Merge remote-tracking branch 'origin/main' into dev

Author: lcbrooks

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

@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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:
@@ -15,12 +15,12 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
-      
+
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck

.github/workflows/pkgdown.yaml

@@ -1,8 +1,10 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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]
   release:
     types: [published]
   workflow_dispatch:
@@ -12,24 +14,33 @@ name: pkgdown
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: pkgdown
+          extra-packages: any::pkgdown, local::.
           needs: website
 
-      - name: Deploy package
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Build site
+        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
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

NEWS.md

@@ -81,6 +81,7 @@ development versions. A ".9999" suffix indicates a development version.
 * Added a `NEWS.md` file to track changes to the package.
 * Implemented `?dplyr::dplyr_extending` for `epi_df`s
   ([#223](https://github.com/cmu-delphi/epiprocess/issues/223)).
+* Fixed various small documentation issues ([#217](https://github.com/cmu-delphi/epiprocess/issues/217)).
 
 # epiprocess 0.5.0:
 
@@ -93,13 +94,13 @@ development versions. A ".9999" suffix indicates a development version.
 
 ## Improvements:
 
-* Fixed `epix_merge`, `<epi_archive>$merge` always raising error on `sync="truncate"`
+* Fixed `epix_merge`, `<epi_archive>$merge` always raising error on `sync="truncate"`.
 
 ## Cleanup:
 
-* Added `Remotes:` entry for `genlasso`, which was removed from CRAN
-* Added `as_epi_archive` tests
-* Added missing `epix_merge` test for `sync="truncate"`
+* Added `Remotes:` entry for `genlasso`, which was removed from CRAN.
+* Added `as_epi_archive` tests.
+* Added missing `epix_merge` test for `sync="truncate"`.
 
 # epiprocess 0.4.0:
 
@@ -142,7 +143,7 @@ development versions. A ".9999" suffix indicates a development version.
   * `epix_<method>` will not mutate input `epi_archive`s, but may alias them
     or alias their fields (which should not be a worry if a user sticks to
     these `epix_*` functions and "regular" R functions with
-    copy-on-write-like behavior, avoiding mutating functions `[.data.table`)
+    copy-on-write-like behavior, avoiding mutating functions `[.data.table`).
   * `x$<method>` may mutate `x`; if it mutates `x`, it will return `x`
     invisibly (where this makes sense), and, for each of its fields, may
     either mutate the object to which it refers or reseat the reference (but
@@ -183,7 +184,7 @@ development versions. A ".9999" suffix indicates a development version.
 * New function `epix_fill_through_version`, method
   `<epi_archive>$fill_through_version`: non-mutating & mutating way to
   ensure that an archive contains versions at least through some
-  `fill_versions_end`, extrapolating according to `how` if necessary
+  `fill_versions_end`, extrapolating according to `how` if necessary.
 * Example archive data object is now constructed on demand from its
   underlying data, so it will be based on the user's version of
   `epi_archive` rather than an outdated R6 implementation from whenever the
@@ -289,7 +290,7 @@ Classes:
   * `epi_cor` calculates Pearson, Kendall, or Spearman correlations
     between two (optionally time-shifted) variables in an `epi_df` within
     user-specified groups.
-  * Convenience function: `is_epi_df`
+  * Convenience function: `is_epi_df`.
 * `epi_archive`: R6 class for version (patch) data for geotemporal
   epidemiological time series data sets. Comes with S3 methods and regular
   functions that wrap around this functionality for those unfamiliar with R6
@@ -298,23 +299,23 @@ Classes:
     containing snapshots and/or patch data for every available version of
     the data set.
   * `as_of`: extracts a snapshot of the data set as of some requested
-    version, in `epi_df` format
+    version, in `epi_df` format.
   * `epix_slide`, `<epi_archive>$slide`: similar to `epi_slide`, but for
     `epi_archive`s; for each requested `ref_time_value` and group, applies
     a time window and user-specified computation to a snapshot of the data
     as of `ref_time_value`.
   * `epix_merge`, `<epi_archive>$merge`: like `merge` for `epi_archive`s,
     but allowing for the last version of each observation to be carried
     forward to fill in gaps in `x` or `y`.
-  * Convenience function: `is_epi_archive`
+  * Convenience function: `is_epi_archive`.
 
 Additional functions:
 * `growth_rate`: estimates growth rate of a time series using one of a few
   built-in `method`s based on relative change, linear regression,
   smoothing splines, or trend filtering.
 * `detect_outlr`: applies one or more outlier detection methods to a given
   signal variable, and optionally aggregates the outputs to create a
-  consensus result
+  consensus result.
 * `detect_outlr_rm`: outlier detection function based on a
   rolling-median-based outlier detection function; one of the methods
   included in `detect_outlr`.

