merge dev, document

Merge branch 'dev' into main-to-dev

# Conflicts:
#	.github/workflows/pkgdown.yaml
#	DESCRIPTION
#	R/layer_population_scaling.R
#	R/step_population_scaling.R
#	_pkgdown.yml
#	man/layer_population_scaling.Rd
#	man/step_population_scaling.Rd
#	tests/testthat/test-arg_is_.R
#	tests/testthat/test-check-training-set.R
#	tests/testthat/test-population_scaling.R
#	tests/testthat/test-snapshots.R
#	tests/testthat/test-target_date_bug.R

Author: dajmcdon

.Rbuildignore

@@ -20,4 +20,5 @@
 ^doc$
 ^Meta$
 ^.lintr$
-^.venv$
+^.venv$
+^inst/templates$

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: epipredict
 Title: Basic epidemiology forecasting methods
-Version: 0.1.0
+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("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"),
@@ -24,6 +24,7 @@ URL: https://github.com/cmu-delphi/epipredict/,
     https://cmu-delphi.github.io/epipredict
 BugReports: https://github.com/cmu-delphi/epipredict/issues/
 Depends:
+    epidatasets,
     epiprocess (>= 0.9.0),
     parsnip (>= 1.0.0),
     R (>= 3.5.0)
@@ -48,7 +49,6 @@ Imports:
     vctrs,
     workflows (>= 1.0.0)
 Suggests:
-    covidcast,
     data.table,
     epidatr (>= 1.0.0),
     fs,
@@ -60,6 +60,7 @@ Suggests:
     quantreg,
     ranger,
     RcppRoll,
+    readr,
     rmarkdown,
     smoothqr,
     testthat (>= 3.0.0),
@@ -69,11 +70,12 @@ VignetteBuilder:
     knitr
 Remotes:
     cmu-delphi/delphidocs,
+    cmu-delphi/epidatasets,
     cmu-delphi/epidatr,
     cmu-delphi/epiprocess,
     dajmcdon/smoothqr
-Config/testthat/edition: 3
 Config/Needs/website: cmu-delphi/delphidocs
+Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)

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
@@ -13,33 +11,71 @@ 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
 
-The [documentation site](https://cmu-delphi.github.io/epipredict/) is built off of the `main` branch. The `dev` version of the site is available at https://cmu-delphi.github.io/epipredict/dev.
-
-The documentation site can be previewed locally by running in R
-
-```r
-pkgdown::build_site(preview=TRUE)
-```
+Our CI builds two versions of the documentation:
 
-The `main` version is available at `file:///<local path>/epidatr/epipredict/index.html` and `dev` at `file:///<local path>/epipredict/docs/dev/index.html`.
+- https://cmu-delphi.github.io/epipredict/ from the `main` branch and
+- https://cmu-delphi.github.io/epipredict/dev from the `dev` branch.
 
-You can also build the docs manually and launch the site with python. From the terminal, this looks like
+Commands for developing the documentation site:
 
