Merge pull request #550 from cmu-delphi/dev

Sync dev -> main

Author: dshemetov

.Rbuildignore

@@ -17,4 +17,8 @@
 ^DEVELOPMENT.md$
 man-roxygen
 ^.venv$
-^sandbox.R$
+^sandbox.R$
+^README.Rmd$
+^README_cache$
+^pkgdown-watch.R$
+^.editorconfig$

.editorconfig

@@ -0,0 +1,21 @@
+# EditorConfig helps developers define and maintain consistent
+# coding styles between different editors and IDEs
+# editorconfig.org
+
+root = true
+
+
+[*]
+
+# Change these settings to your own preference
+indent_style = space
+indent_size = 2
+
+# We recommend you to keep these unchanged
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[*.md]
+trim_trailing_whitespace = false

.gitignore

@@ -13,4 +13,9 @@ docs
 renv/
 renv.lock
 .Rprofile
-sandbox.R
+sandbox.R
+# Vignette caches
+*_cache/
+vignettes/*.html
+vignettes/*.R
+!vignettes/_common.R

DESCRIPTION

@@ -1,7 +1,7 @@
-Type: Package
 Package: epiprocess
+Type: Package
 Title: Tools for basic signal processing in epidemiology
-Version: 0.9.0
+Version: 0.9.6
 Authors@R: c(
     person("Jacob", "Bien", role = "ctb"),
     person("Logan", "Brooks", , "[email protected]", role = c("aut", "cre")),
@@ -20,13 +20,19 @@ Authors@R: c(
     person("Hadley", "Wickham", role = "ctb",
            comment = "Author of included rlang fragments"),
     person("Posit", role = "cph",
-           comment = "Copyright holder of included rlang fragments")
+           comment = "Copyright holder of included rlang fragments"),
+    person("Johns Hopkins University Center for Systems Science and Engineering", role = "dtc",
+            comment = "Owner of COVID-19 cases and deaths data from the COVID-19 Data Repository"),
+    person("Johns Hopkins University", role = "cph",
+            comment = "Copyright holder of COVID-19 cases and deaths data from the COVID-19 Data Repository"),
+    person("Carnegie Mellon University Delphi Group", role = "dtc",
+            comment = "Owner of claims-based CLI data from the Delphi Epidata API")
   )
-Description: This package introduces a common data structure for
-    epidemiological data reported by location and time, provides another
-    data structure to work with revisions to these data sets over time,
-    and offers associated utilities to perform basic signal processing
-    tasks.
+Description: This package introduces common data structures for working with
+    epidemiological data reported by location and time and offers associated
+    utilities to perform basic signal processing tasks. The package is designed
+    to be used in conjunction with `epipredict` for building and evaluating
+    epidemiological models.
 License: MIT + file LICENSE
 URL: https://cmu-delphi.github.io/epiprocess/
 Depends:
@@ -35,7 +41,8 @@ Imports:
     checkmate,
     cli,
     data.table,
-    dplyr (>= 1.0.8),
+    dplyr (>= 1.1.0),
+    epidatasets,
     genlasso,
     ggplot2,
     glue,
@@ -53,17 +60,19 @@ Imports:
     vctrs,
     waldo
 Suggests:
-    covidcast,
     devtools,
     epidatr,
+    here,
     knitr,
     outbreaks,
+    readr,
     rmarkdown,
     testthat (>= 3.1.5),
     withr
 VignetteBuilder:
     knitr
 Remotes:
+    cmu-delphi/epidatasets,
     cmu-delphi/epidatr,
     glmgen/genlasso,
     reconverse/outbreaks
@@ -78,10 +87,9 @@ Collate:
     'archive.R'
     'autoplot.R'
     'correlation.R'
-    'data.R'
     'epi_df.R'
     'epi_df_forbidden_methods.R'
-    'epiprocess.R'
+    'epiprocess-package.R'
     'group_by_epi_df_methods.R'
     'methods-epi_archive.R'
     'grouped_epi_archive.R'

DEVELOPMENT.md

@@ -1,10 +1,8 @@
 ## Setting up the development environment
 
 ```r
-install.packages(c('devtools', 'pkgdown', 'styler', 'lintr')) # install dev dependencies
-devtools::install_deps(dependencies = TRUE) # install package dependencies
-devtools::document() # generate package meta data and man files
-devtools::build() # build package
+install.packages(c('devtools', 'pkgdown', 'styler', 'lintr', 'pak')) # install dev dependencies
+pak::pkg_install(".") # install package and dependencies
 ```
 
