From 0425dd0b9d6fe51327770ac5350693fb647d26e8 Mon Sep 17 00:00:00 2001
From: "George G. Vega Yon" <g.vegayon@gmail.com>
Date: Thu, 14 Nov 2024 11:53:58 -0700
Subject: [PATCH] Initial commit

---
 .Rbuildignore                      |   4 ++
 .github/.gitignore                 |   1 +
 .github/workflows/R-CMD-check.yaml |  49 +++++++++++++++++++++++++
 .gitignore                         |   7 ++++
 DESCRIPTION                        |  16 ++++++++
 NAMESPACE                          |   5 +++
 R/RcppExports.R                    |  12 ++++++
 R/egpkg-package.R                  |   3 ++
 README.Rmd                         |  56 ++++++++++++++++++++++++++++
 README.md                          |  57 +++++++++++++++++++++++++++++
 egpkg.Rproj                        |  21 +++++++++++
 man/figures/README-pressure-1.png  | Bin 0 -> 7324 bytes
 man/rcpp_hello_world.Rd            |  17 +++++++++
 src/.gitignore                     |   3 ++
 src/RcppExports.cpp                |  32 ++++++++++++++++
 src/rcpp_hello_world.cpp           |  18 +++++++++
 16 files changed, 301 insertions(+)
 create mode 100644 .Rbuildignore
 create mode 100644 .github/.gitignore
 create mode 100644 .github/workflows/R-CMD-check.yaml
 create mode 100644 .gitignore
 create mode 100644 DESCRIPTION
 create mode 100644 NAMESPACE
 create mode 100644 R/RcppExports.R
 create mode 100644 R/egpkg-package.R
 create mode 100644 README.Rmd
 create mode 100644 README.md
 create mode 100644 egpkg.Rproj
 create mode 100644 man/figures/README-pressure-1.png
 create mode 100644 man/rcpp_hello_world.Rd
 create mode 100644 src/.gitignore
 create mode 100644 src/RcppExports.cpp
 create mode 100644 src/rcpp_hello_world.cpp

diff --git a/.Rbuildignore b/.Rbuildignore
new file mode 100644
index 0000000..f11ab17
--- /dev/null
+++ b/.Rbuildignore
@@ -0,0 +1,4 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.github$
+^README\.Rmd$
diff --git a/.github/.gitignore b/.github/.gitignore
new file mode 100644
index 0000000..2d19fc7
--- /dev/null
+++ b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
new file mode 100644
index 0000000..a3ac618
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/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: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - 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@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..56843bc
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,7 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+src/*.o
+src/*.so
+src/*.dll
diff --git a/DESCRIPTION b/DESCRIPTION
new file mode 100644
index 0000000..f11a912
--- /dev/null
+++ b/DESCRIPTION
@@ -0,0 +1,16 @@
+Package: egpkg
+Type: Package
+Title: What the Package Does in One 'Title Case' Line
+Version: 1.0
+Date: 2023-02-23
+Author: Your Name
+Maintainer: Your Name <your@email.com>
+Description: One paragraph description of what the package does as
+       one or more full sentences.
+License: GPL (>= 2)
+Imports: 
+    Rcpp
+LinkingTo: Rcpp
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+Encoding: UTF-8
diff --git a/NAMESPACE b/NAMESPACE
new file mode 100644
index 0000000..8f279de
--- /dev/null
+++ b/NAMESPACE
@@ -0,0 +1,5 @@
+# Generated by roxygen2: do not edit by hand
+
+export(rcpp_hello_world)
+importFrom(Rcpp,evalCpp)
+useDynLib(egpkg, .registration = TRUE)
diff --git a/R/RcppExports.R b/R/RcppExports.R
new file mode 100644
index 0000000..03501a9
--- /dev/null
+++ b/R/RcppExports.R
@@ -0,0 +1,12 @@
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#' Hello world from Rcpp
+#' @return A list with two vectors (`x`, `y`).
+#' @examples
+#' rcpp_hello_world()
+#' @export
+rcpp_hello_world <- function() {
+    .Call(`_egpkg_rcpp_hello_world`)
+}
+
diff --git a/R/egpkg-package.R b/R/egpkg-package.R
new file mode 100644
index 0000000..d488f21
--- /dev/null
+++ b/R/egpkg-package.R
@@ -0,0 +1,3 @@
+#' @importFrom Rcpp evalCpp
+#' @useDynLib egpkg, .registration = TRUE
+NULL
diff --git a/README.Rmd b/README.Rmd
new file mode 100644
index 0000000..42aa185
--- /dev/null
+++ b/README.Rmd
@@ -0,0 +1,56 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# egpkg
+
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/UofUEpiBio/egpkg/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/UofUEpiBio/egpkg/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
+
+The goal of egpkg is to ...