-```bash
+```sh
+# Basic build and preview
+R -e 'pkgdown::clean_site()'
 R -e 'devtools::document()'
-python -m http.server -d docs
+R -e 'pkgdown::build_site()'
 ```
 
+If you work without R Studio and want to iterate on documentation, you might
+find [this
+script](https://gist.github.com/gadenbuie/d22e149e65591b91419e41ea5b2e0621)
+helpful.
+
 ## Versioning
 
 Please follow the guidelines in the [PR template document](.github/pull_request_template.md).
 
-## Release process
+## Planned CRAN release process
+
+Open a release issue and then copy and follow this checklist in the issue (modified from the checklist generated by `usethis::use_release_issue(version = "1.0.2")`):
+
+- [ ] `git pull` on `dev` branch.
+- [ ] Make sure all changes are committed and pushed.
+- [ ] Check [current CRAN check results](https://cran.rstudio.org/web/checks/check_results_epipredict.html).
+- [ ] `devtools::check(".", manual = TRUE, env_vars = c(NOT_CRAN = "false"))`.
+  - Aim for 10/10, no notes.
+- [ ] If check works well enough, merge to main. Otherwise open a PR to fix up.
+- [ ] [Polish NEWS](https://github.com/cmu-delphi/epipredict/blob/dev/NEWS.md).
+  - Some [guidelines](https://style.tidyverse.org/news.html#news-release).
+- [ ] `git checkout main`
+- [ ] `git pull`
+- [ ] `urlchecker::url_check()`.
+  - This may choke on the MIT license url, and that's ok.
+- [ ] `devtools::build_readme()`
+- [ ] `devtools::check_win_devel()`
+- [ ] Have maintainer ("cre" in description) check email for problems.
+- [ ] `revdepcheck::revdep_check(num_workers = 4)`.
+  - This may choke, it is very sensitive to the binary versions of packages on a given system. Either bypass or ask someone else to run it if you're concerned.
+- [ ] Update `cran-comments.md`
+- [ ] PR with any changes (and go through the list again) into `dev` and run through the list again.
+
+Submit to CRAN:
+
+- [ ] `devtools::submit_cran()`.
+- [ ] Maintainer approves email.
+
+Wait for CRAN...
 
-TBD
+- [ ] If accepted :tada:, move to next steps. If rejected, fix and resubmit.
+- [ ] Open and merge a PR containing any updates made to `main` back to `dev`.
+- [ ] `usethis::use_github_release(publish = FALSE)` (publish off, otherwise it won't push) will create a draft release based on the commit hash in CRAN-SUBMISSION and push a tag to the GitHub repo.
+- [ ] Go to the repo, verify the release notes, and publish when ready.

NAMESPACE

@@ -19,11 +19,13 @@ S3method(autoplot,canned_epipred)
 S3method(autoplot,epi_workflow)
 S3method(bake,check_enough_train_data)
 S3method(bake,epi_recipe)
+S3method(bake,step_adjust_latency)
 S3method(bake,step_epi_ahead)
 S3method(bake,step_epi_lag)
 S3method(bake,step_epi_slide)
 S3method(bake,step_growth_rate)
 S3method(bake,step_lag_difference)
+S3method(bake,step_panel_normalize)
 S3method(bake,step_population_scaling)
 S3method(bake,step_training_window)
 S3method(detect_layer,frosting)
@@ -58,11 +60,13 @@ S3method(predict,epi_workflow)
 S3method(predict,flatline)
 S3method(prep,check_enough_train_data)
 S3method(prep,epi_recipe)
+S3method(prep,step_adjust_latency)
 S3method(prep,step_epi_ahead)
 S3method(prep,step_epi_lag)
 S3method(prep,step_epi_slide)
 S3method(prep,step_growth_rate)
 S3method(prep,step_lag_difference)
+S3method(prep,step_panel_normalize)
 S3method(prep,step_population_scaling)
 S3method(prep,step_training_window)
 S3method(print,alist)
@@ -87,12 +91,14 @@ S3method(print,layer_quantile_distn)
 S3method(print,layer_residual_quantiles)
 S3method(print,layer_threshold)
 S3method(print,layer_unnest)
+S3method(print,step_adjust_latency)
 S3method(print,step_epi_ahead)
 S3method(print,step_epi_lag)
 S3method(print,step_epi_slide)
 S3method(print,step_growth_rate)
 S3method(print,step_lag_difference)
 S3method(print,step_naomit)
+S3method(print,step_panel_normalize)
 S3method(print,step_population_scaling)
 S3method(print,step_training_window)
 S3method(quantile,dist_quantiles)
@@ -118,6 +124,7 @@ S3method(snap,distribution)
 S3method(tidy,check_enough_train_data)
 S3method(tidy,frosting)
 S3method(tidy,layer)
+S3method(tidy,step_panel_normalize)
 S3method(update,layer)
 S3method(vec_ptype_abbr,dist_quantiles)
 S3method(vec_ptype_full,dist_quantiles)