R/methods-epi_archive.R

@@ -82,7 +82,7 @@ epix_as_of = function(x, max_version, min_time_value = -Inf, all_versions = FALS
 #'  `x`), and returns the updated `x` [invisibly][base::invisible].
 #'
 #' @param x An `epi_archive`
-#' @param fill_versions_end Length-1, same class&type as `%s$version`: the
+#' @param fill_versions_end Length-1, same class&type as `x$version`: the
 #'   version through which to fill in missing version history; this will be the
 #'   result's `$versions_end` unless it already had a later
 #'   `$versions_end`.
@@ -699,9 +699,10 @@ group_by.epi_archive = function(.data, ..., .add=FALSE, .drop=dplyr::group_by_dr
 #' @param new_col_name String indicating the name of the new column that will
 #'   contain the derivative values. Default is "slide_value"; note that setting
 #'   `new_col_name` equal to an existing column name will overwrite this column.
-#' @param as_list_col Should the new column be stored as a list column? Default
-#'   is `FALSE`, in which case a list object returned by `f` would be unnested
-#'   (using `tidyr::unnest()`), and the names of the resulting columns are given
+#' @param as_list_col If the computations return data frames, should the slide
+#'   result hold these in a single list column or try to unnest them? Default is
+#'   `FALSE`, in which case a list object returned by `f` would be unnested
+#'   (using [`tidyr::unnest()`]), and the names of the resulting columns are given
 #'   by prepending `new_col_name` to the names of the list elements.
 #' @param names_sep String specifying the separator to use in `tidyr::unnest()`
 #'   when `as_list_col = FALSE`. Default is "_". Using `NULL` drops the prefix

R/slide.R

@@ -52,9 +52,10 @@
 #' @param new_col_name String indicating the name of the new column that will
 #'   contain the derivative values. Default is "slide_value"; note that setting
 #'   `new_col_name` equal to an existing column name will overwrite this column.
-#' @param as_list_col Should the new column be stored as a list column? Default
-#'   is `FALSE`, in which case a list object returned by `f` would be unnested
-#'   (using `tidyr::unnest()`), and the names of the resulting columns are given
+#' @param as_list_col If the computations return data frames, should the slide
+#'   result hold these in a single list column or try to unnest them? Default is
+#'   `FALSE`, in which case a list object returned by `f` would be unnested
+#'   (using [`tidyr::unnest()`]), and the names of the resulting columns are given
 #'   by prepending `new_col_name` to the names of the list elements.
 #' @param names_sep String specifying the separator to use in `tidyr::unnest()`
 #'   when `as_list_col = FALSE`. Default is "_". Using `NULL` drops the prefix

README.md

@@ -1,7 +1,7 @@
 # epiprocess
 
  <!-- badges: start -->
-  [![R-CMD-check](https://github.com/cmu-delphi/epiprocess/workflows/R-CMD-check/badge.svg)](https://github.com/cmu-delphi/epiprocess/actions)
+  [![R-CMD-check](https://github.com/cmu-delphi/epiprocess/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/cmu-delphi/epiprocess/actions/workflows/R-CMD-check.yaml)
   <!-- badges: end -->
 
 This package introduces a common data structure for epidemiological data sets
@@ -45,10 +45,10 @@ The second main data structure in the package is called
 wrapped around a data table that stores the archive (version history) of some
 signal variables of interest.
 
-By convention, functions in the `epiprocess` package that operate on `epi_df`
-objects begin with `epix` (the "x" is meant to remind you of "archive"). These
-are just wrapper functions around the public methods for the `epi_archive` R6
-class. For example:
+By convention, functions in the `epiprocess` package that operate on
+`epi_archive` objects begin with `epix` (the "x" is meant to remind you of
+"archive"). These are just wrapper functions around the public methods for the
+`epi_archive` R6 class. For example:
 
 - `epix_as_of()`, for generating a snapshot in `epi_df` format from the data
   archive, which represents the most up-to-date values of the signal variables,

_pkgdown.yml

@@ -6,9 +6,11 @@ url: https://cmu-delphi.github.io/epiprocess/
 home:
   links:
   - text: Get the epipredict R package
-    href: https://cmu-delphi.github.io/epiprocess/
+    href: https://cmu-delphi.github.io/epipredict/
   - text: Get the covidcast R package
     href: https://cmu-delphi.github.io/covidcast/covidcastR/
+  - text: Get the epidatr R package
+    href: https://github.com/cmu-delphi/epidatr
 
 articles:
 - title: Using the package
@@ -34,11 +36,11 @@ repo:
 
 
 reference:
-- title: epi_df basics
+- title: "`epi_df` basics"
   desc: Details on `epi_df` format, and basic functionality.
 - contents:
   - matches("epi_df")
-- title: epi_*() functions
+- title: "`epi_*()` functions"
   desc: Functions that act on `epi_df` objects.
 - contents:
   - epi_slide
@@ -50,11 +52,11 @@ reference:
   - detect_outlr
   - detect_outlr_rm
   - detect_outlr_stl
-- title: epi_archive basics
+- title: "`epi_archive` basics"
   desc: Details on `epi_archive`, and basic functionality.
 - contents:
   - matches("archive")
-- title: epix_*() functions
+- title: `epix_*()` functions
   desc: Functions that act on an `epi_archive` and/or `grouped_epi_archive` object.
 - contents:
   - starts_with("epix")