Merge branch 'main' into djm/pkgdown-prettier

Author: dajmcdon

.Rbuildignore

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

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

@@ -1,10 +1,12 @@
 # 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
+#
+# Created with usethis + edited to run on PRs to dev, use API key.
 on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
 
 name: R-CMD-check
 
@@ -27,3 +29,5 @@ jobs:
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
+        env:
+          DELPHI_EPIDATA_KEY: ${{ secrets.SECRET_EPIPROCESS_GHACTIONS_DELPHI_EPIDATA_KEY }}

.github/workflows/pkgdown.yaml

@@ -1,10 +1,12 @@
 # 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
+#
+# Created with usethis + edited to run on PRs to dev, use API key.
 on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
   release:
     types: [published]
   workflow_dispatch:
@@ -13,6 +15,8 @@ name: pkgdown
 
 jobs:
   pkgdown:
+    # only build docs on the main repository and not forks
+    if: github.repository_owner == 'cmu-delphi'
     runs-on: ubuntu-latest
     # Only restrict concurrency for non-PR jobs
     concurrency:
@@ -34,6 +38,8 @@ jobs:
           needs: website
 
       - name: Build site
+        env:
+          DELPHI_EPIDATA_KEY: ${{ secrets.SECRET_EPIPROCESS_GHACTIONS_DELPHI_EPIDATA_KEY }}
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 

DESCRIPTION

@@ -1,32 +1,39 @@
 Type: Package
 Package: epiprocess
 Title: Tools for basic signal processing in epidemiology
-Version: 0.5.0.9999
+Version: 0.7.0
 Authors@R: c(
     person("Jacob", "Bien", role = "ctb"),
     person("Logan", "Brooks", role = "aut"),
     person("Rafael", "Catoia", role = "ctb"),
+    person("Nat", "DeFries", role = "ctb"),
     person("Daniel", "McDonald", role = "aut"),
     person("Rachel", "Lobay", role = "ctb"),
     person("Ken", "Mawer", role = "ctb"),
     person("Chloe", "You", role = "ctb"),
     person("Quang", "Nguyen", role = "ctb"),
     person("Evan", "Ray", role = "aut"),
     person("Dmitry", "Shemetov", role = "ctb"),
-    person("Ryan", "Tibshirani", , "[email protected]", role = c("aut", "cre"))
+    person("Ryan", "Tibshirani", , "[email protected]", role = c("aut", "cre")),
+    person("Lionel", "Henry", role = "ctb", comment = "Author of included rlang fragments"),
+    person("Hadley", "Wickham", role = "ctb", comment = "Author of included rlang fragments"),
+    person("Posit", role = "cph", comment = "Copyright holder of included rlang fragments")
   )
 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.
 License: MIT + file LICENSE
-Imports: 
+Copyright: file inst/COPYRIGHTS
+Imports:
+    cli,
     data.table,
-    dplyr,
+    dplyr (>= 1.0.0),
     fabletools,
     feasts,
     generics,
     genlasso,
+    lifecycle (>= 1.0.1),
     lubridate,
     magrittr,
     purrr,
@@ -35,18 +42,18 @@ Imports:
     slider,
     tibble,
     tidyr,
-    tidyselect,
+    tidyselect (>= 1.2.0),
     tsibble,
-    utils
+    utils,
+    vctrs
 Suggests:
     covidcast,
     epidatr,
     ggplot2,
     knitr,
     outbreaks,
     rmarkdown,
-    testthat (>= 3.0.0),
-    vctrs,
+    testthat (>= 3.1.5),
     waldo (>= 0.3.1),
     withr
 VignetteBuilder: 
@@ -59,7 +66,22 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Depends: 
     R (>= 2.10)
 URL: https://cmu-delphi.github.io/epiprocess/
+Collate: 
+    'archive.R'
+    'correlation.R'
+    'data.R'
+    'epi_df.R'
+    'epiprocess.R'
+    'methods-epi_archive.R'
+    'grouped_epi_archive.R'
+    'growth_rate.R'
+    'methods-epi_df.R'
+    'outliers.R'
+    'reexports.R'
+    'slide.R'
+    'utils.R'
+    'utils_pipe.R'