@@ -195,12 +202,14 @@ export(remove_frosting)
 export(remove_model)
 export(slather)
 export(smooth_quantile_reg)
+export(step_adjust_latency)
 export(step_epi_ahead)
 export(step_epi_lag)
 export(step_epi_naomit)
 export(step_epi_slide)
 export(step_growth_rate)
 export(step_lag_difference)
+export(step_panel_normalize)
 export(step_population_scaling)
 export(step_training_window)
 export(tibble)
@@ -211,6 +220,7 @@ export(update_model)
 export(validate_layer)
 export(weighted_interval_score)
 import(distributional)
+import(epidatasets)
 import(epiprocess)
 import(parsnip)
 import(recipes)
@@ -225,6 +235,7 @@ importFrom(checkmate,test_numeric)
 importFrom(checkmate,test_scalar)
 importFrom(cli,cli_abort)
 importFrom(cli,cli_warn)
+importFrom(dplyr,"%>%")
 importFrom(dplyr,across)
 importFrom(dplyr,all_of)
 importFrom(dplyr,any_of)
@@ -235,13 +246,20 @@ importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
+importFrom(dplyr,group_by_at)
+importFrom(dplyr,join_by)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
+importFrom(dplyr,n)
+importFrom(dplyr,pull)
 importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
+importFrom(dplyr,rowwise)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
+importFrom(dplyr,tibble)
+importFrom(dplyr,tribble)
 importFrom(dplyr,ungroup)
 importFrom(epiprocess,epi_slide)
 importFrom(epiprocess,growth_rate)
@@ -255,18 +273,20 @@ importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_linerange)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_ribbon)
+importFrom(glue,glue)
+importFrom(hardhat,extract_recipe)
 importFrom(hardhat,refresh_blueprint)
 importFrom(hardhat,run_mold)
 importFrom(magrittr,"%>%")
 importFrom(recipes,bake)
+importFrom(recipes,detect_step)
 importFrom(recipes,prep)
 importFrom(recipes,rand_id)
 importFrom(rlang,"!!!")
 importFrom(rlang,"!!")
 importFrom(rlang,"%@%")
 importFrom(rlang,"%||%")
 importFrom(rlang,":=")
-importFrom(rlang,abort)
 importFrom(rlang,arg_match)
 importFrom(rlang,as_function)
 importFrom(rlang,caller_arg)
@@ -276,16 +296,19 @@ importFrom(rlang,enquos)
 importFrom(rlang,expr)
 importFrom(rlang,global_env)
 importFrom(rlang,inject)
+importFrom(rlang,is_empty)
 importFrom(rlang,is_logical)
 importFrom(rlang,is_null)
 importFrom(rlang,is_true)
+importFrom(rlang,list2)
 importFrom(rlang,set_names)
 importFrom(rlang,sym)
 importFrom(stats,as.formula)
 importFrom(stats,family)
 importFrom(stats,lm)
 importFrom(stats,median)
 importFrom(stats,model.frame)
+importFrom(stats,na.omit)
 importFrom(stats,poly)
 importFrom(stats,predict)
 importFrom(stats,qnorm)
@@ -294,6 +317,12 @@ importFrom(stats,residuals)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
 importFrom(tidyr,crossing)
+importFrom(tidyr,drop_na)
+importFrom(tidyr,expand_grid)
+importFrom(tidyr,fill)
+importFrom(tidyr,unnest)
+importFrom(tidyselect,all_of)
+importFrom(utils,capture.output)
 importFrom(vctrs,as_list_of)
 importFrom(vctrs,field)
 importFrom(vctrs,new_rcrd)
@@ -303,3 +332,4 @@ importFrom(vctrs,vec_data)
 importFrom(vctrs,vec_ptype_abbr)
 importFrom(vctrs,vec_ptype_full)
 importFrom(vctrs,vec_recycle_common)
+importFrom(workflows,extract_preprocessor)

NEWS.md

@@ -2,6 +2,25 @@
 
 Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.0.x will indicate PR's.
 
+# epipredict 0.2
+
+## Breaking changes
+
+- Moved example datasets from being hosted in the package to being loaded
+  from the `epidatasets` package. The datasets can no longer be loaded with
+  `data(<dataset name>)`, but can be accessed with 
+  `data(<dataset name>, package = "epidatasets")`, `epidatasets::<dataset name>` 
+  or, after loading the package, the name of the dataset alone (#382).
+
+## Improvements
+
+- Add `step_adjust_latency`, which give several methods to adjust the forecast if the `forecast_date` is after the last day of data.
+- (temporary) ahead negative is allowed for `step_epi_ahead` until we have `step_epi_shift`
+
+## Bug fixes
+- Shifting no columns results in no error for either `step_epi_ahead` and `step_epi_lag`
+- Quantiles produced by `grf` were sometimes out of order.
+
 # epipredict 0.1
 
 - simplify `layer_residual_quantiles()` to avoid timesuck in `utils::methods()`