Merge pull request #443 from cmu-delphi/nh-quantiles

hardhat quantiles

Author: dajmcdon

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: epipredict
 Title: Basic epidemiology forecasting methods
-Version: 0.1.11
+Version: 0.1.12
 Authors@R: c(
     person("Daniel J.", "McDonald", , "[email protected]", role = c("aut", "cre")),
     person("Ryan", "Tibshirani", , "[email protected]", role = "aut"),
@@ -30,13 +30,12 @@ Depends:
 Imports:
     checkmate,
     cli,
-    distributional,
     dplyr,
     epiprocess (>= 0.10.4),
     generics,
     ggplot2,
     glue,
-    hardhat (>= 1.3.0),
+    hardhat (>= 1.4.1),
     lifecycle,
     lubridate,
     magrittr,
@@ -77,6 +76,5 @@ Remotes:
 Config/Needs/website: cmu-delphi/delphidocs
 Config/testthat/edition: 3
 Encoding: UTF-8
-LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2

NAMESPACE

@@ -2,8 +2,6 @@
 
 S3method(Add_model,epi_workflow)
 S3method(Add_model,workflow)
-S3method(Math,dist_quantiles)
-S3method(Ops,dist_quantiles)
 S3method(Remove_model,epi_workflow)
 S3method(Remove_model,workflow)
 S3method(Update_model,epi_workflow)
@@ -41,20 +39,14 @@ S3method(extract_frosting,default)
 S3method(extract_frosting,epi_workflow)
 S3method(extract_layers,frosting)
 S3method(extract_layers,workflow)
-S3method(extrapolate_quantiles,dist_default)
-S3method(extrapolate_quantiles,dist_quantiles)
-S3method(extrapolate_quantiles,distribution)
+S3method(extrapolate_quantiles,quantile_pred)
 S3method(fit,epi_workflow)
 S3method(flusight_hub_formatter,canned_epipred)
 S3method(flusight_hub_formatter,data.frame)
 S3method(forecast,epi_workflow)
-S3method(format,dist_quantiles)
-S3method(is.na,dist_quantiles)
-S3method(is.na,distribution)
 S3method(key_colnames,epi_workflow)
 S3method(key_colnames,recipe)
-S3method(mean,dist_quantiles)
-S3method(median,dist_quantiles)
+S3method(mean,quantile_pred)
 S3method(predict,epi_workflow)
 S3method(predict,flatline)
 S3method(prep,check_enough_train_data)
@@ -86,7 +78,6 @@ S3method(print,layer_naomit)
 S3method(print,layer_point_from_distn)
 S3method(print,layer_population_scaling)
 S3method(print,layer_predict)
-S3method(print,layer_predictive_distn)
 S3method(print,layer_quantile_distn)
 S3method(print,layer_residual_quantiles)
 S3method(print,layer_threshold)
@@ -101,7 +92,7 @@ S3method(print,step_lag_difference)
 S3method(print,step_naomit)
 S3method(print,step_population_scaling)
 S3method(print,step_training_window)
-S3method(quantile,dist_quantiles)
+S3method(quantile,quantile_pred)
 S3method(refresh_blueprint,default_epi_recipe_blueprint)
 S3method(residuals,flatline)
 S3method(run_mold,default_epi_recipe_blueprint)
@@ -112,25 +103,22 @@ S3method(slather,layer_naomit)
 S3method(slather,layer_point_from_distn)
 S3method(slather,layer_population_scaling)
 S3method(slather,layer_predict)
-S3method(slather,layer_predictive_distn)
 S3method(slather,layer_quantile_distn)
 S3method(slather,layer_residual_quantiles)
 S3method(slather,layer_threshold)
 S3method(slather,layer_unnest)
 S3method(snap,default)
-S3method(snap,dist_default)
-S3method(snap,dist_quantiles)
-S3method(snap,distribution)
+S3method(snap,quantile_pred)
 S3method(tidy,check_enough_train_data)
 S3method(tidy,frosting)
 S3method(tidy,layer)
 S3method(update,layer)
-S3method(vec_ptype_abbr,dist_quantiles)
-S3method(vec_ptype_full,dist_quantiles)
-S3method(weighted_interval_score,default)
-S3method(weighted_interval_score,dist_default)
-S3method(weighted_interval_score,dist_quantiles)
-S3method(weighted_interval_score,distribution)
+S3method(vec_arith,quantile_pred)
+S3method(vec_arith.numeric,quantile_pred)
+S3method(vec_arith.quantile_pred,numeric)
+S3method(vec_math,quantile_pred)
+S3method(vec_proxy_equal,quantile_pred)
+S3method(weighted_interval_score,quantile_pred)
 export("%>%")
 export(Add_model)
 export(Remove_model)
@@ -167,6 +155,7 @@ export(epi_workflow)
 export(extract_argument)
 export(extract_frosting)
 export(extract_layers)
+export(extract_quantile_levels)
 export(extrapolate_quantiles)
 export(filter)
 export(fit)
@@ -203,6 +192,7 @@ export(pivot_quantiles_longer)
 export(pivot_quantiles_wider)
 export(pivot_wider)
 export(prep)
+export(quantile_pred)
 export(quantile_reg)
 export(rand_id)
 export(remove_epi_recipe)
@@ -212,6 +202,7 @@ export(rename)
 export(select)
 export(slather)
 export(smooth_quantile_reg)
+export(snap)
 export(step_adjust_latency)
 export(step_climate)
 export(step_epi_ahead)
@@ -230,7 +221,6 @@ export(update_frosting)
 export(update_model)
 export(validate_layer)
 export(weighted_interval_score)
-import(distributional)
 import(epidatasets)
 import(epiprocess)
 import(parsnip)
@@ -290,9 +280,12 @@ importFrom(ggplot2,geom_linerange)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_ribbon)
 importFrom(glue,glue)
+importFrom(hardhat,extract_quantile_levels)
 importFrom(hardhat,extract_recipe)
+importFrom(hardhat,quantile_pred)
 importFrom(hardhat,refresh_blueprint)
 importFrom(hardhat,run_mold)
+importFrom(lifecycle,deprecated)
 importFrom(lubridate,"%m-%")
 importFrom(lubridate,leap_year)
 importFrom(lubridate,month)
@@ -325,14 +318,11 @@ importFrom(rlang,list2)
 importFrom(rlang,set_names)
 importFrom(rlang,sym)
 importFrom(stats,as.formula)
-importFrom(stats,family)
 importFrom(stats,lm)
-importFrom(stats,median)
 importFrom(stats,model.frame)
 importFrom(stats,na.omit)
 importFrom(stats,poly)
 importFrom(stats,predict)
-importFrom(stats,qnorm)
 importFrom(stats,quantile)
 importFrom(stats,residuals)
 importFrom(tibble,as_tibble)
@@ -347,12 +337,11 @@ importFrom(tidyr,unnest)
 importFrom(tidyselect,all_of)
 importFrom(utils,capture.output)
 importFrom(vctrs,as_list_of)
-importFrom(vctrs,field)
-importFrom(vctrs,new_rcrd)
 importFrom(vctrs,new_vctr)
+importFrom(vctrs,vec_arith)
+importFrom(vctrs,vec_arith.numeric)
 importFrom(vctrs,vec_cast)
-importFrom(vctrs,vec_data)
-importFrom(vctrs,vec_ptype_abbr)
-importFrom(vctrs,vec_ptype_full)
+importFrom(vctrs,vec_math)
+importFrom(vctrs,vec_proxy_equal)
 importFrom(vctrs,vec_recycle_common)
 importFrom(workflows,extract_preprocessor)

