diff --git a/.Rbuildignore b/.Rbuildignore index 88b0533..7334216 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,3 +1,5 @@ +^renv$ +^renv\.lock$ ^LICENSE\.md$ ^.*\.Rproj$ ^\.Rproj\.user$ @@ -6,3 +8,5 @@ ^docs$ ^pkgdown$ ^\.lintr$ +^data-raw$ +^renv.* diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index d9de82f..47c376f 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -29,12 +29,12 @@ jobs: - {os: windows-latest, r: '3.6'} # Use older ubuntu to maximise backward compatibility - - {os: ubuntu-18.04, r: 'devel', http-user-agent: 'release'} - - {os: ubuntu-18.04, r: 'release'} - - {os: ubuntu-18.04, r: 'oldrel-1'} - - {os: ubuntu-18.04, r: 'oldrel-2'} - - {os: ubuntu-18.04, r: 'oldrel-3'} - - {os: ubuntu-18.04, r: 'oldrel-4'} + - {os: ubuntu-20.04, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-20.04, r: 'release'} + - {os: ubuntu-20.04, r: 'oldrel-1'} + - {os: ubuntu-20.04, r: 'oldrel-2'} + - {os: ubuntu-20.04, r: 'oldrel-3'} + - {os: ubuntu-20.04, r: 'oldrel-4'} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} @@ -43,19 +43,19 @@ jobs: steps: - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-pandoc@v2 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} http-user-agent: ${{ matrix.config.http-user-agent }} use-public-rspm: true - - uses: r-lib/actions/setup-r-dependencies@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: rcmdcheck + extra-packages: rcmdcheck, knitr - - uses: r-lib/actions/check-r-package@v1 + - uses: r-lib/actions/check-r-package@v2 - name: Show testthat output if: always() diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml index 6388f75..212c4fc 100644 --- a/.github/workflows/lint.yaml +++ b/.github/workflows/lint.yaml @@ -14,16 +14,17 @@ jobs: env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 with: use-public-rspm: true - - uses: r-lib/actions/setup-r-dependencies@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: lintr - name: Lint - run: lintr::lint_package() + run: lintr::lint_package(linters = lintr::linters_with_defaults(object_name_linter = lintr::object_name_linter("camelCase"))) shell: Rscript {0} + diff --git a/.gitignore b/.gitignore index 0dddc4b..fbe71ed 100644 --- a/.gitignore +++ b/.gitignore @@ -40,3 +40,6 @@ vignettes/*.pdf .Renviron inst/doc docs + +.Rprofile +renv/ \ No newline at end of file diff --git a/DESCRIPTION b/DESCRIPTION index e2161da..1658ef4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: DevelExample Title: A Basic R Package to Demonstrate a Cycle of Code Development -Version: 0.0.1 +Version: 0.1.1 Authors@R: person(given = "Joshua", family = "Campbell", @@ -15,10 +15,12 @@ Encoding: UTF-8 biocViews: Clustering LazyData: false Roxygen: list(markdown = TRUE) -RoxygenNote: 7.1.1 +RoxygenNote: 7.2.3 Suggests: knitr, rmarkdown, testthat (>= 3.0.0) Config/testthat/edition: 3 VignetteBuilder: knitr +Depends: + R (>= 2.10) diff --git a/NAMESPACE b/NAMESPACE index 01843dc..6bd620a 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,3 +1,4 @@ # Generated by roxygen2: do not edit by hand +export(euclideanDist) export(hello) diff --git a/NEWS.md b/NEWS.md index 4cd8ae2..8bf56cb 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ -# Changes in Version 0.0.1 (2022-05-08) +# Changes in Version 0.1.1 (2023-04-09) * Created package * Added Hello World function * Added documentation, unit tests, and vignettes * Added a `NEWS.md` file to track changes to the package. +* Added function to calculate euclidean dist diff --git a/R/data.R b/R/data.R new file mode 100644 index 0000000..20b993d --- /dev/null +++ b/R/data.R @@ -0,0 +1,9 @@ +#' Example dataset +#' A dataset containing a matrix with two columns that were generated +#' with a random normal distribution with a mean of 0 and stdev of 1. +#' @format A matrix with 100 rows and 2 columns +#' @keywords datasets +#' @usage data("example_data") +#' @examples +#' data("example_data") +"example_data" \ No newline at end of file diff --git a/R/distance.R b/R/distance.R new file mode 100644 index 0000000..40a8cf7 --- /dev/null +++ b/R/distance.R @@ -0,0 +1,30 @@ +#' @title Euclidean distance +#' @description Calculates Euclidean distance between two vectors. An error will be +#' given if NAs are present in either vector. +#' @param a The first vector to use in the distance calculation. +#' @param b The second vector to use in the distance