Move to CI, include data, clean up dependencies, add examples

.Rbuildignore

@@ -1,3 +1,8 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^\.github$
+^docs$
+^_pkgdown.yml
+^index\.md$
+^data-raw$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/CODEOWNERS

@@ -0,0 +1 @@
+@dajmcdon

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

@@ -0,0 +1,29 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/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]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v2
+
+      - 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
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2

.gitignore

@@ -3,3 +3,4 @@
 .RData
 .Ruserdata
 *.Rproj
+inst/doc

DESCRIPTION

@@ -1,63 +1,56 @@
-Package: epiprocess
 Type: Package
+Package: epiprocess
 Title: Tools for basic signal processing in epidemiology
 Version: 1.0.0
-Authors@R:
-  c(
-  person(given = "Jacob",
-         family = "Bien",
-         role = "ctb"),
-  person(given = "Logan",
-         family = "Brooks",
-         role = "aut"),
-  person(given = "Rafael",
-         family = "Catoia",
-         role = "ctb"),
-  person(given = "Daniel",
-         family = "McDonald",
-         role = "ctb"),
-  person(given = "Quang",
-         family = "Nguyen",
-         role = "ctb"),
-  person(given = "Evan",
-         family = "Ray",
-         role = "aut"),
-  person(given = "Dmitry",
-         family = "Shemetov",
-         role = "ctb"),
-  person(given = "Ryan",
-         family = "Tibshirani",
-         role = c("aut", "cre"),
-         email = "ryantibs@cmu.edu"))
-Description: This package introduces a common data structure for epidemiological
-  data sets measured over space and time, and offers associated utilities to
-  perform basic signal processing tasks.    
+Authors@R: c(
+    person("Jacob", "Bien", role = "ctb"),
+    person("Logan", "Brooks", role = "aut"),
+    person("Rafael", "Catoia", role = "ctb"),
+    person("Daniel", "McDonald", role = "ctb"),
+    person("Quang", "Nguyen", role = "ctb"),
+    person("Evan", "Ray", role = "aut"),
+    person("Dmitry", "Shemetov", role = "ctb"),
+    person("Ryan", "Tibshirani", , "ryantibs@cmu.edu", role = c("aut", "cre"))
+  )
+Description: This package introduces a common data structure for
+    epidemiological data sets measured over space and time, and offers
+    associated utilities to perform basic signal processing tasks.
 License: MIT + file LICENSE
-Encoding: UTF-8
-LazyData: true
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
-Remotes:
-  cmu-delphi/delphi-epidata-r,
-  reconverse/outbreaks
 Imports: 
-  data.table,
-  delphi.epidata,
-  dplyr,
-  fabletools,
-  feasts,
-  genlasso,
-  lubridate,
-  magrittr,
-  purrr,
-  R6,
-  rlang,
-  slider,
-  tibble,
-  tidyselect,
-  tidyr,
-  tsibble
+    data.table,
+    dplyr,
+    fabletools,
+    feasts,
+    generics,
+    genlasso,
+    lubridate,
+    magrittr,
+    purrr,
+    R6,
+    rlang,
+    slider,
+    tibble,
+    tidyr,
+    tidyselect,
+    tsibble,
+    utils
 Suggests:
-  outbreaks,
-  testthat (>= 3.0.0),
+    covidcast,
+    delphi.epidata,
+    ggplot2,
+    knitr,
+    outbreaks,
+    rmarkdown,
+    testthat (>= 3.0.0)
+VignetteBuilder: 
+    knitr
+Remotes:
+    dajmcdon/delphi.epidata,
+    reconverse/outbreaks
 Config/testthat/edition: 3
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.0
+Depends: 
+    R (>= 2.10)

NAMESPACE

@@ -20,8 +20,10 @@ S3method(tail,epi_df)
 S3method(ungroup,epi_df)
 S3method(unnest,epi_df)
 export("%>%")
+export(arrange)
 export(as_epi_archive)
 export(as_epi_df)
+export(as_tsibble)
 export(detect_outlr)
 export(detect_outlr_rm)
 export(detect_outlr_stl)
@@ -31,10 +33,19 @@ export(epi_slide)
 export(epix_as_of)
 export(epix_merge)
 export(epix_slide)
+export(filter)
+export(group_by)
+export(group_modify)
 export(growth_rate)
 export(is_epi_archive)
 export(is_epi_df)
-export(quiet)
+export(mutate)
+export(relocate)
+export(rename)
+export(slice)
+export(ungroup)
+export(unnest)
+importFrom(R6,R6Class)
 importFrom(data.table,as.data.table)
 importFrom(data.table,between)
 importFrom(data.table,key)
@@ -48,6 +59,7 @@ importFrom(dplyr,group_modify)
 importFrom(dplyr,mutate)
 importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
+importFrom(dplyr,select)
 importFrom(dplyr,slice)
 importFrom(dplyr,ungroup)
 importFrom(lubridate,days)
@@ -68,3 +80,5 @@ importFrom(tidyr,unnest)
 importFrom(tidyselect,eval_select)
 importFrom(tidyselect,starts_with)
 importFrom(tsibble,as_tsibble)
+importFrom(utils,head)
+importFrom(utils,tail)