diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..c0f0cf0 --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,19 @@ +^renv$ +^renv\.lock$ +CODE_OF_CONDUCT.md +SECURITY.md +^.*\.Rproj$ +^\.Rproj\.user$ +^_pkgdown\.yml$ +^vignettes/hello\.Rmd$ +^docs$ +^\.github$ +README.* +^\.lintr$ +^staged_dependencies\.yaml$ +coverage.* +^\.pre-commit-config\.yaml$ +^codemeta\.json$ +init.sh +workflows.md +images diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..dfe0770 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,2 @@ +# Auto detect text files and perform LF normalization +* text=auto diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml new file mode 100644 index 0000000..40b4a07 --- /dev/null +++ b/.github/workflows/check.yaml @@ -0,0 +1,79 @@ +--- +name: Check πŸ›  + +on: + pull_request: + types: + - opened + - synchronize + - reopened + - ready_for_review + branches: + - main + push: + branches: + - main + workflow_dispatch: + +jobs: + audit: + name: Audit Dependencies πŸ•΅οΈβ€β™‚οΈ + uses: insightsengineering/r.pkg.template/.github/workflows/audit.yaml@main + r-cmd: + name: R CMD Check 🧬 + uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main + secrets: + REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + additional-env-vars: | + _R_CHECK_CRAN_INCOMING_REMOTE_=false + additional-r-cmd-check-params: --as-cran + coverage: + name: Coverage πŸ“” + uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main + secrets: + REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + linter: + if: github.event_name == 'pull_request' + name: SuperLinter πŸ¦Έβ€β™€οΈ + uses: insightsengineering/r.pkg.template/.github/workflows/linter.yaml@main + roxygen: + name: Roxygen πŸ…Ύ + uses: insightsengineering/r.pkg.template/.github/workflows/roxygen.yaml@main + secrets: + REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + auto-update: true + gitleaks: + name: gitleaks πŸ’§ + uses: insightsengineering/r.pkg.template/.github/workflows/gitleaks.yaml@main + spelling: + if: github.event_name == 'pull_request' + name: Spell Check πŸ†Ž + uses: insightsengineering/r.pkg.template/.github/workflows/spelling.yaml@main + links: + if: github.event_name == 'pull_request' + name: Check URLs 🌐 + uses: insightsengineering/r.pkg.template/.github/workflows/links.yaml@main + vbump: + name: Version Bump πŸ€œπŸ€› + if: github.event_name == 'push' + uses: insightsengineering/r.pkg.template/.github/workflows/version-bump.yaml@main + secrets: + REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + version: + name: Version Check 🏁 + uses: insightsengineering/r.pkg.template/.github/workflows/version.yaml@main + licenses: + name: License Check πŸƒ + uses: insightsengineering/r.pkg.template/.github/workflows/licenses.yaml@main + style: + if: github.event_name == 'pull_request' + name: Style Check πŸ‘— + uses: insightsengineering/r.pkg.template/.github/workflows/style.yaml@main + with: + auto-update: true + grammar: + if: github.event_name == 'pull_request' + name: Grammar Check πŸ”€ + uses: insightsengineering/r.pkg.template/.github/workflows/grammar.yaml@main diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml new file mode 100644 index 0000000..5232d65 --- /dev/null +++ b/.github/workflows/docs.yaml @@ -0,0 +1,41 @@ +--- +name: Docs πŸ“š + +on: + push: + branches: + - main + paths: + - "inst/templates/**" + - "_pkgdown.y[a]ml" + - DESCRIPTION + - "**.md" + - "**.Rmd" + - "man/**" + - "LICENSE.*" + - NAMESPACE + pull_request: + types: + - opened + - synchronize + - reopened + - ready_for_review + branches: + - main + paths: + - "inst/templates/**" + - "_pkgdown.y[a]ml" + - DESCRIPTION + - "**.md" + - "**.Rmd" + - "man/**" + - "LICENSE.*" + - NAMESPACE + workflow_dispatch: + +jobs: + docs: + name: Pkgdown Docs πŸ“š + uses: insightsengineering/r.pkg.template/.github/workflows/pkgdown.yaml@main + secrets: + REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/post-release.yaml.shared b/.github/workflows/post-release.yaml.shared new file mode 100644 index 0000000..6428c79 --- /dev/null +++ b/.github/workflows/post-release.yaml.shared @@ -0,0 +1,15 @@ +--- +name: Post release ✨ + +on: + release: + types: ["released"] + +jobs: + vbump: + name: Version Bump πŸ€œπŸ€› + uses: insightsengineering/r.pkg.template/.github/workflows/version-bump.yaml@main + secrets: + REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + vbump-after-release: true diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml new file mode 100644 index 0000000..5af598c --- /dev/null +++ b/.github/workflows/release.yaml @@ -0,0 +1,54 @@ +--- +name: Release 🎈 + +on: + push: + tags: + - "v*" + workflow_dispatch: + +jobs: + build: + name: Build package 🎁 + needs: release + uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main + secrets: + REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + skip-r-cmd-check: true + skip-r-cmd-install: true + docs: + name: Pkgdown Docs πŸ“š + needs: release + uses: insightsengineering/r.pkg.template/.github/workflows/pkgdown.yaml@main + secrets: + REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + default-landing-page: latest-tag + validation: + name: R Package