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Merge pull request #328 from cmu-delphi/325-workflow-adj
325 workflow adj
2 parents 0c3236c + f043918 commit 5aa7828

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‎NAMESPACE

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@@ -1,8 +1,13 @@
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# Generated by roxygen2: do not edit by hand
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S3method(Add_model,epi_workflow)
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S3method(Add_model,workflow)
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S3method(Math,dist_quantiles)
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S3method(Ops,dist_quantiles)
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S3method(add_model,epi_workflow)
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S3method(Remove_model,epi_workflow)
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S3method(Remove_model,workflow)
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S3method(Update_model,epi_workflow)
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S3method(Update_model,workflow)
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S3method(adjust_epi_recipe,epi_recipe)
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S3method(adjust_epi_recipe,epi_workflow)
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S3method(adjust_frosting,epi_workflow)
@@ -92,7 +97,6 @@ S3method(print,step_population_scaling)
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S3method(print,step_training_window)
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S3method(quantile,dist_quantiles)
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S3method(refresh_blueprint,default_epi_recipe_blueprint)
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S3method(remove_model,epi_workflow)
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S3method(residuals,flatline)
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S3method(run_mold,default_epi_recipe_blueprint)
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S3method(slather,layer_add_forecast_date)
@@ -115,10 +119,12 @@ S3method(tidy,check_enough_train_data)
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S3method(tidy,frosting)
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S3method(tidy,layer)
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S3method(update,layer)
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S3method(update_model,epi_workflow)
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S3method(vec_ptype_abbr,dist_quantiles)
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S3method(vec_ptype_full,dist_quantiles)
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export("%>%")
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export(Add_model)
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export(Remove_model)
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export(Update_model)
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export(add_epi_recipe)
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export(add_frosting)
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export(add_layer)

‎R/epi_workflow.R

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}
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#' Add a model to an `epi_workflow`
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#'
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#' @seealso [workflows::add_model()]
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#' - `add_model()` adds a parsnip model to the `epi_workflow`.
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#'
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#' - `remove_model()` removes the model specification as well as any fitted
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#' model object. Any extra formulas are also removed.
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#'
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#' - `update_model()` first removes the model then adds the new
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#' specification to the workflow.
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#'
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#' @details
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#' Has the same behaviour as [workflows::add_model()] but also ensures
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#' that the returned object is an `epi_workflow`.
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#'
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#' @inheritParams workflows::add_model
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#'
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#' @param x An `epi_workflow`.
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#'
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#' @param spec A parsnip model specification.
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#'
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#' @param ... Not used.
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#'
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#' @return
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#' `x`, updated with a new, updated, or removed model.
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#'
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#' @export
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#' @examples
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#' jhu <- case_death_rate_subset %>%
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#' dplyr::filter(
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#' time_value > "2021-11-01",
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#' geo_value %in% c("ak", "ca", "ny")
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#' )
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#'
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#' r <- epi_recipe(jhu) %>%
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#' step_epi_lag(death_rate, lag = c(0, 7, 14)) %>%
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#' step_epi_ahead(death_rate, ahead = 7)
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#'
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#' rf_model <- rand_forest(mode = "regression")
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#'
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#' wf <- epi_workflow(r)
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#'
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#' wf <- wf %>% add_model(rf_model)
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#' wf
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#'
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#' lm_model <- parsnip::linear_reg()
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#'
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#' wf <- update_model(wf, lm_model)
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#' wf
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#'
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#' wf <- remove_model(wf)
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#' wf
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#' @export
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add_model <- function(x, spec, ..., formula = NULL) {
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UseMethod("add_model")
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}
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#' @rdname add_model
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#' @export
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remove_model <- function(x) {
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UseMethod("remove_model")
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}
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#' @rdname add_model
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#' @export
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update_model <- function(x, spec, ..., formula = NULL) {
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UseMethod("update_model")
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}
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#' @rdname add_model
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#' @export
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add_model.epi_workflow <- function(x, spec, ..., formula = NULL) {
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workflows::add_model(x, spec, ..., formula = formula)
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}
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#' @rdname add_model
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#' @export
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remove_model.epi_workflow <- function(x) {
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workflows:::validate_is_workflow(x)
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if (!workflows:::has_spec(x)) {
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rlang::warn("The workflow has no model to remove.")
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}
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new_epi_workflow(
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pre = x$pre,
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fit = workflows:::new_stage_fit(),
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post = x$post,
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trained = FALSE
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)
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}
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#' @rdname add_model
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#' @export
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update_model.epi_workflow <- function(x, spec, ..., formula = NULL) {
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rlang::check_dots_empty()
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x <- remove_model(x)
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workflows::add_model(x, spec, ..., formula = formula)
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}
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#' Fit an `epi_workflow` object
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#'
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#' @description