calculation. +#' @param verbose Boolean. If \code{TRUE}, a message will be printed. Default \code{TRUE}. +#' @return A numeric value of a distance +#' @examples +#' data(example_data) +#' euclideanDist(example_data[,1], example_data[,2], verbose = FALSE) +#' @export +euclideanDist <- function(a, b, verbose = FALSE) { + if (isTRUE(verbose)) { + message("Calculating distance ...") + } + + # Check validity of data + .check_data(a) + .check_data(b) + + # Perform calculation + res <- sqrt(sum((a-b)^2)) + return(res) +} + +.check_data <- function(input) { + if (any(is.na(input))) { + stop("'input' must not contain NAs") + } +} \ No newline at end of file diff --git a/R/functions.R b/R/functions.R index 5e2937a..e4fa2eb 100644 --- a/R/functions.R +++ b/R/functions.R @@ -1,3 +1,4 @@ + #' @title Hello world #' @description A simple function to print Hello world #' @@ -14,4 +15,4 @@ hello <- function(withExcitement = TRUE) { str <- "Hello world." } return(str) -} + } diff --git a/_pkgdown.yml b/_pkgdown.yml index e69de29..d71acfb 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -0,0 +1,4 @@ +url: ~ +template: + bootstrap: 5 + diff --git a/data-raw/example_data.R b/data-raw/example_data.R new file mode 100644 index 0000000..24efc73 --- /dev/null +++ b/data-raw/example_data.R @@ -0,0 +1,6 @@ +## code to prepare `example_data` dataset goes here +set.seed(123) +a <- rnorm(100) +b <- rnorm(100) +example_data <- cbind(a, b) +usethis::use_data(example_data, overwrite = TRUE) diff --git a/data/example_data.rda b/data/example_data.rda new file mode 100644 index 0000000..ea06561 Binary files /dev/null and b/data/example_data.rda differ diff --git a/man/euclideanDist.Rd b/man/euclideanDist.Rd new file mode 100644 index 0000000..ed10e85 --- /dev/null +++ b/man/euclideanDist.Rd @@ -0,0 +1,26 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/distance.R +\name{euclideanDist} +\alias{euclideanDist} +\title{Euclidean distance} +\usage{ +euclideanDist(a, b, verbose = FALSE) +} +\arguments{ +\item{a}{The first vector to use in the distance calculation.} + +\item{b}{The second vector to use in the distance calculation.} + +\item{verbose}{Boolean. If \code{TRUE}, a message will be printed. Default \code{TRUE}.} +} +\value{ +A numeric value of a distance +} +\description{ +Calculates Euclidean distance between two vectors. An error will be +given if NAs are present in either vector. +} +\examples{ +data(example_data) +euclideanDist(example_data[,1], example_data[,2], verbose = FALSE) +} diff --git a/man/example_data.Rd b/man/example_data.Rd new file mode 100644 index 0000000..be597cf --- /dev/null +++ b/man/example_data.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{example_data} +\alias{example_data} +\title{Example dataset +A dataset containing a matrix with two columns that were generated +with a random normal distribution with a mean of 0 and stdev of 1.} +\format{ +A matrix with 100 rows and 2 columns +} +\usage{ +data("example_data") +} +\description{ +Example dataset +A dataset containing a matrix with two columns that were generated +with a random normal distribution with a mean of 0 and stdev of 1. +} +\examples{ +data("example_data") +} +\keyword{datasets} diff --git a/renv.lock b/renv.lock new file mode 100644 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+ res <- dist(rbind(example_data[, 1], example_data[, 2]))[1] + expect_equal(euclideanDist(example_data[, 1], example_data[, 2]), res) + expect_error(euclideanDist(c(1, 2), c(NA, 2)), regexp = "contain NAs")}) \ No newline at end of file diff --git a/vignettes/DevelExample.Rmd b/vignettes/DevelExample.Rmd index 170fadb..5c30b4d 100644 --- a/vignettes/DevelExample.Rmd +++ b/vignettes/DevelExample.Rmd @@ -39,4 +39,13 @@ It is usually a good idea to show the session information to help with reproduci ```{r session} sessionInfo() ``` +To calculate the euclidean distance between two vectors, we can use the `euclideanDist` function. In this example we will generate two random vectors from normal distributions with two different means and calculate the distance between them: +```{r dist} +set.seed(12345) +v1 <- rnorm(10000, mean = 1) +v2 <- rnorm(10000, mean = 2) +res <- euclideanDist(v1, v2, verbose = FALSE) +res +``` +The `set.seed` function is used for the random number generator and ensures the same vectors will be produced each time for reproducibility.