Merge pull request #247 from cmu-delphi/v0.0.6

v0.0.6 to main

Author: dajmcdon

.Rbuildignore

@@ -12,3 +12,4 @@
 ^musings$
 ^data-raw$
 ^vignettes/articles$
+^.git-blame-ignore-revs$

.github/workflows/styler.yml

@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   workflow_dispatch:
-  pullrequest:
+  pull_request:
     paths:
       [
         "**.[rR]",

DESCRIPTION

@@ -1,14 +1,16 @@
 Package: epipredict
 Title: Basic epidemiology forecasting methods
-Version: 0.0.5
+Version: 0.0.6
 Authors@R: c(
     person("Daniel", "McDonald", , "[email protected]", role = c("aut", "cre")),
     person("Ryan", "Tibshirani", , "[email protected]", role = "aut"),
     person("Logan", "Brooks", role = "aut"),
     person("Rachel", "Lobay", role = "aut"),
-    person("Maggie", "Liu", role = "aut"),
-    person("Ken", "Mawer", role = "aut"),
-    person("Chloe", "You", role = "aut"),
+    person("Dmitry", "Shemetov", email = "[email protected]", role = "ctb"),
+    person("David", "Weber", email = "[email protected]", role = "ctb"),
+    person("Maggie", "Liu", role = "ctb"),
+    person("Ken", "Mawer", role = "ctb"),
+    person("Chloe", "You", role = "ctb"),
     person("Jacob", "Bien", role = "ctb")
   )
 Description: A forecasting "framework" for creating epidemiological
@@ -32,6 +34,7 @@ Imports:
     generics,
     glue,
     hardhat (>= 1.3.0),
+    lifecycle,
     magrittr,
     methods,
     quantreg,

NAMESPACE

@@ -34,6 +34,8 @@ S3method(extrapolate_quantiles,dist_default)
 S3method(extrapolate_quantiles,dist_quantiles)
 S3method(extrapolate_quantiles,distribution)
 S3method(fit,epi_workflow)
+S3method(flusight_hub_formatter,canned_epipred)
+S3method(flusight_hub_formatter,data.frame)
 S3method(format,dist_quantiles)
 S3method(is.na,dist_quantiles)
 S3method(is.na,distribution)
@@ -52,6 +54,7 @@ S3method(print,alist)
 S3method(print,arx_class)
 S3method(print,arx_fcast)
 S3method(print,canned_epipred)
+S3method(print,cdc_baseline_fcast)
 S3method(print,epi_recipe)
 S3method(print,epi_workflow)
 S3method(print,flat_fcast)
@@ -81,6 +84,7 @@ S3method(residuals,flatline)
 S3method(run_mold,default_epi_recipe_blueprint)
 S3method(slather,layer_add_forecast_date)
 S3method(slather,layer_add_target_date)
+S3method(slather,layer_cdc_flatline_quantiles)
 S3method(slather,layer_naomit)
 S3method(slather,layer_point_from_distn)
 S3method(slather,layer_population_scaling)
@@ -108,6 +112,8 @@ export(arx_classifier)
 export(arx_fcast_epi_workflow)
 export(arx_forecaster)
 export(bake)
+export(cdc_baseline_args_list)
+export(cdc_baseline_forecaster)
 export(create_layer)
 export(default_epi_recipe_blueprint)
 export(detect_layer)
@@ -124,6 +130,7 @@ export(fit)
 export(flatline)
 export(flatline_args_list)
 export(flatline_forecaster)
+export(flusight_hub_formatter)
 export(frosting)
 export(get_test_data)
 export(grab_names)
@@ -133,6 +140,7 @@ export(is_layer)
 export(layer)
 export(layer_add_forecast_date)
 export(layer_add_target_date)
+export(layer_cdc_flatline_quantiles)
 export(layer_naomit)
 export(layer_point_from_distn)
 export(layer_population_scaling)
@@ -145,7 +153,8 @@ export(layer_unnest)
 export(nested_quantiles)
 export(new_default_epi_recipe_blueprint)
 export(new_epi_recipe_blueprint)
-export(pivot_quantiles)
+export(pivot_quantiles_longer)
+export(pivot_quantiles_wider)
 export(prep)
 export(quantile_reg)
 export(remove_frosting)
@@ -163,12 +172,13 @@ import(distributional)
 import(epiprocess)
 import(parsnip)
 import(recipes)
-import(vctrs)
+importFrom(cli,cli_abort)
 importFrom(epiprocess,growth_rate)
 importFrom(generics,augment)
 importFrom(generics,fit)
 importFrom(hardhat,refresh_blueprint)
 importFrom(hardhat,run_mold)
+importFrom(lifecycle,deprecated)
 importFrom(magrittr,"%>%")
 importFrom(methods,is)
 importFrom(quantreg,rq)
@@ -183,6 +193,7 @@ importFrom(rlang,caller_env)
 importFrom(rlang,is_empty)
 importFrom(rlang,is_null)
 importFrom(rlang,quos)
+importFrom(smoothqr,smooth_qr)
 importFrom(stats,as.formula)
 importFrom(stats,family)
 importFrom(stats,lm)
@@ -196,3 +207,12 @@ importFrom(stats,residuals)
 importFrom(tibble,as_tibble)
 importFrom(tibble,is_tibble)
 importFrom(tibble,tibble)
+importFrom(vctrs,as_list_of)
+importFrom(vctrs,field)
+importFrom(vctrs,new_rcrd)
+importFrom(vctrs,new_vctr)
+importFrom(vctrs,vec_cast)
+importFrom(vctrs,vec_data)
+importFrom(vctrs,vec_ptype_abbr)
+importFrom(vctrs,vec_ptype_full)
+importFrom(vctrs,vec_recycle_common)