Validation report πŸ“ƒ + needs: release + uses: insightsengineering/r.pkg.template/.github/workflows/validation.yaml@main + secrets: + REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + release: + name: Create release πŸŽ‰ + uses: insightsengineering/r.pkg.template/.github/workflows/release.yaml@main + secrets: + REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + r-cmd: + name: R CMD Check 🧬 + needs: [release, docs] + uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main + secrets: + REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + with: + additional-env-vars: | + _R_CHECK_CRAN_INCOMING_REMOTE_=false + additional-r-cmd-check-params: --as-cran + coverage: + name: Coverage πŸ“” + needs: [release, docs] + uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main + secrets: + REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/scheduled.yaml.shared b/.github/workflows/scheduled.yaml.shared new file mode 100644 index 0000000..b6ff306 --- /dev/null +++ b/.github/workflows/scheduled.yaml.shared @@ -0,0 +1,28 @@ +--- +name: Scheduled πŸ•°οΈ + +on: + schedule: + - cron: '45 3 * * 0' + workflow_dispatch: + +jobs: + dependency-test: + strategy: + fail-fast: false + matrix: + test-strategy: ["min", "release", "max"] + uses: insightsengineering/r.pkg.template/.github/workflows/verdepcheck.yaml@main + name: Dependency Test - ${{ matrix.test-strategy }} πŸ”’ + secrets: + REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GCHAT_WEBHOOK: ${{ secrets.GCHAT_WEBHOOK }} + with: + strategy: ${{ matrix.test-strategy }} + additional-env-vars: | + PKG_SYSREQS_DRY_RUN=true + branch-cleanup: + name: Branch Cleanup 🧹 + uses: insightsengineering/r.pkg.template/.github/workflows/branch-cleanup.yaml@main + secrets: + REPO_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..7065c0b --- /dev/null +++ b/.gitignore @@ -0,0 +1,33 @@ +.DS_Store +.httr-oauth +.project +.RData +.Rhistory +.Rproj.user +.Ruserdata +.settings/** +*.html +*.Rcheck +*.rprof +*.sas.txt +*~ +/.project +devel/* +doc +docs +inst/outputs/* +logs +Meta +packrat/lib*/ +temp +temp_w +templates/ +tmp.* +vignettes/*.html +vignettes/*.md +vignettes/*.R +coverage.* +.vscode/ +node_modules/ +package-lock.json +package.json diff --git a/.lintr b/.lintr new file mode 100644 index 0000000..34473d2 --- /dev/null +++ b/.lintr @@ -0,0 +1,5 @@ +linters: linters_with_defaults( + line_length_linter = line_length_linter(120), + cyclocomp_linter = NULL, + object_usage_linter = NULL + ) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..0229cbf --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,82 @@ +--- +# All available hooks: https://pre-commit.com/hooks.html +# R specific hooks: https://github.com/lorenzwalthert/precommit +repos: + - repo: https://github.com/lorenzwalthert/precommit + rev: v0.3.2.9013 + hooks: + - id: style-files + args: [--style_pkg=styler, --style_fun=tidyverse_style] + - id: roxygenize + additional_dependencies: + - plumber + - shiny + # codemeta must be above use-tidy-description when both are used + # - id: codemeta-description-updated + - id: use-tidy-description + - id: spell-check + exclude: > + (?x)^( + data/.*| + (.*/|)\.Rprofile| + (.*/|)\.Renviron| + (.*/|)\.gitignore| + (.*/|)NAMESPACE| + (.*/|)DESCRIPTION| + (.*/|)WORDLIST| + (.*/|)LICENSE| + (.*/|)\.Rbuildignore| + (.*/|)\.lintr| + (.*/|)_pkgdown.yaml| + (.*/|)staged_dependencies.yaml| + (.*/|)\.pre-commit-.*| + \.github/.*| + .*\.[rR]| + .*\.Rproj| + .*\.py| + .*\.png| + .*\.feather| + .*\.rds| + .*\.Rds| + .*\.sh| + .*\.RData + )$ + - id: lintr + - id: readme-rmd-rendered + - id: parsable-R + - id: no-browser-statement + - id: deps-in-desc + - repo: https://github.com/pre-commit/mirrors-prettier + rev: v3.0.0-alpha.9-for-vscode + hooks: + - id: prettier + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.4.0 + hooks: + - id: check-added-large-files + args: ["--maxkb=200"] + - id: end-of-file-fixer + exclude: '\.Rd' + - id: trailing-whitespace + exclude: '\.Rd' + - id: check-yaml + - id: no-commit-to-branch + - id: mixed-line-ending + args: ["--fix=lf"] + - id: detect-aws-credentials + args: ["--allow-missing-credentials"] + - id: detect-private-key + - id: forbid-new-submodules + - id: check-symlinks + - repo: local + hooks: + - id: forbid-to-commit + name: Don't commit common R artifacts + entry: Cannot commit .Rhistory, .RData, .Rds or .rds. + language: fail + files: '\.Rhistory|\.RData|\.Rds|\.rds$' + # `exclude: ` to allow committing specific files. + - repo: https://github.com/igorshubovych/markdownlint-cli + rev: v0.35.0 + hooks: + - id: markdownlint diff --git a/DESCRIPTION b/DESCRIPTION new file mode 100644 index 0000000..cc4a186 --- /dev/null +++ b/DESCRIPTION @@ -0,0 +1,31 @@ +Type: Package +Package: anthonyverse +Title: R Package Template +Version: 0.1.0 +Date: 2023-07-05 +Authors@R: + person("anthonyokc", , , "anthonyokc@example.com", role = c("aut", "cre")) +Description: R package template with GitHub Actions workflows included. +License: Apache License 2.0 | file LICENSE +URL: https://github.com/anthonyokc/anthonyverse/ +BugReports: https://github.com/anthonyokc/anthonyverse/issues +Depends: + R (>= 