Merge pull request #427 from cmu-delphi/main-to-dev

Main to dev

Author: dajmcdon

.github/workflows/R-CMD-check.yaml

@@ -17,7 +17,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

.github/workflows/pkgdown.yaml

@@ -40,32 +40,12 @@ jobs:
           needs: website
 
       - name: Build site
-        # - target_ref gets the ref from a different variable, depending on the event
-        # - override allows us to set the pkgdown mode and version_label
-        #   - mode: release is the standard build mode, devel places the site in /dev
-        #   - version_label: 'light' and 'success' are CSS labels for Bootswatch: Cosmo
-        #                    https://bootswatch.com/cosmo/
-        # - we use pkgdown:::build_github_pages to build the site because of an issue in pkgdown
-        #   https://github.com/r-lib/pkgdown/issues/2257
-        run: |
-          target_ref <- "${{ github.event_name == 'pull_request' && github.base_ref || github.ref }}"
-          override <- if (target_ref == "main" || target_ref == "refs/heads/main") {
-            list(development = list(mode = "release", version_label = "light"))
-          } else if (target_ref == "dev" || target_ref == "refs/heads/dev") {
-            list(development = list(mode = "devel", version_label = "success"))
-          } else {
-            stop("Unexpected target_ref: ", target_ref)
-          }
-          pkg <- pkgdown::as_pkgdown(".", override = override)
-          cli::cli_rule("Cleaning files from old site...")
-          pkgdown::clean_site(pkg)
-          pkgdown::build_site(pkg, preview = FALSE, install = FALSE, new_process = FALSE)
-          pkgdown:::build_github_pages(pkg)
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

.github/workflows/styler.yml

@@ -21,7 +21,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.gitignore

@@ -9,4 +9,4 @@ inst/doc
 /Meta/
 .Rprofile
 renv.lock
-renv/
+renv/

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: epipredict
 Title: Basic epidemiology forecasting methods
-Version: 0.1.4
+Version: 0.1.5
 Authors@R: c(
     person("Daniel J.", "McDonald", , "[email protected]", role = c("aut", "cre")),
     person("Ryan", "Tibshirani", , "[email protected]", role = "aut"),
-    person("Dmitry", "Shemetov", email = "[email protected]", role = "aut"),
-    person("David", "Weber", email = "[email protected]", role = "aut"),
-    person("CMU's Delphi Research Group", role = c("cph", "fnd")),
+    person("Dmitry", "Shemetov", , "[email protected]", role = "aut"),
+    person("David", "Weber", , "[email protected]", role = "aut"),
+    person("Delphi Research Group", role = c("cph", "fnd")),
     person("Logan", "Brooks", role = "aut"),
     person("Rachel", "Lobay", role = "aut"),
     person("Maggie", "Liu", role = "ctb"),
@@ -24,8 +24,8 @@ URL: https://github.com/cmu-delphi/epipredict/,
     https://cmu-delphi.github.io/epipredict
 BugReports: https://github.com/cmu-delphi/epipredict/issues/
 Depends:
-    epiprocess (>= 0.9.0),
     epidatasets,
+    epiprocess (>= 0.9.0),
     parsnip (>= 1.0.0),
     R (>= 3.5.0)
 Imports:
@@ -69,11 +69,13 @@ Suggests:
 VignetteBuilder:
     knitr
 Remotes:
+    cmu-delphi/delphidocs,
     cmu-delphi/epidatasets,
     cmu-delphi/epidatr,
     cmu-delphi/epiprocess,
     cmu-delphi/epidatasets,
     dajmcdon/smoothqr
+Config/Needs/website: cmu-delphi/delphidocs
 Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true

README.md

@@ -38,25 +38,24 @@ You can view documentation for the `main` branch at
     You should be able to do a reasonably limited amount of
     customization on them. For the basic forecasters, we currently
     provide:
-      - Baseline flatline forecaster
-      - Autoregressive forecaster
-      - Autoregressive classifier
-      - CDC FluSight flatline forecaster
+    - Baseline flatline forecaster
+    - Autoregressive forecaster
+    - Autoregressive classifier
+    - CDC FluSight flatline forecaster
 2.  A framework for creating custom forecasters out of modular
     components. There are four types of components:
-      - Preprocessor: do things to the data before model training
-      - Trainer: train a model on data, resulting in a fitted model
-        object
-      - Predictor: make predictions, using a fitted model object
-      - Postprocessor: do things to the predictions before returning
+    - Preprocessor: do things to the data before model training
+    - Trainer: train a model on data, resulting in a fitted model object
+    - Predictor: make predictions, using a fitted model object
+    - Postprocessor: do things to the predictions before returning
 
 **Target audiences:**
 
-  - Basic. Has data, calls forecaster with default arguments.
-  - Intermediate. Wants to examine changes to the arguments, take
-    advantage of built in flexibility.
-  - Advanced. Wants to write their own forecasters. Maybe willing to
-    build up from some components.
+- Basic. Has data, calls forecaster with default arguments.
+- Intermediate. Wants to examine changes to the arguments, take
+  advantage of built in flexibility.
+- Advanced. Wants to write their own forecasters. Maybe willing to build
+  up from some components.
 