NEWS.md

@@ -1,14 +1,20 @@
 # epipredict (development)
 
+# epipredict 0.0.6
+
+* rename the `dist_quantiles()` to be more descriptive, breaking change)
+* removes previous `pivot_quantiles()` (now `*_wider()`, breaking change)
+* add `pivot_quantiles_wider()` for easier plotting
+* add complement `pivot_quantiles_longer()`
+* add `cdc_baseline_forecaster()` and `flusight_hub_formatter()`
+
 # epipredict 0.0.5
 
 * add `smooth_quantile_reg()`
 * improved printing of various methods / internals
 * canned forecasters get a class
 * fixed quantile bug in `flatline_forecaster()`
 * add functionality to output the unfit workflow from the canned forecasters
-* add `pivot_quantiles()` for easier plotting
-
 
 # epipredict 0.0.4
 

R/arx_classifier.R

@@ -250,7 +250,9 @@ arx_class_args_list <- function(
     method = c("rel_change", "linear_reg", "smooth_spline", "trend_filter"),
     log_scale = FALSE,
     additional_gr_args = list(),
-    nafill_buffer = Inf) {
+    nafill_buffer = Inf,
+    ...) {
+  rlang::check_dots_empty()
   .lags <- lags
   if (is.list(lags)) lags <- unlist(lags)
   method <- match.arg(method)
@@ -305,3 +307,5 @@ print.arx_class <- function(x, ...) {
   name <- "ARX Classifier"
   NextMethod(name = name, ...)
 }
+
+# this is a trivial change to induce a check