3.6) +Imports: + plumber, + shiny, + stringr +Suggests: + future, + httr, + knitr, + shinytest, + testthat (>= 2.0) +VignetteBuilder: + knitr +biocViews: +Encoding: UTF-8 +Language: en-US +LazyData: true +Roxygen: list(markdown = TRUE) +RoxygenNote: 7.2.3 diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..e62ec04 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ +GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/NAMESPACE b/NAMESPACE new file mode 100644 index 0000000..62a3c9a --- /dev/null +++ b/NAMESPACE @@ -0,0 +1,6 @@ +# Generated by roxygen2: do not edit by hand + +export(hello) +export(plumber_api) +export(shiny_app) +importFrom(utils,packageName) diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..cdff1c6 --- /dev/null +++ b/NEWS.md @@ -0,0 +1,13 @@ +# anthonyverse 0.1.0 + +### New features + +* Add an initializer script. + +### Enhancements + +* Documentation on how to use the initialize a package. + +### Bug fixes + +* None. \ No newline at end of file diff --git a/R/covid_eviction_labels.R b/R/covid_eviction_labels.R new file mode 100644 index 0000000..3866cfb --- /dev/null +++ b/R/covid_eviction_labels.R @@ -0,0 +1,102 @@ +covid_eviction_labels <- function(label_data, ..., .labels = FALSE) { + + ojo_labels <- function(.label, data = label_data, .x, .y) { + "Helper: Makes it more efficient to make and edit the aesthetics of all labels at once." + geom_label( + data = data, + label = .label, + aes(x = {{.x}}, y = {{.y}}, group = variable), + fontface = "bold", size = 2.5, hjust = -0.02, + label.size = 0, fill = "#dddddd", color = "#231f20" + ) + } + + # Dates of events are rounded to nearest month for readability + # COVID State of Emergency Declared + date_covid <- ymd("2020-03-01") + # Federal Eviction Moratorium Begins (CARES Act passed 3-24-2020) + date_federalMoratoriumBegins <- ymd("2020-04-01") + # Federal Eviction Moratorium Expires 7/25/2020 + date_federalMoratoriumExpires <- ymd("2020-08-01") + # CDC Moratorium Begins 9/4/2020 + date_cdcMoratoriumBegins <- ymd("2020-09-01") + # CDC Moratorium Expires 7/31/2021 + date_cdcMoratoriumEnds <- ymd("2021-08-01") + + + components <- list( + # Highlight dates where there is an active eviction moratorium or court closure. + annotate( + "rect", + xmin = date_covid, xmax = date_federalMoratoriumExpires, + ymin = -Inf, ymax = Inf, + fill = "#000000", alpha = 0.25, + color = NA + ), + annotate( + "rect", + xmin = date_cdcMoratoriumBegins, xmax = date_cdcMoratoriumEnds, + ymin = -Inf, ymax = Inf, + fill = "#000000", alpha = 0.25, + color = NA + ), + # We use this to make the legend (the x & y values don't matter) + geom_rect( + aes( + xmin = date_covid, xmax = date_federalMoratoriumBegins, + ymin = 0, ymax = Inf, + fill = "Active Eviction Moratorium\nor Court Closure", + color = NULL + ) + ), + scale_fill_manual( + name = "", + values = c("Active Eviction Moratorium\nor Court Closure" = "#00000000"), + guide = guide_legend(override.aes = list(fill = "#000000", alpha = .2)) + ) + ) + + + if (.labels == TRUE) { + components <- append(components, list( + geom_vline(xintercept = date_covid, linetype = "dashed"), + geom_vline(xintercept = date_federalMoratoriumBegins, linetype = "dashed"), + geom_vline(xintercept = date_federalMoratoriumExpires, linetype = "dashed"), + geom_vline(xintercept = date_cdcMoratoriumBegins, linetype = "dashed"), + geom_vline(xintercept = date_cdcMoratoriumEnds, linetype = "dashed"), + ojo_labels( + data = label_data, + .label = "COVID State of Emergency:\nCourt Closes Temporarily", + .x = date_covid, + .y = maxValue * .95 + ), + ojo_labels( + data = label_data, + .label = "CARES Act: Federal Eviction Moratorium Issued", + .x = date_federalMoratoriumBegins, + .y = maxValue * .8 + ), + ojo_labels( + data = label_data, + .label = "Federal Eviction\nMoratorium Expires", + .x = date_federalMoratoriumExpires, + .y = maxValue * .7 + ), + ojo_labels( + data = label_data, + .label = "CDC Eviction\nMoratorium Issued", + .x = date_cdcMoratoriumBegins, + .y = maxValue * .2 + ), + ojo_labels( + data = label_data, + .label = "CDC Eviction\nMoratorium Expires", + .x = date_cdcMoratoriumEnds, + .y = maxValue * .95 + ) + )) + } + + + return(components) +} diff --git a/R/custom_ojo_theme.R b/R/custom_ojo_theme.R new file mode 100644 index 0000000..002211c --- /dev/null +++ b/R/custom_ojo_theme.R @@ -0,0 +1,20 @@ +custom_ojo_theme <- function() { + ggplot2::theme_bw( + base_size = 16, + base_family = "roboto_condensed" + ) %+replace% + ggplot2::theme( + panel.background = ggplot2::element_blank(), + plot.background = ggplot2::element_blank(), + legend.background = ggplot2::element_rect(fill = "transparent", colour = NA), + legend.key = ggplot2::element_rect(fill = "transparent", colour = NA), + legend.position = "top" + ) + + theme( + legend.title = element_blank(), + legend.text = element_text(size = 14), + axis.title = element_blank(), + strip.background = element_blank(), + strip.text = element_text(face = "bold") + ) +} diff --git a/R/hc_theme_ojo.R b/R/hc_theme_ojo.R new file mode 100644 index 0000000..a9ee914 --- /dev/null +++ b/R/hc_theme_ojo.R @@ -0,0 +1,22 @@ +library(highcharter) +library(ojodb) +hc_theme_ojo <- hc_theme_merge( + hc_theme_smpl(), + hc_theme( + colors = ojo_pal, + plotOptions = list( + line = list( + lineWidth = 3, + marker = list( + enabled = TRUE, + lineColor = "#000000", + lineWidth = 1.5 + ) + ) + ), + legend = list( + align = "center", + verticalAlign = "top" + ) + ) +) diff --git a/R/highchart_label_formatter.R b/R/highchart_label_formatter.R new file mode 100644 index 0000000..bb92f3d --- /dev/null +++ b/R/highchart_label_formatter.R @@ -0,0 +1,44 @@ +highchart_label_formatter <- function(variable_name, + prefix = "", + suffix = "", + value_identifier = "this.value", + digits = 0, + dataClass = FALSE + ) { + + if (str_detect(variable_name, "[P|p]ercent")) { + formatted_value <- "Highcharts.numberFormat(this.value * 100, 0) + '%'" + } else if (str_detect(variable_name, "[I|i]ncome|[A|a]mount")) { + formatted_value <- "'$' + Highcharts.numberFormat(this.value, 0)" + } else { + formatted_value <- "Highcharts.numberFormat(this.value, 0)" + } + + if (value_identifier != "this.value") { + formatted_value <- + str_replace_all(formatted_value, "this.value", value_identifier) + } + + if (digits != 0) { + formatted_value <- + str_replace_all(formatted_value, "0\\)", paste0(digits, "\\)")) + } + + if (dataClass == TRUE) { + modified_from <- str_replace_all(formatted_value, "this.value", "this.from") + modified_to <- str_replace_all(formatted_value, "this.value", "this.to") + + return(JS(paste0("function() { + return ", prefix, + modified_from, " + ' β€” ' + ", modified_to, + suffix, ";", " + }")) + ) + } + + return(JS(paste0("function() { + return ", prefix, formatted_value, suffix, ";", " + }")) + ) + +} diff --git a/R/ojo_add_geoid.R b/R/ojo_add_geoid.R new file mode 100644 index 0000000..dfe2887 --- /dev/null +++ b/R/ojo_add_geoid.R @@ -0,0 +1,48 @@ +ojo_add_geoid <- function(data, + geography = c("county", "state"), + year = 2019 + ) { + + rlang::check_installed(pkg = "tidycensus") + + # Variable Handling + .geography = geography[1] + + population_variable <- "POPESTIMATE" + + if (year <= 2019) { + population_variable <- "POP" + } + + df <- tidycensus::get_estimates( + variables = population_variable, + geography = .geography, + year = year, + state = "OK" + ) + + if (.geography == "county") { + df <- + df |> + dplyr::mutate( + district = + NAME |> + stringr::str_remove(" County.*") |> + stringr::str_to_upper() |> + str_replace_all("LE FLORE", "LEFLORE") + ) |> + dplyr::select(district, GEOID) + + data <- + data |> + dplyr::left_join(df) + + return(data) + } + + data <- + data |> + mutate(GEOID = df$GEOID) + + return(data) +} diff --git a/R/ojo_add_geometries.R b/R/ojo_add_geometries.R new file mode 100644 index 0000000..07d2b8a --- /dev/null +++ b/R/ojo_add_geometries.R @@ -0,0 +1,22 @@ +library(tigris) +library(sf) +ojo_add_geometries <- function(data, geography = c("county", "state"), ...) { + geography <- geography[1] + + if (geography == "county") { + data <- counties("OK", progress_bar = FALSE, ...) |> + select(GEOID) |> + left_join(data) + + return(data) + } + + if (geography == "state") { + data <- states(progress_bar = FALSE, ...) |> + filter(NAME == "Oklahoma") |> + select(geometry) |> + cross_join(data) + } + + return(data) +} diff --git a/R/ojo_add_month_and_year.R b/R/ojo_add_month_and_year.R new file mode 100644 index 0000000..f1dc7cc --- /dev/null +++ b/R/ojo_add_month_and_year.R @@ -0,0 +1,29 @@ +library(dplyr) +library(lubridate) +library(purrr) +ojo_add_month_and_year <- function(data, ...) { + "Add month and year columns. Uses columns with 'date' by default but + user can input the ones they want manually." + + cols <- rlang::quos(...) + + # If no specific columns provided, look for columns containing the word 'date' + if (length(cols) == 0) { + cols <- names(data)[grepl("date", names(data))] + } else { + cols <- purrr::map_chr(cols, ~ rlang::quo_text(.)) + } + + for (colname in cols) { + month_name <- if (colname == "date") "month" else paste0("month_", gsub("date_", "", colname)) + year_name <- if (colname == "date") "year" else paste0("year_", gsub("date_", "", colname)) + + data <- data %>% + mutate( + !!month_name := floor_date(!!sym(colname), "month"), + !!year_name := floor_date(!!sym(colname), "year") + ) + } + + return(data) +} diff --git a/R/ojo_add_population.R b/R/ojo_add_population.R new file mode 100644 index 0000000..3553696 --- /dev/null +++ b/R/ojo_add_population.R @@ -0,0 +1,129 @@ +library(tidyr) +library(stringr) +ojo_add_population <- function(data, + geography = c("both", "county", "state"), + year_column, + individual_year = NA, + ... + ) { + + "Adds population data from the Census Population Estimate Program." + + # TODO: Add option for population density + + ## Variable Handling + # By default geography gets both the county and state + .geography <- geography[1] + + # Add GEOIDs + data <- data |> + ojo_add_geoid(geography = "county", 2020) + + if (missing(year_column)) { + # Find year columns in data, select first one in alphabetical order. + year_column <- data |> + select(starts_with("year")) |> + names() |> + sort() |> + nth(1) + } + + years <- data |> + pull({{year_column}}) |> + unique() |> + year() + + get_population_data <- function(years, geography) { + + population_data <- tibble() + + #TODO: Need to use censusapi to get the 2000s and earlier PEP estimates. + # if (any(years %in% 2000:2009)) { + # population_2000s <- tidycensus::get_estimates( + # product = "population", + # geography = geography, + # year = 2009, + # time_series = TRUE, + # state = "OK" + # ) |> + # filter( + # variable == "POP", + # !