Euclidian distance feature

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^LICENSE\.md$
 ^.*\.Rproj$
 ^\.Rproj\.user$
@@ -6,3 +8,5 @@
 ^docs$
 ^pkgdown$
 ^\.lintr$
+renv*
+^data-raw$

.github/workflows/BioC-check.yaml

@@ -25,17 +25,17 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - 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, BiocManager
 

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

@@ -29,33 +29,31 @@ 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'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - 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()

.github/workflows/lint.yaml

@@ -14,16 +14,16 @@ 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}

.gitignore

@@ -2,6 +2,10 @@
 .Rhistory
 .Rapp.history
 
+# R things
+.Rprofile
+renv/
+
 # Session Data files
 .RData
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: DevelExample
 Title: A Basic R Package to Demonstrate a Cycle of Code Development
-Version: 0.0.1
+Version: 0.1.0
 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)

NAMESPACE

@@ -1,3 +1,4 @@
 # Generated by roxygen2: do not edit by hand
 
+export(euclideanDist)
 export(hello)

NEWS.md

@@ -1,3 +1,6 @@
+# Changes in Version 0.1.0 (2022-05-20)
+* Added function to calculate euclidean distance
+
 # Changes in Version 0.0.1 (2022-05-08)
 * Created package
 * Added Hello World function

R/data.R

@@ -0,0 +1,11 @@
+#' 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"

R/distance.R

@@ -0,0 +1,31 @@
+#' @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")
+  }
+}

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: ~
+template:
+  bootstrap: 5
+

data-raw/example_data.R

@@ -0,0 +1,7 @@
+## 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)