 The Advanced user should find their task to be relatively easy. Examples
 of these tasks are illustrated in the [vignettes and
@@ -71,7 +70,7 @@ The package comes with some built-in historical data for illustration,
 but up-to-date versions of this could be downloaded with the
 [`{epidatr}` package](https://cmu-delphi.github.io/epidatr/) and
 processed using
-[`{epiprocess}`](https://cmu-delphi.github.io/epiprocess/).\[1\]
+[`{epiprocess}`](https://cmu-delphi.github.io/epiprocess/).[^1]
 
 ``` r
 library(epipredict)
@@ -114,7 +113,7 @@ two_week_ahead <- arx_forecaster(
 two_week_ahead
 #> ══ A basic forecaster of type ARX Forecaster ═══════════════════════════════
 #> 
-#> This forecaster was fit on 2024-01-29 15:10:01.
+#> This forecaster was fit on 2024-11-11 11:38:31.
 #> 
 #> Training data was an <epi_df> with:
 #> • Geography: state,
@@ -207,7 +206,7 @@ through the end of 2021 for the 14th of January 2022. A prediction for
 the death rate per 100K inhabitants is available for every state
 (`geo_value`) along with a 90% predictive interval.
 
-1.  Other epidemiological signals for non-Covid related illnesses are
+[^1]: Other epidemiological signals for non-Covid related illnesses are
     also available with
     [`{epidatr}`](https://github.com/cmu-delphi/epidatr) which
     interfaces directly to Delphi’s [Epidata

_pkgdown.yml

@@ -1,25 +1,10 @@
 url: https://cmu-delphi.github.io/epipredict/
 
-# This is to give a default value to the `mode` parameter in the
-# `pkgdown::build_site()` function. This is useful when building the site locally,
-# as it will default to `devel` mode. In practice, this should all be handled
-# dynamically by the CI/CD pipeline.
 development:
-  mode: devel
-  version_label: success
+  mode: auto
 
 template:
-  bootstrap: 5
-  bootswatch: cosmo
-  bslib:
-    font_scale: 1.0
-    primary: "#C41230"
-    success: "#B4D43C"
-    link-color: "#C41230"
-
-navbar:
-  bg: primary
-  type: light
+  package: delphidocs
 
 articles:
   - title: Get started
@@ -30,39 +15,40 @@ articles:
       - backtesting
       - arx-classifier
       - update
-
   - title: Advanced methods
     contents:
+      - articles/sliding
       - articles/smooth-qr
-      - articles/symptom-surveys
       - panel-data
 
 repo:
   url:
-    home: https://github.com/cmu-delphi/epipredict/tree/main/
-    source: https://github.com/cmu-delphi/epipredict/blob/main/
+    home: https://github.com/cmu-delphi/epipredict/
+    source: https://github.com/cmu-delphi/epipredict/
     issue: https://github.com/cmu-delphi/epipredict/issues
-    user: https://github.com/
 
 home:
   links:
-    - text: Introduction to Delphi's Tooling Work
-      href: https://cmu-delphi.github.io/delphi-tooling-book/
-    - text: The epiprocess R package
+    - text: The epiprocess package
       href: https://cmu-delphi.github.io/epiprocess/
-    - text: The epidatr R package
-      href: https://github.com/cmu-delphi/epidatr/
-    - text: The epidatasets R package
-      href: https://cmu-delphi.github.io/epidatasets/
-    - text: The covidcast R package
-      href: https://cmu-delphi.github.io/covidcast/covidcastR/
+  sidebar:
+    structure: [links, license, community, citation, authors, dev, related]
+    components:
+      related:
+        title: Delphi packages and resources
+        text: |
+          * [The epidatr package](https://github.com/cmu-delphi/epidatr/)
+          * [The epiprocess package](https://cmu-delphi.github.io/epiprocess/)
+          * [The epidatasets package](https://cmu-delphi.github.io/epidatasets/)
+          * [Introduction to Delphi's Tooling Work](https://cmu-delphi.github.io/delphi-tooling-book/)
 
 reference:
   - title: Simple forecasters
     desc: Complete forecasters that produce reasonable baselines
     contents:
       - contains("forecaster")
       - contains("classifier")
+
   - title: Forecaster modifications
     desc: Constructors to modify forecaster arguments and utilities to produce `epi_workflow` objects
     contents:
@@ -71,12 +57,14 @@ reference:
   - title: Helper functions for Hub submission
     contents:
       - flusight_hub_formatter
+
   - title: Parsnip engines
     desc: Prediction methods not available elsewhere
     contents:
       - quantile_reg
       - smooth_quantile_reg
       - grf_quantiles
+
   - title: Custom panel data forecasting workflows
     contents:
       - epi_recipe
@@ -93,31 +81,37 @@ reference:
     contents:
       - starts_with("step_")
       - contains("bake")
+
   - title: Epi recipe verification checks
     contents:
       - check_enough_train_data
+
   - title: Forecast postprocessing
     desc: Create a series of postprocessing operations
     contents:
       - frosting
       - ends_with("_frosting")
       - get_test_data
       - tidy.frosting
+
   - title: Frosting layers
     contents:
       - contains("layer")
       - contains("slather")
+
   - title: Automatic forecast visualization
     contents:
       - autoplot.epi_workflow
       - autoplot.canned_epipred
+
   - title: Utilities for quantile distribution processing
     contents:
       - dist_quantiles
       - extrapolate_quantiles
       - nested_quantiles
       - weighted_interval_score
       - starts_with("pivot_quantiles")
+
   - title: Other utilities
     contents:
       - clean_f_name