(DATE %in% c(1, 12)) # Excludes years 2010, and 2020 (https://www.census.gov/data/developers/data-sets/popest-popproj/popest/popest-vars/2019.html) + # ) |> + # mutate( + # year = 2000 + (DATE - 2), + # variable = "POPESTIMATE" + # ) + # + # population_data <- population_data |> + # bind_rows(population_2000s) + # } + + if (any(years %in% 2010:2019)) { + population_2010s <- tidycensus::get_estimates( + product = "population", + geography = geography, + year = 2019, + time_series = TRUE, + state = "OK" + ) |> + filter( + variable == "POP", + !(DATE %in% c(1, 12)) + ) |> + mutate( + year = 2010 + (DATE - 2), + variable = "POPESTIMATE" + ) + + population_data <- population_data |> + bind_rows(population_2010s) + } + + if (any(years %in% 2020:2029)) { + population_2020s <- tidycensus::get_estimates( + product = "population", + geography = geography, + time_series = TRUE, + state = "OK" + ) |> + filter(variable == "POPESTIMATE") + + population_data <- population_data |> + bind_rows(population_2020s) + } + + population_data <- population_data |> + pivot_wider(names_from = "variable", values_from = "value") |> + mutate(year = paste0(year, "-01-01") |> ymd()) |> + select(year, GEOID, population_county = POPESTIMATE) + + if (geography == "state") { + population_data <- population_data |> + select(year, population_state = population_county) + } + + return(population_data) + } + + if (.geography %in% c("state", "both")) { + population_state_data <- get_population_data(years, "state") + data <- data |> + left_join(population_state_data, by = join_by(!!year_column == year)) |> + mutate(population_state = as.numeric(population_state)) # as.numeric() is necessary for this to work. + } + if (.geography %in% c("county", "both")) { + population_county_data <- get_population_data(years, "county") + + data <- data |> + left_join(population_county_data, by = join_by(!!year_column == year, GEOID)) |> + mutate(population_county = as.numeric(population_county)) + } + + cat( + paste("Joined population on the", paste0("`", year_column, "`"), "column."), + sep = "\n" + ) + + return(data) +} diff --git a/R/ojo_aggregate.R b/R/ojo_aggregate.R new file mode 100644 index 0000000..dd60bce --- /dev/null +++ b/R/ojo_aggregate.R @@ -0,0 +1,90 @@ +ojo_aggregate <- function(data, + ..., + group_by, + geography = c("county", "state"), + rate = 10^3, + rate_suffix = "1k" + ) { + + # Variable Handling + geography <- geography[1] + variables <- enquos(...) + if (!missing(group_by)) { + group_by_text <- enquos(group_by) |> purrr::map_chr(~ rlang::quo_get_expr(.) |> rlang::as_label()) + } + + if (length(variables) == 0) { + variable_name <- NA + } else { + variable_name <- purrr::map_chr(variables, ~ rlang::as_label(.)) + } + + n_variable_name <- if_else( + is.na(variable_name), + "n", + paste0("n_", variable_name) # E.g., n_eviction_filings + ) + rate_variable_name <- if_else( + is.na(variable_name), + paste0("n_", "per_", rate_suffix), + paste0("n_", variable_name, "_per_", rate_suffix) # E.g., n_eviction_filings_per1k + ) + + data <- data |> + distinct(id, .keep_all = TRUE) + + if (any(is.na(variable_name))) { + variable_name <- "" + + if (geography == "county") { + + data <- data |> + count({{group_by}}, district, population_county, name = n_variable_name) + + } else if (geography == "state") { + + data <- data |> + count({{group_by}}, population_state, name = n_variable_name) + + data <- data |> + mutate( + !!rate_variable_name := .data[[n_variable_name]] / population_state * rate + ) |> + arrange({{group_by}}, !!variable_name) + + return(data) + + } + } else { + if (geography == "county") { + + data <- data |> + count( + {{group_by}}, district, population_county, .data[[variable_name]], + name = n_variable_name + ) + + } else if (geography == "state") { + + data <- data |> + count( + {{group_by}}, district, population_county, .data[[variable_name]], + name = n_variable_name + ) + + data <- data |> + mutate( + !!rate_variable_name := .data[[n_variable_name]] / population_state * rate + ) |> + arrange({{group_by}}, !!variable_name) + + return(data) + } + } + + data <- data |> + mutate(!!rate_variable_name := .data[[n_variable_name]] / population_county * rate) |> + arrange({{group_by}}, district, !!variable_name) + + return(data) +} diff --git a/R/ojo_district_and_date_filters.R b/R/ojo_district_and_date_filters.R new file mode 100644 index 0000000..119f6a9 --- /dev/null +++ b/R/ojo_district_and_date_filters.R @@ -0,0 +1,25 @@ +ojo_district_and_date_filters <- function(data, + districts = "ALL", + date_start = NA, + date_end = NA, + district_variable = "district", + date_variable = "date_filed" + ) { + + "Helper function for commonly used case filters." + + # Variable Handling + .districts <- toupper(districts) + + if (any(districts != "ALL")) { + data <- data |> filter(.data[[district_variable]] %in% .districts) + } + if (!is.na(date_end)) { + data <- data |> filter(.data[[date_variable]] <= date_end) + } + if (!is.na(date_start)) { + data <- data |> filter(.data[[date_variable]] >= date_start) + } + + return(data) +} diff --git a/R/ojo_highchart_map.R b/R/ojo_highchart_map.R new file mode 100644 index 0000000..4acbd58 --- /dev/null +++ b/R/ojo_highchart_map.R @@ -0,0 +1,125 @@ +library(ggthemes) +library(jsonlite) +library(geojsonsf) +library(highcharter) +ojo_highchart_map <- function(data, + variable, + ..., + caption = NULL, + nbins, + map_color_stops = rev(viridis::magma(n = 3)) + ) { + + variable <- enquo(variable) |> rlang::as_label() + + + data_json <- data |> + select(district) |> + geojsonsf::sf_geojson() |> + jsonlite::fromJSON(simplifyVector = FALSE) + + # Highlight around specific areas + # data_hc <- + # data |> + # left_join( + # tibble( + # district = __, + # borderColor = ojo_pal[1], + # borderWidth = 3, + # zIndex = 5000, + # candidate = 1 + # ), + # by = "district" + # ) + + # variable_data <- data_hc |> + variable_data <- data |> + pull({{variable}}) |> + na.omit() + + n_bins <- nclass.FD(variable_data) + if (!missing(nbins)) { + n_bins <- nbins + + if (is.function(nbins)) { + bin_formula <- nbins + n_bins <- bin_formula(variable_data) + } + } + + h <- hist(variable_data, plot = FALSE, breaks = n_bins) + + d <- diff(h$breaks)[1] + + df <- tibble( + x = h$mids, + y = h$counts, + name = sprintf("(%s, %s]", h$mids - d / 2, h$mids + d / 2) + ) + + legend_colors <- color_classes( + breaks = h$breaks, + colors = + color_stops( + n = n_bins, + colors = map_color_stops + ) |> + sapply(function(x) x[[2]]) + ) + + hc <- highchart() |> + hc_add_series_map( + map = data_json, + df = data, + joinBy = "district", + id = "s1", + name = pretty_variable_names(variable), + value = variable, + tooltip = list( + headerFormat = "{point.name}
", + pointFormatter = highchart_label_formatter( + variable, + prefix = "'' + this.district + '
' + this.series.name + ': ' + ", + suffix = " + '
'", + # "+ 'Margin of Error:, + # paste0("this.moe_", variable), + # "±'", + digits = 1 + ) + ), + dataLabels = list( + enabled = TRUE, + format = "{point.district}" + ) + ) |> + hc_caption(text = caption) |> + hc_colorAxis( + labels = list( + format = "{value}", + formatter = highchart_label_formatter(variable) + ), + dataClasses = legend_colors + ) |> + hc_legend( + layout = "vertical", + align = "left", + verticalAlign = "top", + floating = TRUE, + backgroundColor = 'rgba(255,255,255,0.9)', + valueDecimals = 2, + labelFormatter = highchart_label_formatter(variable, dataClass = TRUE), + symbolRadius = 0, + itemMarginBottom = 4, + itemMarginTop = 4, + shadow = TRUE + ) |> + hc_mapNavigation( + enabled = TRUE, + buttonOptions = list( + align = "right" + ) + ) |> + hc_add_theme(hc_theme_ojo) + + return(hc) +} diff --git a/R/ojo_optional_filter.R b/R/ojo_optional_filter.R new file mode 100644 index 0000000..cc6a0f7 --- /dev/null +++ b/R/ojo_optional_filter.R @@ -0,0 +1,9 @@ +ojo_optional_filter <- function(data, variable, variable_values = NA) { + "Helper for optional filtering of variable if not NA." + + if (any(!is.na(variable_values))) { + data <- data |> filter({{variable}} %in% variable_values) + } + + return(data) +} diff --git a/R/ojo_plot_lines.R b/R/ojo_plot_lines.R new file mode 100644 index 0000000..3e6c835 --- /dev/null +++ b/R/ojo_plot_lines.R @@ -0,0 +1,177 @@ +library(ojodb) +library(ggplot2) + +ojo_plot_lines <- function(data, + x, + y, + ..., + color_variable = variable, + facet_variable = NA, + # legend_labels = "default", + # facet_labels = "default", + legend_labels = NA, + facet_labels = NA, + custom_color_palette = NA, + number_of_columns = 1, + data_to_highlight = NA, + highlight_color = "red", + theme = custom_ojo_theme(), + add_covid_labels = FALSE +) { + + + # Create strings from inputs + x_string <- deparse(substitute(x)) + if (is.symbol(substitute(y)) | is.language(substitute(y))) { + y_string <- deparse(substitute(y)) + } else if (is.language(substitute(y))) { + y_string <- sapply(substitute(y)[-1], function(x) deparse(x)) + y_string <- str_flatten(y_string) + } else { + y_string <- y + } + color_variable_string <- deparse(substitute(color_variable)) + facet_variable_string <- deparse(substitute(facet_variable)) + if (color_variable_string == "variable") { + color_variable_string <- "" + } + + # Regex selection of the x, y, and color_variable columns. + regex_columns <-paste0( + x_string, + "|", + if_else( + color_variable_string == "", + "", + paste0(color_variable_string, "|") + ), + y_string + ) + + plotData <- + data |> + select(matches(regex_columns)) + + # Construct wide data to input to ggplot based on the color_variable input + if (color_variable_string == "") { + plotData <- + plotData |> + pivot_longer(!