NEWS.md

@@ -17,6 +17,9 @@ Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.0.x will indicat
   has an `na_rm` argument.
 - Moves `epiprocess` out of depends (#440). No internals have changed, but downstream
   users may need to add `library(epiprocess)` to existing code.
+- Removes dependence on the `distributional` package, replacing the quantiles 
+  with `hardhat::quantile_pred()`. Some associated functions are deprecated with
+  `lifecycle` messages.
 
 ## Improvements
 
@@ -28,6 +31,8 @@ Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.0.x will indicat
 - Add `reference_date` as an argument to `epi_recipe()`
 - Add `step_climate()` to create "climate" predictor in forecast workflows
 - Add `climatological_forecaster()` to automatically create climate baselines
+- Replace `dist_quantiles()` with `hardhat::quantile_pred()`
+- Allow `quantile()` to threshold to an interval if desired (#434)
 
 ## Bug fixes
 

R/autoplot.R

@@ -243,7 +243,7 @@ plot_bands <- function(
   ntarget_dates <- dplyr::n_distinct(predictions$time_value)
 
   predictions <- predictions %>%
-    mutate(.pred_distn = dist_quantiles(quantile(.pred_distn, levels), levels)) %>%
+    mutate(.pred_distn = quantile_pred(quantile(.pred_distn, levels), levels)) %>%
     pivot_quantiles_wider(.pred_distn)
   qnames <- setdiff(names(predictions), innames)
 

R/climatological_forecaster.R

@@ -148,7 +148,7 @@ climatological_forecaster <- function(epi_data,
       .by = all_of(args_list$quantile_by_key)
     ) %>%
     rename(.pred_distn = climate_pred) %>%
-    mutate(.pred_distn = dist_quantiles(.pred_distn, args_list$quantile_levels))
+    mutate(.pred_distn = hardhat::quantile_pred(do.call(rbind, .pred_distn), args_list$quantile_levels))
   # combine them together
   climate_table <- climate_center %>%
     left_join(climate_quantiles, by = c(".idx", args_list$quantile_by_key)) %>%