review code

.Rbuildignore

@@ -1,13 +1,16 @@
-^.*\.Rproj$
-^\.Rproj\.user$
-^README\.Rmd$
-^vignettes/articles$
-^LICENSE\.md$
-^_pkgdown\.yml$
-^docs$
-^pkgdown$
-^\.github$
-^CRAN-SUBMISSION$
-^cran-comments\.md$
-^doc$
-^Meta$
+^.*\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^vignettes/articles$
+^LICENSE\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$
+^CRAN-SUBMISSION$
+^cran-comments\.md$
+^doc$
+^Meta$
+^codecov\.yml$
+^Makefile$
+^Jenkinsfile$

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,126 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
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+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at codeofconduct@posit.co. 
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org

.github/CONTRIBUTING.md

@@ -0,0 +1,47 @@
+# Contributing to genetic.algo.optimizeR
+
+This outlines how to propose a change to genetic.algo.optimizeR.
+For a detailed discussion on contributing to this and other tidyverse packages, please see the [development contributing guide](https://rstd.io/tidy-contrib) and our [code review principles](https://code-review.tidyverse.org/).
+
+## Fixing typos
+
+You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file. 
+This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file. 
+You can find the `.R` file that generates the `.Rd` by reading the comment in the first line.
+
+## Bigger changes
+
+If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed. 
+If you’ve found a bug, please file an issue that illustrates the bug with a minimal 
+[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
+See our guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) for more advice.
+
+### Pull request process
+
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("danymukesha/genetic.algo.optimizeR", fork = TRUE)`.
+
+*   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
+*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
+
+*   Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Fixes #issue-number`.
+
+*  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
+
+### Code style
+
+*   New code should follow the tidyverse [style guide](https://style.tidyverse.org). 
+    You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
+
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.  
+
+*  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. 
+   Contributions with test cases included are easier to accept.  
+
+## Code of Conduct
+
+Please note that the genetic.algo.optimizeR project is released with a
+[Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this
+project you agree to abide by its terms.

.github/ISSUE_TEMPLATE/issue_template.md

@@ -0,0 +1,16 @@
+---
+name: Bug report or feature request
+about: Describe a bug you've seen or make a case for a new feature
+---
+
+Please briefly describe your problem and what output you expect. If you have a question, please don't use this form. Instead, ask on <https://stackoverflow.com/> or <https://community.rstudio.com/>.
+
+Please include a minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](http://reprex.tidyverse.org/) before, start by reading <https://www.tidyverse.org/help/#reprex>.
+
+For more advice on how to write a great issue, see <https://code-review.tidyverse.org/issues/>.
+
+Brief description of the problem
+
+```r
+# insert reprex here
+```

.github/SUPPORT.md

@@ -0,0 +1,35 @@
+# Getting help with genetic.algo.optimizeR
+
+Thanks for using genetic.algo.optimizeR!
+Before filing an issue, there are a few places to explore and pieces to put together to make the process as smooth as possible.
+
+## Make a reprex
+
+Start by making a minimal **repr**oducible **ex**ample using the  [reprex](https://reprex.tidyverse.org/) package. 
+If you haven't heard of or used reprex before, you're in for a treat! 
+Seriously, reprex will make all of your R-question-asking endeavors easier (which is a pretty insane ROI for the five to ten minutes it'll take you to learn what it's all about). 
+For additional reprex pointers, check out the [Get help!](https://www.tidyverse.org/help/) section of the tidyverse site.
+
+## Where to ask?
+
+Armed with your reprex, the next step is to figure out [where to ask](https://www.tidyverse.org/help/#where-to-ask). 
+
+*   If it's a question: start with [community.rstudio.com](https://community.rstudio.com/), and/or StackOverflow. There are more people there to answer questions.  
+
+*   If it's a bug: you're in the right place, [file an issue](https://github.com/danymukesha/genetic.algo.optimizeR/issues/new).  
+
+*   If you're not sure: let the community help you figure it out! 
+    If your problem _is_ a bug or a feature request, you can easily return here and report it. 
+
+Before opening a new issue, be sure to [search issues and pull requests](https://github.com/danymukesha/genetic.algo.optimizeR/issues) to make sure the bug hasn't been reported and/or already fixed in the development version. 
+By default, the search will be pre-populated with `is:issue is:open`. 
+You can [edit the qualifiers](https://help.github.com/articles/searching-issues-and-pull-requests/)  (e.g. `is:pr`, `is:closed`) as needed. 
+For example, you'd simply remove `is:open` to search _all_ issues in the repo, open or closed.
+
+## What happens next?
+
+To be as efficient as possible, development of tidyverse packages tends to be very bursty, so you shouldn't worry if you don't get an immediate response.
+Typically we don't look at a repo until a sufficient quantity of issues accumulates, then there’s a burst of intense activity as we focus our efforts. 
+That makes development more efficient because it avoids expensive context switching between problems, at the cost of taking longer to get back to you. 
+This process makes a good reprex particularly important because it might be multiple months between your initial report and when we start working on it. 
+If we can’t reproduce the bug, we can’t fix it!