R/arx_forecaster.R

@@ -33,7 +33,7 @@
 #' out <- arx_forecaster(jhu, "death_rate",
 #'   c("case_rate", "death_rate"),
 #'   trainer = quantile_reg(),
-#'   args_list = arx_args_list(levels = 1:9 / 10)
+#'   args_list = arx_args_list(quantile_levels = 1:9 / 10)
 #' )
 arx_forecaster <- function(epi_data,
                            outcome,
@@ -99,7 +99,7 @@ arx_forecaster <- function(epi_data,
 #' arx_fcast_epi_workflow(jhu, "death_rate",
 #'   c("case_rate", "death_rate"),
 #'   trainer = quantile_reg(),
-#'   args_list = arx_args_list(levels = 1:9 / 10)
+#'   args_list = arx_args_list(quantile_levels = 1:9 / 10)
 #' )
 arx_fcast_epi_workflow <- function(
     epi_data,
@@ -134,18 +134,20 @@ arx_fcast_epi_workflow <- function(
   # --- postprocessor
   f <- frosting() %>% layer_predict() # %>% layer_naomit()
   if (inherits(trainer, "quantile_reg")) {
-    # add all levels to the forecaster and update postprocessor
-    tau <- sort(compare_quantile_args(
-      args_list$levels,
-      rlang::eval_tidy(trainer$args$tau)
+    # add all quantile_level to the forecaster and update postprocessor
+    quantile_levels <- sort(compare_quantile_args(
+      args_list$quantile_levels,
+      rlang::eval_tidy(trainer$args$quantile_levels)
     ))
-    args_list$levels <- tau
-    trainer$args$tau <- rlang::enquo(tau)
-    f <- layer_quantile_distn(f, levels = tau) %>% layer_point_from_distn()
+    args_list$quantile_levels <- quantile_levels
+    trainer$args$quantile_levels <- rlang::enquo(quantile_levels)
+    f <- layer_quantile_distn(f, quantile_levels = quantile_levels) %>%
+      layer_point_from_distn()
   } else {
     f <- layer_residual_quantiles(
       f,
-      probs = args_list$levels, symmetrize = args_list$symmetrize,
+      quantile_levels = args_list$quantile_levels,
+      symmetrize = args_list$symmetrize,
       by_key = args_list$quantile_by_key
     )
   }
@@ -173,7 +175,7 @@ arx_fcast_epi_workflow <- function(
 #'   The default `NULL` will attempt to determine this automatically.
 #' @param target_date Date. The date for which the forecast is intended.
 #'   The default `NULL` will attempt to determine this automatically.
-#' @param levels Vector or `NULL`. A vector of probabilities to produce
+#' @param quantile_levels Vector or `NULL`. A vector of probabilities to produce
 #'   prediction intervals. These are created by computing the quantiles of
 #'   training residuals. A `NULL` value will result in point forecasts only.
 #' @param symmetrize Logical. The default `TRUE` calculates
@@ -197,6 +199,7 @@ arx_fcast_epi_workflow <- function(
 #'   create a prediction. For this reason, setting `nafill_buffer < min(lags)`
 #'   will be treated as _additional_ allowed recent data rather than the
 #'   total amount of recent data to examine.
+#' @param ... Space to handle future expansions (unused).
 #'
 #'
 #' @return A list containing updated parameter choices with class `arx_flist`.
@@ -205,18 +208,19 @@ arx_fcast_epi_workflow <- function(
 #' @examples
 #' arx_args_list()
 #' arx_args_list(symmetrize = FALSE)
-#' arx_args_list(levels = c(.1, .3, .7, .9), n_training = 120)
+#' arx_args_list(quantile_levels = c(.1, .3, .7, .9), n_training = 120)
 arx_args_list <- function(
     lags = c(0L, 7L, 14L),
     ahead = 7L,
     n_training = Inf,
     forecast_date = NULL,
     target_date = NULL,
-    levels = c(0.05, 0.95),
+    quantile_levels = c(0.05, 0.95),
     symmetrize = TRUE,
     nonneg = TRUE,
     quantile_by_key = character(0L),
-    nafill_buffer = Inf) {
+    nafill_buffer = Inf,
+    ...) {
   # error checking if lags is a list
   .lags <- lags
   if (is.list(lags)) lags <- unlist(lags)
@@ -227,7 +231,7 @@ arx_args_list <- function(
   arg_is_date(forecast_date, target_date, allow_null = TRUE)
   arg_is_nonneg_int(ahead, lags)
   arg_is_lgl(symmetrize, nonneg)
-  arg_is_probabilities(levels, allow_null = TRUE)
+  arg_is_probabilities(quantile_levels, allow_null = TRUE)
   arg_is_pos(n_training)
   if (is.finite(n_training)) arg_is_pos_int(n_training)
   if (is.finite(nafill_buffer)) arg_is_pos_int(nafill_buffer, allow_null = TRUE)
@@ -238,7 +242,7 @@ arx_args_list <- function(
       lags = .lags,
       ahead,
       n_training,
-      levels,
+      quantile_levels,
       forecast_date,
       target_date,
       symmetrize,
@@ -259,8 +263,8 @@ print.arx_fcast <- function(x, ...) {
 }
 
 compare_quantile_args <- function(alist, tlist) {
-  default_alist <- eval(formals(arx_args_list)$levels)
-  default_tlist <- eval(formals(quantile_reg)$tau)
+  default_alist <- eval(formals(arx_args_list)$quantile_level)
+  default_tlist <- eval(formals(quantile_reg)$quantile_level)
   if (setequal(alist, default_alist)) {
     if (setequal(tlist, default_tlist)) {
       return(sort(unique(union(alist, tlist))))

R/canned-epipred.R

@@ -8,13 +8,13 @@ validate_forecaster_inputs <- function(epi_data, outcome, predictors) {
   arg_is_chr(predictors)
   arg_is_chr_scalar(outcome)
   if (!outcome %in% names(epi_data)) {
-    cli::cli_abort("{outcome} was not found in the training data.")
+    cli::cli_abort("{.var {outcome}} was not found in the training data.")
   }
   check <- hardhat::check_column_names(epi_data, predictors)
   if (!check$ok) {
     cli::cli_abort(c(
       "At least one predictor was not found in the training data.",
-      "!" = "The following required columns are missing: {check$missing_names}."
+      "!" = "The following required columns are missing: {.val {check$missing_names}}."
     ))
   }
   invisible(TRUE)
@@ -41,8 +41,8 @@ arx_lags_validator <- function(predictors, lags) {
         predictors_miss <- setdiff(predictors, names(lags))
         cli::cli_abort(c(
           "If lags is a named list, then all predictors must be present.",
-          i = "The predictors are '{predictors}'.",
-          i = "So lags is missing '{predictors_miss}'."
+          i = "The predictors are {.var {predictors}}.",
+          i = "So lags is missing {.var {predictors_miss}}'."
         ))
       }
     }