive_model <- function( #' #' This method transforms data into the format required by the naive model #' by: -#' 1. Identifying required columns for the naive model using -#' [.naive_required_cols()] +#' 1. Identifying required columns for the naive model #' 2. Summarising the data by counting unique combinations of these columns and #' any variables in the model formula using [.summarise_n_by_formula()] #' 3. Converting the summarised data to a naive model object using diff --git a/man/epidist.Rd b/man/epidist.Rd index 7bb69f824..32caa7dac 100644 --- a/man/epidist.Rd +++ b/man/epidist.Rd @@ -52,4 +52,16 @@ These two later options may be useful for model debugging and extensions.} \description{ Fit epidemiological delay distributions using a \code{brms} interface } +\examples{ +fit <- sierra_leone_ebola_data |> + as_epidist_linelist_data( + pdate_lwr = "date_of_symptom_onset", + sdate_lwr = "date_of_sample_tested" + ) |> + as_epidist_aggregate_data() |> + as_epidist_marginal_model() |> + epidist(chains = 2, cores = 2, refresh = ifelse(interactive(), 250, 0)) + +summary(fit) +} \concept{fit} diff --git a/man/epidist_diagnostics.Rd b/man/epidist_diagnostics.Rd index c25181c91..37093f909 100644 --- a/man/epidist_diagnostics.Rd +++ b/man/epidist_diagnostics.Rd @@ -38,8 +38,8 @@ fit <- sierra_leone_ebola_data |> sdate_lwr = "date_of_sample_tested" ) |> as_epidist_aggregate_data() |> - as_epidist_naive_model() |> - epidist() + as_epidist_marginal_model() |> + epidist(chains = 2, cores = 2, refresh = ifelse(interactive(), 250, 0)) epidist_diagnostics(fit) } \concept{diagnostics} diff --git a/man/epidist_transform_data_model.epidist_marginal_model.Rd b/man/epidist_transform_data_model.epidist_marginal_model.Rd index f79757911..930baef98 100644 --- a/man/epidist_transform_data_model.epidist_marginal_model.Rd +++ b/man/epidist_transform_data_model.epidist_marginal_model.Rd @@ -19,8 +19,7 @@ This method transforms data into the format required by the marginal model by: \enumerate{ -\item Identifying required columns for the marginal model using -\code{\link[=.marginal_required_cols]{.marginal_required_cols()}} +\item Identifying required columns for the marginal model \item Summarising the data by counting unique combinations of these columns and any variables in the model formula using \code{\link[=.summarise_n_by_formula]{.summarise_n_by_formula()}} \item Converting the summarised data to a marginal model object using diff --git a/man/epidist_transform_data_model.epidist_naive_model.Rd b/man/epidist_transform_data_model.epidist_naive_model.Rd index a5c5a3d95..5e0a8746e 100644 --- a/man/epidist_transform_data_model.epidist_naive_model.Rd +++ b/man/epidist_transform_data_model.epidist_naive_model.Rd @@ -19,8 +19,7 @@ This method transforms data into the format required by the naive model by: \enumerate{ -\item Identifying required columns for the naive model using -\code{\link[=.naive_required_cols]{.naive_required_cols()}} +\item Identifying required columns for the naive model \item Summarising the data by counting unique combinations of these columns and any variables in the model formula using \code{\link[=.summarise_n_by_formula]{.summarise_n_by_formula()}} \item Converting the summarised data to a naive model object using diff --git a/tests/testthat/test-int-direct_model.R b/tests/testthat/test-int-naive_model.R similarity index 100% rename from tests/testthat/test-int-direct_model.R rename to tests/testthat/test-int-naive_model.R