+
+## Installation
+
+You can install the development version of egpkg from [GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("UofUEpiBio/egpkg")
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+```{r example}
+library(egpkg)
+## basic example code
+```
+
+What is special about using `README.Rmd` instead of just `README.md`? You can include R chunks like so:
+
+```{r cars}
+summary(cars)
+```
+
+You'll still need to render `README.Rmd` regularly, to keep `README.md` up-to-date. `devtools::build_readme()` is handy for this. You could also use GitHub Actions to re-render `README.Rmd` every time you push. An example workflow can be found here: <https://github.com/r-lib/actions/tree/v1/examples>.
+
+You can also embed plots, for example:
+
+```{r pressure, echo = FALSE}
+plot(pressure)
+```
+
+In that case, don't forget to commit and push the resulting figure files, so they display on GitHub and CRAN.
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..57e039d
--- /dev/null
+++ b/README.md
@@ -0,0 +1,57 @@
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# egpkg
+
+<!-- badges: start -->
+
+[![R-CMD-check](https://github.com/UofUEpiBio/egpkg/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/UofUEpiBio/egpkg/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
+
+The goal of egpkg is to …
+
+## Installation
+
+You can install the development version of egpkg from
+[GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("UofUEpiBio/egpkg")
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+``` r
+library(egpkg)
+## basic example code
+```
+
+What is special about using `README.Rmd` instead of just `README.md`?
+You can include R chunks like so:
+
+``` r
+summary(cars)
+#>      speed           dist       
+#>  Min.   : 4.0   Min.   :  2.00  
+#>  1st Qu.:12.0   1st Qu.: 26.00  
+#>  Median :15.0   Median : 36.00  
+#>  Mean   :15.4   Mean   : 42.98  
+#>  3rd Qu.:19.0   3rd Qu.: 56.00  
+#>  Max.   :25.0   Max.   :120.00
+```
+
+You’ll still need to render `README.Rmd` regularly, to keep `README.md`
+up-to-date. `devtools::build_readme()` is handy for this. You could also
+use GitHub Actions to re-render `README.Rmd` every time you push. An
+example workflow can be found here:
+<https://github.com/r-lib/actions/tree/v1/examples>.
+
+You can also embed plots, for example:
+
+<img src="man/figures/README-pressure-1.png" width="100%" />
+
+In that case, don’t forget to commit and push the resulting figure
+files, so they display on GitHub and CRAN.
diff --git a/egpkg.Rproj b/egpkg.Rproj
new file mode 100644
index 0000000..270314b
--- /dev/null
+++ b/egpkg.Rproj
@@ -0,0 +1,21 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+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/man/figures/README-pressure-1.png b/man/figures/README-pressure-1.png
new file mode 100644
index 0000000000000000000000000000000000000000..e208f61cdb5ecd0e71c372902595d01b5baaede4
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diff --git a/man/rcpp_hello_world.Rd b/man/rcpp_hello_world.Rd
new file mode 100644
index 0000000..0a9f57e
--- /dev/null
+++ b/man/rcpp_hello_world.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/RcppExports.R
+\name{rcpp_hello_world}
+\alias{rcpp_hello_world}
+\title{Hello world from Rcpp}
+\usage{
+rcpp_hello_world()
+}
+\value{
+A list with two vectors (\code{x}, \code{y}).
+}
+\description{
+Hello world from Rcpp
+}
+\examples{
+rcpp_hello_world()
+}
diff --git a/src/.gitignore b/src/.gitignore
new file mode 100644
index 0000000..22034c4
--- /dev/null
+++ b/src/.gitignore
@@ -0,0 +1,3 @@
+*.o
+*.so
+*.dll
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
new file mode 100644
index 0000000..4433333
--- /dev/null
+++ b/src/RcppExports.cpp
@@ -0,0 +1,32 @@
+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
+// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#include <Rcpp.h>
+
+using namespace Rcpp;
+
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
+// rcpp_hello_world
+List rcpp_hello_world();
+RcppExport SEXP _egpkg_rcpp_hello_world() {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    rcpp_result_gen = Rcpp::wrap(rcpp_hello_world());
+    return rcpp_result_gen;
+END_RCPP
+}
+
+static const R_CallMethodDef CallEntries[] = {
+    {"_egpkg_rcpp_hello_world", (DL_FUNC) &_egpkg_rcpp_hello_world, 0},
+    {NULL, NULL, 0}
+};
+
+RcppExport void R_init_egpkg(DllInfo *dll) {
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}
diff --git a/src/rcpp_hello_world.cpp b/src/rcpp_hello_world.cpp
new file mode 100644
index 0000000..fe62d77
--- /dev/null
+++ b/src/rcpp_hello_world.cpp
@@ -0,0 +1,18 @@
+
+#include <Rcpp.h>
+using namespace Rcpp;
+
+//' Hello world from Rcpp
+//' @return A list with two vectors (`x`, `y`).
+//' @examples
+//' rcpp_hello_world()
+//' @export
+// [[Rcpp::export]]
+List rcpp_hello_world() {
+
+    CharacterVector x = CharacterVector::create( "foo", "bar" )  ;
+    NumericVector y   = NumericVector::create( 0.0, 1.0 ) ;
+    List z            = List::create( x, y ) ;
+
+    return z ;
+}