 ## Validating the package
@@ -13,8 +11,12 @@ devtools::build() # build package
 styler::style_pkg() # format code
 lintr::lint_package() # lint code
 
+devtools::check() # run R CMD check, which runs everything below
+devtools::document() # generate package meta data and man files
 devtools::test() # test package
-devtools::check() # check package for errors
+devtools::build_vignettes() # build vignettes only
+devtools::run_examples() # run doc examples
+devtools::check(vignettes = FALSE) # check package without vignettes
 ```
 
 ## Developing the documentation site
@@ -24,20 +26,16 @@ Our CI builds two version of the documentation:
 - https://cmu-delphi.github.io/epiprocess/ from the `main` branch and
 - https://cmu-delphi.github.io/epiprocess/dev from the `dev` branch.
 
-The documentation site can be previewed locally by running in R:
-
-```r
-# Should automatically open a browser
-pkgdown::build_site(preview=TRUE)
-```
-
-If the above does not open a browser, you can try using a Python server from the
-command line:
+We include the script `pkgdown-watch.R` that will automatically rebuild the
+documentation locally and preview it. It can be used with:
 
-```bash
-R -e 'devtools::document()'
-R -e 'pkgdown::build_site()'
-python -m http.server -d docs
+```sh
+# Make sure you have servr installed
+R -e 'renv::install("servr")'
+# Will start a local server
+Rscript pkgdown-watch.R
+# You may need to first build the site with
+R -e 'pkgdown::build_site(".", examples = FALSE, devel = TRUE, preview = FALSE)'
 ```
 
 ## Versioning

NAMESPACE

@@ -42,8 +42,6 @@ S3method(key_colnames,default)
 S3method(key_colnames,epi_archive)
 S3method(key_colnames,epi_df)
 S3method(mean,epi_df)
-S3method(next_after,Date)
-S3method(next_after,integer)
 S3method(print,epi_archive)
 S3method(print,epi_df)
 S3method(print,grouped_epi_archive)
@@ -59,8 +57,13 @@ export(as_epi_archive)
 export(as_epi_df)
 export(as_tsibble)
 export(autoplot)
+export(cases_deaths_subset)
 export(clone)
 export(complete)
+export(covid_case_death_rates_extended)
+export(covid_incidence_county_subset)
+export(covid_incidence_outliers)
+export(deprecated_quo_is_present)
 export(detect_outlr)
 export(detect_outlr_rm)
 export(detect_outlr_stl)
@@ -85,11 +88,9 @@ export(guess_period)
 export(is_epi_df)
 export(is_grouped_epi_archive)
 export(key_colnames)
-export(max_version_with_row_in)
 export(mutate)
 export(new_epi_archive)
 export(new_epi_df)
-export(next_after)
 export(relocate)
 export(rename)
 export(revision_summary)
@@ -100,6 +101,7 @@ export(ungroup)
 export(unnest)
 export(validate_epi_archive)
 export(version_column_names)
+import(epidatasets)
 importFrom(checkmate,anyInfinite)
 importFrom(checkmate,anyMissing)
 importFrom(checkmate,assert)

NEWS.md

@@ -2,6 +2,38 @@
 
 Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.x.y will indicate PR's.
 
+# epiprocess 0.10
+
+## Breaking changes
+
+- Moved example datasets from being hosted in the package to being reexported
+  from the `epidatasets` package. The datasets can no longer be loaded with
+  `data()` but can be accessed with `epiprocess::` or, after loading the
+  package, just the name of the dataset (#520). Those with names starting with
+  `jhu` have been renamed to a more uniform scheme and now have names starting
+  with `covid`. The data set previously named `jhu_confirmed_cumulative_num` has
+  been removed from the package, but a renamed version is has been removed from
+  the package, but a renamed version is still available in `epidatasets`.
+
+## Bug fixes
+
+- Removed `.window_size = 1` default from `epi_slide_{mean,sum,opt}`; this
+  argument is now mandatory, and should nearly always be greater than 1 except
+  for testing purposes.
+
+## Improvements
+
+- `epi_slide` and `epix_slide` now provide some hints if you forget a `~` when
+  using a formula to specify the slide computation, and other bits of forgotten
+  syntax.
+- Improved validation of `.window_size` arguments.
+- Rewrote a lot of the package documentation to be more consistent and
+  informative. Simplified and streamlined the vignettes.
+
+## Cleanup
+
+- Removed vignette dependency on `covidcast`.
+
 # epiprocess 0.9
 
 ## Breaking changes