NAMESPACE

@@ -1,24 +1,31 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method("[",epi_df)
-S3method(arrange,epi_df)
+S3method("names<-",epi_df)
 S3method(as_epi_df,data.frame)
 S3method(as_epi_df,epi_df)
 S3method(as_epi_df,tbl_df)
 S3method(as_epi_df,tbl_ts)
+S3method(as_tibble,epi_df)
 S3method(as_tsibble,epi_df)
-S3method(filter,epi_df)
+S3method(dplyr_col_modify,col_modify_recorder_df)
+S3method(dplyr_col_modify,epi_df)
+S3method(dplyr_reconstruct,epi_df)
+S3method(dplyr_row_slice,epi_df)
+S3method(epix_truncate_versions_after,epi_archive)
+S3method(epix_truncate_versions_after,grouped_epi_archive)
+S3method(group_by,epi_archive)
 S3method(group_by,epi_df)
+S3method(group_by,grouped_epi_archive)
+S3method(group_by_drop_default,grouped_epi_archive)
 S3method(group_modify,epi_df)
-S3method(mutate,epi_df)
+S3method(groups,grouped_epi_archive)
 S3method(next_after,Date)
 S3method(next_after,integer)
 S3method(print,epi_df)
-S3method(relocate,epi_df)
-S3method(rename,epi_df)
-S3method(slice,epi_df)
 S3method(summary,epi_df)
 S3method(ungroup,epi_df)
+S3method(ungroup,grouped_epi_archive)
 S3method(unnest,epi_df)
 export("%>%")
 export(archive_cases_dv_subset)
@@ -35,12 +42,14 @@ export(epi_slide)
 export(epix_as_of)
 export(epix_merge)
 export(epix_slide)
+export(epix_truncate_versions_after)
 export(filter)
 export(group_by)
 export(group_modify)
 export(growth_rate)
 export(is_epi_archive)
 export(is_epi_df)
+export(is_grouped_epi_archive)
 export(max_version_with_row_in)
 export(mutate)
 export(new_epi_df)
@@ -60,9 +69,16 @@ importFrom(data.table,key)
 importFrom(data.table,set)
 importFrom(data.table,setkeyv)
 importFrom(dplyr,arrange)
+importFrom(dplyr,bind_rows)
+importFrom(dplyr,dplyr_col_modify)
+importFrom(dplyr,dplyr_reconstruct)
+importFrom(dplyr,dplyr_row_slice)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
+importFrom(dplyr,group_by_drop_default)
 importFrom(dplyr,group_modify)
+importFrom(dplyr,group_vars)
+importFrom(dplyr,groups)
 importFrom(dplyr,mutate)
 importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
@@ -72,20 +88,34 @@ importFrom(dplyr,ungroup)
 importFrom(lubridate,days)
 importFrom(lubridate,weeks)
 importFrom(magrittr,"%>%")
+importFrom(purrr,map_lgl)
 importFrom(rlang,"!!!")
 importFrom(rlang,"!!")
 importFrom(rlang,.data)
 importFrom(rlang,.env)
 importFrom(rlang,arg_match)
+importFrom(rlang,caller_arg)
+importFrom(rlang,caller_env)
 importFrom(rlang,enquo)
 importFrom(rlang,enquos)
+importFrom(rlang,env)
+importFrom(rlang,f_env)
+importFrom(rlang,f_rhs)
+importFrom(rlang,is_environment)
+importFrom(rlang,is_formula)
+importFrom(rlang,is_function)
+importFrom(rlang,is_missing)
 importFrom(rlang,is_quosure)
+importFrom(rlang,missing_arg)
+importFrom(rlang,new_function)
 importFrom(rlang,quo_is_missing)
 importFrom(rlang,sym)
 importFrom(rlang,syms)
 importFrom(stats,cor)
 importFrom(stats,median)
+importFrom(tibble,as_tibble)
 importFrom(tidyr,unnest)
 importFrom(tidyselect,eval_select)
 importFrom(tidyselect,starts_with)
 importFrom(tsibble,as_tsibble)
+importFrom(utils,tail)