DESCRIPTION

@@ -1,31 +1,33 @@
-Package: genetic.algo.optimizeR
 Type: Package
+Package: genetic.algo.optimizeR
 Title: Genetic Algorithm Optimization
 Version: 0.2.4.9000
-Authors@R: c(
+Authors@R: 
     person("Dany", "Mukesha", , "danymukesha@gmail.com", role = c("aut", "cre"),
-      comment = c(ORCID = "0009-0001-9514-751X")
-    )
-  )
+           comment = c(ORCID = "0009-0001-9514-751X"))
 Maintainer: "Dany Mukesha" <danymukesha@gmail.com>
-Description: R package for learning purposes that implements a genetic algorithm optimization process.
+Description: R package for learning purposes that implements a genetic
+    algorithm optimization process.
 License: MIT + file LICENSE
-Encoding: UTF-8
-LazyData: true
-Suggests: 
-    knitr,
-    learnr,
-    rmarkdown,
-    testthat (>= 3.0.0)
-VignetteBuilder: knitr
-RoxygenNote: 7.2.3
-URL: https://danymukesha.github.io/genetic.algo.optimizeR/, https://github.com/danymukesha/genetic.algo.optimizeR
+URL: https://danymukesha.github.io/genetic.algo.optimizeR/,
+    https://github.com/danymukesha/genetic.algo.optimizeR
+BugReports: https://github.com/danymukesha/genetic.algo.optimizeR/issues
 Imports: 
     dplyr,
     ggplot2,
+    magrittr,
     rsconnect,
     stats,
     stringr,
     tinytex
+Suggests: 
+    knitr,
+    learnr,
+    rmarkdown,
+    testthat (>= 3.0.0)
+VignetteBuilder: 
+    knitr
 Config/testthat/edition: 3
-BugReports: https://github.com/danymukesha/genetic.algo.optimizeR/issues
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.2.3

Jenkinsfile

@@ -0,0 +1,21 @@
+pipeline {
+  agent any {
+    stages {
+      stage('Build') {
+        steps {
+          make build
+        }
+      }
+      stage('Check') {
+        steps {
+          make check
+        }
+      }
+      stage('Clean') {
+        steps {
+          make clean
+        }
+      }
+    }
+  }
+}

Makefile

@@ -0,0 +1,26 @@
+# h/t to @jimhester and @yihui for this parse block:
+# https://github.com/yihui/knitr/blob/dc5ead7bcfc0ebd2789fe99c527c7d91afb3de4a/Makefile#L1-L4
+# Note the portability change as suggested in the manual:
+# https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Writing-portable-packages
+PKGNAME = `sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION`
+PKGVERS = `sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION`
+
+
+all: check
+
+build: install_deps
+	R CMD build .
+
+check: build
+	R CMD check --no-manual $(PKGNAME)_$(PKGVERS).tar.gz
+
+install_deps:
+	Rscript \
+	-e 'if (!requireNamespace("remotes")) install.packages("remotes")' \
+	-e 'remotes::install_deps(dependencies = TRUE)'
+
+install: build
+	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
+
+clean:
+	@rm -rf $(PKGNAME)_$(PKGVERS).tar.gz $(PKGNAME).Rcheck

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export("%>%")
 export(crossover)
 export(evaluate_fitness)
 export(initialize_population)
@@ -12,3 +13,4 @@ import(stringr)
 import(tinytex)
 importFrom(dplyr,"%>%")
 importFrom(ggplot2,ggplot)
+importFrom(magrittr,"%>%")

R/crossover.R

@@ -21,7 +21,7 @@
 #' print("Evaluation:")
 #' print(fitness)
 #'
-#' #Selection
+#' # Selection
 #' selected_parents <- selection(population, fitness, num_parents = 2)
 #' print("Selection:")
 #' print(selected_parents)
@@ -44,7 +44,7 @@ crossover <- function(selected_parents, offspring_size) {
     parent2_index <- sample(1:num_parents, 1)
 
     offspring[i] <- (selected_parents[parent1_index] + selected_parents[parent2_index]) / 2
-    offspring[i+1] <- (selected_parents[parent1_index] + selected_parents[parent2_index]) / 2
+    offspring[i + 1] <- (selected_parents[parent1_index] + selected_parents[parent2_index]) / 2
   }
   offspring <- offspring |>
     round(x = _) # facilitate the adaptation of the offspring