Merge pull request #20 from CDCgov/dev

Version Bump 0.1 -> 0.2

.Rbuildignore

@@ -1,3 +1,8 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^.*\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$
+^codecov\.yml$

.github/.gitignore

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

.github/workflows/pkgdown.yaml

@@ -0,0 +1,35 @@
+# 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: [ master, dev ]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: pkgdown
+          needs: website
+
+      - name: Deploy package
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

.github/workflows/r.yml

@@ -42,6 +42,9 @@ jobs:
           extra-packages: rcmdcheck
           cache-version: 2
       - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: '"--no-manual"'
+          error-on: '"error"'
       # - name: Upload check results
       #   if: failure()
       #   uses: actions/upload-artifact@main

.github/workflows/test-coverage.yaml

@@ -0,0 +1,30 @@
+# 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: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: covr
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+docs

DESCRIPTION

@@ -1,9 +1,14 @@
 Package: SaviR
 Type: Package
-Title: ITF Analytics
-Version: 0.1.0
-Author: Authors@R: person("Randy", "Yee", email = "[email protected]", role = c("aut", "cre"))
-Maintainer: Randy Yee <[email protected]>
+Title: ITF Situational Awareness and Visualization
+Version: 0.2.0
+Authors@R:  c(
+    person("Sean", "Browning", email = "[email protected]", role = c("aut", "cre")),
+    person("Kimberly", "Wong", email = "[email protected]", role = "aut"),
+    person("Nartlada", "Chantharojwong", email = "[email protected]", role = "aut"),
+    person("James", "Fuller", role = "aut"),
+    person("Dante", "Bugli", role = "ctb"),
+    person("Randy", "Yee", email = "[email protected]", role = "aut"))
 Description: Data access and management of open-source COVID data for the production of analytic datasets.
 License: Apache + file LICENSE
 Imports: 
@@ -25,6 +30,7 @@ Imports:
     RcppRoll,
     cachem,
     data.table,
+    openxlsx,
     magrittr,
     memoise,
     rgdal,
@@ -34,13 +40,17 @@ Imports:
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.1.2
+Roxygen: list(markdown = TRUE)
 Suggests: 
     rmarkdown,
+    htmltools,
     tidyr,
     webshot,
     knitr,
     vdiffr,
-    testthat (>= 3.0.0)
+    httr,
+    testthat (>= 3.0.0),
+    covr
 Config/testthat/edition: 3
 Depends: 
     R (>= 3.5.0)

NAMESPACE

@@ -1,6 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 export(calc_add_risk)
+export(calc_vax_carryforward)
+export(get_combined_table)
 export(get_country_coords)
 export(get_covid_df)
 export(get_gdeltnews)
@@ -10,6 +12,7 @@ export(get_preferred_tests14)
 export(get_testing)
 export(get_testing_long)
 export(get_vax)
+export(get_vax_dates)
 export(get_vax_manufacturers)
 export(map_burden)
 export(map_template)
@@ -47,6 +50,7 @@ importFrom(cachem,cache_mem)
 importFrom(data.table,fread)
 importFrom(magrittr,`%>%`)
 importFrom(memoise,memoise)
+importFrom(openxlsx,read.xlsx)
 importFrom(purrr,set_names)
 importFrom(rgdal,readOGR)
 importFrom(sp,spTransform)

R/calc_riskmatrix.R

@@ -2,7 +2,7 @@
 
 #' @title calc_add_risk
 #' @description Calculate epi stats a generalized df input.
-#' @param df Dataframe with id (iso3), date, new_cases, new_deaths, cumulative_cases, cumulative_deaths, AND population.
+#' @param df Dataframe with id, date, new_cases, new_deaths, cumulative_cases, cumulative_deaths, AND population.
 #'
 
 #' @importFrom RcppRoll roll_mean
@@ -12,11 +12,10 @@
 #' @examples
 #' \dontrun{
 #' df <- onetable %>%
-#'      right_join(get_covid_df() %>% select(-who_region), by = c("iso2code" = "country_code")) %>%
-#'      filter(!(country == "China" & source == "WHO"))
-#' 
+#'   right_join(get_covid_df(), by = c("iso2code")) %>%
+#'   filter(!(country == "China" & source == "WHO"))
+#'
 #' calc_add_risk(df)
-#' 
 #' }
 #'
 calc_add_risk <- function(df) {

R/calc_vax_carryforward.R

@@ -0,0 +1,41 @@
+#' @title Carry-Forward vaccination metrics to latest date
+#'
+#' @param df (data.frame) Source data frame containing vaccine metrics from [get_vax()]
+#' @param ... (optional) (un-)quoted column names to carry forward. Overwrites standard variable set
+#'
+#' @return df with either columns in \code{...} carried forward, or default set
+#' @section Notes:
+#' By default, function carries forward the following (unless names are passed in \code{...}):
+#' \itemize{
+#'   \item{total_vaccinations}{}
+#'   \item{people_vaccinated}{}
+#'   \item{people_fully_vaccinated}{}
+#'   \item{total_boosters}{}
+#'   \item{total_vaccinations_per_hundred}{}
+#'   \item{people_vaccinated_per_hundred}{}
+#'   \item{people_fully_vaccinated_per_hundred}{}
+#'   \item{total_boosters_per_hundred}{}
+#' }
+#' @export
+calc_vax_carryforward <- function(df, ...) {
+  # Optionally specify vax cols by name if we want to be specific
+  vax_cols <- rlang::enquos(...)
+
+  # If not specified, just take standard set.
+  if (!length(vax_cols)) {
+    vaccine_col_str <- c(
+      "total_vaccinations", "people_vaccinated", "people_fully_vaccinated",
+      "total_boosters", "total_vaccinations_per_hundred", "people_vaccinated_per_hundred",
+      "people_fully_vaccinated_per_hundred", "total_boosters_per_hundred"
+    )
+
+    vax_cols <- lapply(vaccine_col_str, as.name)
+  }
+
+  df %>%
+    arrange(id, date) %>%
+    group_by(id) %>%
+    # Take any cols that
+    mutate_at(vars(!!!vax_cols), zoo::na.locf, na.rm = FALSE) %>%
+    ungroup()
+}