Merge pull request #410 from reichlab/bsweger/cleanup-unused-target-r…

…eferences

Bsweger/cleanup unused target references

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.github$

.github/workflows/r_cmd_check.yaml

@@ -1,36 +1,41 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
 name: R-CMD-check
-on: pull_request
+
 jobs:
   R-CMD-check:
     runs-on: macOS-latest
+
+    name: r-cmd-check
+
+    strategy:
+      fail-fast: false
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
     steps:
       - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-      - uses: r-lib/actions/setup-pandoc@v2
-      - name: Cache R packages
-        uses: actions/cache@v1
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: r-${{ hashFiles('DESCRIPTION') }}
-      - name: Install dependencies
-        run: |
-          install.packages(c("devtools"))
-          devtools::install_github("epiforecasts/scoringutils@v1.2.2")
-          devtools::install_deps(dependencies = TRUE)
-        shell: Rscript {0}
-      - name: Check
-        run: |
-          devtools::check(args = c("--no-tests", "--no-manual", "--no-vignettes"),error_on = "error")
-        shell: Rscript {0}
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          error-on: '"error"'
+          upload-snapshots: true

.gitignore

@@ -10,3 +10,17 @@ inst/doc
 
 # pre-commit isn't part of the team workflow, so don't commit the config
 **/.pre-commit-config.yaml
+
+docs
+Meta
+
+# data generated by test suite and other dev operations
+tests/**/*.csv
+tests/**/*.json
+tests/**/*.rds
+
+# renv artifacts (we're not using renv at the contributor level, so
+# we'll exclude related files from the repo)
+.Rprofile
+renv.lock
+renv/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: covidHubUtils
 Title: Utility functions for the COVID-19 forecast hub
-Version: 0.1.8
+Version: 0.1.9
 Authors@R: c(
     person(given = "Yijin Serena",
            family = "Wang",
@@ -85,7 +85,7 @@ Imports:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
 VignetteBuilder: knitr
 Suggests:
     DT,

NAMESPACE

@@ -12,7 +12,6 @@ export(calc_target_end_date)
 export(calc_target_week_end_date)
 export(date_to_datetime)
 export(download_raw_nytimes)
-export(download_raw_usafacts)
 export(get_all_models)
 export(get_model_designations)
 export(get_model_metadata)
@@ -35,15 +34,12 @@ export(plot_forecasts)
 export(preprocess_hospitalization)
 export(preprocess_jhu)
 export(preprocess_nytimes)
-export(preprocess_truth_for_zoltar)
-export(preprocess_usafacts)
 export(preprocess_visualization_truth)
 export(reformat_forecasts)
-export(save_truth_for_zoltar)
 export(score_forecasts)
 export(setup_zoltar_connection)
 importFrom(doParallel,registerDoParallel)
-importFrom(dplyr,`%>%`)
+importFrom(dplyr,"%>%")
 importFrom(dplyr,any_of)
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)

NEWS.md

@@ -1,6 +1,16 @@
 ## Changes since last release
 - None yet
 
+## covidHubUtils 0.1.9
+
+This update removes truth data functions that are no longer relevant.
+### Updates
+- Remove `download_raw_usafacts` and `preprocess_usafacts` because the last release
+deprecated USAFacts as a truth source.
+- Remove `preprocess_truth_for_zoltar` and `save_truth_for_zoltar`, as the truth
+data being sent to Zoltar (JHU CSSE cases and deaths) stopped updating in March 2023.
+
+
 ## covidHubUtils 0.1.8
 
 This update has minor changes.

R/covidHubUtils-package.R

@@ -2,7 +2,7 @@
 #'
 #' @author Evan L. Ray <elray@umass.edu>
 #' @docType package
-#' @importFrom dplyr `%>%`
+#' @importFrom dplyr %>%
 #' @name covidHubUtils
 #' @aliases covidHubUtils covidHubUtils-package
 #' @description Utility functions for the COVID-19 forecast hub
@@ -12,7 +12,7 @@ NULL
 ##' @name hub_locations
 ##' @title Information on locations in the COVID-19 Forecast Hub
 ##' @docType data
-##' @format A data frame with information and metadata about national, state, and county locations for the US. 3,200 observations on the following 6 variables. 
+##' @format A data frame with information and metadata about national, state, and county locations for the US. 3,200 observations on the following 6 variables.
 ##' \describe{
 ##'   \item{\code{fips}}{the FIPS code for each location}
 ##'   \item{\code{location_name}}{A non-abbreviated name for each location}
@@ -24,4 +24,4 @@ NULL
 ##' @usage data(hub_locations)
 ##' @source JHU CSSE COVID Dashboard (https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data), covidcast API (https://github.com/cmu-delphi/covidcast), COVID-19 Forecast Hub (https://covid19forecasthub.org/).
 ##' @keywords datasets
-NULL
+NULL

R/get_plot_forecast_data.R

@@ -22,7 +22,7 @@
 #' Default to `TRUE`.
 #' @param truth_source character specifying where the truth data will
 #' be loaded from if truth_data is not provided. Currently support `"JHU"`,
-#' `"USAFacts"`, `"NYTimes"` and `"HealthData"`.
+#' `NYTimes"` and `"HealthData"`.
 #' Optional if `truth_data` is provided.
 #' @param  target_variable_to_plot string specifying target type. It should be one of
 #' `"cum death"`, `"inc case"`, `"inc death"`, `"inc hosp"` and `"inc flu hosp"`.
@@ -61,7 +61,7 @@ get_plot_forecast_data <- function(forecast_data,
       "cum death", "inc case",
       "inc death", "inc hosp"
     )
-    valid_truth_sources <- c("JHU", "USAFacts", "NYTimes", "HealthData")
+    valid_truth_sources <- c("JHU", "NYTimes", "HealthData", "USAFacts")
   } else if (hub[1] == "ECDC") {
     valid_location_codes <- covidHubUtils::hub_locations_ecdc$location
     valid_target_variables <- c("inc case", "inc death")
@@ -122,6 +122,9 @@ get_plot_forecast_data <- function(forecast_data,
     }
   } else {
     # validate truth_source
+    if (tolower(truth_source) == "usafacts") {
+      stop("USAFacts can no longer be downloaded. Please use another truth source.")
+    }
     truth_source <- match.arg(truth_source,
       choices = valid_truth_sources,
       several.ok = FALSE