‎R/model-methods.R

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#' Add a model to an `epi_workflow`
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#'
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#' @seealso [workflows::add_model()]
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#' - `Add_model()` adds a parsnip model to the `epi_workflow`.
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#'
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#' - `Remove_model()` removes the model specification as well as any fitted
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#' model object. Any extra formulas are also removed.
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#'
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#' - `Update_model()` first removes the model then adds the new
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#' specification to the workflow.
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#'
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#' @details
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#' Has the same behaviour as [workflows::add_model()] but also ensures
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#' that the returned object is an `epi_workflow`.
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#'
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#' This family is called `Add_*` / `Update_*` / `Remove_*` to avoid
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#' masking the related functions in `{workflows}`. We also provide
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#' aliases with the lower-case names. However, in the event that
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#' `{workflows}` is loaded after `{epipredict}`, these may fail to function
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#' properly.
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#'
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#' @inheritParams workflows::add_model
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#'
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#' @param x An `epi_workflow`.
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#'
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#' @param spec A parsnip model specification.
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#'
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#' @param ... Not used.
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#'
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#' @return
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#' `x`, updated with a new, updated, or removed model.
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#'
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#' @export
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#' @examples
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#' jhu <- case_death_rate_subset %>%
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#' dplyr::filter(
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#' time_value > "2021-11-01",
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#' geo_value %in% c("ak", "ca", "ny")
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#' )
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#'
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#' r <- epi_recipe(jhu) %>%
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#' step_epi_lag(death_rate, lag = c(0, 7, 14)) %>%
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#' step_epi_ahead(death_rate, ahead = 7)
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#'
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#' rf_model <- rand_forest(mode = "regression")
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#'
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#' wf <- epi_workflow(r)
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#'
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#' wf <- wf %>% Add_model(rf_model)
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#' wf
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#'
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#' lm_model <- parsnip::linear_reg()
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#'
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#' wf <- Update_model(wf, lm_model)
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#' wf
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#'
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#' wf <- Remove_model(wf)
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#' wf
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#' @export
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Add_model <- function(x, spec, ..., formula = NULL) {
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UseMethod("Add_model")
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}
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#' @rdname Add_model
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#' @export
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Remove_model <- function(x) {
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UseMethod("Remove_model")
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}
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#' @rdname Add_model
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#' @export
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Update_model <- function(x, spec, ..., formula = NULL) {
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UseMethod("Update_model")
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}
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#' @rdname Add_model
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#' @export
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Add_model.epi_workflow <- function(x, spec, ..., formula = NULL) {
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workflows::add_model(x, spec, ..., formula = formula)
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}
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82+
#' @rdname Add_model
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#' @export
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Remove_model.epi_workflow <- function(x) {
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workflows:::validate_is_workflow(x)
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87+
if (!workflows:::has_spec(x)) {
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rlang::warn("The workflow has no model to remove.")
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}
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new_epi_workflow(
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pre = x$pre,
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fit = workflows:::new_stage_fit(),
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post = x$post,
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trained = FALSE
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)
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}
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#' @rdname Add_model
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#' @export
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Update_model.epi_workflow <- function(x, spec, ..., formula = NULL) {
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rlang::check_dots_empty()
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x <- Remove_model(x)
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Add_model(x, spec, ..., formula = formula)
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}
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#' @rdname Add_model
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#' @export
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Add_model.workflow <- workflows::add_model
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#' @rdname Add_model
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#' @export
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Remove_model.workflow <- workflows::remove_model
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#' @rdname Add_model
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#' @export
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Update_model.workflow <- workflows::update_model
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# Aliases -----------------------------------------------------------------
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#' @rdname Add_model
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#' @export
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add_model <- Add_model
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#' @rdname Add_model
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#' @export
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remove_model <- Remove_model
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#' @rdname Add_model
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#' @export
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update_model <- Update_model

‎_pkgdown.yml

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type: light
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articles:
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- title: Get started
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navbar: ~
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contents:
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- epipredict
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- preprocessing-and-models
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- arx-classifier
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- articles/update
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- title: Get started
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navbar: ~
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contents:
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- epipredict
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- preprocessing-and-models
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- arx-classifier
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- update
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- title: Advanced methods
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contents:
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- articles/sliding
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- articles/smooth-qr
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- articles/symptom-surveys
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- panel-data
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- title: Advanced methods
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contents:
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- articles/sliding
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- articles/smooth-qr
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- articles/symptom-surveys
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- panel-data
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repo:
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url:
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- smooth_quantile_reg
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- title: Custom panel data forecasting workflows
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contents:
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- epi_recipe
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- epi_workflow
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- add_epi_recipe
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- adjust_epi_recipe
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- add_model
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- predict.epi_workflow
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- fit.epi_workflow
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- augment.epi_workflow
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- forecast.epi_workflow
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- epi_recipe
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- epi_workflow
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- add_epi_recipe
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- adjust_epi_recipe
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- Add_model
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- predict.epi_workflow
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- fit.epi_workflow
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- augment.epi_workflow
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- forecast.epi_workflow
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- title: Epi recipe preprocessing steps
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contents:
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- starts_with("step_")

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