{{x}}, names_to = "variable", values_to = "value") + + p <- + plotData |> + ggplot(aes(x = {{x}}, y = value, color = variable)) + + number_of_variables <- + plotData |> + distinct(variable) |> + pull() |> + length() + } else { + plotData <- + plotData |> + pivot_longer( + !any_of(c(x_string, color_variable_string)), + names_to = "variable", values_to = "value" + ) + + p <- + plotData |> + ggplot(aes(x = {{x}}, y = value, color = {{color_variable}})) + + number_of_variables <- + plotData |> + distinct({{color_variable}}) |> + pull() |> + length() + } + + # Format labels for use in ggplot + if (any(!is.na(legend_labels))) { + legend_variables <- plotData |> distinct(variable) |> pull() + names(legend_labels) <- legend_variables + } + # if (any(!is.na(facet_labels))) { + # facets <- plotData |> distinct({{facet_variable}}) |> pull() + # names(facet_labels) <- facets + # } + + # Optional labels for covid eviction moratoriums. + if (add_covid_labels == TRUE) { + labelData <- + plotData |> + summarise(maxValue = max(value), .by = variable) + p <- p + + covid_eviction_labels(label_data = labelData) + } + + p <- p + + geom_line(linewidth = 1.5) + + geom_point(shape = 19, size = 2) + + # Add optional highlighting of certain data points. + if (is.object(data_to_highlight)) { + data_to_highlight <- + data_to_highlight |> + select(matches(regex_columns)) |> + pivot_longer( + !any_of(c(x_string, color_variable_string)), + names_to = "variable", values_to = "value" + ) + + p <- p + + geom_point(data = data_to_highlight, shape = 19, size = 2, color = highlight_color) + } + + p <- p + + geom_point(shape = 21, size = 2, stroke = 1, color = "black") + + if (facet_variable_string != "NA") { + p <- p + + facet_wrap( + vars({{facet_variable}}), ncol = number_of_columns, scales = "free", + labeller = as_labeller(facet_labels) + ) + } + + if (any(!is.na(theme))) { + p <- p + + theme + } + + p <- p + + theme( + axis.title = element_blank() + ) + + if (any(is.na(facet_labels))) + p <- p + + theme( + strip.text = element_blank() + ) + + p <- p + + scale_y_continuous(labels = scales::label_comma()) + + scale_color_manual(values = ojo_pal[1:number_of_variables]) + + guides(color = guide_legend(override.aes = list( + shape = rep(19, number_of_variables), linetype = 0, size = 3, fill = NA + )) + ) + + # Customize color pallette + if (any(!is.na(custom_color_palette))) { + p <- p + + scale_color_manual(values = custom_color_palette[1:number_of_variables]) + } + + # Add custom labels for legend + if (any(!is.na(legend_labels))) { + p <- p + + scale_color_manual( + values = ojo_pal[1:number_of_variables], + labels = legend_labels + ) + } + + return(p) +} diff --git a/R/pretty_variable_names.R b/R/pretty_variable_names.R new file mode 100644 index 0000000..423fbdf --- /dev/null +++ b/R/pretty_variable_names.R @@ -0,0 +1,15 @@ +pretty_variable_names <- function(variable_names) { + + pretty_names <- variable_names |> + snakecase::to_title_case() |> + str_replace_all( + pattern = "Percent Population", + replacement = "% of Population," + ) |> + str_replace_all("Nhpi", "NHPI") |> + str_replace_all("Non Hispanic", "Non-Hispanic") |> + str_replace_all("^N\\s", "Number of ") |> + str_replace_all("\\sN\\s", "Number of ") + + return(pretty_names) +} diff --git a/R/tably.R b/R/tably.R new file mode 100644 index 0000000..dfc6e32 --- /dev/null +++ b/R/tably.R @@ -0,0 +1,42 @@ +tably <- function (data, ..., print_n = NA, top_n = NA, sort = TRUE) { + # TODO: add check for x is missing. + # TODO: add check for using print_n & top_n at the same time. + + # Format arguments + .sort <- sort + dots <- enquos(...) + + df <- + data |> + count(!!!dots, sort = .sort) |> + mutate(percent = n / sum(n) * 100, + total_n = sum(n) + ) + + # if you want to the output to print more than 10. + if (!is.na(print_n)) { + return( + df |> + print(n = print_n) + ) + } + + # Returns the frequency and percent frequency of the top n observations + # and of the observations not in the top n. + if (!is.na(top_n)) { + df <- + df |> + slice(1:top_n) |> + summarise(!!paste0("top", top_n, "_n") := sum(n), + !!paste0("top", top_n, "_percent") := sum(percent), + .by = total_n + ) |> + mutate(!!paste0("non_top", top_n, "_n") := + total_n - !!sym(paste0("top", top_n, "_n")), + !!paste0("non_top", top_n, "_percent") := + 100 - !!sym(paste0("top", top_n, "_percent")) + ) + } + + return(df) +} diff --git a/README.md b/README.md new file mode 100644 index 0000000..68ad9cc --- /dev/null +++ b/README.md @@ -0,0 +1,2 @@ +# anthonyverse + A collection of various R functions I've created for cleaning/wrangling, aggregating, and plotting data that I commonly use across projects. Some may eventually "graduate" to be functions in other packages, in which case a warning will be displayed directing the user the new location for the function. diff --git a/_pkgdown.yml b/_pkgdown.yml new file mode 100644 index 0000000..59d1b42 --- /dev/null +++ b/_pkgdown.yml @@ -0,0 +1,20 @@ +url: https://anthonyokc.github.io/anthonyverse + +template: + bootstrap: 5 + bootswatch: cerulean + includes: + in_header: | + + + + +navbar: + right: + - icon: fa-github + href: https://github.com/anthonyokc/anthonyverse diff --git a/anthonyverse.Rproj b/anthonyverse.Rproj new file mode 100644 index 0000000..cba1b6b --- /dev/null +++ b/anthonyverse.Rproj @@ -0,0 +1,21 @@ +Version: 1.0 + +RestoreWorkspace: No +SaveWorkspace: No +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX + +AutoAppendNewline: Yes +StripTrailingWhitespace: Yes + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source +PackageRoxygenize: rd,collate,namespace diff --git a/inst/WORDLIST b/inst/WORDLIST new file mode 100644 index 0000000..03096e3 --- /dev/null +++ b/inst/WORDLIST @@ -0,0 +1,12 @@ +BiocCheck +CMD +Pkgdown +Pre +Roxygen +SuperLinter +github +gitleaks +initializer +pre +repo +Forkers diff --git a/inst/plumber/hello/plumber.R b/inst/plumber/hello/plumber.R new file mode 100644 index 0000000..f71c7f3 --- /dev/null +++ b/inst/plumber/hello/plumber.R @@ -0,0 +1,4 @@ +#* Personal greeting as a Plumber API +#* @param name Your name (character string; e.g. "john doe"). +#* @get /echo +anthonyverse::hello diff --git a/man/hello.Rd b/man/hello.Rd new file mode 100644 index 0000000..e7eb880 --- /dev/null +++ b/man/hello.Rd @@ -0,0 +1,20 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/hello.R +\name{hello} +\alias{hello} +\title{Personal greeting} +\usage{ +hello(name = "your name") +} +\arguments{ +\item{name}{Your name (character string; e.g. "john doe").} +} +\value{ +A character string, capitalized to title case. +} +\description{ +Greet a person and appropriately capitalize their name. +} +\examples{ +hello("james bond") +} diff --git a/man/plumber_api.Rd b/man/plumber_api.Rd new file mode 100644 index 0000000..84ef92b --- /dev/null +++ b/man/plumber_api.Rd @@ -0,0 +1,18 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/hello.R +\name{plumber_api} +\alias{plumber_api} +\title{Personal greeting as a Plumber API} +\usage{ +plumber_api(...) +} +\arguments{ +\item{...}{Additional arguments to plumber::pr_run()} +} +\value{ +Plumber API showcasing the personal greeting feature. +} +\description{ +Greet a person and appropriately capitalize their name +as a Plumber API. +} diff --git a/man/shiny_app.Rd b/man/shiny_app.Rd new file mode 100644 index 0000000..8171c58 --- /dev/null +++ b/man/shiny_app.Rd @@ -0,0 +1,15 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/hello.R +\name{shiny_app} +\alias{shiny_app} +\title{Personal greeting as a Shiny app} +\usage{ +shiny_app() +} +\value{ +Shiny app showcasing the personal greeting feature. +} +\description{ +Greet a person and appropriately capitalize their name +as a Shiny app. +} diff --git a/staged_dependencies.yaml b/staged_dependencies.yaml new file mode 100644 index 0000000..b068aa4 --- /dev/null +++ b/staged_dependencies.yaml @@ -0,0 +1,7 @@ +--- +# Information about this file: https://github.com/openpharma/staged.dependencies +current_repo: + repo: anthonyokc/anthonyverse + host: https://github.com +upstream_repos: +downstream_repos: diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 0000000..00dc32a --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,3 @@ +pkg_name <- "anthonyverse" +library(pkg_name, character.only = TRUE) +testthat::test_check(pkg_name) diff --git a/tests/testthat/shiny-app/app.R b/tests/testthat/shiny-app/app.R new file mode 100644 index 0000000..27c86e1 --- /dev/null +++ b/tests/testthat/shiny-app/app.R @@ -0,0 +1 @@ +anthonyverse::shiny_app() diff --git a/tests/testthat/test-api.R b/tests/testthat/test-api.R new file mode 100644 index 0000000..ee1574b --- /dev/null +++ b/tests/testthat/test-api.R @@ -0,0 +1,30 @@ +test_that("API greets the person", { + host <- "127.0.0.1" + port <- 9000 + + # Start the API + future::plan(future::multisession) + future::future( + anthonyverse::plumber_api(host = host, port = port) + ) + Sys.sleep(3) + + # Make request + res <- httr::GET( + url = paste0( + "http://", + host, + ":", + port, + "/echo" + ), + query = "name=tim" + ) + + # Get response + result <- httr::content(res)[[1]] + + # Compare + expected <- "Hello, Tim" + expect_identical(result, expected) +}) diff --git a/tests/testthat/test-hello.R b/tests/testthat/test-hello.R new file mode 100644 index 0000000..4dccc45 --- /dev/null +++ b/tests/testthat/test-hello.R @@ -0,0 +1,5 @@ +test_that("hello greets the entity", { + result <- hello("foo") + expected <- "Hello, Foo" + expect_identical(result, expected) +}) diff --git a/tests/testthat/test-shiny.R b/tests/testthat/test-shiny.R new file mode 100644 index 0000000..6fed2d6 --- /dev/null +++ b/tests/testthat/test-shiny.R @@ -0,0 +1,25 @@ +test_that("The Shiny App returns a proper greeting", { + library(shinytest) + app <- ShinyDriver$new( + "shiny-app/", + loadTimeout = 1e5, + debug = "all", + phantomTimeout = 1e5, + seed = 123 + ) + app$getDebugLog() + + # Set input + app$setInputs(name = "john") + app$setInputs(greet = "click") + output <- app$getValue(name = "greeting") + + # test + expect_equal(output, "Hello, John") + + # wait for the process to close gracefully + # this allows covr to write out the coverage results + p <- app$.__enclos_env__$private$shinyProcess + p$interrupt() + p$wait() +}) diff --git a/vignettes/hello.Rmd b/vignettes/hello.Rmd new file mode 100644 index 0000000..405e244 --- /dev/null +++ b/vignettes/hello.Rmd @@ -0,0 +1,12 @@ + +--- +title: "Hello" +date: "`r Sys.Date()`" +--- + +Hello World! + +```{r} +library(anthonyverse) +hello("anthonyverse!") +```